[med-svn] [python-pbcore] 01/12: Imported Upstream version 1.2.3+dfsg
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Sep 20 08:25:26 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit 0d7b8ea2775a5d678d354c0bce99829bd1a99c03
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Sep 17 18:46:47 2015 -0700
Imported Upstream version 1.2.3+dfsg
---
CHANGELOG.org | 6 +
bin/dataset.py | 3 +
doc/pacbio-theme/static/headerGradient.jpg | Bin 0 -> 7099 bytes
doc/pacbio-theme/static/pacbio.css | 238 +
doc/pacbio-theme/static/pacbioLogo.png | Bin 0 -> 3128 bytes
doc/pacbio-theme/static/pygments.css | 55 +
doc/pacbio-theme/theme.conf | 4 +
pbcore/__init__.py | 2 +-
pbcore/data/Makefile | 28 +-
pbcore/data/__init__.py | 3 +
pbcore/data/datasets/__init__.py | 20 +-
pbcore/data/datasets/alignment.dataset.xml | 157 +-
pbcore/data/datasets/barcode.dataset.xml | 39 +-
pbcore/data/datasets/ccsaligned.dataset.xml | 48 +
pbcore/data/datasets/ccsread.dataset.xml | 61 +-
pbcore/data/datasets/contig.dataset.xml | 54 +-
pbcore/data/datasets/fofn.fofn | 2 +-
pbcore/data/datasets/lambda.alignmentset.xml | 15 +
pbcore/data/datasets/lambda.pbalign.xml | 2 -
pbcore/data/datasets/lambda.reference.xml | 2 -
pbcore/data/datasets/lambda.referenceset.xml | 19 +
pbcore/data/datasets/pbalchemysim.alignmentset.xml | 57 +
.../data/datasets/pbalchemysim.hdfsubreadset.xml | 11 +
pbcore/data/datasets/pbalchemysim.pbalign.xml | 2 -
.../pbalchemysim0.alignmentset.chunk0contigs.xml | 47 +
.../pbalchemysim0.alignmentset.chunk1contigs.xml | 47 +
.../data/datasets/pbalchemysim0.alignmentset.xml | 15 +
.../data/datasets/pbalchemysim0.hdfsubreadset.xml | 10 +
pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi | Bin 2115 -> 2147 bytes
.../pbalchemysim0.pbalign.chunk0contigs.xml | 2 -
.../pbalchemysim0.pbalign.chunk1contigs.xml | 2 -
pbcore/data/datasets/pbalchemysim0.pbalign.xml | 2 -
pbcore/data/datasets/pbalchemysim0.reference.xml | 77 -
.../data/datasets/pbalchemysim0.referenceset.xml | 77 +
pbcore/data/datasets/pbalchemysim0.subread.xml | 2 -
.../data/datasets/pbalchemysim0.subreads.bam.bai | Bin 0 -> 16 bytes
.../data/datasets/pbalchemysim0.subreads.bam.pbi | Bin 0 -> 1003 bytes
pbcore/data/datasets/pbalchemysim0.subreadset.xml | 10 +
.../data/datasets/pbalchemysim1.alignmentset.xml | 15 +
.../data/datasets/pbalchemysim1.hdfsubreadset.xml | 10 +
pbcore/data/datasets/pbalchemysim1.pbalign.xml | 2 -
pbcore/data/datasets/pbalchemysim1.subread.xml | 2 -
.../data/datasets/pbalchemysim1.subreads.bam.bai | Bin 0 -> 16 bytes
.../data/datasets/pbalchemysim1.subreads.bam.pbi | Bin 0 -> 945 bytes
pbcore/data/datasets/pbalchemysim1.subreadset.xml | 10 +
pbcore/data/datasets/reference.dataset.xml | 69 +-
pbcore/data/datasets/subread.dataset.xml | 1014 +-
pbcore/data/datasets/subreadSetWithStats.xml | 2262 ++-
.../datasets/transformed_rs_subread.dataset.xml | 152 +-
pbcore/data/empty.ccs.bam | Bin 0 -> 540 bytes
pbcore/data/empty.ccs.bam.pbi | Bin 0 -> 67 bytes
pbcore/io/BasH5IO.py | 18 +-
pbcore/io/GffIO.py | 64 +
pbcore/io/align/BamAlignment.py | 29 +-
pbcore/io/align/BamIO.py | 5 +-
pbcore/io/align/PacBioBamIndex.py | 2 +-
pbcore/io/align/_bgzf.py | 55 +-
pbcore/io/dataset/DataSetIO.py | 2898 ++--
pbcore/io/dataset/DataSetMembers.py | 191 +-
pbcore/io/dataset/DataSetReader.py | 100 +-
pbcore/io/dataset/DataSetValidator.py | 2 +
pbcore/io/dataset/DataSetWriter.py | 145 +-
pbcore/io/dataset/DataSetXsd.py | 13884 ++-----------------
pbcore/io/dataset/EntryPoints.py | 63 +-
pbcore/io/dataset/_pbbase.py | 4563 ++++++
pbcore/io/dataset/_pbds.py | 3435 +++++
pbcore/io/dataset/_pbmeta.py | 2056 +++
pbcore/io/dataset/_pbpn.py | 507 +
pbcore/io/dataset/_pbrk.py | 1218 ++
pbcore/io/dataset/_pbsample.py | 632 +
pbcore/io/dataset/utils.py | 125 +
tests/test_pbcore_io_AlnFileReaders.py | 9 +
tests/test_pbcore_io_GffIO.py | 67 +-
tests/test_pbcore_io_bgzf.py | 42 +
tests/test_pbdataset.py | 389 +-
tests/test_pbdataset_subtypes.py | 319 +-
76 files changed, 19382 insertions(+), 16091 deletions(-)
diff --git a/CHANGELOG.org b/CHANGELOG.org
index 466bdf7..c00d28e 100644
--- a/CHANGELOG.org
+++ b/CHANGELOG.org
@@ -1,3 +1,9 @@
+* Version 1.2.3
+- Updated for newer dataset schema
+- BAM access speed improvements
+- BGZF fixed for large bam.pbi files
+- readsInRange iteration order parity between different dataset sources
+
* Version 1.2.2
- Bug fixes and speed improvements to the
- Dataset constructor APIs enhanced
diff --git a/bin/dataset.py b/bin/dataset.py
index 1d3cc3d..e5fcef8 100755
--- a/bin/dataset.py
+++ b/bin/dataset.py
@@ -24,6 +24,7 @@ def get_subparsers():
('split', EntryPoints.split_options),
('validate', EntryPoints.validate_options),
('loadstats', EntryPoints.loadStatsXml_options),
+ ('summarize', EntryPoints.summarize_options),
('consolidate', EntryPoints.consolidate_options)]
return sps
@@ -44,6 +45,8 @@ def get_parser():
help="Turn on debug level logging")
parser.add_argument("--strict", default=False, action='store_true',
help="Turn on strict tests, raise all errors")
+ parser.add_argument("--skipCounts", default=False, action='store_true',
+ help="Turn on strict tests, raise all errors")
subparser_list = get_subparsers()
parser = add_subparsers(parser, subparser_list)
return parser
diff --git a/doc/pacbio-theme/static/headerGradient.jpg b/doc/pacbio-theme/static/headerGradient.jpg
new file mode 100644
index 0000000..883f147
Binary files /dev/null and b/doc/pacbio-theme/static/headerGradient.jpg differ
diff --git a/doc/pacbio-theme/static/pacbio.css b/doc/pacbio-theme/static/pacbio.css
new file mode 100644
index 0000000..b4ab87f
--- /dev/null
+++ b/doc/pacbio-theme/static/pacbio.css
@@ -0,0 +1,238 @@
+/**
+ * Sphinx stylesheet -- default theme
+ * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ */
+
+ at import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+ font-family: Arial, sans-serif;
+ font-size: 100%;
+ background-color: #555;
+ color: #555;
+ margin: 0;
+ padding: 0;
+ min-width: 500px;
+ max-width: 956px;
+ margin: 0 auto;
+}
+
+div.documentwrapper {
+ float: left;
+ width: 100%;
+}
+
+div.bodywrapper {
+ margin: 0 0 0 230px;
+}
+
+hr{
+ border: 1px solid #B1B4B6;
+
+}
+
+div.document {
+ background-color: #eee;
+}
+
+div.body {
+ background-color: #ffffff;
+ color: #3E4349;
+ padding: 30px 30px 30px 30px;
+ font-size: 0.8em;
+}
+
+div.footer {
+ color: #555;
+ background-color: #fff;
+ padding: 13px 0;
+ text-align: center;
+ font-size: 75%;
+
+}
+div.footer a {
+ color: #444;
+ text-decoration: underline;
+}
+
+div.related {
+ background: #fff url(headerGradient.jpg);
+ line-height: 80px;
+ color: #fff;
+ font-size: 0.80em;
+ height: 79px;
+ z-index: -1;
+}
+
+div.related ul {
+ background: url(pacbioLogo.png) 10px no-repeat;
+ padding: 0 0 0 200px;
+}
+
+div.related a {
+ color: #E2F3CC;
+}
+
+div.sphinxsidebar {
+ font-size: 0.75em;
+ line-height: 1.5em;
+}
+
+div.sphinxsidebarwrapper{
+ padding: 20px 0;
+}
+
+div.sphinxsidebar h3,
+div.sphinxsidebar h4 {
+ font-family: Arial, sans-serif;
+ color: #222;
+ font-size: 1.2em;
+ font-weight: bold;
+ margin: 0;
+ padding: 5px 10px 0 10px;
+}
+
+div.sphinxsidebar h4{
+ font-size: 1.1em;
+}
+
+div.sphinxsidebar h3 a {
+ color: #444;
+}
+
+
+div.sphinxsidebar p {
+ color: #888;
+ padding: 0px 20px;
+ margin-top: 5px;
+}
+
+div.sphinxsidebar p.topless {
+}
+
+div.sphinxsidebar ul {
+ margin: 5px 20px 10px 20px;
+ padding: 0;
+ color: #000;
+}
+
+div.sphinxsidebar a {
+ color: #444;
+}
+
+div.sphinxsidebar input {
+ border: 1px solid #ccc;
+ font-family: sans-serif;
+ font-size: 1em;
+}
+
+div.sphinxsidebar input[type=text]{
+ margin-left: 20px;
+}
+
+/* -- body styles ----------------------------------------------------------- */
+
+a {
+ color: #005B81;
+ text-decoration: none;
+}
+
+a:hover {
+ color: #E32E00;
+ text-decoration: underline;
+}
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+ font-family: Arial, sans-serif;
+ font-weight: bold;
+ color: #264868;
+ margin: 30px 0px 10px 0px;
+ padding: 5px 0 5px 0px;
+}
+
+div.body h1 { border-top: 20px solid white; margin-top: 0; font-size: 180%; font-weight: normal; }
+div.body h2 { font-size: 125%; }
+div.body h3 { font-size: 110%; }
+div.body h4 { font-size: 100%; }
+div.body h5 { font-size: 100%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+ color: #c60f0f;
+ font-size: 0.8em;
+ padding: 0 4px 0 4px;
+ text-decoration: none;
+}
+
+a.headerlink:hover {
+ background-color: #c60f0f;
+ color: white;
+}
+
+div.body p, div.body dd, div.body li {
+ line-height: 1.5em;
+ font-size: 1em;
+}
+
+div.admonition p.admonition-title + p {
+ display: inline;
+}
+
+div.highlight{
+ background-color: white;
+}
+
+div.note {
+ background-color: #eee;
+ border: 1px solid #ccc;
+}
+
+div.seealso {
+ background-color: #ffc;
+ border: 1px solid #ff6;
+}
+
+div.topic {
+ background-color: #eee;
+}
+
+div.warning {
+ background-color: #ffe4e4;
+ border: 1px solid #f66;
+}
+
+p.admonition-title {
+ display: inline;
+}
+
+p.admonition-title:after {
+ content: ":";
+}
+
+pre {
+ padding: 10px;
+ background-color: White;
+ color: #222;
+ line-height: 1.2em;
+ border: 1px solid #C6C9CB;
+ font-size: 1.2em;
+ margin: 1.5em 0 1.5em 0;
+ -webkit-box-shadow: 1px 1px 1px #d8d8d8;
+ -moz-box-shadow: 1px 1px 1px #d8d8d8;
+}
+
+tt {
+ background-color: #ecf0f3;
+ color: #222;
+ padding: 1px 2px;
+ font-size: 1.2em;
+ font-family: monospace;
+}
+
diff --git a/doc/pacbio-theme/static/pacbioLogo.png b/doc/pacbio-theme/static/pacbioLogo.png
new file mode 100644
index 0000000..b2e4887
Binary files /dev/null and b/doc/pacbio-theme/static/pacbioLogo.png differ
diff --git a/doc/pacbio-theme/static/pygments.css b/doc/pacbio-theme/static/pygments.css
new file mode 100644
index 0000000..4588cde
--- /dev/null
+++ b/doc/pacbio-theme/static/pygments.css
@@ -0,0 +1,55 @@
+.c { color: #999988; font-style: italic } /* Comment */
+.k { font-weight: bold } /* Keyword */
+.o { font-weight: bold } /* Operator */
+.cm { color: #999988; font-style: italic } /* Comment.Multiline */
+.cp { color: #999999; font-weight: bold } /* Comment.preproc */
+.c1 { color: #999988; font-style: italic } /* Comment.Single */
+.gd { color: #000000; background-color: #ffdddd } /* Generic.Deleted */
+.ge { font-style: italic } /* Generic.Emph */
+.gr { color: #aa0000 } /* Generic.Error */
+.gh { color: #999999 } /* Generic.Heading */
+.gi { color: #000000; background-color: #ddffdd } /* Generic.Inserted */
+.go { color: #111 } /* Generic.Output */
+.gp { color: #555555 } /* Generic.Prompt */
+.gs { font-weight: bold } /* Generic.Strong */
+.gu { color: #aaaaaa } /* Generic.Subheading */
+.gt { color: #aa0000 } /* Generic.Traceback */
+.kc { font-weight: bold } /* Keyword.Constant */
+.kd { font-weight: bold } /* Keyword.Declaration */
+.kp { font-weight: bold } /* Keyword.Pseudo */
+.kr { font-weight: bold } /* Keyword.Reserved */
+.kt { color: #445588; font-weight: bold } /* Keyword.Type */
+.m { color: #009999 } /* Literal.Number */
+.s { color: #bb8844 } /* Literal.String */
+.na { color: #008080 } /* Name.Attribute */
+.nb { color: #999999 } /* Name.Builtin */
+.nc { color: #445588; font-weight: bold } /* Name.Class */
+.no { color: #ff99ff } /* Name.Constant */
+.ni { color: #800080 } /* Name.Entity */
+.ne { color: #990000; font-weight: bold } /* Name.Exception */
+.nf { color: #990000; font-weight: bold } /* Name.Function */
+.nn { color: #555555 } /* Name.Namespace */
+.nt { color: #000080 } /* Name.Tag */
+.nv { color: purple } /* Name.Variable */
+.ow { font-weight: bold } /* Operator.Word */
+.mf { color: #009999 } /* Literal.Number.Float */
+.mh { color: #009999 } /* Literal.Number.Hex */
+.mi { color: #009999 } /* Literal.Number.Integer */
+.mo { color: #009999 } /* Literal.Number.Oct */
+.sb { color: #bb8844 } /* Literal.String.Backtick */
+.sc { color: #bb8844 } /* Literal.String.Char */
+.sd { color: #bb8844 } /* Literal.String.Doc */
+.s2 { color: #bb8844 } /* Literal.String.Double */
+.se { color: #bb8844 } /* Literal.String.Escape */
+.sh { color: #bb8844 } /* Literal.String.Heredoc */
+.si { color: #bb8844 } /* Literal.String.Interpol */
+.sx { color: #bb8844 } /* Literal.String.Other */
+.sr { color: #808000 } /* Literal.String.Regex */
+.s1 { color: #bb8844 } /* Literal.String.Single */
+.ss { color: #bb8844 } /* Literal.String.Symbol */
+.bp { color: #999999 } /* Name.Builtin.Pseudo */
+.vc { color: #ff99ff } /* Name.Variable.Class */
+.vg { color: #ff99ff } /* Name.Variable.Global */
+.vi { color: #ff99ff } /* Name.Variable.Instance */
+.il { color: #009999 } /* Literal.Number.Integer.Long */
+
diff --git a/doc/pacbio-theme/theme.conf b/doc/pacbio-theme/theme.conf
new file mode 100644
index 0000000..dd24a1a
--- /dev/null
+++ b/doc/pacbio-theme/theme.conf
@@ -0,0 +1,4 @@
+[theme]
+inherit = default
+stylesheet = pacbio.css
+pygments_style = tango
diff --git a/pbcore/__init__.py b/pbcore/__init__.py
index 937e2f1..466ec29 100644
--- a/pbcore/__init__.py
+++ b/pbcore/__init__.py
@@ -28,4 +28,4 @@
# POSSIBILITY OF SUCH DAMAGE.
#################################################################################
-__VERSION__ = "1.2.2"
+__VERSION__ = "1.2.3"
diff --git a/pbcore/data/Makefile b/pbcore/data/Makefile
index 99fbcf0..4182217 100644
--- a/pbcore/data/Makefile
+++ b/pbcore/data/Makefile
@@ -16,29 +16,35 @@ $(MOVIE1).aligned_subreads.cmp.h5: $(MOVIE1).1.bax.h5 lambdaNEB.fa
pbalign-2.3 --forQuiver --metrics IPD,DeletionQV,DeletionTag,InsertionQV,MergeQV,SubstitutionQV $^ $@
testdata:
- dataset.py create --type ReferenceSet --relative datasets/pbalchemysim0.reference.xml datasets/pbalchemysim0.reference.fasta
+ dataset.py create --type ReferenceSet --relative datasets/pbalchemysim0.referenceset.xml datasets/pbalchemysim0.reference.fasta
bax2bam datasets/pbalchemysim0.bas.h5 -o datasets/pbalchemysim0 --pulsefeatures DeletionTag,DeletionQV,InsertionQV,MergeQV,SubstitutionQV && \
samtools index datasets/pbalchemysim0.subreads.bam
pbindex datasets/pbalchemysim0.subreads.bam
- dataset.py create --type SubreadSet --relative datasets/pbalchemysim0.subread.xml datasets/pbalchemysim0.subreads.bam
+ dataset.py create --type SubreadSet --relative datasets/pbalchemysim0.subreadset.xml datasets/pbalchemysim0.subreads.bam
pbalign datasets/pbalchemysim0.subreads.bam datasets/pbalchemysim0.reference.fasta datasets/pbalchemysim0.pbalign.bam && \
- dataset.py create --type AlignmentSet --relative datasets/pbalchemysim0.pbalign.xml datasets/pbalchemysim0.pbalign.bam
- dataset.py split --contigs --chunks 2 datasets/pbalchemysim0.pbalign.xml
+ dataset.py create --type AlignmentSet --relative datasets/pbalchemysim0.alignmentset.xml datasets/pbalchemysim0.pbalign.bam
+ dataset.py split --contigs --chunks 2 datasets/pbalchemysim0.alignmentset.xml
+ dataset.py create --type AlignmentSet --relative datasets/pbalchemysim0.alignmentset.chunk0contigs.xml datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
+ dataset.py create --type AlignmentSet --relative datasets/pbalchemysim0.alignmentset.chunk1contigs.xml datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
bax2bam datasets/pbalchemysim1.bas.h5 -o datasets/pbalchemysim1 --pulsefeatures DeletionTag,DeletionQV,InsertionQV,MergeQV,SubstitutionQV && \
samtools index datasets/pbalchemysim1.subreads.bam
pbindex datasets/pbalchemysim1.subreads.bam
- dataset.py create --type SubreadSet --relative datasets/pbalchemysim1.subread.xml datasets/pbalchemysim1.subreads.bam
+ dataset.py create --type SubreadSet --relative datasets/pbalchemysim1.subreadset.xml datasets/pbalchemysim1.subreads.bam
pbalign datasets/pbalchemysim1.subreads.bam datasets/pbalchemysim0.reference.fasta datasets/pbalchemysim1.pbalign.bam && \
- dataset.py create --type AlignmentSet --relative datasets/pbalchemysim1.pbalign.xml datasets/pbalchemysim1.pbalign.bam
- dataset.py create --type AlignmentSet --relative datasets/pbalchemysim.pbalign.xml datasets/pbalchemysim0.pbalign.bam datasets/pbalchemysim1.pbalign.bam
- dataset.py create --type SubreadSet --relative datasets/subreadSetWithStats.xml datasets/pbalchemysim0.subread.xml
+ dataset.py create --type AlignmentSet --relative datasets/pbalchemysim1.alignmentset.xml datasets/pbalchemysim1.pbalign.bam
+ dataset.py create --type AlignmentSet --relative datasets/pbalchemysim.alignmentset.xml datasets/pbalchemysim0.alignmentset.xml datasets/pbalchemysim1.alignmentset.xml
+ dataset.py create --type SubreadSet --relative datasets/subreadSetWithStats.xml datasets/pbalchemysim0.subreadset.xml
dataset.py loadstats datasets/subreadSetWithStats.xml datasets/m150430_142051_Mon_p1_b25.sts.xml
dataset.py loadstats datasets/subreadSetWithStats.xml datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml
+ dataset.py create --type SubreadSet --relative datasets/subreadSetWithStats.xml datasets/subreadSetWithStats.xml
+ dataset.py create --type HdfSubreadSet --relative datasets/pbalchemysim0.hdfsubreadset.xml datasets/pbalchemysim0.bas.h5
+ dataset.py create --type HdfSubreadSet --relative datasets/pbalchemysim1.hdfsubreadset.xml datasets/pbalchemysim1.bas.h5
+ dataset.py create --type HdfSubreadSet --relative datasets/pbalchemysim.hdfsubreadset.xml datasets/pbalchemysim0.bas.h5 datasets/pbalchemysim1.bas.h5
upstream_testdata:
- dataset.py create --type ReferenceSet --relative datasets/lambda.reference.xml lambdaNEB.fa
- dataset.py create --type AlignmentSet --relative datasets/lambda.pbalign.xml $(MOVIE1).aligned_subreads.bam
+ dataset.py create --type ReferenceSet --relative datasets/lambda.referenceset.xml lambdaNEB.fa
+ dataset.py create --type AlignmentSet --relative datasets/lambda.alignmentset.xml $(MOVIE1).aligned_subreads.bam
xsdupdate:
- cp ../../../doc/FileFormats/examples/datasets/*.xml datasets/.
+ cp ../../../../../doc/FileFormats/examples/datasets/*.xml datasets/.
diff --git a/pbcore/data/__init__.py b/pbcore/data/__init__.py
index dbc4b19..433b5bf 100644
--- a/pbcore/data/__init__.py
+++ b/pbcore/data/__init__.py
@@ -168,3 +168,6 @@ def getUnalignedBam():
Get the unaligned BAM file, corresponding to the same bax above
"""
return _getAbsPath("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam")
+
+def getEmptyBam():
+ return _getAbsPath("empty.ccs.bam")
diff --git a/pbcore/data/datasets/__init__.py b/pbcore/data/datasets/__init__.py
index 30357fb..843faae 100755
--- a/pbcore/data/datasets/__init__.py
+++ b/pbcore/data/datasets/__init__.py
@@ -11,15 +11,19 @@ XML_FILES = ["alignment.dataset.xml", #0
"subread.dataset.xml",
"transformed_rs_subread_dataset.xml",
"hdfsubread_dataset.xml",
- "pbalchemysim0.pbalign.xml",
- "pbalchemysim0.reference.xml", #9
- "pbalchemysim0.subread.xml",
- "pbalchemysim1.pbalign.xml",
- "pbalchemysim.pbalign.xml", # both sim0 and sim1 bam files
- "pbalchemysim1.subread.xml",
+ "pbalchemysim0.alignmentset.xml",
+ "pbalchemysim0.referenceset.xml", #9
+ "pbalchemysim0.subreadset.xml",
+ "pbalchemysim1.alignmentset.xml",
+ "pbalchemysim.alignmentset.xml", # both sim0 and sim1 bam files
+ "pbalchemysim1.subreadset.xml",
"subreadSetWithStats.xml", #14
- "pbalchemysim0.pbalign.chunk0contigs.xml",
- "pbalchemysim0.pbalign.chunk1contigs.xml",
+ "pbalchemysim0.alignmentset.chunk0contigs.xml",
+ "pbalchemysim0.alignmentset.chunk1contigs.xml",
+ "pbalchemysim0.hdfsubreadset.xml",
+ "pbalchemysim1.hdfsubreadset.xml",
+ "pbalchemysim.hdfsubreadset.xml", #19
+ "ccsaligned.dataset.xml",
]
BAM_FILES = ["pbalchemysim0.pbalign.bam",
"pbalchemysim1.pbalign.bam",
diff --git a/pbcore/data/datasets/alignment.dataset.xml b/pbcore/data/datasets/alignment.dataset.xml
index b45f24e..f20f4c3 100644
--- a/pbcore/data/datasets/alignment.dataset.xml
+++ b/pbcore/data/datasets/alignment.dataset.xml
@@ -1,56 +1,105 @@
<?xml version="1.0" encoding="utf-8"?>
-<AlignmentSet xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" MetaType="PacBio.DataSet.AlignmentSet" Name="DataSet_AlignmentSet" Tags="barcode moreTags mapping mytags" UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" CreatedAt="2015-01-27T09:00:01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource Name="First Alignments BAM" Description="Points to an example Alignments BAM file." MetaType="PacBio.AlignmentFile.AlignmentBamFile" ResourceId="file:///mnt/path/to/alignments0.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/alignments0.pbi"/>
- </FileIndices>
- <ExternalResources>
- <ExternalResource Name="Reference used to produce BAM file" Description="Points to the reference used to generate the above BAM file." MetaType="PacBio.ReferenceFile.ReferenceFastaFile" ResourceId="file:///mnt/path/to/reference.fasta" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.SaWriterIndex" ResourceId="file:///mnt/path/to/reference.fasta.sa"/>
- <FileIndex MetaType="PacBio.Index.SamIndex" ResourceId="file:///mnt/path/to/reference.fasta.fai"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- </ExternalResource>
- <ExternalResource Name="Second Alignments BAM" Description="Points to another example Alignments BAM file, by relative path." MetaType="PacBio.AlignmentFile.AlignmentBamFile" ResourceId="file:./alignments1.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/alignments1.pbi"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- <DataSets>
- <DataSet UniqueId="ab95d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" Name="HighQuality Read Alignments">
- <ExternalResources>
- <ExternalResource/> <!-- This is a hack to make alignment set validate. Clearly the labelled subset needs a little more thought. -->
- </ExternalResources>
- <Filters> <!-- These Filters are in addition to those above. This provides a means to subset and label the parent DataSet further. -->
- <Filter>
- <Properties>
- <Property Name="rq" Value="0.85" Operator=">"/>
- </Properties>
- </Filter>
- </Filters>
- </DataSet>
- <DataSet UniqueId="ac95d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" Name="Alignments to chromosome 1">
- <ExternalResources>
+<pbds:AlignmentSet
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd"
+ xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ Tags="barcode moreTags mapping mytags"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="alignmentset_150304_231155"
+ MetaType="PacBio.DataSet.AlignmentSet"
+ Name="Uber alignment set"
+ Version="2.3.0"
+ CreatedAt="2015-01-27T09:00:01">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ Name="First Alignments BAM"
+ Description="Points to an example Alignments BAM file."
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5293"
+ TimeStampedName="alignment_bam_150304_231155"
+ MetaType="PacBio.AlignmentFile.AlignmentBamFile"
+ ResourceId="file:///mnt/path/to/alignments0.bam" Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5393"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/alignments0.pbi"/>
+ </pbbase:FileIndices>
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ Name="Reference used to produce BAM file"
+ Description="Points to the reference used to generate the above BAM file."
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5493"
+ TimeStampedName="reference_fasta_150304_231155"
+ MetaType="PacBio.ReferenceFile.ReferenceFastaFile"
+ ResourceId="file:///mnt/path/to/reference.fasta" Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5593"
+ TimeStampedName="sawriter_index_150304_231155"
+ MetaType="PacBio.Index.SaWriterIndex"
+ ResourceId="file:///mnt/path/to/reference.fasta.sa"/>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5693"
+ TimeStampedName="sam_index_150304_231155"
+ MetaType="PacBio.Index.SamIndex"
+ ResourceId="file:///mnt/path/to/reference.fasta.fai"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ </pbbase:ExternalResource>
+ <!-- Is this second BAM necessary? <pbbase:ExternalResource Name="Second Alignments BAM" Description="Points to another example Alignments BAM file, by relative path." MetaType="PacBio.AlignmentFile.AlignmentBamFile" ResourceId="file:./alignments1.bam" Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/alignments1.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>-->
+
+ </pbbase:ExternalResources>
+<!-- START use IDREF here for External Resources, or just duplicate them? <pbds:DataSets>
+ <pbds:DataSet
+ UniqueId="ab95d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="alignmentset_150304_231155"
+ MetaType="PacBio.DataSet.AlignmentSet"
+ Version="2.3.0"
+ Name="HighQuality Read Alignments">
+ <pbbase:ExternalResources>
<ExternalResource/>
- </ExternalResources>
- <Filters>
- <Filter>
- <Properties>
- <Property Name="RNAME" Value="chr1" Operator="=="/>
- </Properties>
- </Filter>
- </Filters>
- </DataSet>
- </DataSets>
- <DataSetMetadata>
- <TotalLength>50000</TotalLength>
- <NumRecords>5000</NumRecords>
- <Provenance CreatedBy="AnalysisJob">
- <ParentTool Name="pbalign" Version="0.1.0" Description="pbalign subreads.dataset.xml reference.dataset.xml"/>
- </Provenance>
- </DataSetMetadata>
-</AlignmentSet>
+ </pbbase:ExternalResources>
+ <pbds:Filters> These Filters are in addition to those above. This provides a means to subset and label the parent DataSet further.
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rq" Value="0.85" Operator=">"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ </pbds:Filters>
+ </pbds:DataSet>
+ <pbds:DataSet
+ UniqueId="ac95d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="alignmentset_150304_231155"
+ MetaType="PacBio.DataSet.AlignmentSet"
+ Version="2.3.0"
+ Name="Alignments to chromosome 1">
+ <pbbase:ExternalResources>
+ <ExternalResource/>
+ </pbbase:ExternalResources>
+ <pbds:Filters>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="RNAME" Value="chr1" Operator="=="/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ </pbds:Filters>
+ </pbds:DataSet>
+ </pbds:DataSets>
+ -->
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>50000</pbds:TotalLength>
+ <pbds:NumRecords>5000</pbds:NumRecords>
+ <pbds:Provenance CreatedBy="AnalysisJob">
+ <pbds:ParentTool Name="pbalign" Version="0.1.0" Description="pbalign subreads.dataset.xml reference.dataset.xml"/>
+ </pbds:Provenance>
+ </pbds:DataSetMetadata>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/barcode.dataset.xml b/pbcore/data/datasets/barcode.dataset.xml
index a32acd3..f4c9f54 100644
--- a/pbcore/data/datasets/barcode.dataset.xml
+++ b/pbcore/data/datasets/barcode.dataset.xml
@@ -1,11 +1,30 @@
<?xml version="1.0" encoding="utf-8"?>
-<BarcodeSet xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" MetaType="PacBio.DataSet.BarcodeSet" Name="DataSet_BarcodeSet" Tags="barcode moreTags mapping mytags" UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" CreatedAt="2015-01-27T09:00:01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource Name="First Barcodes FASTA" Description="Points to an example Barcodes FASTA file." MetaType="BarcodeFile.BarcodeFastaFile" ResourceId="file:///mnt/path/to/barcode.fasta" Tags="Example"/>
- </ExternalResources>
- <DataSetMetadata>
- <TotalLength>400</TotalLength>
- <NumRecords>30</NumRecords>
- <BarcodeConstruction>paired</BarcodeConstruction>
- </DataSetMetadata>
-</BarcodeSet>
+<pbds:BarcodeSet
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="barcodeset_150304_231155"
+ MetaType="PacBio.DataSet.BarcodeSet"
+ Name="DataSet_BarcodeSet"
+ Tags="barcode moreTags mapping mytags"
+ Version="2.3.0"
+ CreatedAt="2015-01-27T09:00:01">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ Name="First Barcodes FASTA"
+ Description="Points to an example Barcodes FASTA file."
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe719c"
+ MetaType="PacBio.BarcodeFile.BarcodeFastaFile"
+ TimeStampedName="barcode_fasta_150304_231155"
+ ResourceId="file:///mnt/path/to/barcode.fasta"
+ Tags="Example"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>400</pbds:TotalLength>
+ <pbds:NumRecords>30</pbds:NumRecords>
+ <pbds:BarcodeConstruction>paired</pbds:BarcodeConstruction>
+ </pbds:DataSetMetadata>
+</pbds:BarcodeSet>
diff --git a/pbcore/data/datasets/ccsaligned.dataset.xml b/pbcore/data/datasets/ccsaligned.dataset.xml
new file mode 100644
index 0000000..ce9592f
--- /dev/null
+++ b/pbcore/data/datasets/ccsaligned.dataset.xml
@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="utf-8"?>
+<pbds:ConsensusAlignmentSet
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="consensusreadset_150304_231155"
+ MetaType="PacBio.DataSet.ConsensusAlignmentSet"
+ Name="DataSet_ConsensusAlignmentSet"
+ Tags="barcode moreTags mapping mytags"
+ Version="2.3.0"
+ CreatedAt="2015-01-27T09:00:01">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5193"
+ TimeStampedName="consensusread_bam_150304_231155"
+ MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile"
+ Name="First ConsensusRead BAM"
+ Description="Points to an example ConsensusRead BAM file."
+ ResourceId="file:///mnt/path/to/ccsreads0.bam"
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5293"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/ccsreads0.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5393"
+ TimeStampedName="consensusread_bam_150304_231155"
+ MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile"
+ Name="Second ConsensusRead BAM"
+ Description="Points to an example ConsensusRead BAM file."
+ ResourceId="file:///mnt/path/to/ccsreads1.bam"
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5493"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/ccsreads0.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+</pbds:ConsensusAlignmentSet>
diff --git a/pbcore/data/datasets/ccsread.dataset.xml b/pbcore/data/datasets/ccsread.dataset.xml
index 529a457..ba1b506 100644
--- a/pbcore/data/datasets/ccsread.dataset.xml
+++ b/pbcore/data/datasets/ccsread.dataset.xml
@@ -1,15 +1,48 @@
<?xml version="1.0" encoding="utf-8"?>
-<ConsensusReadSet xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" MetaType="PacBio.DataSet.ConsensusReadSet" Name="DataSet_ConsensusReadSet" Tags="barcode moreTags mapping mytags" UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" CreatedAt="2015-01-27T09:00:01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource Name="First ConsensusRead BAM" Description="Points to an example ConsensusRead BAM file." MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile" ResourceId="file:///mnt/path/to/ccsreads0.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/ccsreads0.pbi"/>
- </FileIndices>
- </ExternalResource>
- <ExternalResource Name="Second ConsensusRead BAM" Description="Points to another example ConsensusRead BAM file." MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile" ResourceId="file:///mnt/path/to/ccsreads1.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/ccsreads0.pbi"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
-</ConsensusReadSet>
+<pbds:ConsensusReadSet
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="consensusreadset_150304_231155"
+ MetaType="PacBio.DataSet.ConsensusReadSet"
+ Name="DataSet_ConsensusReadSet"
+ Tags="barcode moreTags mapping mytags"
+ Version="2.3.0"
+ CreatedAt="2015-01-27T09:00:01">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5193"
+ TimeStampedName="consensusread_bam_150304_231155"
+ MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile"
+ Name="First ConsensusRead BAM"
+ Description="Points to an example ConsensusRead BAM file."
+ ResourceId="file:///mnt/path/to/ccsreads0.bam"
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5293"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/ccsreads0.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5393"
+ TimeStampedName="consensusread_bam_150304_231155"
+ MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile"
+ Name="Second ConsensusRead BAM"
+ Description="Points to an example ConsensusRead BAM file."
+ ResourceId="file:///mnt/path/to/ccsreads1.bam"
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5493"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/ccsreads0.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+</pbds:ConsensusReadSet>
diff --git a/pbcore/data/datasets/contig.dataset.xml b/pbcore/data/datasets/contig.dataset.xml
index 2995a82..c71a80f 100644
--- a/pbcore/data/datasets/contig.dataset.xml
+++ b/pbcore/data/datasets/contig.dataset.xml
@@ -1,18 +1,36 @@
-<?xml version="1.0" encoding="utf-8"?>
-<ContigSet xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" MetaType="PacBio.DataSet.ContigSet" Name="DataSet_ContigSet" Tags="AHAcontigs" UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" CreatedAt="2015-01-27T09:00:01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource Name="First References FASTA" Description="Points to an example references FASTA file." MetaType="PacBio.ReferenceFile.ReferenceFastaFile" ResourceId="file:///mnt/path/to/reference.fasta" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.SaWriterIndex" ResourceId="file:///mnt/path/to/reference.fasta.sa"/>
- <FileIndex MetaType="PacBio.Index.SamIndex" ResourceId="file:///mnt/path/to/reference.fasta.fai"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- <DataSetMetadata>
- <TotalLength>5000000</TotalLength>
- <NumRecords>500</NumRecords>
- <Contigs>
- <Contig Name="gi|229359445|emb|AM181176.4|" Description="Pseudomonas fluorescens SBW25 complete genome|quiver" Length="6722109" Digest="f627c795efad7ce0050ed42b942d408e"/>
- </Contigs>
- </DataSetMetadata>
-</ContigSet>
+<?xml version="1.0" encoding="utf-8"?>
+<pbds:ContigSet
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="contigset_150304_231155"
+ MetaType="PacBio.DataSet.ContigSet"
+ Name="DataSet_ContigSet"
+ Tags="HGAP"
+ Version="2.3.0"
+ CreatedAt="2015-01-27T09:00:01"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe529c"
+ TimeStampedName="contig_fasta_150304_231155"
+ MetaType="PacBio.ContigFile.ContigFastaFile"
+ Name="First Contigs FASTA"
+ Description="Points to an example contigs FASTA file e.g. from HGAP."
+ ResourceId="file:///mnt/path/to/contigs.fasta" Tags="Example">
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>5000000</pbds:TotalLength>
+ <pbds:NumRecords>500</pbds:NumRecords>
+ <pbds:Contigs>
+ <pbds:Contig
+ Name="gi|229359445|emb|AM181176.4|"
+ Description="Pseudomonas fluorescens SBW25 complete genome|quiver"
+ Length="6722109"
+ Digest="f627c795efad7ce0050ed42b942d408e"/>
+ </pbds:Contigs>
+ </pbds:DataSetMetadata>
+</pbds:ContigSet>
diff --git a/pbcore/data/datasets/fofn.fofn b/pbcore/data/datasets/fofn.fofn
index fef9353..d068f2e 100644
--- a/pbcore/data/datasets/fofn.fofn
+++ b/pbcore/data/datasets/fofn.fofn
@@ -1,2 +1,2 @@
-pbalchemysim0.pbalign.xml
+pbalchemysim0.alignmentset.xml
pbalchemysim1.pbalign.bam
diff --git a/pbcore/data/datasets/lambda.alignmentset.xml b/pbcore/data/datasets/lambda.alignmentset.xml
new file mode 100644
index 0000000..4a5c490
--- /dev/null
+++ b/pbcore/data/datasets/lambda.alignmentset.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" ?>
+<pbds:AlignmentSet CreatedAt="2015-08-05T10:24:09" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="" UniqueId="0714f33d-1dd3-1301-c923-1ae2c96c5eb1" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioData [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="../m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_172409" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="../m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_172409" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="../m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_172409" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>60467</pbds:TotalLength>
+ <pbds:NumRecords>112</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/lambda.pbalign.xml b/pbcore/data/datasets/lambda.pbalign.xml
deleted file mode 100644
index 4e6b034..0000000
--- a/pbcore/data/datasets/lambda.pbalign.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<AlignmentSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:42" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" UniqueId="6ed2c3bd-b54d-c6b2-0fac-b724ab4e60d4" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="../m140905_042212_sidney_c100564852550000001823085 [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/lambda.reference.xml b/pbcore/data/datasets/lambda.reference.xml
deleted file mode 100644
index 7d297e6..0000000
--- a/pbcore/data/datasets/lambda.reference.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<ReferenceSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:42" MetaType="PacBio.DataSet.ReferenceSet" Name="" Tags="" UniqueId="fd07c0d2-5f6e-67ac-646a-d200c03eacef" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="" ResourceId="../lambdaNEB.fa"><FileIndices><FileIndex MetaType="PacBio.Index.SamIndex" ResourceI [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/lambda.referenceset.xml b/pbcore/data/datasets/lambda.referenceset.xml
new file mode 100644
index 0000000..9d299fe
--- /dev/null
+++ b/pbcore/data/datasets/lambda.referenceset.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" ?>
+<pbds:ReferenceSet CreatedAt="2015-08-05T10:24:09" MetaType="PacBio.DataSet.ReferenceSet" Name="" Tags="" TimeStampedName="" UniqueId="20a27082-8ffc-24dc-cc80-55628f526859" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioData [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="" ResourceId="../lambdaNEB.fa" TimeStampedName="-150805_172409" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.SamIndex" ResourceId="../lambdaNEB.fa.fai" TimeStampedName="PacBio.Index.SamIndex-150805_172409" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>48502</pbds:TotalLength>
+ <pbds:NumRecords>1</pbds:NumRecords>
+ <pbds:Organism/>
+ <pbds:Ploidy/>
+ <pbds:Contigs>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="48502" Name="lambda_NEB3011"/>
+ </pbds:Contigs>
+ </pbds:DataSetMetadata>
+</pbds:ReferenceSet>
diff --git a/pbcore/data/datasets/pbalchemysim.alignmentset.xml b/pbcore/data/datasets/pbalchemysim.alignmentset.xml
new file mode 100644
index 0000000..88339c5
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim.alignmentset.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0" ?>
+<pbds:AlignmentSet CreatedAt="2015-08-05T10:43:42" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="" UniqueId="4be3b4e4-6915-dac6-bccb-8f1eb791c6e6" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioData [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_172518" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim0.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim0.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_174342" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim1.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim1.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>240674</pbds:TotalLength>
+ <pbds:NumRecords>177</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+ <DataSets>
+ <AlignmentSet CreatedAt="2015-08-05T10:43:42" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="" UniqueId="67473387-ff6e-8320-f9ac-f5d2fe878d29" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_172518" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim0.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim0.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_174342" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim1.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim1.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>240674</pbds:TotalLength>
+ <pbds:NumRecords>177</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+ </AlignmentSet>
+ <AlignmentSet CreatedAt="2015-08-05T10:43:42" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="" UniqueId="795a907f-37c3-8e8a-5642-ff677d4e466a" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_174342" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim1.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim1.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>117086</pbds:TotalLength>
+ <pbds:NumRecords>85</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+ </AlignmentSet>
+ </DataSets>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml b/pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml
new file mode 100644
index 0000000..17c33c1
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" ?>
+<pbds:HdfSubreadSet CreatedAt="2015-08-07T13:57:03" MetaType="PacBio.DataSet.HdfSubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.HdfSubreadSet-150807_205703" UniqueId="832b12ed-7c0f-f620-a791-49aa02198c53" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocati [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.BasFile" ResourceId="pbalchemysim0.bas.h5" TimeStampedName="PacBio.SubreadFile.BasFile-150807_205703" UniqueId="24837e10-e3dd-4f8d-8cee-fef459b5f907"/>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.BasFile" ResourceId="pbalchemysim1.bas.h5" TimeStampedName="PacBio.SubreadFile.BasFile-150807_205703" UniqueId="de557acf-ac6c-4827-ba71-a1e41afc0174"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>249482</pbds:TotalLength>
+ <pbds:NumRecords>18</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:HdfSubreadSet>
diff --git a/pbcore/data/datasets/pbalchemysim.pbalign.xml b/pbcore/data/datasets/pbalchemysim.pbalign.xml
deleted file mode 100644
index 955343e..0000000
--- a/pbcore/data/datasets/pbalchemysim.pbalign.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<AlignmentSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:36" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" UniqueId="ddc7ca6d-8a64-2375-3b65-626b11c3d560" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam"><FileIndices><FileIndex [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml b/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
new file mode 100644
index 0000000..c8f38ac
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
@@ -0,0 +1,47 @@
+<?xml version="1.0" ?>
+<pbds:AlignmentSet CreatedAt="2015-08-05T10:25:18" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.AlignmentSet-150807_210959" UniqueId="e09f7fc7-a9a7-d142-e280-13680de85722" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_172518" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim0.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim0.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>52023</pbds:TotalLength>
+ <pbds:NumRecords>40</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+ <Filters>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="C.beijerinckii.9"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="R.sphaeroides.1"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="S.epidermidis.3"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="S.epidermidis.4"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="B.vulgatus.4"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="C.beijerinckii.14"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ </Filters>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml b/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
new file mode 100644
index 0000000..9b72fc1
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
@@ -0,0 +1,47 @@
+<?xml version="1.0" ?>
+<pbds:AlignmentSet CreatedAt="2015-08-05T10:25:18" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.AlignmentSet-150807_211009" UniqueId="9a49c1d9-ab09-f14e-8410-678d2e9986f4" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_172518" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim0.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim0.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>71565</pbds:TotalLength>
+ <pbds:NumRecords>52</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+ <Filters>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="E.faecalis.2"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="E.faecalis.1"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="S.epidermidis.2"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="B.vulgatus.5"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="E.coli.6"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rname" Operator="=" Value="C.beijerinckii.13"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ </Filters>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/pbalchemysim0.alignmentset.xml b/pbcore/data/datasets/pbalchemysim0.alignmentset.xml
new file mode 100644
index 0000000..8684c77
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim0.alignmentset.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" ?>
+<pbds:AlignmentSet CreatedAt="2015-08-05T10:25:18" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="" UniqueId="cb534760-6ed0-614e-e6cf-3d2a1b968206" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioData [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_172518" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim0.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim0.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_172518" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>123588</pbds:TotalLength>
+ <pbds:NumRecords>92</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml b/pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml
new file mode 100644
index 0000000..c94a87e
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" ?>
+<pbds:HdfSubreadSet CreatedAt="2015-08-07T13:56:03" MetaType="PacBio.DataSet.HdfSubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.HdfSubreadSet-150807_205603" UniqueId="d41f7d4b-0663-d35a-ec47-ac2f47a73c8f" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocati [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.BasFile" ResourceId="pbalchemysim0.bas.h5" TimeStampedName="PacBio.SubreadFile.BasFile-150807_205603" UniqueId="f135275c-7c69-4a28-b736-fafaef3e7612"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>128093</pbds:TotalLength>
+ <pbds:NumRecords>9</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:HdfSubreadSet>
diff --git a/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi b/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi
index 126ebb7..1ae468c 100644
Binary files a/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi and b/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi differ
diff --git a/pbcore/data/datasets/pbalchemysim0.pbalign.chunk0contigs.xml b/pbcore/data/datasets/pbalchemysim0.pbalign.chunk0contigs.xml
deleted file mode 100644
index ac10d5e..0000000
--- a/pbcore/data/datasets/pbalchemysim0.pbalign.chunk0contigs.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<AlignmentSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:29" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" UniqueId="c35c10ea-504f-fc3f-ef9b-7f8934061c44" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="/home/UNIXHOME/mdsmith/p4/mainline/software/smrtan [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim0.pbalign.chunk1contigs.xml b/pbcore/data/datasets/pbalchemysim0.pbalign.chunk1contigs.xml
deleted file mode 100644
index 0b6aa73..0000000
--- a/pbcore/data/datasets/pbalchemysim0.pbalign.chunk1contigs.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<AlignmentSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:29" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" UniqueId="02da8218-8636-10ae-89e9-413908e60b18" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="/home/UNIXHOME/mdsmith/p4/mainline/software/smrtan [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim0.pbalign.xml b/pbcore/data/datasets/pbalchemysim0.pbalign.xml
deleted file mode 100644
index 3f4838e..0000000
--- a/pbcore/data/datasets/pbalchemysim0.pbalign.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<AlignmentSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:29" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" UniqueId="ece766a0-e7df-a647-ea6b-abaeaaad164c" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.pbalign.bam"><FileIndices><FileIndex [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim0.reference.xml b/pbcore/data/datasets/pbalchemysim0.reference.xml
deleted file mode 100644
index 0bc2b06..0000000
--- a/pbcore/data/datasets/pbalchemysim0.reference.xml
+++ /dev/null
@@ -1,77 +0,0 @@
-<?xml version="1.0" ?>
-<ReferenceSet CreatedAt="2015-07-20T15:34:19" MetaType="PacBio.DataSet.ReferenceSet" Name="" Tags="" UniqueId="45a23d37-50b1-9d86-2253-085f10cc0bc1" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource MetaType="PacBio.ReferenceFile.ReferenceFastaFile" ResourceId="pbalchemysim0.reference.fasta">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.SamIndex" ResourceId="pbalchemysim0.reference.fasta.fai"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- <DataSetMetadata>
- <TotalLength>85774</TotalLength>
- <NumRecords>59</NumRecords>
- <Organism/>
- <Ploidy/>
- <Contigs>
- <Contig Description="" Digest="DEPRECATED" Length="1458" Name="A.baumannii.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1462" Name="A.odontolyticus.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="B.cereus.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1473" Name="B.cereus.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="B.cereus.4"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="B.cereus.6"/>
- <Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.3"/>
- <Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.4"/>
- <Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.5"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.3"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.4"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.5"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.6"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.7"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.8"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.9"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.10"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.11"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.12"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.13"/>
- <Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.14"/>
- <Contig Description="" Digest="DEPRECATED" Length="1423" Name="D.radiodurans.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1423" Name="D.radiodurans.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1482" Name="E.faecalis.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1482" Name="E.faecalis.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.4"/>
- <Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.5"/>
- <Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.6"/>
- <Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.7"/>
- <Contig Description="" Digest="DEPRECATED" Length="1424" Name="H.pylori.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1494" Name="L.gasseri.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.3"/>
- <Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.5"/>
- <Contig Description="" Digest="DEPRECATED" Length="1462" Name="N.meningitidis.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1446" Name="P.acnes.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1457" Name="P.aeruginosa.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1457" Name="P.aeruginosa.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1386" Name="R.sphaeroides.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1388" Name="R.sphaeroides.3"/>
- <Contig Description="" Digest="DEPRECATED" Length="1473" Name="S.aureus.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1473" Name="S.aureus.4"/>
- <Contig Description="" Digest="DEPRECATED" Length="1473" Name="S.aureus.5"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.3"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.4"/>
- <Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.5"/>
- <Contig Description="" Digest="DEPRECATED" Length="1470" Name="S.agalactiae.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1478" Name="S.mutans.1"/>
- <Contig Description="" Digest="DEPRECATED" Length="1478" Name="S.mutans.2"/>
- <Contig Description="" Digest="DEPRECATED" Length="1467" Name="S.pneumoniae.1"/>
- </Contigs>
- </DataSetMetadata>
-</ReferenceSet>
diff --git a/pbcore/data/datasets/pbalchemysim0.referenceset.xml b/pbcore/data/datasets/pbalchemysim0.referenceset.xml
new file mode 100644
index 0000000..4a60abe
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim0.referenceset.xml
@@ -0,0 +1,77 @@
+<?xml version="1.0" ?>
+<pbds:ReferenceSet CreatedAt="2015-08-05T10:24:51" MetaType="PacBio.DataSet.ReferenceSet" Name="" Tags="" TimeStampedName="" UniqueId="76c0ea62-7887-fd36-d6f6-dd87526b4109" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioData [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.ReferenceFile.ReferenceFastaFile" ResourceId="pbalchemysim0.reference.fasta" TimeStampedName="PacBio.ReferenceFile.ReferenceFastaFile-150805_172451" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.SamIndex" ResourceId="pbalchemysim0.reference.fasta.fai" TimeStampedName="PacBio.Index.SamIndex-150805_172451" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>85774</pbds:TotalLength>
+ <pbds:NumRecords>59</pbds:NumRecords>
+ <pbds:Organism/>
+ <pbds:Ploidy/>
+ <pbds:Contigs>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1458" Name="A.baumannii.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1462" Name="A.odontolyticus.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="B.cereus.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1473" Name="B.cereus.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="B.cereus.4"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="B.cereus.6"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.3"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.4"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1449" Name="B.vulgatus.5"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.3"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.4"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.5"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.6"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.7"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.8"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.9"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.10"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.11"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.12"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.13"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1433" Name="C.beijerinckii.14"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1423" Name="D.radiodurans.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1423" Name="D.radiodurans.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1482" Name="E.faecalis.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1482" Name="E.faecalis.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.4"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.5"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.6"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1463" Name="E.coli.7"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1424" Name="H.pylori.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1494" Name="L.gasseri.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.3"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1471" Name="L.monocytogenes.5"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1462" Name="N.meningitidis.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1446" Name="P.acnes.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1457" Name="P.aeruginosa.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1457" Name="P.aeruginosa.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1386" Name="R.sphaeroides.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1388" Name="R.sphaeroides.3"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1473" Name="S.aureus.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1473" Name="S.aureus.4"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1473" Name="S.aureus.5"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.3"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.4"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1472" Name="S.epidermidis.5"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1470" Name="S.agalactiae.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1478" Name="S.mutans.1"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1478" Name="S.mutans.2"/>
+ <pbds:Contig Description="" Digest="DEPRECATED" Length="1467" Name="S.pneumoniae.1"/>
+ </pbds:Contigs>
+ </pbds:DataSetMetadata>
+</pbds:ReferenceSet>
diff --git a/pbcore/data/datasets/pbalchemysim0.subread.xml b/pbcore/data/datasets/pbalchemysim0.subread.xml
deleted file mode 100644
index 803644c..0000000
--- a/pbcore/data/datasets/pbalchemysim0.subread.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<SubreadSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:25" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" UniqueId="a3c23749-a427-3072-bc56-5e2409e287b4" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.subreads.bam"><FileIndices /></ExternalR [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim0.subreads.bam.bai b/pbcore/data/datasets/pbalchemysim0.subreads.bam.bai
new file mode 100644
index 0000000..a4d59b6
Binary files /dev/null and b/pbcore/data/datasets/pbalchemysim0.subreads.bam.bai differ
diff --git a/pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi b/pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi
new file mode 100644
index 0000000..0930a2e
Binary files /dev/null and b/pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi differ
diff --git a/pbcore/data/datasets/pbalchemysim0.subreadset.xml b/pbcore/data/datasets/pbalchemysim0.subreadset.xml
new file mode 100644
index 0000000..ced5930
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim0.subreadset.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" ?>
+<pbds:SubreadSet CreatedAt="2015-08-06T17:07:36" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.SubreadSet-150807_000736" UniqueId="dd7edc7d-0c24-0823-f918-394d4cbd0f9d" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http: [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.subreads.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150807_000736" UniqueId="c55c8ed2-4821-4c48-9395-94625363fe6d"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>-1</pbds:TotalLength>
+ <pbds:NumRecords>-1</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:SubreadSet>
diff --git a/pbcore/data/datasets/pbalchemysim1.alignmentset.xml b/pbcore/data/datasets/pbalchemysim1.alignmentset.xml
new file mode 100644
index 0000000..3cb6ba9
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim1.alignmentset.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" ?>
+<pbds:AlignmentSet CreatedAt="2015-08-05T10:43:42" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" TimeStampedName="" UniqueId="4be3b4e4-6915-dac6-bccb-8f1eb791c6e6" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioData [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.pbalign.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150805_174342" UniqueId="6699f7d3-8def-0af8-fd4d-19238d2352b2">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="pbalchemysim1.pbalign.bam.pbi" TimeStampedName="PacBio.Index.PacBioIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ <pbbase:FileIndex MetaType="PacBio.Index.BamIndex" ResourceId="pbalchemysim1.pbalign.bam.bai" TimeStampedName="PacBio.Index.BamIndex-150805_174342" UniqueId="370dc654-d2a5-e575-92cc-6f9c75a403f4"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>117086</pbds:TotalLength>
+ <pbds:NumRecords>85</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:AlignmentSet>
diff --git a/pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml b/pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml
new file mode 100644
index 0000000..7b933bc
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" ?>
+<pbds:HdfSubreadSet CreatedAt="2015-08-07T13:56:30" MetaType="PacBio.DataSet.HdfSubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.HdfSubreadSet-150807_205630" UniqueId="87e2ec76-dbc4-4ce2-e9f1-f274d0e204db" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocati [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.BasFile" ResourceId="pbalchemysim1.bas.h5" TimeStampedName="PacBio.SubreadFile.BasFile-150807_205630" UniqueId="8180f7fb-845c-4ce1-af1e-518e70874fe4"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>121389</pbds:TotalLength>
+ <pbds:NumRecords>9</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:HdfSubreadSet>
diff --git a/pbcore/data/datasets/pbalchemysim1.pbalign.xml b/pbcore/data/datasets/pbalchemysim1.pbalign.xml
deleted file mode 100644
index b2091b1..0000000
--- a/pbcore/data/datasets/pbalchemysim1.pbalign.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<AlignmentSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:35" MetaType="PacBio.DataSet.AlignmentSet" Name="" Tags="" UniqueId="768de2d3-3c72-4868-006d-56c38569b0f5" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.pbalign.bam"><FileIndices><FileIndex [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim1.subread.xml b/pbcore/data/datasets/pbalchemysim1.subread.xml
deleted file mode 100644
index 2e4a21c..0000000
--- a/pbcore/data/datasets/pbalchemysim1.subread.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<SubreadSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" CreatedAt="2015-07-09T17:04:30" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" UniqueId="cdbacc75-70cc-bd40-f2cb-ce984e7fd4a3" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"><ExternalResources><ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.subreads.bam"><FileIndices /></ExternalR [...]
\ No newline at end of file
diff --git a/pbcore/data/datasets/pbalchemysim1.subreads.bam.bai b/pbcore/data/datasets/pbalchemysim1.subreads.bam.bai
new file mode 100644
index 0000000..5db0891
Binary files /dev/null and b/pbcore/data/datasets/pbalchemysim1.subreads.bam.bai differ
diff --git a/pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi b/pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi
new file mode 100644
index 0000000..d637f58
Binary files /dev/null and b/pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi differ
diff --git a/pbcore/data/datasets/pbalchemysim1.subreadset.xml b/pbcore/data/datasets/pbalchemysim1.subreadset.xml
new file mode 100644
index 0000000..5e272d7
--- /dev/null
+++ b/pbcore/data/datasets/pbalchemysim1.subreadset.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" ?>
+<pbds:SubreadSet CreatedAt="2015-08-06T17:07:38" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.SubreadSet-150807_000738" UniqueId="6d5ce5ad-cd98-ffe3-2607-ca3788b593e0" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http: [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim1.subreads.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150807_000738" UniqueId="83272dbe-56ed-44da-b88f-8a62d8587abb"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>-1</pbds:TotalLength>
+ <pbds:NumRecords>-1</pbds:NumRecords>
+ </pbds:DataSetMetadata>
+</pbds:SubreadSet>
diff --git a/pbcore/data/datasets/reference.dataset.xml b/pbcore/data/datasets/reference.dataset.xml
index 02ea01d..e71c176 100644
--- a/pbcore/data/datasets/reference.dataset.xml
+++ b/pbcore/data/datasets/reference.dataset.xml
@@ -1,20 +1,51 @@
<?xml version="1.0" encoding="utf-8"?>
-<ReferenceSet xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" MetaType="PacBio.DataSet.ReferenceSet" Name="DataSet_ReferenceSet" Tags="barcode moreTags mapping mytags" UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" CreatedAt="2015-01-27T09:00:01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource Name="First References FASTA" Description="Points to an example references FASTA file." MetaType="PacBio.ReferenceFile.ReferenceFastaFile" ResourceId="file:///mnt/path/to/reference.fasta" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.SaWriterIndex" ResourceId="file:///mnt/path/to/reference.fasta.sa"/>
- <FileIndex MetaType="PacBio.Index.SamIndex" ResourceId="file:///mnt/path/to/reference.fasta.fai"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- <DataSetMetadata>
- <TotalLength>5000000</TotalLength>
- <NumRecords>500</NumRecords>
- <Organism>Tribble</Organism>
- <Ploidy>Diploid</Ploidy>
- <Contigs>
- <Contig Name="gi|229359445|emb|AM181176.4|" Description="Pseudomonas fluorescens SBW25 complete genome|quiver" Length="6722109" Digest="f627c795efad7ce0050ed42b942d408e"/>
- </Contigs>
- </DataSetMetadata>
-</ReferenceSet>
+<pbds:ReferenceSet
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="referenceset_150304_231155"
+ MetaType="PacBio.DataSet.ReferenceSet"
+ Name="DataSet_ReferenceSet"
+ Tags="barcode moreTags mapping mytags"
+ Version="2.3.0"
+ CreatedAt="2015-01-27T09:00:01">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ Name="First References FASTA"
+ Description="Points to an example references FASTA file."
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5293"
+ TimeStampedName="referencefasta_150304_231155"
+ MetaType="PacBio.ReferenceFile.ReferenceFastaFile"
+ ResourceId="file:///mnt/path/to/reference.fasta"
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5393"
+ TimeStampedName="sawriter_index_150304_231155"
+ MetaType="PacBio.Index.SaWriterIndex"
+ ResourceId="file:///mnt/path/to/reference.fasta.sa"/>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5493"
+ TimeStampedName="sam_index_150304_231155"
+ MetaType="PacBio.Index.SamIndex"
+ ResourceId="file:///mnt/path/to/reference.fasta.fai"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>5000000</pbds:TotalLength>
+ <pbds:NumRecords>500</pbds:NumRecords>
+ <pbds:Organism>Tribble</pbds:Organism>
+ <pbds:Ploidy>Diploid</pbds:Ploidy>
+ <pbds:Contigs>
+ <pbds:Contig
+ Name="gi|229359445|emb|AM181176.4|"
+ Description="Pseudomonas fluorescens SBW25 complete genome|quiver"
+ Length="6722109"
+ Digest="f627c795efad7ce0050ed42b942d408e"/>
+ </pbds:Contigs>
+ </pbds:DataSetMetadata>
+</pbds:ReferenceSet>
diff --git a/pbcore/data/datasets/subread.dataset.xml b/pbcore/data/datasets/subread.dataset.xml
index 98a6ae0..890d4b0 100644
--- a/pbcore/data/datasets/subread.dataset.xml
+++ b/pbcore/data/datasets/subread.dataset.xml
@@ -1,472 +1,544 @@
<?xml version="1.0" encoding="utf-8"?>
-<SubreadSet xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" MetaType="PacBio.DataSet.SubreadSet" Name="DataSet_SubreadSet" Tags="barcode moreTags mapping mytags" UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c" Version="2.3.0" CreatedAt="2015-01-27T09:00:01" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
-<ExternalResources>
- <ExternalResource Name="First Subreads BAM" Description="Points to an example Subreads BAM file." MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="file:///mnt/path/to/subreads0.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/subreads0.pbi"/>
- </FileIndices>
- <ExternalResources>
- <ExternalResource Name="First scraps BAM" Description="Points to an example scraps BAM file." MetaType="PacBio.SubreadFile.ScrapsBamFile" ResourceId="file:///mnt/path/to/scraps0.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/scraps0.pbi"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- </ExternalResource>
- <ExternalResource Name="Second Subreads BAM" Description="Points to another example Subreads BAM file." MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="file:///mnt/path/to/subreads1.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/subreads0.pbi"/>
- </FileIndices>
- <ExternalResources>
- <ExternalResource Name="Second scraps BAM" Description="Points to another example scraps BAM file." MetaType="PacBio.SubreadFile.ScrapsBamFile" ResourceId="file:///mnt/path/to/scraps1.bam" Tags="Example">
- <FileIndices>
- <FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/scraps1.pbi"/>
- </FileIndices>
- </ExternalResource>
- </ExternalResources>
- </ExternalResource>
-</ExternalResources>
-<Filters>
- <Filter>
- <Properties>
- <Property Name="rq" Value="0.75" Operator=">"/>
- </Properties>
- </Filter>
- <Filter>
- <Properties>
- <Property Name="QNAME" Value="100/0/0_100" Operator="=="/>
- </Properties>
- </Filter>
-</Filters>
-<DataSetMetadata>
- <TotalLength>500000</TotalLength>
- <NumRecords>500</NumRecords>
- <Collections>
- <CollectionMetadata Context="m152720_092723_00114_c100480560100000001823075906281381_s1_p0" InstrumentName="RS" InstrumentId="43210">
- <InstCtrlVer>2.3.0.0.140640</InstCtrlVer>
- <SigProcVer>NRT at 172.31.128.10:8082, SwVer=2300.140640, HwVer=1.0</SigProcVer>
- <RunDetails>
- <RunId>e903682f-e502-465c-a2b6-9dd77c9f43fc</RunId>
- <Name>beta4_130726_biotin_DEV_vs_MFG_PB11K_9458p</Name>
- </RunDetails>
- <WellSample Name="Well Sample 1" UniqueId="aaa2df90-d44f-4a48-9f35-3b99473c68f5">
- <PlateId>2014-12-24_141_NGAT_Igor_bisPNA Enrichment_Mag Bead Elution Buffers</PlateId>
- <WellName>B01</WellName>
- <Concentration>10</Concentration>
- <SampleReuseEnabled>true</SampleReuseEnabled>
- <StageHotstartEnabled>true</StageHotstartEnabled>
- <SizeSelectionEnabled>true</SizeSelectionEnabled>
- <UseCount>0</UseCount>
- <Comments>Lorem ipsum</Comments>
- <BioSamplePointers>
- <BioSamplePointer>abc2df90-d44f-4a48-9f35-3b99473c68f5</BioSamplePointer>
- </BioSamplePointers>
- </WellSample>
- <Automation>
- <AutomationParameters>
- <AutomationParameter/>
- </AutomationParameters>
- </Automation>
- <CollectionNumber>0</CollectionNumber>
- <CellIndex>0</CellIndex>
- <CellPac Barcode="100480560100000001823075906281381"/>
- <Primary>
- <AutomationName>BasecallerV1</AutomationName>
- <ConfigFileName>1-3-0_Standard_C2.xml</ConfigFileName>
- <SequencingCondition/>
- <ResultsFolder>Analysis_Results</ResultsFolder>
- <CollectionPathUri>rsy://mp-rsync/vol56//RS_DATA_STAGING//2014-12-24_141_NGAT_Igor_bisPNA%20Enrichment_Mag%20Bead%20Elution%20Buffers_1094/B01_1</CollectionPathUri>
- <CopyFiles>
- <CollectionFileCopy>Bam</CollectionFileCopy>
- </CopyFiles>
- </Primary>
- </CollectionMetadata>
- </Collections>
- <BioSamples>
- <BioSample UniqueId="abc2df90-d44f-4a48-9f35-3b99473c68f5" Name="consectetur purus" Description="Risus sit amet lectus vehicula vulputate quisque porta accumsan venenatis." CreatedAt="2015-01-20T13:27:23.9271737-08:00"/>
- </BioSamples>
- <SummaryStats>
- <AdapterDimerFraction>0.1</AdapterDimerFraction>
- <ShortInsertFraction>0.1</ShortInsertFraction>
- <NumSequencingZmws>0</NumSequencingZmws>
- <ProdDist>
- <NumBins>4</NumBins>
- <BinCounts>
- <BinCount>1576</BinCount>
- <BinCount>901</BinCount>
- <BinCount>399</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <MetricDescription>Productivity</MetricDescription>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>Productive</BinLabel>
- <BinLabel>Other</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ProdDist>
- <ReadTypeDist>
- <NumBins>9</NumBins>
- <BinCounts>
- <BinCount>1474</BinCount>
- <BinCount>799</BinCount>
- <BinCount>4</BinCount>
- <BinCount>181</BinCount>
- <BinCount>92</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>326</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <MetricDescription>Read Type</MetricDescription>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>FullHqRead0</BinLabel>
- <BinLabel>FullHqRead1</BinLabel>
- <BinLabel>PartialHqRead0</BinLabel>
- <BinLabel>PartialHqRead1</BinLabel>
- <BinLabel>PartialHqRead2</BinLabel>
- <BinLabel>Multiload</BinLabel>
- <BinLabel>Indeterminate</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ReadTypeDist>
- <ReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>4528.69384765625</SampleMean>
- <SampleMed>5227</SampleMed>
- <SampleStd>2322.8055598026981</SampleStd>
- <Sample95thPct>7367</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>62</BinCount>
- <BinCount>39</BinCount>
- <BinCount>36</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>19</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>32</BinCount>
- <BinCount>32</BinCount>
- <BinCount>40</BinCount>
- <BinCount>45</BinCount>
- <BinCount>54</BinCount>
- <BinCount>73</BinCount>
- <BinCount>77</BinCount>
- <BinCount>97</BinCount>
- <BinCount>95</BinCount>
- <BinCount>49</BinCount>
- <BinCount>17</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinWidth>418.89999389648438</BinWidth>
- <MinOutlierValue>77</MinOutlierValue>
- <MinBinValue>77</MinBinValue>
- <MaxBinValue>12225.1025390625</MaxBinValue>
- <MaxOutlierValue>12644</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- </ReadLenDist>
- <ReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.82736450433731079</SampleMean>
- <SampleMed>0.83167940378189087</SampleMed>
- <SampleStd>0.029663275550147809</SampleStd>
- <Sample95thPct>0.86801999807357788</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>12</BinCount>
- <BinCount>8</BinCount>
- <BinCount>11</BinCount>
- <BinCount>10</BinCount>
- <BinCount>17</BinCount>
- <BinCount>11</BinCount>
- <BinCount>20</BinCount>
- <BinCount>24</BinCount>
- <BinCount>24</BinCount>
- <BinCount>34</BinCount>
- <BinCount>25</BinCount>
- <BinCount>38</BinCount>
- <BinCount>52</BinCount>
- <BinCount>33</BinCount>
- <BinCount>45</BinCount>
- <BinCount>48</BinCount>
- <BinCount>57</BinCount>
- <BinCount>47</BinCount>
- <BinCount>69</BinCount>
- <BinCount>65</BinCount>
- <BinCount>55</BinCount>
- <BinCount>51</BinCount>
- <BinCount>57</BinCount>
- <BinCount>42</BinCount>
- <BinCount>29</BinCount>
- <BinCount>12</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- <BinWidth>0.0049052196554839611</BinWidth>
- <MinOutlierValue>0.7500004768371582</MinOutlierValue>
- <MinBinValue>0.7500004768371582</MinBinValue>
- <MaxBinValue>0.89225196838378906</MaxBinValue>
- <MaxOutlierValue>0.89715707302093506</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- </ReadQualDist>
- <ControlReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>4528.69384765625</SampleMean>
- <SampleMed>5227</SampleMed>
- <SampleStd>2322.8055598026981</SampleStd>
- <Sample95thPct>7367</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>62</BinCount>
- <BinCount>39</BinCount>
- <BinCount>36</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>19</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>32</BinCount>
- <BinCount>32</BinCount>
- <BinCount>40</BinCount>
- <BinCount>45</BinCount>
- <BinCount>54</BinCount>
- <BinCount>73</BinCount>
- <BinCount>77</BinCount>
- <BinCount>97</BinCount>
- <BinCount>95</BinCount>
- <BinCount>49</BinCount>
- <BinCount>17</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinWidth>418.89999389648438</BinWidth>
- <MinOutlierValue>77</MinOutlierValue>
- <MinBinValue>77</MinBinValue>
- <MaxBinValue>12225.1025390625</MaxBinValue>
- <MaxOutlierValue>12644</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- </ControlReadLenDist>
- <ControlReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.82736450433731079</SampleMean>
- <SampleMed>0.83167940378189087</SampleMed>
- <SampleStd>0.029663275550147809</SampleStd>
- <Sample95thPct>0.86801999807357788</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>12</BinCount>
- <BinCount>8</BinCount>
- <BinCount>11</BinCount>
- <BinCount>10</BinCount>
- <BinCount>17</BinCount>
- <BinCount>11</BinCount>
- <BinCount>20</BinCount>
- <BinCount>24</BinCount>
- <BinCount>24</BinCount>
- <BinCount>34</BinCount>
- <BinCount>25</BinCount>
- <BinCount>38</BinCount>
- <BinCount>52</BinCount>
- <BinCount>33</BinCount>
- <BinCount>45</BinCount>
- <BinCount>48</BinCount>
- <BinCount>57</BinCount>
- <BinCount>47</BinCount>
- <BinCount>69</BinCount>
- <BinCount>65</BinCount>
- <BinCount>55</BinCount>
- <BinCount>51</BinCount>
- <BinCount>57</BinCount>
- <BinCount>42</BinCount>
- <BinCount>29</BinCount>
- <BinCount>12</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- <BinWidth>0.0049052196554839611</BinWidth>
- <MinOutlierValue>0.7500004768371582</MinOutlierValue>
- <MinBinValue>0.7500004768371582</MinBinValue>
- <MaxBinValue>0.89225196838378906</MaxBinValue>
- <MaxOutlierValue>0.89715707302093506</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- </ControlReadQualDist>
- <MedianInsertDist>
- <SampleSize>973</SampleSize>
- <SampleMean>513.21990966796875</SampleMean>
- <SampleMed>350</SampleMed>
- <SampleStd>575.83020626506971</SampleStd>
- <Sample95thPct>1322</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>714</BinCount>
- <BinCount>101</BinCount>
- <BinCount>32</BinCount>
- <BinCount>18</BinCount>
- <BinCount>13</BinCount>
- <BinCount>8</BinCount>
- <BinCount>5</BinCount>
- <BinCount>6</BinCount>
- <BinCount>7</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>1</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>4</BinCount>
- <BinCount>6</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>7</BinCount>
- <BinCount>1</BinCount>
- <BinCount>3</BinCount>
- <BinCount>4</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>1</BinCount>
- <BinCount>9</BinCount>
- </BinCounts>
- <BinWidth>93.333335876464844</BinWidth>
- <MinOutlierValue>289</MinOutlierValue>
- <MinBinValue>289</MinBinValue>
- <MaxBinValue>2995.666259765625</MaxBinValue>
- <MaxOutlierValue>6278</MaxOutlierValue>
- <MetricDescription>Median Insert</MetricDescription>
- </MedianInsertDist>
- <InsertReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>4528.69384765625</SampleMean>
- <SampleMed>5227</SampleMed>
- <SampleStd>2322.8055598026981</SampleStd>
- <Sample95thPct>7367</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>62</BinCount>
- <BinCount>39</BinCount>
- <BinCount>36</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>19</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>32</BinCount>
- <BinCount>32</BinCount>
- <BinCount>40</BinCount>
- <BinCount>45</BinCount>
- <BinCount>54</BinCount>
- <BinCount>73</BinCount>
- <BinCount>77</BinCount>
- <BinCount>97</BinCount>
- <BinCount>95</BinCount>
- <BinCount>49</BinCount>
- <BinCount>17</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinWidth>418.89999389648438</BinWidth>
- <MinOutlierValue>77</MinOutlierValue>
- <MinBinValue>77</MinBinValue>
- <MaxBinValue>12225.1025390625</MaxBinValue>
- <MaxOutlierValue>12644</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- </InsertReadLenDist>
- <InsertReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.82736450433731079</SampleMean>
- <SampleMed>0.83167940378189087</SampleMed>
- <SampleStd>0.029663275550147809</SampleStd>
- <Sample95thPct>0.86801999807357788</Sample95thPct>
- <NumBins>30</NumBins>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>12</BinCount>
- <BinCount>8</BinCount>
- <BinCount>11</BinCount>
- <BinCount>10</BinCount>
- <BinCount>17</BinCount>
- <BinCount>11</BinCount>
- <BinCount>20</BinCount>
- <BinCount>24</BinCount>
- <BinCount>24</BinCount>
- <BinCount>34</BinCount>
- <BinCount>25</BinCount>
- <BinCount>38</BinCount>
- <BinCount>52</BinCount>
- <BinCount>33</BinCount>
- <BinCount>45</BinCount>
- <BinCount>48</BinCount>
- <BinCount>57</BinCount>
- <BinCount>47</BinCount>
- <BinCount>69</BinCount>
- <BinCount>65</BinCount>
- <BinCount>55</BinCount>
- <BinCount>51</BinCount>
- <BinCount>57</BinCount>
- <BinCount>42</BinCount>
- <BinCount>29</BinCount>
- <BinCount>12</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- <BinWidth>0.0049052196554839611</BinWidth>
- <MinOutlierValue>0.7500004768371582</MinOutlierValue>
- <MinBinValue>0.7500004768371582</MinBinValue>
- <MaxBinValue>0.89225196838378906</MaxBinValue>
- <MaxOutlierValue>0.89715707302093506</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- </InsertReadQualDist>
- </SummaryStats>
-</DataSetMetadata>
-</SubreadSet>
+<pbds:SubreadSet
+ xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
+ xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd"
+ xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd"
+ xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
+ TimeStampedName="subreadset_150304_231155"
+ MetaType="PacBio.DataSet.SubreadSet"
+ Name="DataSet_SubreadSet"
+ Tags="barcode moreTags mapping mytags"
+ Version="3.0.0"
+ CreatedAt="2015-01-27T09:00:01">
+<pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5193"
+ TimeStampedName="subread_bam_150304_231155"
+ MetaType="PacBio.SubreadFile.SubreadBamFile"
+ ResourceId="file:///mnt/path/to/subreads0.bam"
+ Name="First Subreads BAM"
+ Description="Points to an example Subreads BAM file."
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5194"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/subreads0.pbi"/>
+ </pbbase:FileIndices>
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ UniqueId="b096d0a3-94b8-4918-b3af-a3f81bbe5195"
+ TimeStampedName="scraps_bam_150304_231155"
+ MetaType="PacBio.SubreadFile.ScrapsBamFile"
+ ResourceId="file:///mnt/path/to/scraps0.bam"
+ Tags="Example"
+ Name="First scraps BAM"
+ Description="Points to an example scraps BAM file.">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b096d0a3-94b8-4918-b3af-a3f81bbe5196"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/scraps0.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ </pbbase:ExternalResource>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5197"
+ TimeStampedName="subread_bam_150304_231155"
+ MetaType="PacBio.SubreadFile.SubreadBamFile"
+ ResourceId="file:///mnt/path/to/subreads1.bam"
+ Name="Second Subreads BAM"
+ Description="Points to another example Subreads BAM file."
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b096d0a3-94b8-4918-b3af-a3f81bbe5198"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/subreads0.pbi"/>
+ </pbbase:FileIndices>
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5199"
+ TimeStampedName="scraps_bam_150304_231155"
+ MetaType="PacBio.SubreadFile.ScrapsBamFile"
+ ResourceId="file:///mnt/path/to/scraps1.bam"
+ Name="Second scraps BAM" Description="Points to another example scraps BAM file."
+ Tags="Example">
+ <pbbase:FileIndices>
+ <pbbase:FileIndex
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5190"
+ TimeStampedName="bam_index_150304_231155"
+ MetaType="PacBio.Index.PacBioIndex"
+ ResourceId="file:///mnt/path/to/scraps1.pbi"/>
+ </pbbase:FileIndices>
+ </pbbase:ExternalResource>
+ </pbbase:ExternalResources>
+ </pbbase:ExternalResource>
+</pbbase:ExternalResources>
+<pbds:Filters>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="rq" Value="0.75" Operator=">"/>
+ </pbbase:Properties>
+ </pbds:Filter>
+ <pbds:Filter>
+ <pbbase:Properties>
+ <pbbase:Property Name="QNAME" Value="100/0/0_100" Operator="=="/>
+ </pbbase:Properties>
+ </pbds:Filter>
+</pbds:Filters>
+<pbds:DataSetMetadata>
+ <pbds:TotalLength>500000</pbds:TotalLength>
+ <pbds:NumRecords>500</pbds:NumRecords>
+ <pbmeta:Collections>
+ <pbmeta:CollectionMetadata
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5393"
+ TimeStampedName="collection_150304_231155"
+ MetaType="PacBio.CollectionMetadata"
+ Context="m152720_092723_00114_c100480560100000001823075906281381_s1_p0"
+ InstrumentName="RS"
+ InstrumentId="43210">
+ <pbmeta:InstCtrlVer>2.3.0.0.140640</pbmeta:InstCtrlVer>
+ <pbmeta:SigProcVer>NRT at 172.31.128.10:8082, SwVer=2300.140640, HwVer=1.0</pbmeta:SigProcVer>
+ <pbmeta:RunDetails>
+ <pbmeta:RunId>e903682f-e502-465c-a2b6-9dd77c9f43fc</pbmeta:RunId>
+ <pbmeta:Name>beta4_130726_biotin_DEV_vs_MFG_PB11K_9458p</pbmeta:Name>
+ </pbmeta:RunDetails>
+ <pbmeta:WellSample Name="Well Sample 1">
+ <pbmeta:PlateId>2014-12-24_141_NGAT_Igor_bisPNA Enrichment_Mag Bead Elution Buffers</pbmeta:PlateId>
+ <pbmeta:WellName>B01</pbmeta:WellName>
+ <pbmeta:Concentration>10</pbmeta:Concentration>
+ <pbmeta:SampleReuseEnabled>true</pbmeta:SampleReuseEnabled>
+ <pbmeta:StageHotstartEnabled>true</pbmeta:StageHotstartEnabled>
+ <pbmeta:SizeSelectionEnabled>true</pbmeta:SizeSelectionEnabled>
+ <pbmeta:UseCount>0</pbmeta:UseCount>
+ <pbsample:BioSamplePointers>
+ <pbsample:BioSamplePointer>abc2df90-d44f-4a48-9f35-3b99473c68f5</pbsample:BioSamplePointer>
+ </pbsample:BioSamplePointers>
+ </pbmeta:WellSample>
+ <pbmeta:Automation>
+ <pbbase:AutomationParameters>
+ <pbbase:AutomationParameter/>
+ </pbbase:AutomationParameters>
+ </pbmeta:Automation>
+ <pbmeta:CollectionNumber>0</pbmeta:CollectionNumber>
+ <pbmeta:CellIndex>0</pbmeta:CellIndex>
+ <pbmeta:CellPac Barcode="100480560100000001823075906281381"/>
+ <pbmeta:Primary>
+ <pbmeta:AutomationName>BasecallerV1</pbmeta:AutomationName>
+ <pbmeta:ConfigFileName>1-3-0_Standard_C2.xml</pbmeta:ConfigFileName>
+ <pbmeta:SequencingCondition/>
+ <pbmeta:OutputOptions>
+ <pbmeta:ResultsFolder>Analysis_Results</pbmeta:ResultsFolder>
+ <pbmeta:CollectionPathUri>rsy://mp-rsync/vol56//RS_DATA_STAGING//2014-12-24_141_NGAT_Igor_bisPNA%20Enrichment_Mag%20Bead%20Elution%20Buffers_1094/B01_1</pbmeta:CollectionPathUri>
+ <pbmeta:CopyFiles>
+ <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+ </pbmeta:CopyFiles>
+ <pbmeta:Readout>Bases</pbmeta:Readout>
+ <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+ </pbmeta:OutputOptions>
+ </pbmeta:Primary>
+ </pbmeta:CollectionMetadata>
+ </pbmeta:Collections>
+ <pbsample:BioSamples>
+ <pbsample:BioSample
+ UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5293"
+ TimeStampedName="biosample_150304_231155"
+ MetaType="PacBio.BioSample"
+ Name="consectetur purus"
+ Description="Risus sit amet lectus vehicula vulputate quisque porta accumsan venenatis."
+ CreatedAt="2015-01-20T13:27:23.9271737-08:00"/>
+ </pbsample:BioSamples>
+ <pbds:SummaryStats>
+ <pbds:AdapterDimerFraction>0.1</pbds:AdapterDimerFraction>
+ <pbds:ShortInsertFraction>0.1</pbds:ShortInsertFraction>
+ <pbds:NumSequencingZmws>0</pbds:NumSequencingZmws>
+ <pbds:ProdDist>
+ <pbbase:NumBins>4</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>1576</pbbase:BinCount>
+ <pbbase:BinCount>901</pbbase:BinCount>
+ <pbbase:BinCount>399</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:MetricDescription>Productivity</pbbase:MetricDescription>
+ <pbbase:BinLabels>
+ <pbbase:BinLabel>Empty</pbbase:BinLabel>
+ <pbbase:BinLabel>Productive</pbbase:BinLabel>
+ <pbbase:BinLabel>Other</pbbase:BinLabel>
+ <pbbase:BinLabel>NotDefined</pbbase:BinLabel>
+ </pbbase:BinLabels>
+ </pbds:ProdDist>
+ <pbds:ReadTypeDist>
+ <pbbase:NumBins>9</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>1474</pbbase:BinCount>
+ <pbbase:BinCount>799</pbbase:BinCount>
+ <pbbase:BinCount>4</pbbase:BinCount>
+ <pbbase:BinCount>181</pbbase:BinCount>
+ <pbbase:BinCount>92</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>326</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:MetricDescription>Read Type</pbbase:MetricDescription>
+ <pbbase:BinLabels>
+ <pbbase:BinLabel>Empty</pbbase:BinLabel>
+ <pbbase:BinLabel>FullHqRead0</pbbase:BinLabel>
+ <pbbase:BinLabel>FullHqRead1</pbbase:BinLabel>
+ <pbbase:BinLabel>PartialHqRead0</pbbase:BinLabel>
+ <pbbase:BinLabel>PartialHqRead1</pbbase:BinLabel>
+ <pbbase:BinLabel>PartialHqRead2</pbbase:BinLabel>
+ <pbbase:BinLabel>Multiload</pbbase:BinLabel>
+ <pbbase:BinLabel>Indeterminate</pbbase:BinLabel>
+ <pbbase:BinLabel>NotDefined</pbbase:BinLabel>
+ </pbbase:BinLabels>
+ </pbds:ReadTypeDist>
+ <pbds:ReadLenDist>
+ <pbbase:SampleSize>901</pbbase:SampleSize>
+ <pbbase:SampleMean>4528.69384765625</pbbase:SampleMean>
+ <pbbase:SampleMed>5227</pbbase:SampleMed>
+ <pbbase:SampleStd>2322.8055598026981</pbbase:SampleStd>
+ <pbbase:Sample95thPct>7367</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>62</pbbase:BinCount>
+ <pbbase:BinCount>39</pbbase:BinCount>
+ <pbbase:BinCount>36</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>37</pbbase:BinCount>
+ <pbbase:BinCount>19</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>37</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>40</pbbase:BinCount>
+ <pbbase:BinCount>45</pbbase:BinCount>
+ <pbbase:BinCount>54</pbbase:BinCount>
+ <pbbase:BinCount>73</pbbase:BinCount>
+ <pbbase:BinCount>77</pbbase:BinCount>
+ <pbbase:BinCount>97</pbbase:BinCount>
+ <pbbase:BinCount>95</pbbase:BinCount>
+ <pbbase:BinCount>49</pbbase:BinCount>
+ <pbbase:BinCount>17</pbbase:BinCount>
+ <pbbase:BinCount>2</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>418.89999389648438</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>77</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>77</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>12225.1025390625</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>12644</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Polymerase Read Length</pbbase:MetricDescription>
+ </pbds:ReadLenDist>
+ <pbds:ReadQualDist>
+ <pbbase:SampleSize>901</pbbase:SampleSize>
+ <pbbase:SampleMean>0.82736450433731079</pbbase:SampleMean>
+ <pbbase:SampleMed>0.83167940378189087</pbbase:SampleMed>
+ <pbbase:SampleStd>0.029663275550147809</pbbase:SampleStd>
+ <pbbase:Sample95thPct>0.86801999807357788</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>12</pbbase:BinCount>
+ <pbbase:BinCount>8</pbbase:BinCount>
+ <pbbase:BinCount>11</pbbase:BinCount>
+ <pbbase:BinCount>10</pbbase:BinCount>
+ <pbbase:BinCount>17</pbbase:BinCount>
+ <pbbase:BinCount>11</pbbase:BinCount>
+ <pbbase:BinCount>20</pbbase:BinCount>
+ <pbbase:BinCount>24</pbbase:BinCount>
+ <pbbase:BinCount>24</pbbase:BinCount>
+ <pbbase:BinCount>34</pbbase:BinCount>
+ <pbbase:BinCount>25</pbbase:BinCount>
+ <pbbase:BinCount>38</pbbase:BinCount>
+ <pbbase:BinCount>52</pbbase:BinCount>
+ <pbbase:BinCount>33</pbbase:BinCount>
+ <pbbase:BinCount>45</pbbase:BinCount>
+ <pbbase:BinCount>48</pbbase:BinCount>
+ <pbbase:BinCount>57</pbbase:BinCount>
+ <pbbase:BinCount>47</pbbase:BinCount>
+ <pbbase:BinCount>69</pbbase:BinCount>
+ <pbbase:BinCount>65</pbbase:BinCount>
+ <pbbase:BinCount>55</pbbase:BinCount>
+ <pbbase:BinCount>51</pbbase:BinCount>
+ <pbbase:BinCount>57</pbbase:BinCount>
+ <pbbase:BinCount>42</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>12</pbbase:BinCount>
+ <pbbase:BinCount>3</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>0.0049052196554839611</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>0.7500004768371582</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>0.7500004768371582</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>0.89225196838378906</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>0.89715707302093506</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Polymerase Read Quality</pbbase:MetricDescription>
+ </pbds:ReadQualDist>
+ <pbds:ControlReadLenDist>
+ <pbbase:SampleSize>901</pbbase:SampleSize>
+ <pbbase:SampleMean>4528.69384765625</pbbase:SampleMean>
+ <pbbase:SampleMed>5227</pbbase:SampleMed>
+ <pbbase:SampleStd>2322.8055598026981</pbbase:SampleStd>
+ <pbbase:Sample95thPct>7367</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>62</pbbase:BinCount>
+ <pbbase:BinCount>39</pbbase:BinCount>
+ <pbbase:BinCount>36</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>37</pbbase:BinCount>
+ <pbbase:BinCount>19</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>37</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>40</pbbase:BinCount>
+ <pbbase:BinCount>45</pbbase:BinCount>
+ <pbbase:BinCount>54</pbbase:BinCount>
+ <pbbase:BinCount>73</pbbase:BinCount>
+ <pbbase:BinCount>77</pbbase:BinCount>
+ <pbbase:BinCount>97</pbbase:BinCount>
+ <pbbase:BinCount>95</pbbase:BinCount>
+ <pbbase:BinCount>49</pbbase:BinCount>
+ <pbbase:BinCount>17</pbbase:BinCount>
+ <pbbase:BinCount>2</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>418.89999389648438</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>77</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>77</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>12225.1025390625</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>12644</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Polymerase Read Length</pbbase:MetricDescription>
+ </pbds:ControlReadLenDist>
+ <pbds:ControlReadQualDist>
+ <pbbase:SampleSize>901</pbbase:SampleSize>
+ <pbbase:SampleMean>0.82736450433731079</pbbase:SampleMean>
+ <pbbase:SampleMed>0.83167940378189087</pbbase:SampleMed>
+ <pbbase:SampleStd>0.029663275550147809</pbbase:SampleStd>
+ <pbbase:Sample95thPct>0.86801999807357788</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>12</pbbase:BinCount>
+ <pbbase:BinCount>8</pbbase:BinCount>
+ <pbbase:BinCount>11</pbbase:BinCount>
+ <pbbase:BinCount>10</pbbase:BinCount>
+ <pbbase:BinCount>17</pbbase:BinCount>
+ <pbbase:BinCount>11</pbbase:BinCount>
+ <pbbase:BinCount>20</pbbase:BinCount>
+ <pbbase:BinCount>24</pbbase:BinCount>
+ <pbbase:BinCount>24</pbbase:BinCount>
+ <pbbase:BinCount>34</pbbase:BinCount>
+ <pbbase:BinCount>25</pbbase:BinCount>
+ <pbbase:BinCount>38</pbbase:BinCount>
+ <pbbase:BinCount>52</pbbase:BinCount>
+ <pbbase:BinCount>33</pbbase:BinCount>
+ <pbbase:BinCount>45</pbbase:BinCount>
+ <pbbase:BinCount>48</pbbase:BinCount>
+ <pbbase:BinCount>57</pbbase:BinCount>
+ <pbbase:BinCount>47</pbbase:BinCount>
+ <pbbase:BinCount>69</pbbase:BinCount>
+ <pbbase:BinCount>65</pbbase:BinCount>
+ <pbbase:BinCount>55</pbbase:BinCount>
+ <pbbase:BinCount>51</pbbase:BinCount>
+ <pbbase:BinCount>57</pbbase:BinCount>
+ <pbbase:BinCount>42</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>12</pbbase:BinCount>
+ <pbbase:BinCount>3</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>0.0049052196554839611</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>0.7500004768371582</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>0.7500004768371582</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>0.89225196838378906</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>0.89715707302093506</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Polymerase Read Quality</pbbase:MetricDescription>
+ </pbds:ControlReadQualDist>
+ <pbds:MedianInsertDist>
+ <pbbase:SampleSize>973</pbbase:SampleSize>
+ <pbbase:SampleMean>513.21990966796875</pbbase:SampleMean>
+ <pbbase:SampleMed>350</pbbase:SampleMed>
+ <pbbase:SampleStd>575.83020626506971</pbbase:SampleStd>
+ <pbbase:Sample95thPct>1322</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>714</pbbase:BinCount>
+ <pbbase:BinCount>101</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>18</pbbase:BinCount>
+ <pbbase:BinCount>13</pbbase:BinCount>
+ <pbbase:BinCount>8</pbbase:BinCount>
+ <pbbase:BinCount>5</pbbase:BinCount>
+ <pbbase:BinCount>6</pbbase:BinCount>
+ <pbbase:BinCount>7</pbbase:BinCount>
+ <pbbase:BinCount>10</pbbase:BinCount>
+ <pbbase:BinCount>10</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>2</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>4</pbbase:BinCount>
+ <pbbase:BinCount>6</pbbase:BinCount>
+ <pbbase:BinCount>3</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>7</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>3</pbbase:BinCount>
+ <pbbase:BinCount>4</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>3</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>2</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>9</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>93.333335876464844</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>289</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>289</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>2995.666259765625</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>6278</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Median Insert</pbbase:MetricDescription>
+ </pbds:MedianInsertDist>
+ <pbds:InsertReadLenDist>
+ <pbbase:SampleSize>901</pbbase:SampleSize>
+ <pbbase:SampleMean>4528.69384765625</pbbase:SampleMean>
+ <pbbase:SampleMed>5227</pbbase:SampleMed>
+ <pbbase:SampleStd>2322.8055598026981</pbbase:SampleStd>
+ <pbbase:Sample95thPct>7367</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>62</pbbase:BinCount>
+ <pbbase:BinCount>39</pbbase:BinCount>
+ <pbbase:BinCount>36</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>37</pbbase:BinCount>
+ <pbbase:BinCount>19</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>37</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>32</pbbase:BinCount>
+ <pbbase:BinCount>40</pbbase:BinCount>
+ <pbbase:BinCount>45</pbbase:BinCount>
+ <pbbase:BinCount>54</pbbase:BinCount>
+ <pbbase:BinCount>73</pbbase:BinCount>
+ <pbbase:BinCount>77</pbbase:BinCount>
+ <pbbase:BinCount>97</pbbase:BinCount>
+ <pbbase:BinCount>95</pbbase:BinCount>
+ <pbbase:BinCount>49</pbbase:BinCount>
+ <pbbase:BinCount>17</pbbase:BinCount>
+ <pbbase:BinCount>2</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>418.89999389648438</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>77</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>77</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>12225.1025390625</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>12644</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Polymerase Read Length</pbbase:MetricDescription>
+ </pbds:InsertReadLenDist>
+ <pbds:InsertReadQualDist>
+ <pbbase:SampleSize>901</pbbase:SampleSize>
+ <pbbase:SampleMean>0.82736450433731079</pbbase:SampleMean>
+ <pbbase:SampleMed>0.83167940378189087</pbbase:SampleMed>
+ <pbbase:SampleStd>0.029663275550147809</pbbase:SampleStd>
+ <pbbase:Sample95thPct>0.86801999807357788</pbbase:Sample95thPct>
+ <pbbase:NumBins>30</pbbase:NumBins>
+ <pbbase:BinCounts>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>12</pbbase:BinCount>
+ <pbbase:BinCount>8</pbbase:BinCount>
+ <pbbase:BinCount>11</pbbase:BinCount>
+ <pbbase:BinCount>10</pbbase:BinCount>
+ <pbbase:BinCount>17</pbbase:BinCount>
+ <pbbase:BinCount>11</pbbase:BinCount>
+ <pbbase:BinCount>20</pbbase:BinCount>
+ <pbbase:BinCount>24</pbbase:BinCount>
+ <pbbase:BinCount>24</pbbase:BinCount>
+ <pbbase:BinCount>34</pbbase:BinCount>
+ <pbbase:BinCount>25</pbbase:BinCount>
+ <pbbase:BinCount>38</pbbase:BinCount>
+ <pbbase:BinCount>52</pbbase:BinCount>
+ <pbbase:BinCount>33</pbbase:BinCount>
+ <pbbase:BinCount>45</pbbase:BinCount>
+ <pbbase:BinCount>48</pbbase:BinCount>
+ <pbbase:BinCount>57</pbbase:BinCount>
+ <pbbase:BinCount>47</pbbase:BinCount>
+ <pbbase:BinCount>69</pbbase:BinCount>
+ <pbbase:BinCount>65</pbbase:BinCount>
+ <pbbase:BinCount>55</pbbase:BinCount>
+ <pbbase:BinCount>51</pbbase:BinCount>
+ <pbbase:BinCount>57</pbbase:BinCount>
+ <pbbase:BinCount>42</pbbase:BinCount>
+ <pbbase:BinCount>29</pbbase:BinCount>
+ <pbbase:BinCount>12</pbbase:BinCount>
+ <pbbase:BinCount>3</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ <pbbase:BinCount>0</pbbase:BinCount>
+ <pbbase:BinCount>1</pbbase:BinCount>
+ </pbbase:BinCounts>
+ <pbbase:BinWidth>0.0049052196554839611</pbbase:BinWidth>
+ <pbbase:MinOutlierValue>0.7500004768371582</pbbase:MinOutlierValue>
+ <pbbase:MinBinValue>0.7500004768371582</pbbase:MinBinValue>
+ <pbbase:MaxBinValue>0.89225196838378906</pbbase:MaxBinValue>
+ <pbbase:MaxOutlierValue>0.89715707302093506</pbbase:MaxOutlierValue>
+ <pbbase:MetricDescription>Polymerase Read Quality</pbbase:MetricDescription>
+ </pbds:InsertReadQualDist>
+ </pbds:SummaryStats>
+</pbds:DataSetMetadata>
+</pbds:SubreadSet>
diff --git a/pbcore/data/datasets/subreadSetWithStats.xml b/pbcore/data/datasets/subreadSetWithStats.xml
index 6bacfad..db4e337 100644
--- a/pbcore/data/datasets/subreadSetWithStats.xml
+++ b/pbcore/data/datasets/subreadSetWithStats.xml
@@ -1,1137 +1,1131 @@
<?xml version="1.0" ?>
-<DataSet CreatedAt="2015-07-09T17:04:25" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" UniqueId="a3c23749-a427-3072-bc56-5e2409e287b4" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="/home/UNIXHOME/mdsmith/p4/mainline/software/smrtanalysis/bioinformatics/lib/python/pbcore/pbcore/data/datasets/pbalchemysim0.subreads.bam">
- <FileIndices/>
- </ExternalResource>
- </ExternalResources>
- <DataSetMetadata>
- <NumRecords>-1</NumRecords>
- <TotalLength>-1</TotalLength>
- <SummaryStats>
- <NumSequencingZmws>153168.0</NumSequencingZmws>
- <AdapterDimerFraction>1.28301765719e-05</AdapterDimerFraction>
- <ShortInsertFraction>3.20754414298e-05</ShortInsertFraction>
- <ProdDist>
- <NumBins>4</NumBins>
- <MetricDescription>Productivity</MetricDescription>
- <BinCounts>
- <BinCount>120979</BinCount>
- <BinCount>25123</BinCount>
- <BinCount>7066</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>Productive</BinLabel>
- <BinLabel>Other</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ProdDist>
- <ReadTypeDist>
- <NumBins>9</NumBins>
- <MetricDescription>Read Type</MetricDescription>
- <BinCounts>
- <BinCount>89042</BinCount>
- <BinCount>14534</BinCount>
- <BinCount>199</BinCount>
- <BinCount>4367</BinCount>
- <BinCount>8126</BinCount>
- <BinCount>110</BinCount>
- <BinCount>0</BinCount>
- <BinCount>36790</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>FullHqRead0</BinLabel>
- <BinLabel>FullHqRead1</BinLabel>
- <BinLabel>PartialHqRead0</BinLabel>
- <BinLabel>PartialHqRead1</BinLabel>
- <BinLabel>PartialHqRead2</BinLabel>
- <BinLabel>Multiload</BinLabel>
- <BinLabel>Indeterminate</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ReadTypeDist>
- <ReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>4528.69384765625</SampleMean>
- <SampleMed>5227</SampleMed>
- <SampleStd>2322.8055598026981</SampleStd>
- <Sample95thPct>7367</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>418.89999389648438</BinWidth>
- <MinOutlierValue>77</MinOutlierValue>
- <MinBinValue>77</MinBinValue>
- <MaxBinValue>12225.1025390625</MaxBinValue>
- <MaxOutlierValue>12644</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>62</BinCount>
- <BinCount>39</BinCount>
- <BinCount>36</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>19</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>32</BinCount>
- <BinCount>32</BinCount>
- <BinCount>40</BinCount>
- <BinCount>45</BinCount>
- <BinCount>54</BinCount>
- <BinCount>73</BinCount>
- <BinCount>77</BinCount>
- <BinCount>97</BinCount>
- <BinCount>95</BinCount>
- <BinCount>49</BinCount>
- <BinCount>17</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- </ReadLenDist>
- <ReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.82736450433731079</SampleMean>
- <SampleMed>0.83167940378189087</SampleMed>
- <SampleStd>0.029663275550147809</SampleStd>
- <Sample95thPct>0.86801999807357788</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.0049052196554839611</BinWidth>
- <MinOutlierValue>0.7500004768371582</MinOutlierValue>
- <MinBinValue>0.7500004768371582</MinBinValue>
- <MaxBinValue>0.89225196838378906</MaxBinValue>
- <MaxOutlierValue>0.89715707302093506</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>12</BinCount>
- <BinCount>8</BinCount>
- <BinCount>11</BinCount>
- <BinCount>10</BinCount>
- <BinCount>17</BinCount>
- <BinCount>11</BinCount>
- <BinCount>20</BinCount>
- <BinCount>24</BinCount>
- <BinCount>24</BinCount>
- <BinCount>34</BinCount>
- <BinCount>25</BinCount>
- <BinCount>38</BinCount>
- <BinCount>52</BinCount>
- <BinCount>33</BinCount>
- <BinCount>45</BinCount>
- <BinCount>48</BinCount>
- <BinCount>57</BinCount>
- <BinCount>47</BinCount>
- <BinCount>69</BinCount>
- <BinCount>65</BinCount>
- <BinCount>55</BinCount>
- <BinCount>51</BinCount>
- <BinCount>57</BinCount>
- <BinCount>42</BinCount>
- <BinCount>29</BinCount>
- <BinCount>12</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </ReadQualDist>
- <InsertReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>460.4583740234375</SampleMean>
- <SampleMed>350</SampleMed>
- <SampleStd>592.13342124584449</SampleStd>
- <Sample95thPct>751</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>98</BinWidth>
- <MinOutlierValue>78</MinOutlierValue>
- <MinBinValue>78</MinBinValue>
- <MaxBinValue>2920</MaxBinValue>
- <MaxOutlierValue>5969</MaxOutlierValue>
- <MetricDescription>Read Length of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>21</BinCount>
- <BinCount>25</BinCount>
- <BinCount>621</BinCount>
- <BinCount>151</BinCount>
- <BinCount>23</BinCount>
- <BinCount>10</BinCount>
- <BinCount>7</BinCount>
- <BinCount>4</BinCount>
- <BinCount>4</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>2</BinCount>
- <BinCount>5</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>15</BinCount>
- </BinCounts>
- </InsertReadLenDist>
- <InsertReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.96519893407821655</SampleMean>
- <SampleMed>0.99638187885284424</SampleMed>
- <SampleStd>0.063829474832070937</SampleStd>
- <Sample95thPct>0.9987713098526001</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.0082235373556613922</BinWidth>
- <MinOutlierValue>0.75223779678344727</MinOutlierValue>
- <MinBinValue>0.75223779678344727</MinBinValue>
- <MaxBinValue>0.990720272064209</MaxBinValue>
- <MaxOutlierValue>0.99894392490386963</MaxOutlierValue>
- <MetricDescription>Read Quality of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>6</BinCount>
- <BinCount>3</BinCount>
- <BinCount>7</BinCount>
- <BinCount>11</BinCount>
- <BinCount>14</BinCount>
- <BinCount>13</BinCount>
- <BinCount>12</BinCount>
- <BinCount>13</BinCount>
- <BinCount>6</BinCount>
- <BinCount>5</BinCount>
- <BinCount>3</BinCount>
- <BinCount>9</BinCount>
- <BinCount>3</BinCount>
- <BinCount>2</BinCount>
- <BinCount>3</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>5</BinCount>
- <BinCount>3</BinCount>
- <BinCount>9</BinCount>
- <BinCount>9</BinCount>
- <BinCount>11</BinCount>
- <BinCount>16</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>16</BinCount>
- <BinCount>24</BinCount>
- <BinCount>35</BinCount>
- <BinCount>59</BinCount>
- <BinCount>579</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </InsertReadQualDist>
- <MedianInsertDist>
- <SampleSize>973</SampleSize>
- <SampleMean>513.21990966796875</SampleMean>
- <SampleMed>350</SampleMed>
- <SampleStd>575.83020626506971</SampleStd>
- <Sample95thPct>1322</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>93.333335876464844</BinWidth>
- <MinOutlierValue>289</MinOutlierValue>
- <MinBinValue>289</MinBinValue>
- <MaxBinValue>2995.666259765625</MaxBinValue>
- <MaxOutlierValue>6278</MaxOutlierValue>
- <MetricDescription>Median Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>714</BinCount>
- <BinCount>101</BinCount>
- <BinCount>32</BinCount>
- <BinCount>18</BinCount>
- <BinCount>13</BinCount>
- <BinCount>8</BinCount>
- <BinCount>5</BinCount>
- <BinCount>6</BinCount>
- <BinCount>7</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>1</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>4</BinCount>
- <BinCount>6</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>7</BinCount>
- <BinCount>1</BinCount>
- <BinCount>3</BinCount>
- <BinCount>4</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>1</BinCount>
- <BinCount>9</BinCount>
- </BinCounts>
- </MedianInsertDist>
- <ReadLenDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>13965.3232421875</SampleMean>
- <SampleMed>11484</SampleMed>
- <SampleStd>10580.691922120142</SampleStd>
- <Sample95thPct>34936</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>2078.2333984375</BinWidth>
- <MinOutlierValue>63</MinOutlierValue>
- <MinBinValue>63</MinBinValue>
- <MaxBinValue>60331.7890625</MaxBinValue>
- <MaxOutlierValue>62410</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>2564</BinCount>
- <BinCount>2649</BinCount>
- <BinCount>2135</BinCount>
- <BinCount>1875</BinCount>
- <BinCount>1977</BinCount>
- <BinCount>1829</BinCount>
- <BinCount>1533</BinCount>
- <BinCount>1304</BinCount>
- <BinCount>1148</BinCount>
- <BinCount>1065</BinCount>
- <BinCount>919</BinCount>
- <BinCount>854</BinCount>
- <BinCount>803</BinCount>
- <BinCount>650</BinCount>
- <BinCount>605</BinCount>
- <BinCount>609</BinCount>
- <BinCount>646</BinCount>
- <BinCount>562</BinCount>
- <BinCount>333</BinCount>
- <BinCount>132</BinCount>
- <BinCount>23</BinCount>
- <BinCount>5</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- </ReadLenDist>
- <ReadQualDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>0.85828709602355957</SampleMean>
- <SampleMed>0.868025004863739</SampleMed>
- <SampleStd>0.030875069589002442</SampleStd>
- <Sample95thPct>0.88995635509490967</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.00517143402248621</BinWidth>
- <MinOutlierValue>0.75007820129394531</MinOutlierValue>
- <MinBinValue>0.75007820129394531</MinBinValue>
- <MaxBinValue>0.90004932880401611</MaxBinValue>
- <MaxOutlierValue>0.90522122383117676</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>122</BinCount>
- <BinCount>136</BinCount>
- <BinCount>130</BinCount>
- <BinCount>144</BinCount>
- <BinCount>163</BinCount>
- <BinCount>177</BinCount>
- <BinCount>186</BinCount>
- <BinCount>213</BinCount>
- <BinCount>237</BinCount>
- <BinCount>251</BinCount>
- <BinCount>280</BinCount>
- <BinCount>338</BinCount>
- <BinCount>412</BinCount>
- <BinCount>426</BinCount>
- <BinCount>527</BinCount>
- <BinCount>563</BinCount>
- <BinCount>686</BinCount>
- <BinCount>790</BinCount>
- <BinCount>925</BinCount>
- <BinCount>1095</BinCount>
- <BinCount>1377</BinCount>
- <BinCount>1525</BinCount>
- <BinCount>1775</BinCount>
- <BinCount>2133</BinCount>
- <BinCount>2515</BinCount>
- <BinCount>2973</BinCount>
- <BinCount>2823</BinCount>
- <BinCount>1192</BinCount>
- <BinCount>103</BinCount>
- <BinCount>4</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </ReadQualDist>
- <MedianInsertDist>
- <SampleSize>570</SampleSize>
- <SampleMean>5406.65625</SampleMean>
- <SampleMed>2860</SampleMed>
- <SampleStd>6322.1968204214045</SampleStd>
- <Sample95thPct>18508</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>1090.199951171875</BinWidth>
- <MinOutlierValue>0</MinOutlierValue>
- <MinBinValue>0</MinBinValue>
- <MaxBinValue>31615.791015625</MaxBinValue>
- <MaxOutlierValue>64092</MaxOutlierValue>
- <MetricDescription>Median Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>28</BinCount>
- <BinCount>159</BinCount>
- <BinCount>125</BinCount>
- <BinCount>65</BinCount>
- <BinCount>30</BinCount>
- <BinCount>26</BinCount>
- <BinCount>25</BinCount>
- <BinCount>9</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>12</BinCount>
- <BinCount>7</BinCount>
- <BinCount>11</BinCount>
- <BinCount>11</BinCount>
- <BinCount>3</BinCount>
- <BinCount>3</BinCount>
- <BinCount>9</BinCount>
- <BinCount>3</BinCount>
- <BinCount>5</BinCount>
- <BinCount>4</BinCount>
- <BinCount>2</BinCount>
- <BinCount>2</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>4</BinCount>
- </BinCounts>
- </MedianInsertDist>
- <InsertReadQualDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>0.86046397686004639</SampleMean>
- <SampleMed>0.8684546947479248</SampleMed>
- <SampleStd>0.035067464845073885</SampleStd>
- <Sample95thPct>0.89117431640625</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.0082973875105381012</BinWidth>
- <MinOutlierValue>0.75007820129394531</MinOutlierValue>
- <MinBinValue>0.75007820129394531</MinBinValue>
- <MaxBinValue>0.99070233106613159</MaxBinValue>
- <MaxOutlierValue>0.998999834060669</MaxOutlierValue>
- <MetricDescription>Read Quality of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>196</BinCount>
- <BinCount>221</BinCount>
- <BinCount>249</BinCount>
- <BinCount>282</BinCount>
- <BinCount>308</BinCount>
- <BinCount>392</BinCount>
- <BinCount>438</BinCount>
- <BinCount>619</BinCount>
- <BinCount>701</BinCount>
- <BinCount>871</BinCount>
- <BinCount>1141</BinCount>
- <BinCount>1465</BinCount>
- <BinCount>1989</BinCount>
- <BinCount>2463</BinCount>
- <BinCount>3213</BinCount>
- <BinCount>4186</BinCount>
- <BinCount>4264</BinCount>
- <BinCount>744</BinCount>
- <BinCount>10</BinCount>
- <BinCount>9</BinCount>
- <BinCount>4</BinCount>
- <BinCount>7</BinCount>
- <BinCount>10</BinCount>
- <BinCount>32</BinCount>
- <BinCount>51</BinCount>
- <BinCount>13</BinCount>
- <BinCount>21</BinCount>
- <BinCount>29</BinCount>
- <BinCount>46</BinCount>
- <BinCount>247</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </InsertReadQualDist>
- <InsertReadLenDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>12747.7919921875</SampleMean>
- <SampleMed>10937</SampleMed>
- <SampleStd>9364.0618727600377</SampleStd>
- <Sample95thPct>29948</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>1436.566650390625</BinWidth>
- <MinOutlierValue>1</MinOutlierValue>
- <MinBinValue>1</MinBinValue>
- <MaxBinValue>41661.4296875</MaxBinValue>
- <MaxOutlierValue>43098</MaxOutlierValue>
- <MetricDescription>Read Length of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>1660</BinCount>
- <BinCount>2384</BinCount>
- <BinCount>1828</BinCount>
- <BinCount>1455</BinCount>
- <BinCount>1315</BinCount>
- <BinCount>1302</BinCount>
- <BinCount>1365</BinCount>
- <BinCount>1296</BinCount>
- <BinCount>1200</BinCount>
- <BinCount>1088</BinCount>
- <BinCount>965</BinCount>
- <BinCount>856</BinCount>
- <BinCount>822</BinCount>
- <BinCount>820</BinCount>
- <BinCount>878</BinCount>
- <BinCount>756</BinCount>
- <BinCount>747</BinCount>
- <BinCount>754</BinCount>
- <BinCount>654</BinCount>
- <BinCount>535</BinCount>
- <BinCount>382</BinCount>
- <BinCount>321</BinCount>
- <BinCount>275</BinCount>
- <BinCount>181</BinCount>
- <BinCount>167</BinCount>
- <BinCount>117</BinCount>
- <BinCount>64</BinCount>
- <BinCount>22</BinCount>
- <BinCount>9</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </InsertReadLenDist>
- </SummaryStats>
- </DataSetMetadata>
+<pbds:SubreadSet CreatedAt="2015-08-06T17:07:36" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.SubreadSet-150807_000736" UniqueId="dd7edc7d-0c24-0823-f918-394d4cbd0f9d" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbstats="http://pacificbiosciences.com/PipelineStats/PipeStats.xsd" xmlns [...]
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.subreads.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150807_000736" UniqueId="c55c8ed2-4821-4c48-9395-94625363fe6d"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>-1</pbds:TotalLength>
+ <pbds:NumRecords>-1</pbds:NumRecords>
+ <pbstats:SummaryStats>
+ <pbstats:NumSequencingZmws>153168.0</pbstats:NumSequencingZmws>
+ <pbstats:AdapterDimerFraction>1.28301765719e-05</pbstats:AdapterDimerFraction>
+ <pbstats:ShortInsertFraction>3.20754414298e-05</pbstats:ShortInsertFraction>
+ <pbstats:ProdDist>
+ <pbstats:NumBins>4</pbstats:NumBins>
+ <pbstats:MetricDescription>Productivity</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>120979</pbstats:BinCount>
+ <pbstats:BinCount>25123</pbstats:BinCount>
+ <pbstats:BinCount>7066</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ <pbstats:BinLabels>
+ <pbstats:BinLabel>Empty</pbstats:BinLabel>
+ <pbstats:BinLabel>Productive</pbstats:BinLabel>
+ <pbstats:BinLabel>Other</pbstats:BinLabel>
+ <pbstats:BinLabel>NotDefined</pbstats:BinLabel>
+ </pbstats:BinLabels>
+ </pbstats:ProdDist>
+ <pbstats:ReadTypeDist>
+ <pbstats:NumBins>9</pbstats:NumBins>
+ <pbstats:MetricDescription>Read Type</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>89042</pbstats:BinCount>
+ <pbstats:BinCount>14534</pbstats:BinCount>
+ <pbstats:BinCount>199</pbstats:BinCount>
+ <pbstats:BinCount>4367</pbstats:BinCount>
+ <pbstats:BinCount>8126</pbstats:BinCount>
+ <pbstats:BinCount>110</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>36790</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ <pbstats:BinLabels>
+ <pbstats:BinLabel>Empty</pbstats:BinLabel>
+ <pbstats:BinLabel>FullHqRead0</pbstats:BinLabel>
+ <pbstats:BinLabel>FullHqRead1</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead0</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead1</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead2</pbstats:BinLabel>
+ <pbstats:BinLabel>Multiload</pbstats:BinLabel>
+ <pbstats:BinLabel>Indeterminate</pbstats:BinLabel>
+ <pbstats:BinLabel>NotDefined</pbstats:BinLabel>
+ </pbstats:BinLabels>
+ </pbstats:ReadTypeDist>
+ <pbstats:ReadLenDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>4528.69384765625</pbstats:SampleMean>
+ <pbstats:SampleMed>5227</pbstats:SampleMed>
+ <pbstats:SampleStd>2322.8055598026981</pbstats:SampleStd>
+ <pbstats:Sample95thPct>7367</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>418.89999389648438</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>77</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>77</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>12225.1025390625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>12644</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Length</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>62</pbstats:BinCount>
+ <pbstats:BinCount>39</pbstats:BinCount>
+ <pbstats:BinCount>36</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>37</pbstats:BinCount>
+ <pbstats:BinCount>19</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>37</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>40</pbstats:BinCount>
+ <pbstats:BinCount>45</pbstats:BinCount>
+ <pbstats:BinCount>54</pbstats:BinCount>
+ <pbstats:BinCount>73</pbstats:BinCount>
+ <pbstats:BinCount>77</pbstats:BinCount>
+ <pbstats:BinCount>97</pbstats:BinCount>
+ <pbstats:BinCount>95</pbstats:BinCount>
+ <pbstats:BinCount>49</pbstats:BinCount>
+ <pbstats:BinCount>17</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadLenDist>
+ <pbstats:ReadQualDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>0.82736450433731079</pbstats:SampleMean>
+ <pbstats:SampleMed>0.83167940378189087</pbstats:SampleMed>
+ <pbstats:SampleStd>0.029663275550147809</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.86801999807357788</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.0049052196554839611</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.7500004768371582</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.7500004768371582</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.89225196838378906</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.89715707302093506</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Quality</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>8</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>17</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>20</pbstats:BinCount>
+ <pbstats:BinCount>24</pbstats:BinCount>
+ <pbstats:BinCount>24</pbstats:BinCount>
+ <pbstats:BinCount>34</pbstats:BinCount>
+ <pbstats:BinCount>25</pbstats:BinCount>
+ <pbstats:BinCount>38</pbstats:BinCount>
+ <pbstats:BinCount>52</pbstats:BinCount>
+ <pbstats:BinCount>33</pbstats:BinCount>
+ <pbstats:BinCount>45</pbstats:BinCount>
+ <pbstats:BinCount>48</pbstats:BinCount>
+ <pbstats:BinCount>57</pbstats:BinCount>
+ <pbstats:BinCount>47</pbstats:BinCount>
+ <pbstats:BinCount>69</pbstats:BinCount>
+ <pbstats:BinCount>65</pbstats:BinCount>
+ <pbstats:BinCount>55</pbstats:BinCount>
+ <pbstats:BinCount>51</pbstats:BinCount>
+ <pbstats:BinCount>57</pbstats:BinCount>
+ <pbstats:BinCount>42</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadQualDist>
+ <pbstats:InsertReadLenDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>460.4583740234375</pbstats:SampleMean>
+ <pbstats:SampleMed>350</pbstats:SampleMed>
+ <pbstats:SampleStd>592.13342124584449</pbstats:SampleStd>
+ <pbstats:Sample95thPct>751</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>98</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>78</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>78</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>2920</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>5969</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Length of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>21</pbstats:BinCount>
+ <pbstats:BinCount>25</pbstats:BinCount>
+ <pbstats:BinCount>621</pbstats:BinCount>
+ <pbstats:BinCount>151</pbstats:BinCount>
+ <pbstats:BinCount>23</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>15</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadLenDist>
+ <pbstats:InsertReadQualDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>0.96519893407821655</pbstats:SampleMean>
+ <pbstats:SampleMed>0.99638187885284424</pbstats:SampleMed>
+ <pbstats:SampleStd>0.063829474832070937</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.9987713098526001</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.0082235373556613922</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.75223779678344727</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.75223779678344727</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.990720272064209</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.99894392490386963</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Quality of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>14</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>16</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>16</pbstats:BinCount>
+ <pbstats:BinCount>24</pbstats:BinCount>
+ <pbstats:BinCount>35</pbstats:BinCount>
+ <pbstats:BinCount>59</pbstats:BinCount>
+ <pbstats:BinCount>579</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadQualDist>
+ <pbstats:MedianInsertDist>
+ <pbstats:SampleSize>973</pbstats:SampleSize>
+ <pbstats:SampleMean>513.21990966796875</pbstats:SampleMean>
+ <pbstats:SampleMed>350</pbstats:SampleMed>
+ <pbstats:SampleStd>575.83020626506971</pbstats:SampleStd>
+ <pbstats:Sample95thPct>1322</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>93.333335876464844</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>289</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>289</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>2995.666259765625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>6278</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Median Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>714</pbstats:BinCount>
+ <pbstats:BinCount>101</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>18</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>8</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:MedianInsertDist>
+ <pbstats:ReadLenDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>13965.3232421875</pbstats:SampleMean>
+ <pbstats:SampleMed>11484</pbstats:SampleMed>
+ <pbstats:SampleStd>10580.691922120142</pbstats:SampleStd>
+ <pbstats:Sample95thPct>34936</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>2078.2333984375</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>63</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>63</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>60331.7890625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>62410</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Length</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2564</pbstats:BinCount>
+ <pbstats:BinCount>2649</pbstats:BinCount>
+ <pbstats:BinCount>2135</pbstats:BinCount>
+ <pbstats:BinCount>1875</pbstats:BinCount>
+ <pbstats:BinCount>1977</pbstats:BinCount>
+ <pbstats:BinCount>1829</pbstats:BinCount>
+ <pbstats:BinCount>1533</pbstats:BinCount>
+ <pbstats:BinCount>1304</pbstats:BinCount>
+ <pbstats:BinCount>1148</pbstats:BinCount>
+ <pbstats:BinCount>1065</pbstats:BinCount>
+ <pbstats:BinCount>919</pbstats:BinCount>
+ <pbstats:BinCount>854</pbstats:BinCount>
+ <pbstats:BinCount>803</pbstats:BinCount>
+ <pbstats:BinCount>650</pbstats:BinCount>
+ <pbstats:BinCount>605</pbstats:BinCount>
+ <pbstats:BinCount>609</pbstats:BinCount>
+ <pbstats:BinCount>646</pbstats:BinCount>
+ <pbstats:BinCount>562</pbstats:BinCount>
+ <pbstats:BinCount>333</pbstats:BinCount>
+ <pbstats:BinCount>132</pbstats:BinCount>
+ <pbstats:BinCount>23</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadLenDist>
+ <pbstats:ReadQualDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>0.85828709602355957</pbstats:SampleMean>
+ <pbstats:SampleMed>0.868025004863739</pbstats:SampleMed>
+ <pbstats:SampleStd>0.030875069589002442</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.88995635509490967</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.00517143402248621</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.75007820129394531</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.75007820129394531</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.90004932880401611</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.90522122383117676</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Quality</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>122</pbstats:BinCount>
+ <pbstats:BinCount>136</pbstats:BinCount>
+ <pbstats:BinCount>130</pbstats:BinCount>
+ <pbstats:BinCount>144</pbstats:BinCount>
+ <pbstats:BinCount>163</pbstats:BinCount>
+ <pbstats:BinCount>177</pbstats:BinCount>
+ <pbstats:BinCount>186</pbstats:BinCount>
+ <pbstats:BinCount>213</pbstats:BinCount>
+ <pbstats:BinCount>237</pbstats:BinCount>
+ <pbstats:BinCount>251</pbstats:BinCount>
+ <pbstats:BinCount>280</pbstats:BinCount>
+ <pbstats:BinCount>338</pbstats:BinCount>
+ <pbstats:BinCount>412</pbstats:BinCount>
+ <pbstats:BinCount>426</pbstats:BinCount>
+ <pbstats:BinCount>527</pbstats:BinCount>
+ <pbstats:BinCount>563</pbstats:BinCount>
+ <pbstats:BinCount>686</pbstats:BinCount>
+ <pbstats:BinCount>790</pbstats:BinCount>
+ <pbstats:BinCount>925</pbstats:BinCount>
+ <pbstats:BinCount>1095</pbstats:BinCount>
+ <pbstats:BinCount>1377</pbstats:BinCount>
+ <pbstats:BinCount>1525</pbstats:BinCount>
+ <pbstats:BinCount>1775</pbstats:BinCount>
+ <pbstats:BinCount>2133</pbstats:BinCount>
+ <pbstats:BinCount>2515</pbstats:BinCount>
+ <pbstats:BinCount>2973</pbstats:BinCount>
+ <pbstats:BinCount>2823</pbstats:BinCount>
+ <pbstats:BinCount>1192</pbstats:BinCount>
+ <pbstats:BinCount>103</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadQualDist>
+ <pbstats:MedianInsertDist>
+ <pbstats:SampleSize>570</pbstats:SampleSize>
+ <pbstats:SampleMean>5406.65625</pbstats:SampleMean>
+ <pbstats:SampleMed>2860</pbstats:SampleMed>
+ <pbstats:SampleStd>6322.1968204214045</pbstats:SampleStd>
+ <pbstats:Sample95thPct>18508</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>1090.199951171875</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>31615.791015625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>64092</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Median Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>28</pbstats:BinCount>
+ <pbstats:BinCount>159</pbstats:BinCount>
+ <pbstats:BinCount>125</pbstats:BinCount>
+ <pbstats:BinCount>65</pbstats:BinCount>
+ <pbstats:BinCount>30</pbstats:BinCount>
+ <pbstats:BinCount>26</pbstats:BinCount>
+ <pbstats:BinCount>25</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:MedianInsertDist>
+ <pbstats:InsertReadQualDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>0.86046397686004639</pbstats:SampleMean>
+ <pbstats:SampleMed>0.8684546947479248</pbstats:SampleMed>
+ <pbstats:SampleStd>0.035067464845073885</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.89117431640625</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.0082973875105381012</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.75007820129394531</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.75007820129394531</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.99070233106613159</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.998999834060669</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Quality of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>196</pbstats:BinCount>
+ <pbstats:BinCount>221</pbstats:BinCount>
+ <pbstats:BinCount>249</pbstats:BinCount>
+ <pbstats:BinCount>282</pbstats:BinCount>
+ <pbstats:BinCount>308</pbstats:BinCount>
+ <pbstats:BinCount>392</pbstats:BinCount>
+ <pbstats:BinCount>438</pbstats:BinCount>
+ <pbstats:BinCount>619</pbstats:BinCount>
+ <pbstats:BinCount>701</pbstats:BinCount>
+ <pbstats:BinCount>871</pbstats:BinCount>
+ <pbstats:BinCount>1141</pbstats:BinCount>
+ <pbstats:BinCount>1465</pbstats:BinCount>
+ <pbstats:BinCount>1989</pbstats:BinCount>
+ <pbstats:BinCount>2463</pbstats:BinCount>
+ <pbstats:BinCount>3213</pbstats:BinCount>
+ <pbstats:BinCount>4186</pbstats:BinCount>
+ <pbstats:BinCount>4264</pbstats:BinCount>
+ <pbstats:BinCount>744</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>51</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>21</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>46</pbstats:BinCount>
+ <pbstats:BinCount>247</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadQualDist>
+ <pbstats:InsertReadLenDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>12747.7919921875</pbstats:SampleMean>
+ <pbstats:SampleMed>10937</pbstats:SampleMed>
+ <pbstats:SampleStd>9364.0618727600377</pbstats:SampleStd>
+ <pbstats:Sample95thPct>29948</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>1436.566650390625</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>1</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>1</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>41661.4296875</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>43098</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Length of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1660</pbstats:BinCount>
+ <pbstats:BinCount>2384</pbstats:BinCount>
+ <pbstats:BinCount>1828</pbstats:BinCount>
+ <pbstats:BinCount>1455</pbstats:BinCount>
+ <pbstats:BinCount>1315</pbstats:BinCount>
+ <pbstats:BinCount>1302</pbstats:BinCount>
+ <pbstats:BinCount>1365</pbstats:BinCount>
+ <pbstats:BinCount>1296</pbstats:BinCount>
+ <pbstats:BinCount>1200</pbstats:BinCount>
+ <pbstats:BinCount>1088</pbstats:BinCount>
+ <pbstats:BinCount>965</pbstats:BinCount>
+ <pbstats:BinCount>856</pbstats:BinCount>
+ <pbstats:BinCount>822</pbstats:BinCount>
+ <pbstats:BinCount>820</pbstats:BinCount>
+ <pbstats:BinCount>878</pbstats:BinCount>
+ <pbstats:BinCount>756</pbstats:BinCount>
+ <pbstats:BinCount>747</pbstats:BinCount>
+ <pbstats:BinCount>754</pbstats:BinCount>
+ <pbstats:BinCount>654</pbstats:BinCount>
+ <pbstats:BinCount>535</pbstats:BinCount>
+ <pbstats:BinCount>382</pbstats:BinCount>
+ <pbstats:BinCount>321</pbstats:BinCount>
+ <pbstats:BinCount>275</pbstats:BinCount>
+ <pbstats:BinCount>181</pbstats:BinCount>
+ <pbstats:BinCount>167</pbstats:BinCount>
+ <pbstats:BinCount>117</pbstats:BinCount>
+ <pbstats:BinCount>64</pbstats:BinCount>
+ <pbstats:BinCount>22</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadLenDist>
+ </pbstats:SummaryStats>
+ </pbds:DataSetMetadata>
<DataSets>
- <DataSet CreatedAt="2015-07-09T17:04:25" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" UniqueId="d3ece804-9945-e736-3be0-91b7a104dd71" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="/home/UNIXHOME/mdsmith/p4/mainline/software/smrtanalysis/bioinformatics/lib/python/pbcore/pbcore/data/datasets/pbalchemysim0.subreads.bam">
- <FileIndices/>
- </ExternalResource>
- </ExternalResources>
- <DataSetMetadata>
- <NumRecords>-1</NumRecords>
- <TotalLength>-1</TotalLength>
- <SummaryStats>
- <NumSequencingZmws>2876</NumSequencingZmws>
- <AdapterDimerFraction>0</AdapterDimerFraction>
- <ShortInsertFraction>0</ShortInsertFraction>
- <ProdDist>
- <NumBins>4</NumBins>
- <MetricDescription>Productivity</MetricDescription>
- <BinCounts>
- <BinCount>1576</BinCount>
- <BinCount>901</BinCount>
- <BinCount>399</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>Productive</BinLabel>
- <BinLabel>Other</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ProdDist>
- <ReadTypeDist>
- <NumBins>9</NumBins>
- <MetricDescription>Read Type</MetricDescription>
- <BinCounts>
- <BinCount>1474</BinCount>
- <BinCount>799</BinCount>
- <BinCount>4</BinCount>
- <BinCount>181</BinCount>
- <BinCount>92</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>326</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>FullHqRead0</BinLabel>
- <BinLabel>FullHqRead1</BinLabel>
- <BinLabel>PartialHqRead0</BinLabel>
- <BinLabel>PartialHqRead1</BinLabel>
- <BinLabel>PartialHqRead2</BinLabel>
- <BinLabel>Multiload</BinLabel>
- <BinLabel>Indeterminate</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ReadTypeDist>
- <ReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>4528.69384765625</SampleMean>
- <SampleMed>5227</SampleMed>
- <SampleStd>2322.8055598026981</SampleStd>
- <Sample95thPct>7367</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>418.89999389648438</BinWidth>
- <MinOutlierValue>77</MinOutlierValue>
- <MinBinValue>77</MinBinValue>
- <MaxBinValue>12225.1025390625</MaxBinValue>
- <MaxOutlierValue>12644</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>62</BinCount>
- <BinCount>39</BinCount>
- <BinCount>36</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>19</BinCount>
- <BinCount>29</BinCount>
- <BinCount>37</BinCount>
- <BinCount>32</BinCount>
- <BinCount>32</BinCount>
- <BinCount>40</BinCount>
- <BinCount>45</BinCount>
- <BinCount>54</BinCount>
- <BinCount>73</BinCount>
- <BinCount>77</BinCount>
- <BinCount>97</BinCount>
- <BinCount>95</BinCount>
- <BinCount>49</BinCount>
- <BinCount>17</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- </ReadLenDist>
- <ReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.82736450433731079</SampleMean>
- <SampleMed>0.83167940378189087</SampleMed>
- <SampleStd>0.029663275550147809</SampleStd>
- <Sample95thPct>0.86801999807357788</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.0049052196554839611</BinWidth>
- <MinOutlierValue>0.7500004768371582</MinOutlierValue>
- <MinBinValue>0.7500004768371582</MinBinValue>
- <MaxBinValue>0.89225196838378906</MaxBinValue>
- <MaxOutlierValue>0.89715707302093506</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>12</BinCount>
- <BinCount>8</BinCount>
- <BinCount>11</BinCount>
- <BinCount>10</BinCount>
- <BinCount>17</BinCount>
- <BinCount>11</BinCount>
- <BinCount>20</BinCount>
- <BinCount>24</BinCount>
- <BinCount>24</BinCount>
- <BinCount>34</BinCount>
- <BinCount>25</BinCount>
- <BinCount>38</BinCount>
- <BinCount>52</BinCount>
- <BinCount>33</BinCount>
- <BinCount>45</BinCount>
- <BinCount>48</BinCount>
- <BinCount>57</BinCount>
- <BinCount>47</BinCount>
- <BinCount>69</BinCount>
- <BinCount>65</BinCount>
- <BinCount>55</BinCount>
- <BinCount>51</BinCount>
- <BinCount>57</BinCount>
- <BinCount>42</BinCount>
- <BinCount>29</BinCount>
- <BinCount>12</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </ReadQualDist>
- <InsertReadLenDist>
- <SampleSize>901</SampleSize>
- <SampleMean>460.4583740234375</SampleMean>
- <SampleMed>350</SampleMed>
- <SampleStd>592.13342124584449</SampleStd>
- <Sample95thPct>751</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>98</BinWidth>
- <MinOutlierValue>78</MinOutlierValue>
- <MinBinValue>78</MinBinValue>
- <MaxBinValue>2920</MaxBinValue>
- <MaxOutlierValue>5969</MaxOutlierValue>
- <MetricDescription>Read Length of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>21</BinCount>
- <BinCount>25</BinCount>
- <BinCount>621</BinCount>
- <BinCount>151</BinCount>
- <BinCount>23</BinCount>
- <BinCount>10</BinCount>
- <BinCount>7</BinCount>
- <BinCount>4</BinCount>
- <BinCount>4</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>2</BinCount>
- <BinCount>5</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>15</BinCount>
- </BinCounts>
- </InsertReadLenDist>
- <InsertReadQualDist>
- <SampleSize>901</SampleSize>
- <SampleMean>0.96519893407821655</SampleMean>
- <SampleMed>0.99638187885284424</SampleMed>
- <SampleStd>0.063829474832070937</SampleStd>
- <Sample95thPct>0.9987713098526001</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.0082235373556613922</BinWidth>
- <MinOutlierValue>0.75223779678344727</MinOutlierValue>
- <MinBinValue>0.75223779678344727</MinBinValue>
- <MaxBinValue>0.990720272064209</MaxBinValue>
- <MaxOutlierValue>0.99894392490386963</MaxOutlierValue>
- <MetricDescription>Read Quality of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>6</BinCount>
- <BinCount>3</BinCount>
- <BinCount>7</BinCount>
- <BinCount>11</BinCount>
- <BinCount>14</BinCount>
- <BinCount>13</BinCount>
- <BinCount>12</BinCount>
- <BinCount>13</BinCount>
- <BinCount>6</BinCount>
- <BinCount>5</BinCount>
- <BinCount>3</BinCount>
- <BinCount>9</BinCount>
- <BinCount>3</BinCount>
- <BinCount>2</BinCount>
- <BinCount>3</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>5</BinCount>
- <BinCount>3</BinCount>
- <BinCount>9</BinCount>
- <BinCount>9</BinCount>
- <BinCount>11</BinCount>
- <BinCount>16</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>16</BinCount>
- <BinCount>24</BinCount>
- <BinCount>35</BinCount>
- <BinCount>59</BinCount>
- <BinCount>579</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </InsertReadQualDist>
- <MedianInsertDist>
- <SampleSize>973</SampleSize>
- <SampleMean>513.21990966796875</SampleMean>
- <SampleMed>350</SampleMed>
- <SampleStd>575.83020626506971</SampleStd>
- <Sample95thPct>1322</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>93.333335876464844</BinWidth>
- <MinOutlierValue>289</MinOutlierValue>
- <MinBinValue>289</MinBinValue>
- <MaxBinValue>2995.666259765625</MaxBinValue>
- <MaxOutlierValue>6278</MaxOutlierValue>
- <MetricDescription>Median Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>714</BinCount>
- <BinCount>101</BinCount>
- <BinCount>32</BinCount>
- <BinCount>18</BinCount>
- <BinCount>13</BinCount>
- <BinCount>8</BinCount>
- <BinCount>5</BinCount>
- <BinCount>6</BinCount>
- <BinCount>7</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>1</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>4</BinCount>
- <BinCount>6</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>7</BinCount>
- <BinCount>1</BinCount>
- <BinCount>3</BinCount>
- <BinCount>4</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>3</BinCount>
- <BinCount>0</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>1</BinCount>
- <BinCount>9</BinCount>
- </BinCounts>
- </MedianInsertDist>
- </SummaryStats>
- </DataSetMetadata>
- </DataSet>
- <DataSet CreatedAt="2015-07-09T17:04:25" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" UniqueId="d3ece804-9945-e736-3be0-91b7a104dd71" Version="2.3.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
- <ExternalResources>
- <ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="/home/UNIXHOME/mdsmith/p4/mainline/software/smrtanalysis/bioinformatics/lib/python/pbcore/pbcore/data/datasets/pbalchemysim0.subreads.bam">
- <FileIndices/>
- </ExternalResource>
- </ExternalResources>
- <DataSetMetadata>
- <NumRecords>-1</NumRecords>
- <TotalLength>-1</TotalLength>
- <SummaryStats>
- <NumSequencingZmws>150292</NumSequencingZmws>
- <AdapterDimerFraction>1.3307428206424827E-05</AdapterDimerFraction>
- <ShortInsertFraction>3.3268570516062067E-05</ShortInsertFraction>
- <ProdDist>
- <NumBins>4</NumBins>
- <MetricDescription>Productivity</MetricDescription>
- <BinCounts>
- <BinCount>119403</BinCount>
- <BinCount>24222</BinCount>
- <BinCount>6667</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>Productive</BinLabel>
- <BinLabel>Other</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ProdDist>
- <ReadTypeDist>
- <NumBins>9</NumBins>
- <MetricDescription>Read Type</MetricDescription>
- <BinCounts>
- <BinCount>87568</BinCount>
- <BinCount>13735</BinCount>
- <BinCount>195</BinCount>
- <BinCount>4186</BinCount>
- <BinCount>8034</BinCount>
- <BinCount>110</BinCount>
- <BinCount>0</BinCount>
- <BinCount>36464</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- <BinLabels>
- <BinLabel>Empty</BinLabel>
- <BinLabel>FullHqRead0</BinLabel>
- <BinLabel>FullHqRead1</BinLabel>
- <BinLabel>PartialHqRead0</BinLabel>
- <BinLabel>PartialHqRead1</BinLabel>
- <BinLabel>PartialHqRead2</BinLabel>
- <BinLabel>Multiload</BinLabel>
- <BinLabel>Indeterminate</BinLabel>
- <BinLabel>NotDefined</BinLabel>
- </BinLabels>
- </ReadTypeDist>
- <ReadLenDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>13965.3232421875</SampleMean>
- <SampleMed>11484</SampleMed>
- <SampleStd>10580.691922120142</SampleStd>
- <Sample95thPct>34936</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>2078.2333984375</BinWidth>
- <MinOutlierValue>63</MinOutlierValue>
- <MinBinValue>63</MinBinValue>
- <MaxBinValue>60331.7890625</MaxBinValue>
- <MaxOutlierValue>62410</MaxOutlierValue>
- <MetricDescription>Polymerase Read Length</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>2564</BinCount>
- <BinCount>2649</BinCount>
- <BinCount>2135</BinCount>
- <BinCount>1875</BinCount>
- <BinCount>1977</BinCount>
- <BinCount>1829</BinCount>
- <BinCount>1533</BinCount>
- <BinCount>1304</BinCount>
- <BinCount>1148</BinCount>
- <BinCount>1065</BinCount>
- <BinCount>919</BinCount>
- <BinCount>854</BinCount>
- <BinCount>803</BinCount>
- <BinCount>650</BinCount>
- <BinCount>605</BinCount>
- <BinCount>609</BinCount>
- <BinCount>646</BinCount>
- <BinCount>562</BinCount>
- <BinCount>333</BinCount>
- <BinCount>132</BinCount>
- <BinCount>23</BinCount>
- <BinCount>5</BinCount>
- <BinCount>2</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- </BinCounts>
- </ReadLenDist>
- <ReadQualDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>0.85828709602355957</SampleMean>
- <SampleMed>0.868025004863739</SampleMed>
- <SampleStd>0.030875069589002442</SampleStd>
- <Sample95thPct>0.88995635509490967</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.00517143402248621</BinWidth>
- <MinOutlierValue>0.75007820129394531</MinOutlierValue>
- <MinBinValue>0.75007820129394531</MinBinValue>
- <MaxBinValue>0.90004932880401611</MaxBinValue>
- <MaxOutlierValue>0.90522122383117676</MaxOutlierValue>
- <MetricDescription>Polymerase Read Quality</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>122</BinCount>
- <BinCount>136</BinCount>
- <BinCount>130</BinCount>
- <BinCount>144</BinCount>
- <BinCount>163</BinCount>
- <BinCount>177</BinCount>
- <BinCount>186</BinCount>
- <BinCount>213</BinCount>
- <BinCount>237</BinCount>
- <BinCount>251</BinCount>
- <BinCount>280</BinCount>
- <BinCount>338</BinCount>
- <BinCount>412</BinCount>
- <BinCount>426</BinCount>
- <BinCount>527</BinCount>
- <BinCount>563</BinCount>
- <BinCount>686</BinCount>
- <BinCount>790</BinCount>
- <BinCount>925</BinCount>
- <BinCount>1095</BinCount>
- <BinCount>1377</BinCount>
- <BinCount>1525</BinCount>
- <BinCount>1775</BinCount>
- <BinCount>2133</BinCount>
- <BinCount>2515</BinCount>
- <BinCount>2973</BinCount>
- <BinCount>2823</BinCount>
- <BinCount>1192</BinCount>
- <BinCount>103</BinCount>
- <BinCount>4</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </ReadQualDist>
- <InsertReadLenDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>12747.7919921875</SampleMean>
- <SampleMed>10937</SampleMed>
- <SampleStd>9364.0618727600377</SampleStd>
- <Sample95thPct>29948</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>1436.566650390625</BinWidth>
- <MinOutlierValue>1</MinOutlierValue>
- <MinBinValue>1</MinBinValue>
- <MaxBinValue>41661.4296875</MaxBinValue>
- <MaxOutlierValue>43098</MaxOutlierValue>
- <MetricDescription>Read Length of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>1660</BinCount>
- <BinCount>2384</BinCount>
- <BinCount>1828</BinCount>
- <BinCount>1455</BinCount>
- <BinCount>1315</BinCount>
- <BinCount>1302</BinCount>
- <BinCount>1365</BinCount>
- <BinCount>1296</BinCount>
- <BinCount>1200</BinCount>
- <BinCount>1088</BinCount>
- <BinCount>965</BinCount>
- <BinCount>856</BinCount>
- <BinCount>822</BinCount>
- <BinCount>820</BinCount>
- <BinCount>878</BinCount>
- <BinCount>756</BinCount>
- <BinCount>747</BinCount>
- <BinCount>754</BinCount>
- <BinCount>654</BinCount>
- <BinCount>535</BinCount>
- <BinCount>382</BinCount>
- <BinCount>321</BinCount>
- <BinCount>275</BinCount>
- <BinCount>181</BinCount>
- <BinCount>167</BinCount>
- <BinCount>117</BinCount>
- <BinCount>64</BinCount>
- <BinCount>22</BinCount>
- <BinCount>9</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </InsertReadLenDist>
- <InsertReadQualDist>
- <SampleSize>24222</SampleSize>
- <SampleMean>0.86046397686004639</SampleMean>
- <SampleMed>0.8684546947479248</SampleMed>
- <SampleStd>0.035067464845073885</SampleStd>
- <Sample95thPct>0.89117431640625</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>0.0082973875105381012</BinWidth>
- <MinOutlierValue>0.75007820129394531</MinOutlierValue>
- <MinBinValue>0.75007820129394531</MinBinValue>
- <MaxBinValue>0.99070233106613159</MaxBinValue>
- <MaxOutlierValue>0.998999834060669</MaxOutlierValue>
- <MetricDescription>Read Quality of Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>196</BinCount>
- <BinCount>221</BinCount>
- <BinCount>249</BinCount>
- <BinCount>282</BinCount>
- <BinCount>308</BinCount>
- <BinCount>392</BinCount>
- <BinCount>438</BinCount>
- <BinCount>619</BinCount>
- <BinCount>701</BinCount>
- <BinCount>871</BinCount>
- <BinCount>1141</BinCount>
- <BinCount>1465</BinCount>
- <BinCount>1989</BinCount>
- <BinCount>2463</BinCount>
- <BinCount>3213</BinCount>
- <BinCount>4186</BinCount>
- <BinCount>4264</BinCount>
- <BinCount>744</BinCount>
- <BinCount>10</BinCount>
- <BinCount>9</BinCount>
- <BinCount>4</BinCount>
- <BinCount>7</BinCount>
- <BinCount>10</BinCount>
- <BinCount>32</BinCount>
- <BinCount>51</BinCount>
- <BinCount>13</BinCount>
- <BinCount>21</BinCount>
- <BinCount>29</BinCount>
- <BinCount>46</BinCount>
- <BinCount>247</BinCount>
- <BinCount>1</BinCount>
- </BinCounts>
- </InsertReadQualDist>
- <MedianInsertDist>
- <SampleSize>570</SampleSize>
- <SampleMean>5406.65625</SampleMean>
- <SampleMed>2860</SampleMed>
- <SampleStd>6322.1968204214045</SampleStd>
- <Sample95thPct>18508</Sample95thPct>
- <NumBins>30</NumBins>
- <BinWidth>1090.199951171875</BinWidth>
- <MinOutlierValue>0</MinOutlierValue>
- <MinBinValue>0</MinBinValue>
- <MaxBinValue>31615.791015625</MaxBinValue>
- <MaxOutlierValue>64092</MaxOutlierValue>
- <MetricDescription>Median Insert</MetricDescription>
- <BinCounts>
- <BinCount>0</BinCount>
- <BinCount>28</BinCount>
- <BinCount>159</BinCount>
- <BinCount>125</BinCount>
- <BinCount>65</BinCount>
- <BinCount>30</BinCount>
- <BinCount>26</BinCount>
- <BinCount>25</BinCount>
- <BinCount>9</BinCount>
- <BinCount>10</BinCount>
- <BinCount>10</BinCount>
- <BinCount>12</BinCount>
- <BinCount>7</BinCount>
- <BinCount>11</BinCount>
- <BinCount>11</BinCount>
- <BinCount>3</BinCount>
- <BinCount>3</BinCount>
- <BinCount>9</BinCount>
- <BinCount>3</BinCount>
- <BinCount>5</BinCount>
- <BinCount>4</BinCount>
- <BinCount>2</BinCount>
- <BinCount>2</BinCount>
- <BinCount>3</BinCount>
- <BinCount>1</BinCount>
- <BinCount>1</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>0</BinCount>
- <BinCount>2</BinCount>
- <BinCount>4</BinCount>
- </BinCounts>
- </MedianInsertDist>
- </SummaryStats>
- </DataSetMetadata>
- </DataSet>
+ <SubreadSet CreatedAt="2015-08-06T17:07:36" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.SubreadSet-150807_000736" UniqueId="57850a3a-992e-2286-59b0-e189320d1dbc" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.subreads.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150807_000736" UniqueId="c55c8ed2-4821-4c48-9395-94625363fe6d"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>-1</pbds:TotalLength>
+ <pbds:NumRecords>-1</pbds:NumRecords>
+ <pbstats:SummaryStats>
+ <pbstats:NumSequencingZmws>2876</pbstats:NumSequencingZmws>
+ <pbstats:AdapterDimerFraction>0</pbstats:AdapterDimerFraction>
+ <pbstats:ShortInsertFraction>0</pbstats:ShortInsertFraction>
+ <pbstats:ProdDist>
+ <pbstats:NumBins>4</pbstats:NumBins>
+ <pbstats:MetricDescription>Productivity</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>1576</pbstats:BinCount>
+ <pbstats:BinCount>901</pbstats:BinCount>
+ <pbstats:BinCount>399</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ <pbstats:BinLabels>
+ <pbstats:BinLabel>Empty</pbstats:BinLabel>
+ <pbstats:BinLabel>Productive</pbstats:BinLabel>
+ <pbstats:BinLabel>Other</pbstats:BinLabel>
+ <pbstats:BinLabel>NotDefined</pbstats:BinLabel>
+ </pbstats:BinLabels>
+ </pbstats:ProdDist>
+ <pbstats:ReadTypeDist>
+ <pbstats:NumBins>9</pbstats:NumBins>
+ <pbstats:MetricDescription>Read Type</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>1474</pbstats:BinCount>
+ <pbstats:BinCount>799</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>181</pbstats:BinCount>
+ <pbstats:BinCount>92</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>326</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ <pbstats:BinLabels>
+ <pbstats:BinLabel>Empty</pbstats:BinLabel>
+ <pbstats:BinLabel>FullHqRead0</pbstats:BinLabel>
+ <pbstats:BinLabel>FullHqRead1</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead0</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead1</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead2</pbstats:BinLabel>
+ <pbstats:BinLabel>Multiload</pbstats:BinLabel>
+ <pbstats:BinLabel>Indeterminate</pbstats:BinLabel>
+ <pbstats:BinLabel>NotDefined</pbstats:BinLabel>
+ </pbstats:BinLabels>
+ </pbstats:ReadTypeDist>
+ <pbstats:ReadLenDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>4528.69384765625</pbstats:SampleMean>
+ <pbstats:SampleMed>5227</pbstats:SampleMed>
+ <pbstats:SampleStd>2322.8055598026981</pbstats:SampleStd>
+ <pbstats:Sample95thPct>7367</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>418.89999389648438</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>77</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>77</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>12225.1025390625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>12644</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Length</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>62</pbstats:BinCount>
+ <pbstats:BinCount>39</pbstats:BinCount>
+ <pbstats:BinCount>36</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>37</pbstats:BinCount>
+ <pbstats:BinCount>19</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>37</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>40</pbstats:BinCount>
+ <pbstats:BinCount>45</pbstats:BinCount>
+ <pbstats:BinCount>54</pbstats:BinCount>
+ <pbstats:BinCount>73</pbstats:BinCount>
+ <pbstats:BinCount>77</pbstats:BinCount>
+ <pbstats:BinCount>97</pbstats:BinCount>
+ <pbstats:BinCount>95</pbstats:BinCount>
+ <pbstats:BinCount>49</pbstats:BinCount>
+ <pbstats:BinCount>17</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadLenDist>
+ <pbstats:ReadQualDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>0.82736450433731079</pbstats:SampleMean>
+ <pbstats:SampleMed>0.83167940378189087</pbstats:SampleMed>
+ <pbstats:SampleStd>0.029663275550147809</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.86801999807357788</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.0049052196554839611</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.7500004768371582</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.7500004768371582</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.89225196838378906</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.89715707302093506</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Quality</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>8</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>17</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>20</pbstats:BinCount>
+ <pbstats:BinCount>24</pbstats:BinCount>
+ <pbstats:BinCount>24</pbstats:BinCount>
+ <pbstats:BinCount>34</pbstats:BinCount>
+ <pbstats:BinCount>25</pbstats:BinCount>
+ <pbstats:BinCount>38</pbstats:BinCount>
+ <pbstats:BinCount>52</pbstats:BinCount>
+ <pbstats:BinCount>33</pbstats:BinCount>
+ <pbstats:BinCount>45</pbstats:BinCount>
+ <pbstats:BinCount>48</pbstats:BinCount>
+ <pbstats:BinCount>57</pbstats:BinCount>
+ <pbstats:BinCount>47</pbstats:BinCount>
+ <pbstats:BinCount>69</pbstats:BinCount>
+ <pbstats:BinCount>65</pbstats:BinCount>
+ <pbstats:BinCount>55</pbstats:BinCount>
+ <pbstats:BinCount>51</pbstats:BinCount>
+ <pbstats:BinCount>57</pbstats:BinCount>
+ <pbstats:BinCount>42</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadQualDist>
+ <pbstats:InsertReadLenDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>460.4583740234375</pbstats:SampleMean>
+ <pbstats:SampleMed>350</pbstats:SampleMed>
+ <pbstats:SampleStd>592.13342124584449</pbstats:SampleStd>
+ <pbstats:Sample95thPct>751</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>98</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>78</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>78</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>2920</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>5969</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Length of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>21</pbstats:BinCount>
+ <pbstats:BinCount>25</pbstats:BinCount>
+ <pbstats:BinCount>621</pbstats:BinCount>
+ <pbstats:BinCount>151</pbstats:BinCount>
+ <pbstats:BinCount>23</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>15</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadLenDist>
+ <pbstats:InsertReadQualDist>
+ <pbstats:SampleSize>901</pbstats:SampleSize>
+ <pbstats:SampleMean>0.96519893407821655</pbstats:SampleMean>
+ <pbstats:SampleMed>0.99638187885284424</pbstats:SampleMed>
+ <pbstats:SampleStd>0.063829474832070937</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.9987713098526001</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.0082235373556613922</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.75223779678344727</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.75223779678344727</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.990720272064209</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.99894392490386963</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Quality of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>14</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>16</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>16</pbstats:BinCount>
+ <pbstats:BinCount>24</pbstats:BinCount>
+ <pbstats:BinCount>35</pbstats:BinCount>
+ <pbstats:BinCount>59</pbstats:BinCount>
+ <pbstats:BinCount>579</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadQualDist>
+ <pbstats:MedianInsertDist>
+ <pbstats:SampleSize>973</pbstats:SampleSize>
+ <pbstats:SampleMean>513.21990966796875</pbstats:SampleMean>
+ <pbstats:SampleMed>350</pbstats:SampleMed>
+ <pbstats:SampleStd>575.83020626506971</pbstats:SampleStd>
+ <pbstats:Sample95thPct>1322</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>93.333335876464844</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>289</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>289</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>2995.666259765625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>6278</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Median Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>714</pbstats:BinCount>
+ <pbstats:BinCount>101</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>18</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>8</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>6</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:MedianInsertDist>
+ </pbstats:SummaryStats>
+ </pbds:DataSetMetadata>
+ </SubreadSet>
+ <SubreadSet CreatedAt="2015-08-06T17:07:36" MetaType="PacBio.DataSet.SubreadSet" Name="" Tags="" TimeStampedName="PacBio.DataSet.SubreadSet-150807_000736" UniqueId="57850a3a-992e-2286-59b0-e189320d1dbc" Version="3.0.0" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
+ <pbbase:ExternalResources>
+ <pbbase:ExternalResource MetaType="PacBio.SubreadFile.SubreadBamFile" ResourceId="pbalchemysim0.subreads.bam" TimeStampedName="PacBio.SubreadFile.SubreadBamFile-150807_000736" UniqueId="c55c8ed2-4821-4c48-9395-94625363fe6d"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>-1</pbds:TotalLength>
+ <pbds:NumRecords>-1</pbds:NumRecords>
+ <pbstats:SummaryStats>
+ <pbstats:NumSequencingZmws>150292</pbstats:NumSequencingZmws>
+ <pbstats:AdapterDimerFraction>1.3307428206424827E-05</pbstats:AdapterDimerFraction>
+ <pbstats:ShortInsertFraction>3.3268570516062067E-05</pbstats:ShortInsertFraction>
+ <pbstats:ProdDist>
+ <pbstats:NumBins>4</pbstats:NumBins>
+ <pbstats:MetricDescription>Productivity</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>119403</pbstats:BinCount>
+ <pbstats:BinCount>24222</pbstats:BinCount>
+ <pbstats:BinCount>6667</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ <pbstats:BinLabels>
+ <pbstats:BinLabel>Empty</pbstats:BinLabel>
+ <pbstats:BinLabel>Productive</pbstats:BinLabel>
+ <pbstats:BinLabel>Other</pbstats:BinLabel>
+ <pbstats:BinLabel>NotDefined</pbstats:BinLabel>
+ </pbstats:BinLabels>
+ </pbstats:ProdDist>
+ <pbstats:ReadTypeDist>
+ <pbstats:NumBins>9</pbstats:NumBins>
+ <pbstats:MetricDescription>Read Type</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>87568</pbstats:BinCount>
+ <pbstats:BinCount>13735</pbstats:BinCount>
+ <pbstats:BinCount>195</pbstats:BinCount>
+ <pbstats:BinCount>4186</pbstats:BinCount>
+ <pbstats:BinCount>8034</pbstats:BinCount>
+ <pbstats:BinCount>110</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>36464</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ <pbstats:BinLabels>
+ <pbstats:BinLabel>Empty</pbstats:BinLabel>
+ <pbstats:BinLabel>FullHqRead0</pbstats:BinLabel>
+ <pbstats:BinLabel>FullHqRead1</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead0</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead1</pbstats:BinLabel>
+ <pbstats:BinLabel>PartialHqRead2</pbstats:BinLabel>
+ <pbstats:BinLabel>Multiload</pbstats:BinLabel>
+ <pbstats:BinLabel>Indeterminate</pbstats:BinLabel>
+ <pbstats:BinLabel>NotDefined</pbstats:BinLabel>
+ </pbstats:BinLabels>
+ </pbstats:ReadTypeDist>
+ <pbstats:ReadLenDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>13965.3232421875</pbstats:SampleMean>
+ <pbstats:SampleMed>11484</pbstats:SampleMed>
+ <pbstats:SampleStd>10580.691922120142</pbstats:SampleStd>
+ <pbstats:Sample95thPct>34936</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>2078.2333984375</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>63</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>63</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>60331.7890625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>62410</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Length</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2564</pbstats:BinCount>
+ <pbstats:BinCount>2649</pbstats:BinCount>
+ <pbstats:BinCount>2135</pbstats:BinCount>
+ <pbstats:BinCount>1875</pbstats:BinCount>
+ <pbstats:BinCount>1977</pbstats:BinCount>
+ <pbstats:BinCount>1829</pbstats:BinCount>
+ <pbstats:BinCount>1533</pbstats:BinCount>
+ <pbstats:BinCount>1304</pbstats:BinCount>
+ <pbstats:BinCount>1148</pbstats:BinCount>
+ <pbstats:BinCount>1065</pbstats:BinCount>
+ <pbstats:BinCount>919</pbstats:BinCount>
+ <pbstats:BinCount>854</pbstats:BinCount>
+ <pbstats:BinCount>803</pbstats:BinCount>
+ <pbstats:BinCount>650</pbstats:BinCount>
+ <pbstats:BinCount>605</pbstats:BinCount>
+ <pbstats:BinCount>609</pbstats:BinCount>
+ <pbstats:BinCount>646</pbstats:BinCount>
+ <pbstats:BinCount>562</pbstats:BinCount>
+ <pbstats:BinCount>333</pbstats:BinCount>
+ <pbstats:BinCount>132</pbstats:BinCount>
+ <pbstats:BinCount>23</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadLenDist>
+ <pbstats:ReadQualDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>0.85828709602355957</pbstats:SampleMean>
+ <pbstats:SampleMed>0.868025004863739</pbstats:SampleMed>
+ <pbstats:SampleStd>0.030875069589002442</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.88995635509490967</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.00517143402248621</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.75007820129394531</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.75007820129394531</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.90004932880401611</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.90522122383117676</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Polymerase Read Quality</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>122</pbstats:BinCount>
+ <pbstats:BinCount>136</pbstats:BinCount>
+ <pbstats:BinCount>130</pbstats:BinCount>
+ <pbstats:BinCount>144</pbstats:BinCount>
+ <pbstats:BinCount>163</pbstats:BinCount>
+ <pbstats:BinCount>177</pbstats:BinCount>
+ <pbstats:BinCount>186</pbstats:BinCount>
+ <pbstats:BinCount>213</pbstats:BinCount>
+ <pbstats:BinCount>237</pbstats:BinCount>
+ <pbstats:BinCount>251</pbstats:BinCount>
+ <pbstats:BinCount>280</pbstats:BinCount>
+ <pbstats:BinCount>338</pbstats:BinCount>
+ <pbstats:BinCount>412</pbstats:BinCount>
+ <pbstats:BinCount>426</pbstats:BinCount>
+ <pbstats:BinCount>527</pbstats:BinCount>
+ <pbstats:BinCount>563</pbstats:BinCount>
+ <pbstats:BinCount>686</pbstats:BinCount>
+ <pbstats:BinCount>790</pbstats:BinCount>
+ <pbstats:BinCount>925</pbstats:BinCount>
+ <pbstats:BinCount>1095</pbstats:BinCount>
+ <pbstats:BinCount>1377</pbstats:BinCount>
+ <pbstats:BinCount>1525</pbstats:BinCount>
+ <pbstats:BinCount>1775</pbstats:BinCount>
+ <pbstats:BinCount>2133</pbstats:BinCount>
+ <pbstats:BinCount>2515</pbstats:BinCount>
+ <pbstats:BinCount>2973</pbstats:BinCount>
+ <pbstats:BinCount>2823</pbstats:BinCount>
+ <pbstats:BinCount>1192</pbstats:BinCount>
+ <pbstats:BinCount>103</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:ReadQualDist>
+ <pbstats:InsertReadLenDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>12747.7919921875</pbstats:SampleMean>
+ <pbstats:SampleMed>10937</pbstats:SampleMed>
+ <pbstats:SampleStd>9364.0618727600377</pbstats:SampleStd>
+ <pbstats:Sample95thPct>29948</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>1436.566650390625</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>1</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>1</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>41661.4296875</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>43098</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Length of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>1660</pbstats:BinCount>
+ <pbstats:BinCount>2384</pbstats:BinCount>
+ <pbstats:BinCount>1828</pbstats:BinCount>
+ <pbstats:BinCount>1455</pbstats:BinCount>
+ <pbstats:BinCount>1315</pbstats:BinCount>
+ <pbstats:BinCount>1302</pbstats:BinCount>
+ <pbstats:BinCount>1365</pbstats:BinCount>
+ <pbstats:BinCount>1296</pbstats:BinCount>
+ <pbstats:BinCount>1200</pbstats:BinCount>
+ <pbstats:BinCount>1088</pbstats:BinCount>
+ <pbstats:BinCount>965</pbstats:BinCount>
+ <pbstats:BinCount>856</pbstats:BinCount>
+ <pbstats:BinCount>822</pbstats:BinCount>
+ <pbstats:BinCount>820</pbstats:BinCount>
+ <pbstats:BinCount>878</pbstats:BinCount>
+ <pbstats:BinCount>756</pbstats:BinCount>
+ <pbstats:BinCount>747</pbstats:BinCount>
+ <pbstats:BinCount>754</pbstats:BinCount>
+ <pbstats:BinCount>654</pbstats:BinCount>
+ <pbstats:BinCount>535</pbstats:BinCount>
+ <pbstats:BinCount>382</pbstats:BinCount>
+ <pbstats:BinCount>321</pbstats:BinCount>
+ <pbstats:BinCount>275</pbstats:BinCount>
+ <pbstats:BinCount>181</pbstats:BinCount>
+ <pbstats:BinCount>167</pbstats:BinCount>
+ <pbstats:BinCount>117</pbstats:BinCount>
+ <pbstats:BinCount>64</pbstats:BinCount>
+ <pbstats:BinCount>22</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadLenDist>
+ <pbstats:InsertReadQualDist>
+ <pbstats:SampleSize>24222</pbstats:SampleSize>
+ <pbstats:SampleMean>0.86046397686004639</pbstats:SampleMean>
+ <pbstats:SampleMed>0.8684546947479248</pbstats:SampleMed>
+ <pbstats:SampleStd>0.035067464845073885</pbstats:SampleStd>
+ <pbstats:Sample95thPct>0.89117431640625</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>0.0082973875105381012</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0.75007820129394531</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0.75007820129394531</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>0.99070233106613159</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>0.998999834060669</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Read Quality of Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>196</pbstats:BinCount>
+ <pbstats:BinCount>221</pbstats:BinCount>
+ <pbstats:BinCount>249</pbstats:BinCount>
+ <pbstats:BinCount>282</pbstats:BinCount>
+ <pbstats:BinCount>308</pbstats:BinCount>
+ <pbstats:BinCount>392</pbstats:BinCount>
+ <pbstats:BinCount>438</pbstats:BinCount>
+ <pbstats:BinCount>619</pbstats:BinCount>
+ <pbstats:BinCount>701</pbstats:BinCount>
+ <pbstats:BinCount>871</pbstats:BinCount>
+ <pbstats:BinCount>1141</pbstats:BinCount>
+ <pbstats:BinCount>1465</pbstats:BinCount>
+ <pbstats:BinCount>1989</pbstats:BinCount>
+ <pbstats:BinCount>2463</pbstats:BinCount>
+ <pbstats:BinCount>3213</pbstats:BinCount>
+ <pbstats:BinCount>4186</pbstats:BinCount>
+ <pbstats:BinCount>4264</pbstats:BinCount>
+ <pbstats:BinCount>744</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>32</pbstats:BinCount>
+ <pbstats:BinCount>51</pbstats:BinCount>
+ <pbstats:BinCount>13</pbstats:BinCount>
+ <pbstats:BinCount>21</pbstats:BinCount>
+ <pbstats:BinCount>29</pbstats:BinCount>
+ <pbstats:BinCount>46</pbstats:BinCount>
+ <pbstats:BinCount>247</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:InsertReadQualDist>
+ <pbstats:MedianInsertDist>
+ <pbstats:SampleSize>570</pbstats:SampleSize>
+ <pbstats:SampleMean>5406.65625</pbstats:SampleMean>
+ <pbstats:SampleMed>2860</pbstats:SampleMed>
+ <pbstats:SampleStd>6322.1968204214045</pbstats:SampleStd>
+ <pbstats:Sample95thPct>18508</pbstats:Sample95thPct>
+ <pbstats:NumBins>30</pbstats:NumBins>
+ <pbstats:BinWidth>1090.199951171875</pbstats:BinWidth>
+ <pbstats:MinOutlierValue>0</pbstats:MinOutlierValue>
+ <pbstats:MinBinValue>0</pbstats:MinBinValue>
+ <pbstats:MaxBinValue>31615.791015625</pbstats:MaxBinValue>
+ <pbstats:MaxOutlierValue>64092</pbstats:MaxOutlierValue>
+ <pbstats:MetricDescription>Median Insert</pbstats:MetricDescription>
+ <pbstats:BinCounts>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>28</pbstats:BinCount>
+ <pbstats:BinCount>159</pbstats:BinCount>
+ <pbstats:BinCount>125</pbstats:BinCount>
+ <pbstats:BinCount>65</pbstats:BinCount>
+ <pbstats:BinCount>30</pbstats:BinCount>
+ <pbstats:BinCount>26</pbstats:BinCount>
+ <pbstats:BinCount>25</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>10</pbstats:BinCount>
+ <pbstats:BinCount>12</pbstats:BinCount>
+ <pbstats:BinCount>7</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>11</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>9</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>5</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>3</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>1</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>0</pbstats:BinCount>
+ <pbstats:BinCount>2</pbstats:BinCount>
+ <pbstats:BinCount>4</pbstats:BinCount>
+ </pbstats:BinCounts>
+ </pbstats:MedianInsertDist>
+ </pbstats:SummaryStats>
+ </pbds:DataSetMetadata>
+ </SubreadSet>
</DataSets>
-</DataSet>
+</pbds:SubreadSet>
diff --git a/pbcore/data/datasets/transformed_rs_subread.dataset.xml b/pbcore/data/datasets/transformed_rs_subread.dataset.xml
index 668817a..6aa1152 100644
--- a/pbcore/data/datasets/transformed_rs_subread.dataset.xml
+++ b/pbcore/data/datasets/transformed_rs_subread.dataset.xml
@@ -1,72 +1,84 @@
<?xml version="1.0" encoding="UTF-8"?>
-<HdfSubreadSet xmlns:uuid="java:java.util.UUID" xmlns:bax="http://whatever"
- xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd"
- xmlns:xs="http://www.w3.org/2001/XMLSchema"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:fn="http://www.w3.org/2005/xpath-functions"
- Name="Subreads from run
 r000004_42268_150307"
- MetaType="PacBio.DataSet.SubreadSet"
- Tags="pacbio.secondary.instrument=RS"
- Version="0.5"
- UniqueId="a8c1f8c5-a0ca-4a90-95c7-bc291c389e09">
- <ExternalResources>
- <ExternalResource MetaType="PacBio.SubreadFile.BaxFile"
- ResourceId="file:///C:/Users/aklammer/aklammer_laptop_2015/aklammer_laptop_2015/depot/software/smrtanalysis/bioinformatics/doc/FileFormats/examples/datasets/Analysis_Results/rs.1.bax.h5"/>
- <ExternalResource MetaType="PacBio.SubreadFile.BaxFile"
- ResourceId="file:///C:/Users/aklammer/aklammer_laptop_2015/aklammer_laptop_2015/depot/software/smrtanalysis/bioinformatics/doc/FileFormats/examples/datasets/Analysis_Results/rs.2.bax.h5"/>
- <ExternalResource MetaType="PacBio.SubreadFile.BaxFile"
- ResourceId="file:///C:/Users/aklammer/aklammer_laptop_2015/aklammer_laptop_2015/depot/software/smrtanalysis/bioinformatics/doc/FileFormats/examples/datasets/Analysis_Results/rs.3.bax.h5"/>
- </ExternalResources>
- <DataSetMetadata>
- <TotalLength>50000000</TotalLength>
- <NumRecords>150000</NumRecords>
- <Collections>
- <CollectionMetadata Context="rs" InstrumentName="42268" InstrumentId="1">
- <InstCtrlVer>2.3.0.1.142990</InstCtrlVer>
- <SigProcVer>NRT at 172.31.128.10:8082, SwVer=2301.142990, HwVer=1.0</SigProcVer>
- <RunDetails>
- <RunId>r000004_42268_150307</RunId>
- <Name>Inst42268-030715-2kb-P4-0.05nM-6Chips-FAT2_3</Name>
- </RunDetails>
- <WellSample Name="Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3">
- <PlateId>Inst42268-030715-2kb-P4-0.05nM-6Chips-FAT2_3</PlateId>
- <WellName>Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3</WellName>
- <Concentration>0</Concentration>
- <SampleReuseEnabled>false</SampleReuseEnabled>
- <StageHotstartEnabled>true</StageHotstartEnabled>
- <SizeSelectionEnabled>
+<pbds:HdfSubreadSet xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
+ UniqueId="a4040047-9ae2-4d77-8683-2ae1bd231c75"
+ TimeStampedName="hdfsubreadset_2015-08-04T19:12:20.971-08:00"
+ MetaType="PacBio.DataSet.SubreadSet"
+ Name="Subreads from runr000004_42268_150307"
+ Tags="pacbio.secondary.instrument=RS"
+ Version="0.5">
+ <pbbase:ExternalResources xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+ <pbbase:ExternalResource UniqueId="afde5e9a-0461-4bd1-8bd1-476b87d4f70d"
+ TimeStampedName="hdfsubread_file_2015-08-04T19:12:20.971-08:00"
+ MetaType="PacBio.SubreadFile.BaxFile"
+ ResourceId="file:///C:/Users/aklammer/aklammer_laptop_2015/aklammer_laptop_2015/depot/software/smrtanalysis/bioinformatics/doc/FileFormats/examples/datasets/Analysis_Results/rs.1.bax.h5"/>
+ <pbbase:ExternalResource UniqueId="a0bc77b6-281c-47a3-a532-389c7d5c0736"
+ TimeStampedName="hdfsubread_file_2015-08-04T19:12:20.971-08:00"
+ MetaType="PacBio.SubreadFile.BaxFile"
+ ResourceId="file:///C:/Users/aklammer/aklammer_laptop_2015/aklammer_laptop_2015/depot/software/smrtanalysis/bioinformatics/doc/FileFormats/examples/datasets/Analysis_Results/rs.2.bax.h5"/>
+ <pbbase:ExternalResource UniqueId="ac274355-9abd-4c45-9040-bb97241bb6e6"
+ TimeStampedName="hdfsubreadset_file_2015-08-04T19:12:20.971-08:00"
+ MetaType="PacBio.SubreadFile.BaxFile"
+ ResourceId="file:///C:/Users/aklammer/aklammer_laptop_2015/aklammer_laptop_2015/depot/software/smrtanalysis/bioinformatics/doc/FileFormats/examples/datasets/Analysis_Results/rs.3.bax.h5"/>
+ </pbbase:ExternalResources>
+ <pbds:DataSetMetadata>
+ <pbds:TotalLength>50000000</pbds:TotalLength>
+ <pbds:NumRecords>150000</pbds:NumRecords>
+ <pbmeta:Collections xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+ <pbmeta:CollectionMetadata UniqueId="ad41c283-cd37-455b-97a8-23dde1fd7cee" TimeStampedName="rs"
+ MetaType="PacBio.Collection"
+ Context="rs"
+ InstrumentName="42268"
+ InstrumentId="1">
+ <pbmeta:InstCtrlVer>2.3.0.1.142990</pbmeta:InstCtrlVer>
+ <pbmeta:SigProcVer>NRT at 172.31.128.10:8082, SwVer=2301.142990, HwVer=1.0</pbmeta:SigProcVer>
+ <pbmeta:RunDetails>
+ <pbmeta:RunId>r000004_42268_150307</pbmeta:RunId>
+ <pbmeta:Name>Inst42268-030715-2kb-P4-0.05nM-6Chips-FAT2_3</pbmeta:Name>
+ </pbmeta:RunDetails>
+ <pbmeta:WellSample Name="Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3">
+ <pbmeta:PlateId>Inst42268-030715-2kb-P4-0.05nM-6Chips-FAT2_3</pbmeta:PlateId>
+ <pbmeta:WellName>Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3</pbmeta:WellName>
+ <pbmeta:Concentration>0</pbmeta:Concentration>
+ <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+ <pbmeta:StageHotstartEnabled>true</pbmeta:StageHotstartEnabled>
+ <pbmeta:SizeSelectionEnabled>
false
- </SizeSelectionEnabled>
- <UseCount>1</UseCount>
- <Comments>Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3</Comments>
- <BioSamplePointers>
- <BioSamplePointer>ad236d1c-2dd2-444e-9001-bba691cedad8</BioSamplePointer>
- </BioSamplePointers>
- </WellSample>
- <Automation>
- <AutomationParameters>
- <AutomationParameter/>
- </AutomationParameters>
- </Automation>
- <CollectionNumber>6</CollectionNumber>
- <CellIndex>1</CellIndex>
- <CellPac Barcode="10078306255000000182317020825155"/>
- <Primary>
- <AutomationName>BasecallerV1</AutomationName>
- <ConfigFileName>2-0-0_P4-C2.xml</ConfigFileName>
- <SequencingCondition/>
- <ResultsFolder>Analysis_Results</ResultsFolder>
- <CollectionPathUri>rsy://mp-rsync/vol55//RS_DATA_STAGING/42268/Inst42268-030715-2kb-P4-0.05nM-6Chips-FAT2_3_4/B01_2/</CollectionPathUri>
- <CopyFiles>
- <CollectionFileCopy>Fasta</CollectionFileCopy>
- </CopyFiles>
- </Primary>
- </CollectionMetadata>
- </Collections>
- <BioSamples>
- <BioSample Name="Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3"
- Description="Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3"
- UniqueId="ad236d1c-2dd2-444e-9001-bba691cedad8"/>
- </BioSamples>
- </DataSetMetadata>
-</HdfSubreadSet>
\ No newline at end of file
+ </pbmeta:SizeSelectionEnabled>
+ <pbmeta:UseCount>1</pbmeta:UseCount>
+ <pbsample:BioSamplePointers xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd">
+ <pbsample:BioSamplePointer>a0ad6e5b-a522-405b-8e50-d622e1ca9858</pbsample:BioSamplePointer>
+ </pbsample:BioSamplePointers>
+ </pbmeta:WellSample>
+ <pbmeta:Automation>
+ <pbbase:AutomationParameters xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+ <pbbase:AutomationParameter/>
+ </pbbase:AutomationParameters>
+ </pbmeta:Automation>
+ <pbmeta:CollectionNumber>6</pbmeta:CollectionNumber>
+ <pbmeta:CellIndex>1</pbmeta:CellIndex>
+ <pbmeta:CellPac Barcode="10078306255000000182317020825155"/>
+ <pbmeta:Primary>
+ <pbmeta:AutomationName>BasecallerV1</pbmeta:AutomationName>
+ <pbmeta:ConfigFileName>2-0-0_P4-C2.xml</pbmeta:ConfigFileName>
+ <pbmeta:SequencingCondition/>
+ <pbmeta:OutputOptions>
+ <pbmeta:ResultsFolder>Analysis_Results</pbmeta:ResultsFolder>
+ <pbmeta:CollectionPathUri>rsy://mp-rsync/vol55//RS_DATA_STAGING/42268/Inst42268-030715-2kb-P4-0.05nM-6Chips-FAT2_3_4/B01_2/</pbmeta:CollectionPathUri>
+ <pbmeta:CopyFiles>
+ <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+ </pbmeta:CopyFiles>
+ <pbmeta:Readout>Bases</pbmeta:Readout>
+ <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+ </pbmeta:OutputOptions>
+ </pbmeta:Primary>
+ </pbmeta:CollectionMetadata>
+ </pbmeta:Collections>
+ <pbsample:BioSamples xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd">
+ <pbsample:BioSample UniqueId="a0ad6e5b-a522-405b-8e50-d622e1ca9858"
+ TimeStampedName="biosample_2015-08-04T19:12:20.971-08:00"
+ MetaType="PacBio.Sample"
+ Name="Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3"
+ Description="Inst42268-030715-2kb-P4-0.05nM-2Chips-FAT3"/>
+ </pbsample:BioSamples>
+ </pbds:DataSetMetadata>
+</pbds:HdfSubreadSet>
\ No newline at end of file
diff --git a/pbcore/data/empty.ccs.bam b/pbcore/data/empty.ccs.bam
new file mode 100644
index 0000000..704abbe
Binary files /dev/null and b/pbcore/data/empty.ccs.bam differ
diff --git a/pbcore/data/empty.ccs.bam.pbi b/pbcore/data/empty.ccs.bam.pbi
new file mode 100644
index 0000000..9e7fd4e
Binary files /dev/null and b/pbcore/data/empty.ccs.bam.pbi differ
diff --git a/pbcore/io/BasH5IO.py b/pbcore/io/BasH5IO.py
index 2dd4b2e..8552bf6 100644
--- a/pbcore/io/BasH5IO.py
+++ b/pbcore/io/BasH5IO.py
@@ -218,6 +218,14 @@ class Zmw(CommonEqualityMixin):
raise ValueError, "No CCS reads in this file"
return self.baxH5._ccsNumPasses[self.index]
+ @property
+ def numEvents(self):
+ """
+ Total number of basecall events in the ZMW
+ """
+ offsets = self.baxH5._offsetsByHole[self.holeNumber]
+ return offsets[1] - offsets[0]
+
#
# The following calls return one or more ZmwRead objects.
#
@@ -249,10 +257,8 @@ class Zmw(CommonEqualityMixin):
"""
if not self.baxH5.hasRawBasecalls:
raise ValueError, "No raw reads in this file"
- offsets = self.baxH5._offsetsByHole[self.holeNumber]
- numEvent = offsets[1] - offsets[0]
polymeraseBegin = 0
- polymeraseEnd = numEvent
+ polymeraseEnd = self.numEvents
readStart = polymeraseBegin if readStart is None else readStart
readEnd = polymeraseEnd if readEnd is None else readEnd
return ZmwRead(self.baxH5, self.holeNumber, readStart, readEnd)
@@ -271,7 +277,7 @@ class Zmw(CommonEqualityMixin):
if not self.baxH5.hasRawBasecalls:
raise ValueError, "No raw reads in this file"
return [ self.read(readStart, readEnd)
- for (readStart, readEnd) in self.unclippedInsertRegions ]
+ for (readStart, readEnd) in self.insertRegionsNoQC ]
@property
def subreads(self):
@@ -313,7 +319,7 @@ class Zmw(CommonEqualityMixin):
if not self.baxH5.hasRawBasecalls:
raise ValueError, "No raw reads in this file"
return [ self.read(readStart, readEnd)
- for (readStart, readEnd) in self.unclippedAdapterRegions ]
+ for (readStart, readEnd) in self.adapterRegionsNoQC ]
@property
def ccsRead(self):
@@ -403,6 +409,8 @@ class ZmwRead(CommonEqualityMixin):
SubstitutionQV = _makeQvAccessor("SubstitutionQV")
SubstitutionTag = _makeQvAccessor("SubstitutionTag")
+ PulseIndex = _makeQvAccessor("PulseIndex")
+
class CCSZmwRead(ZmwRead):
"""
diff --git a/pbcore/io/GffIO.py b/pbcore/io/GffIO.py
index 1a3a2ce..c3313f3 100644
--- a/pbcore/io/GffIO.py
+++ b/pbcore/io/GffIO.py
@@ -44,6 +44,9 @@ __all__ = [ "Gff3Record",
from .base import ReaderBase, WriterBase
from collections import OrderedDict
from copy import copy as shallow_copy
+import tempfile
+import os.path
+
class Gff3Record(object):
"""
@@ -161,6 +164,9 @@ class Gff3Record(object):
def put(self, name, value):
setattr(self, name, value)
+ def __cmp__(self, other):
+ return cmp((self.seqid, self.start), (other.seqid, other.start))
+
class GffReader(ReaderBase):
"""
A GFF file reader class
@@ -231,3 +237,61 @@ def grok(s):
def tupleFromGffAttribute(s):
k, v = s.split("=")
return k, grok(v)
+
+
+def sort_gff(file_name, output_file_name=None):
+ """
+ Sort a single GFF file by genomic location (seqid, start).
+ """
+ if output_file_name is None:
+ output_file_name = os.path.splitext(file_name)[0] + "_sorted.gff"
+ with GffReader(file_name) as f:
+ records = [ rec for rec in f ]
+ records.sort()
+ with open(output_file_name, "w") as out:
+ gff_out = GffWriter(out)
+ map(gff_out.writeHeader, f.headers)
+ for rec in records:
+ gff_out.writeRecord(rec)
+ return output_file_name
+
+
+def _merge_gffs(gff1, gff2, out):
+ out = GffWriter(out)
+ n_rec = 0
+ with GffReader(gff1) as f1:
+ map(out.writeHeader, f1.headers)
+ with GffReader(gff2) as f2:
+ rec1 = [ rec for rec in f1 ]
+ rec2 = [ rec for rec in f2 ]
+ i = j = 0
+ while i < len(rec1) and j < len(rec2):
+ if (rec1[i] > rec2[j]):
+ out.writeRecord(rec2[j])
+ j += 1
+ else:
+ out.writeRecord(rec1[i])
+ i += 1
+ for rec in rec1[i:]:
+ out.writeRecord(rec)
+ i += 1
+ for rec in rec2[j:]:
+ out.writeRecord(rec)
+ j += 2
+ return i + j
+
+
+def merge_gffs(gff_files, output_file_name):
+ """
+ Utility function to combine a set of N (>= 2) GFF files, with records
+ ordered by genomic location. (Assuming each input file is already sorted.)
+ """
+ if len(gff_files) == 1: return gff_files[0]
+ while len(gff_files) > 2:
+ tmpout = tempfile.NamedTemporaryFile()
+ _merge_gffs(gff_files[0], gff_files[1], tmpout)
+ tmpout.seek(0)
+ gff_files = [tmpout] + gff_files[2:]
+ with open(output_file_name, "w") as f:
+ _merge_gffs(gff_files[0], gff_files[1], f)
+ return output_file_name
diff --git a/pbcore/io/align/BamAlignment.py b/pbcore/io/align/BamAlignment.py
index 19b33a2..3ed36d7 100644
--- a/pbcore/io/align/BamAlignment.py
+++ b/pbcore/io/align/BamAlignment.py
@@ -76,7 +76,7 @@ def requiresReference(method):
def requiresPbi(method):
@wraps(method)
def f(bamAln, *args, **kwargs):
- if bamAln.rowNumber is None:
+ if not bamAln.hasPbi:
raise UnavailableFeature, "this feature requires a PacBio BAM index"
else:
return method(bamAln, *args, **kwargs)
@@ -124,6 +124,10 @@ class BamAlignment(AlignmentRecordMixin):
return self.bam
@property
+ def hasPbi(self):
+ return self.rowNumber is not None
+
+ @property
def qId(self):
return self.readGroupInfo.ID
@@ -238,6 +242,20 @@ class BamAlignment(AlignmentRecordMixin):
return self.bam.readGroupInfo(rgAsInt(self.peer.opt("RG")))
@property
+ def readScore(self):
+ """
+ Return the "read score", a de novo prediction (not using any
+ alignment) of the accuracy (between 0 and 1) of this read.
+
+ .. note::
+
+ This capability was not available in `cmp.h5` files, so
+ use of this property can result in code that won't work on
+ legacy data.
+ """
+ return 0.001 * self.peer.opt("rq")
+
+ @property
def readType(self):
return self.readGroupInfo.ReadType
@@ -265,7 +283,7 @@ class BamAlignment(AlignmentRecordMixin):
@property
@requiresMapping
def identity(self):
- if self.rowNumber is not None:
+ if self.hasPbi is not None:
# Fast (has pbi)
if self.readLength == 0:
return 0.
@@ -577,8 +595,11 @@ class BamAlignment(AlignmentRecordMixin):
raise AttributeError, "no such column in pbi index"
def __dir__(self):
- if self.bam.pbi is not None:
- return self.bam.pbi.columnNames
+ basicDir = self.__dict__.keys()
+ if self.hasPbi:
+ return basicDir + self.bam.pbi.columnNames
+ else:
+ return basicDir
class ClippedBamAlignment(BamAlignment):
def __init__(self, aln, tStart, tEnd, aStart, aEnd, unrolledCigar):
diff --git a/pbcore/io/align/BamIO.py b/pbcore/io/align/BamIO.py
index 107e8c2..824674c 100644
--- a/pbcore/io/align/BamIO.py
+++ b/pbcore/io/align/BamIO.py
@@ -388,8 +388,9 @@ class IndexedBamReader(_BamReaderBase, IndexedAlignmentReaderMixin):
return self[ix]
def __iter__(self):
- for rn in xrange(len(self.pbi)):
- yield self.atRowNumber(rn)
+ self.peer.reset()
+ for (rowNumber, peerRecord) in enumerate(self.peer):
+ yield BamAlignment(self, peerRecord, rowNumber)
def __len__(self):
return len(self.pbi)
diff --git a/pbcore/io/align/PacBioBamIndex.py b/pbcore/io/align/PacBioBamIndex.py
index d9cff21..642593e 100644
--- a/pbcore/io/align/PacBioBamIndex.py
+++ b/pbcore/io/align/PacBioBamIndex.py
@@ -190,7 +190,7 @@ class PacBioBamIndex(object):
def _checkForBrokenColumns(self):
if ((self.pbiFlags & PBI_FLAGS_MAPPED) and
- np.all((self.nM == 0) & (self.nMM == 0))):
+ (len(self) > 0) and np.all((self.nM == 0) & (self.nMM == 0))):
raise IncompatibleFile, \
"This bam.pbi file was generated by a version of pbindex with" \
" a bug. Please rerun pbindex."
diff --git a/pbcore/io/align/_bgzf.py b/pbcore/io/align/_bgzf.py
index 457fb2d..cf94d70 100644
--- a/pbcore/io/align/_bgzf.py
+++ b/pbcore/io/align/_bgzf.py
@@ -630,35 +630,38 @@ class BgzfReader(object):
# self.tell(), self._block_start_offset, self._within_block_offset)
return virtual_offset
+
+ def _readHelper(self, size):
+ # yields uncompressed hunks of data, which we will be joined
+ # together by read
+ while size > 0:
+ if self._within_block_offset + size <= len(self._buffer):
+ # This may leave us right at the end of a block
+ # (lazy loading, don't load the next block unless we have too)
+ data = self._buffer[self._within_block_offset:self._within_block_offset + size]
+ self._within_block_offset += size
+ assert data # Must be at least 1 byte
+ size -= len(data)
+ yield data
+ else:
+ data = self._buffer[self._within_block_offset:]
+ size -= len(data)
+ self._load_block() # will reset offsets
+ # TODO - Test with corner case of an empty block followed by
+ # a non-empty block
+ if not self._buffer:
+ # EOF
+ yield data
+ return
+ else:
+ yield data
+ assert size == 0, "BGZF: Internal logic error!"
+
+
def read(self, size=-1):
if size < 0:
raise NotImplementedError("Don't be greedy, that could be massive!")
- elif size == 0:
- if self._text:
- return ""
- else:
- return b""
- elif self._within_block_offset + size <= len(self._buffer):
- # This may leave us right at the end of a block
- # (lazy loading, don't load the next block unless we have too)
- data = self._buffer[self._within_block_offset:self._within_block_offset + size]
- self._within_block_offset += size
- assert data # Must be at least 1 byte
- return data
- else:
- data = self._buffer[self._within_block_offset:]
- size -= len(data)
- self._load_block() # will reset offsets
- # TODO - Test with corner case of an empty block followed by
- # a non-empty block
- if not self._buffer:
- return data # EOF
- elif size:
- # TODO - Avoid recursion
- return data + self.read(size)
- else:
- # Only needed the end of the last block
- return data
+ return "".join(self._readHelper(size))
def readline(self):
i = self._buffer.find(self._newline, self._within_block_offset)
diff --git a/pbcore/io/dataset/DataSetIO.py b/pbcore/io/dataset/DataSetIO.py
index 02b4868..d0fe999 100755
--- a/pbcore/io/dataset/DataSetIO.py
+++ b/pbcore/io/dataset/DataSetIO.py
@@ -1,11 +1,11 @@
"""
-Classes representing the elements of the DataSet type
-
-These classes are often instantiated by the parser and passed to the DataSet,
-where they are stored, manipulated, filtered, merged, etc.
+Classes representing DataSets of various types.
"""
+from collections import defaultdict
import hashlib
+import datetime
+import math
import copy
import os
import errno
@@ -13,7 +13,6 @@ import logging
import xml.dom.minidom
import tempfile
from functools import wraps
-import itertools
import numpy as np
from urlparse import urlparse
from pbcore.util.Process import backticks
@@ -21,18 +20,20 @@ from pbcore.io.opener import (openAlignmentFile, openIndexedAlignmentFile,
FastaReader, IndexedFastaReader, CmpH5Reader,
IndexedBamReader)
from pbcore.io.FastaIO import splitFastaHeader, FastaWriter
-from pbcore.io import PacBioBamIndex, BaxH5Reader
+from pbcore.io import BaxH5Reader
from pbcore.io.align._BamSupport import UnavailableFeature
from pbcore.io.dataset.DataSetReader import (parseStats, populateDataSet,
- resolveLocation, wrapNewResource,
- xmlRootType)
+ resolveLocation, xmlRootType,
+ wrapNewResource, openFofnFile)
from pbcore.io.dataset.DataSetWriter import toXml
from pbcore.io.dataset.DataSetValidator import validateString
from pbcore.io.dataset.DataSetMembers import (DataSetMetadata,
SubreadSetMetadata,
ContigSetMetadata,
BarcodeSetMetadata,
- ExternalResources, Filters)
+ ExternalResources,
+ ExternalResource, Filters)
+from pbcore.io.dataset.utils import consolidateBams, _infixFname
log = logging.getLogger(__name__)
@@ -74,22 +75,60 @@ def _dsIdToSuffix(x):
suffix += '.xml'
return suffix
-def openDataSet(*files, **kwargs):
- # infer from the first:
- first = DataSet(files[0], **kwargs)
- dsId = first.objMetadata.get('MetaType')
- # hdfsubreadset metatypes are subreadset. Fix:
- if files[0].endswith('xml'):
- xml_rt = xmlRootType(files[0])
- if _dsIdToName(dsId) != xml_rt:
- log.warn("XML metatype does not match root tag")
- if xml_rt == 'HdfSubreadSet':
- dsId = _toDsId(xml_rt)
+def _typeDataSet(dset):
+ xml_rt = xmlRootType(dset)
+ dsId = _toDsId(xml_rt)
tbrType = _dsIdToType(dsId)
- if tbrType:
- return tbrType(*files, **kwargs)
+ return tbrType
+
+def openDataSet(*files, **kwargs):
+ if not files[0].endswith('xml'):
+ raise TypeError("openDataSet requires that the first file is an XML")
+ tbrType = _typeDataSet(files[0])
+ return tbrType(*files, **kwargs)
+
+def openDataFile(*files, **kwargs):
+ possibleTypes = [AlignmentSet, SubreadSet, ConsensusReadSet,
+ ConsensusAlignmentSet, ReferenceSet, HdfSubreadSet]
+ origFiles = files
+ fileMap = defaultdict(list)
+ for dstype in possibleTypes:
+ for ftype in dstype._metaTypeMapping():
+ fileMap[ftype].append(dstype)
+ ext = _fileType(files[0])
+ if ext == 'fofn':
+ files = openFofnFile(files[0])
+ ext = _fileType(files[0])
+ if ext == 'xml':
+ dsType = _typeDataSet(files[0])
+ return dsType(*origFiles, **kwargs)
+ options = fileMap[ext]
+ if len(options) == 1:
+ return options[0](*origFiles, **kwargs)
else:
- return DataSet(*files, **kwargs)
+ # peek in the files to figure out the best match
+ if ReferenceSet in options:
+ log.warn("Fasta files aren't unambiguously reference vs contig, "
+ "opening as ReferenceSet")
+ return ReferenceSet(*origFiles, **kwargs)
+ elif AlignmentSet in options:
+ # it is a bam file
+ bam = openAlignmentFile(files[0])
+ if bam.isMapped:
+ if bam.readType == "CCS":
+ return ConsensusAlignmentSet(*origFiles, **kwargs)
+ else:
+ return AlignmentSet(*origFiles, **kwargs)
+ else:
+ if bam.readType == "CCS":
+ return ConsensusReadSet(*origFiles, **kwargs)
+ else:
+ return SubreadSet(*origFiles, **kwargs)
+
+def _stackRecArrays(recArrays):
+ tbr = np.concatenate(recArrays)
+ tbr = tbr.view(np.recarray)
+ return tbr
class DataSetMetaTypes(object):
@@ -123,6 +162,7 @@ def _fileType(fname):
ftype = ftype.strip('.')
return ftype
+
class DataSet(object):
"""The record containing the DataSet information, with possible type
specific subclasses"""
@@ -143,14 +183,12 @@ class DataSet(object):
Doctest:
>>> import os, tempfile
>>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet, SubreadSet
+ >>> from pbcore.io import AlignmentSet, SubreadSet
>>> # Prog like pbalign provides a .bam file:
- >>> # e.g. d = DataSet("aligned.bam")
+ >>> # e.g. d = AlignmentSet("aligned.bam")
>>> # Something like the test files we have:
>>> inBam = data.getBam()
- >>> inBam.endswith('.bam')
- True
- >>> d = DataSet(inBam)
+ >>> d = AlignmentSet(inBam)
>>> # A UniqueId is generated, despite being a BAM input
>>> bool(d.uuid)
True
@@ -161,36 +199,26 @@ class DataSet(object):
>>> outXml = os.path.join(outdir, 'tempfile.xml')
>>> d.write(outXml)
>>> # And then recover the same XML:
- >>> d = DataSet(outXml)
+ >>> d = AlignmentSet(outXml)
>>> # The UniqueId will be the same
>>> d.uuid == dOldUuid
True
>>> # Inputs can be many and varied
- >>> ds1 = DataSet(data.getXml(8), data.getBam(1))
+ >>> ds1 = AlignmentSet(data.getXml(8), data.getBam(1))
>>> ds1.numExternalResources
2
- >>> ds1 = DataSet(data.getFofn())
+ >>> ds1 = AlignmentSet(data.getFofn())
>>> ds1.numExternalResources
2
>>> # Constructors should be used directly
>>> SubreadSet(data.getSubreadSet()) # doctest:+ELLIPSIS
<SubreadSet...
>>> # Even with untyped inputs
- >>> DataSet(data.getBam()) # doctest:+ELLIPSIS
- <DataSet...
- >>> SubreadSet(data.getBam()) # doctest:+ELLIPSIS
- <SubreadSet...
- >>> # You can also cast up and down, but casting between siblings
- >>> # is limited (abuse at your own risk)
- >>> DataSet(data.getBam()).copy(asType='SubreadSet')
- ... # doctest:+ELLIPSIS
- <SubreadSet...
- >>> SubreadSet(data.getBam()).copy(asType='DataSet')
- ... # doctest:+ELLIPSIS
- <DataSet...
- >>> # DataSets can also be manipulated after opening:
+ >>> AlignmentSet(data.getBam()) # doctest:+ELLIPSIS
+ <AlignmentSet...
+ >>> # AlignmentSets can also be manipulated after opening:
>>> # Add external Resources:
- >>> ds = DataSet()
+ >>> ds = AlignmentSet()
>>> _ = ds.externalResources.addResources(["IdontExist.bam"])
>>> ds.externalResources[-1].resourceId == "IdontExist.bam"
True
@@ -225,23 +253,61 @@ class DataSet(object):
log.debug('Containers specified')
populateDataSet(self, files)
log.debug('Done populating')
- # update uuid
+
+ # DataSet base class shouldn't really be used. It is ok-ish for just
+ # basic xml mainpulation. May start warning at some point, but
+ # openDataSet uses it, which would warn unnecessarily.
+ baseDataSet = False
+ if isinstance(self.datasetType, tuple):
+ baseDataSet = True
+
+ if self._strict and baseDataSet:
+ raise InvalidDataSetIOError("DataSet is an abstract class")
+
+ # Populate required metadata
if not self.uuid:
self.newUuid()
-
self.objMetadata.setdefault("Name", "")
self.objMetadata.setdefault("Tags", "")
- dsType = self.objMetadata.setdefault(
- "MetaType", "PacBio.DataSet." + self.__class__.__name__)
- if self._strict:
- if dsType != _toDsId('DataSet'):
- if dsType not in self._castableDataSetTypes:
- if not (isinstance(self, HdfSubreadSet) and
- dsType == 'PacBio.DataSet.SubreadSet'):
- raise IOError(errno.EIO,
- "Cannot create {c} from {f}".format(
- c=self.datasetType, f=dsType),
- files[0])
+ if not baseDataSet:
+ dsType = self.objMetadata.setdefault("MetaType", self.datasetType)
+ else:
+ dsType = self.objMetadata.setdefault("MetaType",
+ _toDsId('DataSet'))
+ if not self.objMetadata.get("TimeStampedName", ""):
+ self.objMetadata["TimeStampedName"] = self._getTimeStampedName(
+ self.objMetadata["MetaType"])
+
+ # Don't allow for creating datasets from inappropriate sources
+ # (XML files with mismatched types)
+ if not baseDataSet:
+ # use _castableDataSetTypes to contain good casts
+ if dsType not in self._castableDataSetTypes:
+ # But make an exception for HdfSubreadSet, which has a
+ # mismatched MetaType
+ if not (isinstance(self, HdfSubreadSet) and
+ dsType == 'PacBio.DataSet.SubreadSet'):
+ raise IOError(errno.EIO,
+ "Cannot create {c} from {f}".format(
+ c=self.datasetType, f=dsType),
+ files[0])
+
+ # Don't allow for creating datasets from inappropriate file types
+ # (external resources of improper types)
+ if not baseDataSet:
+ for fname in self.toExternalFiles():
+ # due to h5 file types, must be unpythonic:
+ found = False
+ for allowed in self._metaTypeMapping().keys():
+ if fname.endswith(allowed):
+ found = True
+ break
+ if not found:
+ allowed = self._metaTypeMapping().keys()
+ raise IOError(errno.EIO,
+ "Cannot create {c} with resource of type "
+ "{t}, only {a}".format(c=dsType, t=fname,
+ a=allowed))
# State tracking:
self._cachedFilters = []
@@ -249,6 +315,9 @@ class DataSet(object):
self._openReaders = []
self._referenceInfoTable = None
self._referenceDict = {}
+ self._indexMap = None
+ self._stackedReferenceInfoTable = False
+ self._index = None
# update counts
if files:
@@ -304,45 +373,68 @@ class DataSet(object):
return self.merge(otherDataset)
def merge(self, other, copyOnMerge=True):
+ """Merge an 'other' dataset with this dataset, same as add operator,
+ but can take argumens
+ """
if (other.__class__.__name__ == self.__class__.__name__ or
other.__class__.__name__ == 'DataSet' or
self.__class__.__name__ == 'DataSet'):
+ # determine whether or not this is the merge that is populating a
+ # dataset for the first time
firstIn = False
- if not self.toExternalFiles():
+ if len(self.externalResources) == 0:
firstIn = True
+
+ # Block on filters?
if (not firstIn and
not self.filters.testCompatibility(other.filters)):
log.warning("Filter incompatibility has blocked the addition "
"of two datasets")
return None
else:
- self.addFilters(other.filters)
+ self.addFilters(other.filters, underConstruction=True)
+
+ # reset the filters, just in case
self._cachedFilters = []
+
+ # block on object metadata?
self._checkObjMetadata(other.objMetadata)
+
# There is probably a cleaner way to do this:
self.objMetadata.update(other.objMetadata)
if copyOnMerge:
result = self.copy()
else:
result = self
- result.addMetadata(other.metadata)
+
+ # add in the metadata (not to be confused with obj metadata)
+ if firstIn:
+ result.metadata = other.metadata
+ else:
+ result.addMetadata(other.metadata)
+
# skip updating counts because other's metadata should be up to
# date
result.addExternalResources(other.externalResources,
updateCount=False)
+
# DataSets may only be merged if they have identical filters,
# So there is nothing new to add.
- if other.subdatasets or not firstIn:
- if copyOnMerge:
- result.addDatasets(other.copy())
- else:
- result.addDatasets(other)
+
# If this dataset has no subsets representing it, add self as a
# subdataset to the result
# TODO: this is a stopgap to prevent spurious subdatasets when
# creating datasets from dataset xml files...
if not self.subdatasets and not firstIn:
result.addDatasets(self.copy())
+
+ # add subdatasets
+ if other.subdatasets or not firstIn:
+ #if copyOnMerge:
+ result.addDatasets(other.copy())
+ #else:
+ #result.addDatasets(other)
+
return result
else:
raise TypeError('DataSets can only be merged with records of the '
@@ -362,6 +454,7 @@ class DataSet(object):
tbr.filters = copy.deepcopy(self._filters, memo)
tbr.subdatasets = copy.deepcopy(self.subdatasets, memo)
tbr.fileNames = copy.deepcopy(self.fileNames, memo)
+ tbr._skipCounts = False
return tbr
def __eq__(self, other):
@@ -457,7 +550,7 @@ class DataSet(object):
Doctest:
>>> import pbcore.data.datasets as data
>>> from pbcore.io import DataSet, SubreadSet
- >>> ds1 = DataSet(data.getXml())
+ >>> ds1 = DataSet(data.getXml(12))
>>> # Deep copying datasets is easy:
>>> ds2 = ds1.copy()
>>> # But the resulting uuid's should be different.
@@ -529,7 +622,8 @@ class DataSet(object):
return result
def split(self, chunks=0, ignoreSubDatasets=False, contigs=False,
- maxChunks=0, breakContigs=False):
+ maxChunks=0, breakContigs=False, targetSize=5000, zmws=False,
+ barcodes=False, byRecords=False, updateCounts=False):
"""Deep copy the DataSet into a number of new DataSets containing
roughly equal chunks of the ExternalResources or subdatasets.
@@ -568,7 +662,7 @@ class DataSet(object):
>>> import pbcore.data.datasets as data
>>> from pbcore.io import AlignmentSet
>>> # splitting is pretty intuitive:
- >>> ds1 = AlignmentSet(data.getXml())
+ >>> ds1 = AlignmentSet(data.getXml(12))
>>> # but divides up extRes's, so have more than one:
>>> ds1.numExternalResources > 1
True
@@ -612,7 +706,14 @@ class DataSet(object):
True
"""
if contigs:
- return self._split_contigs(chunks, maxChunks, breakContigs)
+ return self._split_contigs(chunks, maxChunks, breakContigs,
+ targetSize=targetSize,
+ byRecords=byRecords,
+ updateCounts=updateCounts)
+ elif zmws:
+ return self._split_zmws(chunks)
+ elif barcodes:
+ return self._split_barcodes(chunks)
# Lets only split on datasets if actual splitting will occur,
# And if all subdatasets have the required balancing key (totalLength)
@@ -656,6 +757,16 @@ class DataSet(object):
# TODO
return results
+ def _split_contigs(self, chunks, maxChunks=0, breakContigs=False,
+ targetSize=5000, byRecords=False, updateCounts=False):
+ raise TypeError("Only AlignmentSets may be split by contigs")
+
+ def _split_barcodes(self, chunks):
+ raise TypeError("Only ReadSets may be split by contigs")
+
+ def _split_zmws(self, chunks):
+ raise TypeError("Only ReadSets may be split by ZMWs")
+
def _split_atoms(self, atoms, num_chunks):
"""Divide up atomic units (e.g. contigs) into chunks (refId, size,
segments)
@@ -665,110 +776,6 @@ class DataSet(object):
largest[2] += 1
return atoms
- def _split_contigs(self, chunks, maxChunks=0, breakContigs=False,
- targetSize=5000):
- """Split a dataset into reference windows based on contigs.
-
- Args:
- chunks: The number of chunks to emit. If chunks < # contigs,
- contigs are grouped by size. If chunks == contigs, one
- contig is assigned to each dataset regardless of size. If
- chunks >= contigs, contigs are split into roughly equal
- chunks (<= 1.0 contig per file).
-
- """
- # removed the non-trivial case so that it is still filtered to just
- # contigs with associated records
-
- # The format is rID, start, end, for a reference window
- log.debug("Fetching reference names and lengths")
- # pull both at once so you only have to mess with the
- # referenceInfoTable once.
- refLens = self.refLengths
- refNames = refLens.keys()
- log.debug("{i} references found".format(i=len(refNames)))
- log.debug("Finding contigs")
- if len(refNames) < 100:
- atoms = [(rn, 0, 0) for rn in refNames if
- next(self._indexReadsInReference(rn), None)]
- else:
- log.debug("Skipping records for each reference check")
- atoms = [(rn, 0, 0) for rn in refNames]
-
- # The window length is used for balancing
- # TODO switch it to countRecords?
- balanceKey = lambda x: x[2] - x[1]
-
- # By providing maxChunks and not chunks, this combination will set
- # chunks down to < len(atoms) < maxChunks
- if not chunks:
- chunks = len(atoms)
- if maxChunks and chunks > maxChunks:
- chunks = maxChunks
-
- # Decide whether to intelligently limit chunk size:
- if maxChunks and breakContigs:
- # The bounds:
- minNum = 2
- maxNum = maxChunks
- # Adjust
- dataSize = self.numRecords
- chunks = int(dataSize/targetSize)
- # Respect bounds:
- chunks = minNum if chunks < minNum else chunks
- chunks = maxNum if chunks > maxNum else chunks
-
- # refwindow format: rId, start, end
- if chunks > len(atoms):
- # splitting atom format is slightly different (but more compatible
- # going forward with countRecords): (rId, size, segments)
- atoms = [[rn, refLens[rn], 1] for rn, _, _ in atoms]
- log.debug("Splitting atoms")
- atoms = self._split_atoms(atoms, chunks)
- segments = []
- for atom in atoms:
- segment_size = atom[1]/atom[2]
- sub_segments = [(atom[0], segment_size * i, segment_size *
- (i + 1)) for i in range(atom[2])]
- # if you can't divide it evenly you may have some messiness
- # with the last window. Fix it:
- tmp = sub_segments.pop()
- tmp = (tmp[0], tmp[1], refLens[tmp[0]])
- sub_segments.append(tmp)
- segments.extend(sub_segments)
- atoms = segments
- log.debug("Done defining {n} chunks".format(n=chunks))
-
- # duplicate
- log.debug("Making copies")
- results = [self.copy() for _ in range(chunks)]
-
- # replace default (complete) ExternalResource lists
- log.debug("Distributing chunks")
- chunks = self._chunkList(atoms, chunks, balanceKey)
- log.debug("Done chunking")
- log.debug("Modifying filters or resources")
- for result, chunk in zip(results, chunks):
- if atoms[0][2]:
- result.filters.addRequirement(
- rname=[('=', c[0]) for c in chunk],
- tStart=[('>', c[1]) for c in chunk],
- tEnd=[('<', c[2]) for c in chunk])
- else:
- result.filters.addRequirement(
- rname=[('=', c[0]) for c in chunk])
-
- # UniqueId was regenerated when the ExternalResource list was
- # whole, therefore we need to regenerate it again here
- log.debug("Generating new UUID")
- for result in results:
- result.newUuid()
-
- # Update the basic metadata for the new DataSets from external
- # resources, or at least mark as dirty
- # TODO
- return results
-
def _split_subdatasets(self, chunks):
"""Split on subdatasets
@@ -800,7 +807,8 @@ class DataSet(object):
results.append(newCopy)
return results
- def write(self, outFile, validate=True, relPaths=False, pretty=True):
+ def write(self, outFile, validate=True, modPaths=False,
+ relPaths=False, pretty=True):
"""Write to disk as an XML file
Args:
@@ -822,7 +830,7 @@ class DataSet(object):
True
"""
# fix paths if validate:
- if validate:
+ if validate and modPaths:
if relPaths:
self.makePathsRelative(os.path.dirname(outFile))
else:
@@ -894,7 +902,7 @@ class DataSet(object):
# the cache dirty. See disableFilters/enableFilters
if self._cachedFilters:
return self._cachedFilters
- filters = self.filters.tests()
+ filters = self.filters.tests(readType=self._filterType())
# Having no filters means no opportunity to pass. Fix by filling with
# always-true (similar to disableFilters())
if not filters:
@@ -903,6 +911,17 @@ class DataSet(object):
self._cachedFilters = filters
return filters
+ def _filterType(self):
+ raise NotImplementedError()
+
+ def checkAndResolve(self, fname, possibleRelStart='.'):
+ """Try and skip resolveLocation if possible"""
+ if fname.startswith(os.path.sep):
+ return fname
+ else:
+ log.debug('Unable to assume path is already absolute')
+ return resolveLocation(fname, possibleRelStart)
+
def makePathsAbsolute(self, curStart="."):
"""As part of the validation process, make all ResourceIds absolute
URIs rather than relative paths. Generally not called by API users.
@@ -910,8 +929,9 @@ class DataSet(object):
Args:
curStart: The location from which relative paths should emanate.
"""
+ log.debug("Making paths absolute")
self._changePaths(
- lambda x, s=curStart: resolveLocation(x, s))
+ lambda x, s=curStart: self.checkAndResolve(x, s))
def makePathsRelative(self, outDir=False):
"""Make things easier for writing test cases: make all
@@ -922,6 +942,7 @@ class DataSet(object):
outDir: The location from which relative paths should originate
"""
+ log.debug("Making paths relative")
if outDir:
self._changePaths(lambda x, s=outDir: os.path.relpath(x, s))
else:
@@ -970,8 +991,9 @@ class DataSet(object):
self._updateMetaType(item)
try:
stack.extend(list(item.indices))
+ stack.extend(list(item.externalResources))
except AttributeError:
- # Some things just don't have indices
+ # Some things just don't have indices or subresources
pass
# check all DataSetMetadata
@@ -989,6 +1011,14 @@ class DataSet(object):
if not resource.metaType:
file_type = _fileType(resource.resourceId)
resource.metaType = self._metaTypeMapping().get(file_type, "")
+ if not resource.timeStampedName:
+ mtype = resource.metaType
+ tsName = self._getTimeStampedName(mtype)
+ resource.timeStampedName = tsName
+
+ def _getTimeStampedName(self, mType):
+ time = datetime.datetime.utcnow().strftime("%y%m%d_%H%M%S")
+ return "{m}-{t}".format(m=mType, t=time)
@staticmethod
def _metaTypeMapping():
@@ -1003,15 +1033,16 @@ class DataSet(object):
def disableFilters(self):
"""Disable read filtering for this object"""
+ self.reFilter()
self.noFiltering = True
self._cachedFilters = [lambda x: True]
def enableFilters(self):
"""Re-enable read filtering for this object"""
+ self.reFilter()
self.noFiltering = False
- self._cachedFilters = []
- def addFilters(self, newFilters):
+ def addFilters(self, newFilters, underConstruction=False):
"""Add new or extend the current list of filters. Public because there
is already a reasonably compelling reason (the console script entry
point). Most often used by the __add__ method.
@@ -1036,7 +1067,7 @@ class DataSet(object):
( rname = E.faecalis...
"""
self.filters.merge(copy.deepcopy(newFilters))
- self._cachedFilters = []
+ self.reFilter(light=underConstruction)
def _checkObjMetadata(self, newMetadata):
"""Check new object metadata (as opposed to dataset metadata) against
@@ -1050,8 +1081,8 @@ class DataSet(object):
if newMetadata.get('Version') > self.objMetadata.get('Version'):
raise ValueError("Wrong dataset version for merging {v1} vs "
"{v2}".format(
- v1=newMetadata.get('Version'),
- v2=self.objMetadata.get('Version')))
+ v1=newMetadata.get('Version'),
+ v2=self.objMetadata.get('Version')))
def addMetadata(self, newMetadata, **kwargs):
@@ -1107,7 +1138,7 @@ class DataSet(object):
self.metadata.merge(newMetadata)
# or initialize
else:
- self._metadata = newMetadata
+ self.metadata = newMetadata
for key, value in kwargs.items():
self.metadata.addMetadata(key, value)
@@ -1116,28 +1147,6 @@ class DataSet(object):
self.metadata.totalLength = -1
self.metadata.numRecords = -1
- def assertIndexed(self):
- if not self._openReaders:
- try:
- tmp = self._strict
- self._openFiles()
- except Exception:
- # Catch everything to recover the strictness status, then raise
- # whatever error was found.
- self._strict = tmp
- raise
- finally:
- self._strict = tmp
- else:
- for fname, reader in zip(self.toExternalFiles(),
- self.resourceReaders()):
- if (not isinstance(reader, IndexedBamReader) and
- not isinstance(reader, CmpH5Reader)):
- raise IOError(errno.EIO,
- "File not indexed: {f}".format(f=fname),
- fname)
-
-
def addExternalResources(self, newExtResources, updateCount=True):
"""Add additional ExternalResource objects, ensuring no duplicate
resourceIds. Most often used by the __add__ method, rather than
@@ -1174,23 +1183,15 @@ class DataSet(object):
>>> ds.externalResources.addResources(
... ["test3.bam"])[0].addIndices(["test3.bam.bai"])
"""
- # Build list of current resourceIds
- resourceIds = [extRes.resourceId for extRes in
- self.externalResources]
-
- for newExtRes in newExtResources:
- if isinstance(newExtRes, str):
- newExtRes = wrapNewResource(newExtRes)
-
- # merge duplicates instead of adding them
- if newExtRes.resourceId in resourceIds:
- first = resourceIds.index(newExtRes.resourceId)
- self.externalResources[first].merge(newExtRes)
-
- # add non-duplicates, update the list of current resourceIds
- else:
- self.externalResources.append(newExtRes)
- resourceIds.append(newExtRes.resourceId)
+ if not isinstance(newExtResources, ExternalResources):
+ tmp = ExternalResources()
+ # have to wrap them here, as wrapNewResource does quite a bit and
+ # importing into members would create a circular inport
+ tmp.addResources([wrapNewResource(res)
+ if not isinstance(res, ExternalResource) else res
+ for res in newExtResources])
+ newExtResources = tmp
+ self.externalResources.merge(newExtResources)
if updateCount:
self._openFiles()
self.updateCounts()
@@ -1211,93 +1212,11 @@ class DataSet(object):
else:
self.subdatasets.append(otherDataSet)
- def _openFiles(self, refFile=None):
- """Open the files (assert they exist, assert they are of the proper
- type before accessing any file)
- """
- if self._openReaders:
- log.debug("Closing old readers...")
- self.close()
- log.debug("Opening resources")
- for extRes in self.externalResources:
- location = urlparse(extRes.resourceId).path
- try:
- resource = openIndexedAlignmentFile(
- location,
- referenceFastaFname=refFile)
- except (IOError, ValueError):
- if not self._strict:
- log.info("pbi file missing for {f}, operating with "
- "reduced speed and functionality".format(
- f=location))
- resource = openAlignmentFile(location,
- referenceFastaFname=refFile)
- else:
- raise
- if not resource:
- raise IOError(errno.EIO,
- "{f} fails to open".format(f=location),
- location)
- self._openReaders.append(resource)
- log.debug("Done opening resources")
-
-
- def resourceReaders(self, refName=False):
- """A generator of Indexed*Reader objects for the ExternalResources
- in this DataSet.
-
- Args:
- refName: Only yield open resources if they have refName in their
- referenceInfoTable
-
- Yields:
- An open indexed alignment file
-
- Doctest:
- >>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet
- >>> ds = DataSet(data.getBam())
- >>> for seqFile in ds.resourceReaders():
- ... for record in seqFile:
- ... print 'hn: %i' % record.holeNumber # doctest:+ELLIPSIS
- hn: ...
-
- """
- if refName:
- if (not refName in self.refNames and
- not refName in self.fullRefNames):
- _ = int(refName)
- refName = self._idToRname(refName)
-
- if not self._openReaders:
- self._openFiles()
- if refName:
- return [resource for resource in self._openReaders
- if refName in resource.referenceInfoTable['FullName'] or
- refName in resource.referenceInfoTable['Name']]
- else:
- return self._openReaders
-
- @property
- def indexRecords(self):
- """Yields chunks of recarray summarizing all of the records in all of
- the resources that conform to those filters addressing parameters
- cached in the pbi.
- """
- self.assertIndexed()
- for rr in self.resourceReaders():
- indices = rr.index
- if not self._filters or self.noFiltering:
- yield indices
- continue
- nameMap = {name: n
- for n, name in enumerate(rr.referenceInfoTable['Name'])}
+ def _openFiles(self):
+ raise RuntimeError("Not defined for this type of DataSet")
- passes = self._filters.filterIndexRecords(indices, nameMap)
- # This is faster than np.extract or iterating over zip
- for i in xrange(len(indices)):
- if passes[i]:
- yield indices[i]
+ def resourceReaders(self):
+ raise RuntimeError("Not defined for this type of DataSet")
@property
@filtered
@@ -1311,8 +1230,8 @@ class DataSet(object):
Doctest:
>>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet
- >>> ds = DataSet(data.getBam())
+ >>> from pbcore.io import AlignmentSet
+ >>> ds = AlignmentSet(data.getBam())
>>> for record in ds.records:
... print 'hn: %i' % record.holeNumber # doctest:+ELLIPSIS
hn: ...
@@ -1352,21 +1271,951 @@ class DataSet(object):
for read in self.records:
yield read
+ # FIXME this is a workaround for the lack of support for ZMW chunking in
+ # pbbam, and should probably go away once that is available.
@property
- def refWindows(self):
- """Going to be tricky unless the filters are really focused on
- windowing the reference. Much nesting or duplication and the correct
- results are really not guaranteed"""
- windowTuples = []
- nameIDs = self.refInfo('Name')
- refLens = None
- for name, refID in nameIDs:
- for filt in self._filters:
- thisOne = False
- for param in filt:
- if param.name == 'rname':
- if param.value == name:
- thisOne = True
+ def zmwRanges(self):
+ """
+ Return the end-inclusive range of ZMWs covered by the dataset if this
+ was explicitly set by filters via DataSet.split(zmws=True).
+
+ """
+ ranges = []
+ for filt in self._filters:
+ movie, start, end = None, 0, 0
+ values = []
+ for param in filt:
+ if param.name == "movie":
+ movie = param.value
+ elif param.name == "zm":
+ ival = int(param.value)
+ if param.operator == '>':
+ ival += 1
+ elif param.operator == '<':
+ ival -= 1
+ values.append(ival)
+ ranges.append((movie, min(values), max(values)))
+ return ranges
+
+ def toFofn(self, outfn=None, uri=False, relative=False):
+ """Return a list of resource filenames (and write to optional outfile)
+
+ Args:
+ outfn: (None) the file to which the resouce filenames are to be
+ written. If None, the only emission is a returned list of
+ file names.
+ uri: (t/F) write the resource filenames as URIs.
+ relative: (t/F) emit paths relative to outfofn or '.' if no
+ outfofn
+
+ Returns:
+ A list of filenames or uris
+
+ Writes:
+ (Optional) A file containing a list of filenames or uris
+
+ Doctest:
+ >>> from pbcore.io import DataSet
+ >>> DataSet("bam1.bam", "bam2.bam", strict=False).toFofn(uri=False)
+ ['bam1.bam', 'bam2.bam']
+ """
+ lines = [er.resourceId for er in self.externalResources]
+ if not uri:
+ lines = [urlparse(line).path for line in lines]
+ if relative is True:
+ # make it relative to the fofn location
+ if outfn:
+ lines = [os.path.relpath(line, os.path.dirname(outfn))
+ for line in lines]
+ # or current location
+ else:
+ lines = [os.path.relpath(line) for line in lines]
+ if outfn:
+ with open(outfn, 'w') as outFile:
+ outFile.writelines(line + '\n' for line in lines)
+ return lines
+
+ def toExternalFiles(self):
+ """Returns a list of top level external resources (no indices)."""
+ return self.externalResources.resourceIds
+
+ @property
+ def _castableDataSetTypes(self):
+ if isinstance(self.datasetType, tuple):
+ return self.datasetType
+ else:
+ return (_toDsId('DataSet'), self.datasetType)
+
+ @classmethod
+ def castableTypes(cls):
+ """The types to which this DataSet type may be cast. This is a property
+ instead of a member variable as we can enforce casting limits here (and
+ modify if needed by overriding them in subclasses).
+
+ Returns:
+ A dictionary of MetaType->Class mappings, e.g. 'DataSet': DataSet
+ """
+ if cls.__name__ != 'DataSet':
+ return {'DataSet': DataSet,
+ cls.__name__: cls}
+ return {'DataSet': DataSet,
+ 'SubreadSet': SubreadSet,
+ 'HdfSubreadSet': HdfSubreadSet,
+ 'AlignmentSet': AlignmentSet,
+ 'ContigSet': ContigSet,
+ 'ConsensusReadSet': ConsensusReadSet,
+ 'ConsensusAlignmentSet': ConsensusAlignmentSet,
+ 'ReferenceSet': ReferenceSet,
+ 'BarcodeSet': BarcodeSet}
+ @property
+ def metadata(self):
+ """Return the DataSet metadata as a DataSetMetadata object. Attributes
+ should be populated intuitively, but see DataSetMetadata documentation
+ for more detail."""
+ return self._metadata
+
+ @metadata.setter
+ def metadata(self, newDict):
+ """Set the metadata for this object. This is reasonably dangerous, as
+ the argument must be a properly formated data structure, as specified
+ in the DataSetMetadata documentation. This setter is primarily used
+ by other DataSet objects, rather than users or API consumers."""
+ if isinstance(newDict, DataSetMetadata):
+ self._metadata = newDict
+ else:
+ self._metadata = self._metadata.__class__(newDict)
+
+ @property
+ def filters(self):
+ """Limit setting to ensure cache hygiene and filter compatibility"""
+ self._filters.registerCallback(lambda x=self: x.reFilter())
+ return self._filters
+
+ @filters.setter
+ def filters(self, value):
+ """Limit setting to ensure cache hygiene and filter compatibility"""
+ self._filters = value
+
+ def reFilter(self, light=True):
+ """
+ The filters on this dataset have changed, update DataSet state as
+ needed
+ """
+ self._cachedFilters = []
+ self._index = None
+ self._indexMap = None
+ if not light:
+ self.metadata.totalLength = -1
+ self.metadata.numRecords = -1
+ if self.metadata.summaryStats:
+ self.metadata.removeChildren('SummaryStats')
+
+ @property
+ def numRecords(self):
+ """The number of records in this DataSet (from the metadata)"""
+ return self._metadata.numRecords
+
+ @numRecords.setter
+ def numRecords(self, value):
+ """The number of records in this DataSet (from the metadata)"""
+ self._metadata.numRecords = value
+
+ @property
+ def totalLength(self):
+ """The total length of this DataSet"""
+ return self._metadata.totalLength
+
+ @totalLength.setter
+ def totalLength(self, value):
+ """The total length of this DataSet"""
+ self._metadata.totalLength = value
+
+ @property
+ def uuid(self):
+ """The UniqueId of this DataSet"""
+ return self.objMetadata.get('UniqueId')
+
+ @property
+ def name(self):
+ """The name of this DataSet"""
+ return self.objMetadata.get('Name', '')
+
+ @name.setter
+ def name(self, value):
+ """The name of this DataSet"""
+ self.objMetadata['Name'] = value
+
+ @property
+ def numExternalResources(self):
+ """The number of ExternalResources in this DataSet"""
+ return len(self.externalResources)
+
+ def _pollResources(self, func):
+ """Collect the responses to func on each resource (or those with reads
+ mapping to refName)."""
+ return [func(resource) for resource in self.resourceReaders()]
+
+ def _unifyResponses(self, responses, keyFunc=lambda x: x,
+ eqFunc=lambda x, y: x == y):
+ """Make sure all of the responses from resources are the same."""
+ if len(responses) > 1:
+ # Check the rest against the first:
+ for res in responses[1:]:
+ if not eqFunc(keyFunc(responses[0]), keyFunc(res)):
+ raise ResourceMismatchError(responses)
+ return responses[0]
+
+ def hasPulseFeature(self, featureName):
+ responses = self._pollResources(
+ lambda x: x.hasPulseFeature(featureName))
+ return self._unifyResponses(responses)
+
+ def pulseFeaturesAvailable(self):
+ responses = self._pollResources(lambda x: x.pulseFeaturesAvailable())
+ return self._unifyResponses(responses)
+
+ @property
+ def sequencingChemistry(self):
+ return self._checkIdentical('sequencingChemistry')
+
+ @property
+ def isEmpty(self):
+ return self._checkIdentical('isEmpty')
+
+ @property
+ def readType(self):
+ return self._checkIdentical('readType')
+
+ def _checkIdentical(self, key):
+ responses = self._pollResources(lambda x: getattr(x, key))
+ return self._unifyResponses(responses)
+
+ def _chunkList(self, inlist, chunknum, balanceKey=len):
+ """Divide <inlist> members into <chunknum> chunks roughly evenly using
+ a round-robin binning system, return list of lists.
+
+ This is a method so that balanceKey functions can access self."""
+ chunks = [[] for _ in range(chunknum)]
+ # a lightweight accounting of how big (entry 0) each sublist (numbered
+ # by entry 1) is getting
+ chunkSizes = [[0, i] for i in range(chunknum)]
+ for i, item in enumerate(sorted(inlist, key=balanceKey, reverse=True)):
+ # Refresh measure of bin fullness
+ chunkSizes.sort()
+ # Add one to the emptiest bin
+ chunks[chunkSizes[0][1]].append(item)
+ mass = balanceKey(item)
+ if mass == 0:
+ mass += 1
+ chunkSizes[0][0] += mass
+ return chunks
+
+ @property
+ def index(self):
+ if self._index is None:
+ log.debug("Populating index")
+ self.assertIndexed()
+ self._index = self._indexRecords()
+ log.debug("Done populating index")
+ return self._index
+
+ def _indexRecords(self):
+ raise NotImplementedError()
+
+ def assertIndexed(self):
+ raise NotImplementedError()
+
+ def _assertIndexed(self, acceptableTypes):
+ if not self._openReaders:
+ try:
+ tmp = self._strict
+ self._strict = True
+ self._openFiles()
+ except Exception:
+ # Catch everything to recover the strictness status, then raise
+ # whatever error was found.
+ self._strict = tmp
+ raise
+ finally:
+ self._strict = tmp
+ else:
+ for fname, reader in zip(self.toExternalFiles(),
+ self.resourceReaders()):
+ if not isinstance(reader, acceptableTypes):
+ raise IOError(errno.EIO, "File not indexed", fname)
+ return True
+
+
+ def __getitem__(self, index):
+ """Should respect filters for free, as _indexMap should only be
+ populated by filtered reads. Only pbi filters considered, however."""
+ # TODO: add _getRecords for list of indices support
+ if self._indexMap is None:
+ _ = self.index
+ rrNo, recNo = self._indexMap[index]
+ return self.resourceReaders()[rrNo][recNo]
+
+
+class InvalidDataSetIOError(Exception):
+ """The base class for all DataSetIO related custom exceptions (hopefully)
+ """
+
+
+class ResourceMismatchError(InvalidDataSetIOError):
+
+ def __init__(self, responses):
+ super(ResourceMismatchError, self).__init__()
+ self.responses = responses
+
+ def __str__(self):
+ return "Resources responded differently: " + ', '.join(
+ map(str, self.responses))
+
+
+class ReadSet(DataSet):
+ """Base type for read sets, should probably never be used as a concrete
+ class"""
+
+ def __init__(self, *files, **kwargs):
+ super(ReadSet, self).__init__(*files, **kwargs)
+ self._metadata = SubreadSetMetadata(self._metadata)
+
+ def _openFiles(self):
+ """Open the files (assert they exist, assert they are of the proper
+ type before accessing any file)
+ """
+ if self._openReaders:
+ log.debug("Closing old readers...")
+ self.close()
+ log.debug("Opening ReadSet resources")
+ for extRes in self.externalResources:
+ refFile = extRes.reference
+ if refFile:
+ log.debug("Using reference: {r}".format(r=refFile))
+ location = urlparse(extRes.resourceId).path
+ resource = None
+ try:
+ resource = openIndexedAlignmentFile(
+ location,
+ referenceFastaFname=refFile)
+ except (IOError, ValueError):
+ if not self._strict and not extRes.pbi:
+ log.warn("pbi file missing for {f}, operating with "
+ "reduced speed and functionality".format(
+ f=location))
+ resource = openAlignmentFile(
+ location, referenceFastaFname=refFile)
+ else:
+ raise
+ #if resource is None:
+ #assert not self._strict
+ #resource = openAlignmentFile(
+ #location, referenceFastaFname=refFile)
+ if not resource.isEmpty:
+ self._openReaders.append(resource)
+ if len(self._openReaders) == 0 and len(self.toExternalFiles()) != 0:
+ raise IOError("No files were openable or reads found")
+ log.debug("Done opening resources")
+
+ def _filterType(self):
+ return 'bam'
+
+ @property
+ def hasPbi(self):
+ """Test whether all resources are opened as IndexedBamReader objects"""
+ try:
+ res = self._pollResources(lambda x: isinstance(x,
+ IndexedBamReader))
+ return self._unifyResponses(res)
+ except ResourceMismatchError:
+ if not self._strict:
+ log.error("Resources inconsistently indexed")
+ return False
+ else:
+ raise
+
+ def _split_barcodes(self, chunks=0):
+ """Split a readset into chunks by barcodes.
+
+ Args:
+ chunks: The number of chunks to emit. If chunks < # barcodes,
+ barcodes are grouped by size. If chunks == # barcodes, one
+ barcode is assigned to each dataset regardless of size. If
+ chunks >= # barcodes, only # barcodes chunks are emitted
+
+ """
+ # Find all possible barcodes and counts for each
+ # TODO: switch this over to the pbi when bc information is exposed
+ barcodes = defaultdict(int)
+ for read in self.records:
+ barcodes[tuple(read.peer.opt("bc"))] += 1
+
+ log.debug("{i} barcodes found".format(i=len(barcodes.keys())))
+
+ atoms = barcodes.items()
+
+ # The number of reads per barcode is used for balancing
+ balanceKey = lambda x: x[1]
+
+ # Find the appropriate number of chunks
+ if chunks <= 0 or chunks > len(atoms):
+ chunks = len(atoms)
+
+ log.debug("Making copies")
+ results = [self.copy() for _ in range(chunks)]
+
+ log.debug("Distributing chunks")
+ chunks = self._chunkList(atoms, chunks, balanceKey)
+ log.debug("Done chunking")
+ log.debug("Modifying filters or resources")
+ for result, chunk in zip(results, chunks):
+ result.filters.addRequirement(
+ bc=[('=', list(c[0])) for c in chunk])
+
+ # UniqueId was regenerated when the ExternalResource list was
+ # whole, therefore we need to regenerate it again here
+ log.debug("Generating new UUID")
+ for result in results:
+ result.newUuid()
+
+ # Update the basic metadata for the new DataSets from external
+ # resources, or at least mark as dirty
+ # TODO
+ return results
+
+ def _split_zmws(self, chunks):
+ files_to_movies = defaultdict(list)
+ n_bam = 0
+ for bam in self.resourceReaders():
+ n_bam += 1
+ if len(bam.readGroupTable) > 1:
+ raise RuntimeError("Multiple read groups in single .bam")
+ if chunks < n_bam:
+ return self.split(chunks=chunks)
+ n_chunks_per_bam = max(1, int(math.floor(float(chunks) / n_bam)))
+ if n_chunks_per_bam < 2:
+ log.warn("%d ZMW chunks requested but there are %d files" %
+ (chunks, n_bam))
+ n_chunks = n_bam * n_chunks_per_bam
+ if n_chunks != chunks:
+ log.info("Adjusted number of chunks to %d" % n_chunks)
+ log.debug("Making copies")
+ results = [self.copy() for _ in range(n_chunks)]
+ j_chunk = 0
+ for bam in self.resourceReaders():
+ rg = bam.readGroupTable[0]
+ n_reads = len(bam.holeNumber)
+ chunk_size = int(math.ceil(float(n_reads / n_chunks_per_bam)))
+ i_read = 0
+ for i_chunk in range(n_chunks_per_bam):
+ if i_read >= n_reads:
+ break
+ result = results[j_chunk]
+ j_chunk += 1
+ zmw_start = bam.holeNumber[i_read]
+ if i_chunk == n_chunks_per_bam - 1:
+ zmw_end = bam.holeNumber.max()
+ else:
+ i_read += chunk_size
+ zmw_end = bam.holeNumber[min(i_read, n_reads-1)]
+ while i_read < n_reads-1:
+ if zmw_end == bam.holeNumber[i_read+1]:
+ i_read += 1
+ zmw_end = bam.holeNumber[i_read]
+ else:
+ break
+ result.filters.addRequirement(
+ movie=[('=', rg.MovieName)],
+ zm=[('<', zmw_end+1)])
+ result.filters.addRequirement(
+ zm=[('>', zmw_start-1)])
+ i_read += 1
+
+ # UniqueId was regenerated when the ExternalResource list was
+ # whole, therefore we need to regenerate it again here
+ log.debug("Generating new UUID")
+ for result in results:
+ result.newUuid()
+
+ # Update the basic metadata for the new DataSets from external
+ # resources, or at least mark as dirty
+ # TODO
+ return results
+
+ @property
+ def readGroupTable(self):
+ """Combine the readGroupTables of each external resource"""
+ responses = self._pollResources(lambda x: x.readGroupTable)
+ if len(responses) > 1:
+ tbr = reduce(np.append, responses)
+ return tbr
+ else:
+ return responses[0]
+
+ def assertIndexed(self):
+ self._assertIndexed((IndexedBamReader, CmpH5Reader))
+
+ @property
+ def isCmpH5(self):
+ """Test whether all resources are cmp.h5 files"""
+ res = self._pollResources(lambda x: isinstance(x, CmpH5Reader))
+ return self._unifyResponses(res)
+
+ def _indexRecords(self):
+ """Returns index recarray summarizing all of the records in all of
+ the resources that conform to those filters addressing parameters
+ cached in the pbi.
+ """
+
+ recArrays = []
+ self._indexMap = []
+ for rrNum, rr in enumerate(self.resourceReaders()):
+ indices = rr.index
+
+ if not self._filters or self.noFiltering:
+ recArrays.append(indices._tbl)
+ self._indexMap.extend([(rrNum, i) for i in
+ range(len(indices._tbl))])
+ else:
+ # Filtration will be necessary:
+ nameMap = {}
+ if not rr.referenceInfoTable is None:
+ nameMap = {name: n
+ for n, name in enumerate(
+ rr.referenceInfoTable['Name'])}
+
+ passes = self._filters.filterIndexRecords(indices._tbl,
+ nameMap)
+ newInds = indices._tbl[passes]
+ recArrays.append(newInds)
+ self._indexMap.extend([(rrNum, i) for i in
+ np.nonzero(passes)[0]])
+ self._indexMap = np.array(self._indexMap)
+ return _stackRecArrays(recArrays)
+
+ def resourceReaders(self):
+ """Open the files in this ReadSet"""
+ if not self._openReaders:
+ self._openFiles()
+ return self._openReaders
+
+ @property
+ def _length(self):
+ """Used to populate metadata in updateCounts. We're using the pbi here,
+ which is necessary and sufficient for both subreadsets and
+ alignmentsets, but doesn't work for hdfsubreadsets. Rather than
+ duplicate code, we'll implement the hdf specific _length as an
+ overriding function where needed.
+
+ ..note:: Both mapped and unmapped bams can be either indexed or
+ unindexed. This makes life more difficult, but we should
+ expect a pbi for both subreadsets and alignmentsets
+
+ """
+ count = len(self.index)
+ length = sum(self.index.qEnd - self.index.qStart)
+ return count, length
+
+ def _resourceSizes(self):
+ sizes = []
+ for rr in self.resourceReaders():
+ sizes.append((len(rr.index), sum(rr.index.qEnd - rr.index.qStart)))
+ return sizes
+
+ def addMetadata(self, newMetadata, **kwargs):
+ """Add metadata specific to this subtype, while leaning on the
+ superclass method for generic metadata. Also enforce metadata type
+ correctness."""
+ # Validate, clean and prep input data
+ if newMetadata:
+ if isinstance(newMetadata, dict):
+ newMetadata = SubreadSetMetadata(newMetadata)
+ elif isinstance(newMetadata, SubreadSetMetadata) or (
+ type(newMetadata).__name__ == 'DataSetMetadata'):
+ newMetadata = SubreadSetMetadata(newMetadata.record)
+ else:
+ raise TypeError("Cannot extend SubreadSetMetadata with "
+ "{t}".format(t=type(newMetadata).__name__))
+
+ # Pull generic values, kwargs, general treatment in super
+ super(ReadSet, self).addMetadata(newMetadata, **kwargs)
+
+ def consolidate(self, dataFile, numFiles=1):
+ """Consolidate a larger number of bam files to a smaller number of bam
+ files (min 1)
+
+ Args:
+ dataFile: The name of the output file. If numFiles >1 numbers will
+ be added.
+ numFiles: The number of data files to be produced.
+
+ """
+ if numFiles > 1:
+ assert len(self.resourceReaders()) == len(self.toExternalFiles())
+ resSizes = [[i, size[0], size[1]]
+ for i, size in enumerate(self._resourceSizes())]
+ chunks = self._chunkList(resSizes, numFiles, lambda x: x[1])
+ resLists = []
+ for chunk in chunks:
+ thisResList = []
+ for i in chunk:
+ thisResList.append(self.toExternalFiles()[i[0]])
+ resLists.append(thisResList)
+ fnames = [_infixFname(dataFile, str(i)) for i in range(numFiles)]
+ for resList, fname in zip(resLists, fnames):
+ consolidateBams(resList, fname, filterDset=self)
+ log.debug("Replacing resources")
+ self.externalResources = ExternalResources()
+ self.addExternalResources(fnames)
+ else:
+ consolidateBams(self.toExternalFiles(), dataFile, filterDset=self)
+ log.debug("Replacing resources")
+ self.externalResources = ExternalResources()
+ self.addExternalResources([dataFile])
+
+ def __len__(self):
+ if self.numRecords == -1:
+ if self._filters:
+ self.updateCounts()
+ else:
+ count = 0
+ for reader in self.resourceReaders():
+ count += len(reader)
+ self.numRecords = count
+ return self.numRecords
+
+ def updateCounts(self):
+ if self._skipCounts:
+ log.debug("SkipCounts is true, skipping updateCounts()")
+ self.metadata.totalLength = -1
+ self.metadata.numRecords = -1
+ return
+ try:
+ self.assertIndexed()
+ log.debug('Updating counts')
+ numRecords, totalLength = self._length
+ self.metadata.totalLength = totalLength
+ self.metadata.numRecords = numRecords
+ except (IOError, UnavailableFeature):
+ if not self._strict:
+ log.debug("File problem, metadata not populated")
+ self.metadata.totalLength = -1
+ self.metadata.numRecords = -1
+ else:
+ raise
+
+
+class HdfSubreadSet(ReadSet):
+
+ datasetType = DataSetMetaTypes.HDF_SUBREAD
+
+ def __init__(self, *files, **kwargs):
+ log.debug("Opening HdfSubreadSet")
+ super(HdfSubreadSet, self).__init__(*files, **kwargs)
+
+ # The metatype for this dataset type is inconsistent, plaster over it
+ # here:
+ self.objMetadata["MetaType"] = "PacBio.DataSet.SubreadSet"
+ self.objMetadata["TimeStampedName"] = self._getTimeStampedName(
+ self.objMetadata["MetaType"])
+
+ def _openFiles(self):
+ """Open the files (assert they exist, assert they are of the proper
+ type before accessing any file)
+ """
+ if self._openReaders:
+ log.debug("Closing old readers...")
+ self.close()
+ log.debug("Opening resources")
+ for extRes in self.externalResources:
+ location = urlparse(extRes.resourceId).path
+ resource = BaxH5Reader(location)
+ self._openReaders.append(resource)
+ if len(self._openReaders) == 0 and len(self.toExternalFiles()) != 0:
+ raise IOError("No files were openable or reads found")
+ log.debug("Done opening resources")
+
+ @property
+ def _length(self):
+ """Used to populate metadata in updateCounts"""
+ length = 0
+ count = 0
+ for rec in self.records:
+ count += 1
+ hqReg = rec.hqRegion
+ length += hqReg[1] - hqReg[0]
+ return count, length
+
+ def updateCounts(self):
+ """Overriding here so we don't have to assertIndexed"""
+ if self._skipCounts:
+ log.debug("SkipCounts is true, skipping updateCounts()")
+ self.metadata.totalLength = -1
+ self.metadata.numRecords = -1
+ return
+ try:
+ log.debug('Updating counts')
+ numRecords, totalLength = self._length
+ self.metadata.totalLength = totalLength
+ self.metadata.numRecords = numRecords
+ except (IOError, UnavailableFeature):
+ if not self._strict:
+ log.debug("File problem, metadata not populated")
+ self.metadata.totalLength = -1
+ self.metadata.numRecords = -1
+ else:
+ raise
+
+ def consolidate(self, dataFile, numFiles=1):
+ raise NotImplementedError()
+
+ @staticmethod
+ def _metaTypeMapping():
+ return {'bax.h5':'PacBio.SubreadFile.BaxFile',
+ 'bas.h5':'PacBio.SubreadFile.BasFile', }
+
+
+class SubreadSet(ReadSet):
+ """DataSet type specific to Subreads
+
+ DocTest:
+
+ >>> from pbcore.io import SubreadSet
+ >>> from pbcore.io.dataset.DataSetMembers import ExternalResources
+ >>> import pbcore.data.datasets as data
+ >>> ds1 = SubreadSet(data.getXml(no=5))
+ >>> ds2 = SubreadSet(data.getXml(no=5))
+ >>> # So they don't conflict:
+ >>> ds2.externalResources = ExternalResources()
+ >>> ds1 # doctest:+ELLIPSIS
+ <SubreadSet...
+ >>> ds1._metadata # doctest:+ELLIPSIS
+ <SubreadSetMetadata...
+ >>> ds1._metadata # doctest:+ELLIPSIS
+ <SubreadSetMetadata...
+ >>> ds1.metadata # doctest:+ELLIPSIS
+ <SubreadSetMetadata...
+ >>> len(ds1.metadata.collections)
+ 1
+ >>> len(ds2.metadata.collections)
+ 1
+ >>> ds3 = ds1 + ds2
+ >>> len(ds3.metadata.collections)
+ 2
+ >>> ds4 = SubreadSet(data.getSubreadSet())
+ >>> ds4 # doctest:+ELLIPSIS
+ <SubreadSet...
+ >>> ds4._metadata # doctest:+ELLIPSIS
+ <SubreadSetMetadata...
+ >>> len(ds4.metadata.collections)
+ 1
+ """
+
+ datasetType = DataSetMetaTypes.SUBREAD
+
+ def __init__(self, *files, **kwargs):
+ log.debug("Opening SubreadSet")
+ super(SubreadSet, self).__init__(*files, **kwargs)
+
+ @staticmethod
+ def _metaTypeMapping():
+ # This doesn't work for scraps.bam, whenever that is implemented
+ return {'bam':'PacBio.SubreadFile.SubreadBamFile',
+ 'bai':'PacBio.Index.BamIndex',
+ 'pbi':'PacBio.Index.PacBioIndex',
+ }
+
+
+class AlignmentSet(ReadSet):
+ """DataSet type specific to Alignments. No type specific Metadata exists,
+ so the base class version is OK (this just ensures type representation on
+ output and expandability"""
+
+ datasetType = DataSetMetaTypes.ALIGNMENT
+
+ def __init__(self, *files, **kwargs):
+ """ An AlignmentSet
+
+ Args:
+ *files: handled by super
+ referenceFastaFname=None: the reference fasta filename for this
+ alignment.
+ strict=False: see base class
+ skipCounts=False: see base class
+ """
+ log.debug("Opening AlignmentSet with {f}".format(f=files))
+ super(AlignmentSet, self).__init__(*files, **kwargs)
+ fname = kwargs.get('referenceFastaFname', None)
+ if fname:
+ self.addReference(fname)
+
+ def consolidate(self, *args, **kwargs):
+ if self.isCmpH5:
+ raise NotImplementedError()
+ else:
+ return super(AlignmentSet, self).consolidate(*args, **kwargs)
+
+ def addReference(self, fname):
+ if isinstance(fname, ReferenceSet):
+ reference = fname.externalResources.resourceIds
+ else:
+ reference = ReferenceSet(fname).externalResources.resourceIds
+ if len(reference) > 1:
+ if len(reference) != self.numExternalResources:
+ raise ResourceMismatchError(
+ "More than one reference found, but not enough for one "
+ "per resource")
+ for res, ref in zip(self.externalResources, reference):
+ res.reference = ref
+ else:
+ for res in self.externalResources:
+ res.reference = reference[0]
+ self._openFiles()
+
+ def _indexRecords(self, correctIds=True):
+ """Returns index records summarizing all of the records in all of
+ the resources that conform to those filters addressing parameters
+ cached in the pbi.
+
+ """
+ recArrays = []
+ log.debug("Processing resource pbis")
+ self._indexMap = []
+ for rrNum, rr in enumerate(self.resourceReaders()):
+ indices = rr.index
+
+ if correctIds and self._stackedReferenceInfoTable:
+ log.debug("Must correct index tId's")
+ tIdMap = {n: name
+ for n, name in enumerate(
+ rr.referenceInfoTable['Name'])}
+ nameMap = self.refIds
+
+ if not self._filters or self.noFiltering:
+ if correctIds and self._stackedReferenceInfoTable:
+ for i in range(len(indices._tbl)):
+ indices._tbl.tId[i] = nameMap[
+ tIdMap[indices._tbl.tId[i]]]
+ recArrays.append(indices._tbl)
+ self._indexMap.extend([(rrNum, i) for i in
+ range(len(indices._tbl))])
+ else:
+ # Filtration will be necessary:
+ nameMap = {name: n
+ for n, name in enumerate(
+ rr.referenceInfoTable['Name'])}
+
+ passes = self._filters.filterIndexRecords(indices._tbl,
+ nameMap)
+ if correctIds and self._stackedReferenceInfoTable:
+ for i in range(len(indices._tbl)):
+ indices._tbl.tId[i] = nameMap[
+ tIdMap[indices._tbl.tId[i]]]
+ newInds = indices._tbl[passes]
+ recArrays.append(newInds)
+ self._indexMap.extend([(rrNum, i) for i in
+ np.nonzero(passes)[0]])
+ self._indexMap = np.array(self._indexMap)
+ return _stackRecArrays(recArrays)
+
+ def resourceReaders(self, refName=False):
+ """A generator of Indexed*Reader objects for the ExternalResources
+ in this DataSet.
+
+ Args:
+ refName: Only yield open resources if they have refName in their
+ referenceInfoTable
+
+ Yields:
+ An open indexed alignment file
+
+ Doctest:
+ >>> import pbcore.data.datasets as data
+ >>> from pbcore.io import AlignmentSet
+ >>> ds = AlignmentSet(data.getBam())
+ >>> for seqFile in ds.resourceReaders():
+ ... for record in seqFile:
+ ... print 'hn: %i' % record.holeNumber # doctest:+ELLIPSIS
+ hn: ...
+
+ """
+ if refName:
+ if (not refName in self.refNames and
+ not refName in self.fullRefNames):
+ _ = int(refName)
+ refName = self._idToRname(refName)
+
+ if not self._openReaders:
+ self._openFiles()
+ if refName:
+ return [resource for resource in self._openReaders
+ if refName in resource.referenceInfoTable['FullName'] or
+ refName in resource.referenceInfoTable['Name']]
+ else:
+ return self._openReaders
+
+ @property
+ def refNames(self):
+ """A list of reference names (id)."""
+ if self.isCmpH5:
+ return [self._cleanCmpName(name) for _, name in
+ self.refInfo('FullName')]
+ return sorted([name for _, name in self.refInfo('Name')])
+
+ def _indexReadsInReference(self, refName):
+ # This can probably be deprecated for all but the official reads in
+ # range (and maybe reads in reference)
+ refName = self.guaranteeName(refName)
+
+ desiredTid = self.refIds[refName]
+ tIds = self.index.tId
+ passes = tIds == desiredTid
+ return self.index[passes]
+
+ def _resourceSizes(self):
+ sizes = []
+ for rr in self.resourceReaders():
+ sizes.append((len(rr.index), sum(rr.index.aEnd - rr.index.aStart)))
+ return sizes
+
+ def _countMappedReads(self):
+ """It is too slow for large datasets to use _indexReadsInReference"""
+ counts = {rId: 0 for _, rId in self.refIds.items()}
+ for ind in self.index:
+ counts[ind["tId"]] += 1
+ tbr = {}
+ idMap = {rId: name for name, rId in self.refIds.items()}
+ for key, value in counts.iteritems():
+ tbr[idMap[key]] = value
+ return tbr
+
+ def _getMappedReads(self):
+ """It is too slow for large datasets to use _indexReadsInReference for
+ each reference"""
+ counts = {rId: 0 for _, rId in self.refIds.items()}
+ for ind in self.index:
+ counts[ind["tId"]].append(ind)
+ tbr = {}
+ idMap = {rId: name for name, rId in self.refIds.items()}
+ for key, value in counts.iteritems():
+ tbr[idMap[key]] = value
+ return tbr
+
+ @property
+ def refWindows(self):
+ """Going to be tricky unless the filters are really focused on
+ windowing the reference. Much nesting or duplication and the correct
+ results are really not guaranteed"""
+ windowTuples = []
+ nameIDs = self.refInfo('Name')
+ refLens = None
+ for name, refID in nameIDs:
+ for filt in self._filters:
+ thisOne = False
+ for param in filt:
+ if param.name == 'rname':
+ if param.value == name:
+ thisOne = True
if thisOne:
winstart = 0
winend = -1
@@ -1389,134 +2238,414 @@ class DataSet(object):
refLens = self.refLengths
refLen = refLens[name]
windowTuples.append((refId, 0, refLen))
- return windowTuples
+ return sorted(windowTuples)
- @property
- def refNames(self):
- """A list of reference names (id)."""
- if self.isCmpH5:
- return [self._cleanCmpName(name) for _, name in
- self.refInfo('FullName')]
- return sorted([name for _, name in self.refInfo('Name')])
+ def countRecords(self, rname=None, winStart=None, winEnd=None):
+ """Count the number of records mapped to 'rname' that overlap with
+ 'window'"""
+ if rname and winStart != None and winEnd != None:
+ return len(self._indexReadsInRange(rname, winStart, winEnd))
+ elif rname:
+ return len(self._indexReadsInReference(rname))
+ else:
+ return len(self.index)
- def _cleanCmpName(self, name):
- return splitFastaHeader(name)[0]
+ @filtered
+ def readsInReference(self, refName):
+ """A generator of (usually) BamAlignment objects for the
+ reads in one or more Bam files pointed to by the ExternalResources in
+ this DataSet that are mapped to the specified reference genome.
- @property
- def refLengths(self):
- """A dict of refName: refLength"""
- return {name: length for name, length in self.refInfo('Length')}
+ Args:
+ refName: the name of the reference that we are sampling.
- @property
- def refIds(self):
- """A dict of refName: refId"""
- return {name: rId for name, rId in self.refInfo('ID')}
+ Yields:
+ BamAlignment objects
- def refLength(self, rname):
- """The length of reference 'rname'. This is expensive, so if you're
- going to do many lookups cache self.refLengths locally and use that."""
- lut = self.refLengths
- return lut[rname]
+ Doctest:
+ >>> import pbcore.data.datasets as data
+ >>> from pbcore.io import AlignmentSet
+ >>> ds = AlignmentSet(data.getBam())
+ >>> for read in ds.readsInReference(ds.refNames[15]):
+ ... print 'hn: %i' % read.holeNumber # doctest:+ELLIPSIS
+ hn: ...
- @property
- def fullRefNames(self):
- """A list of reference full names (full header)."""
- return [name for _, name in self.refInfo('FullName')]
+ """
- def refInfo(self, key):
- """The reference names present in the referenceInfoTable of the
- ExtResources.
+ if isinstance(refName, np.int64):
+ refName = str(refName)
+ if refName.isdigit():
+ if (not refName in self.refNames
+ and not refName in self.fullRefNames):
+ try:
+ refName = self._idToRname(int(refName))
+ except AttributeError:
+ raise StopIteration
+
+ # I would love to use readsInRange(refName, None, None), but
+ # IndexedBamReader breaks this (works for regular BamReader).
+ # So I have to do a little hacking...
+ refLen = 0
+ for resource in self.resourceReaders():
+ if (refName in resource.referenceInfoTable['Name'] or
+ refName in resource.referenceInfoTable['FullName']):
+ refLen = resource.referenceInfo(refName).Length
+ break
+ if refLen:
+ for read in self.readsInRange(refName, 0, refLen):
+ yield read
+
+ def _intervalContour(self, rname):
+ """Take a set of index records and build a pileup of intervals, or
+ "contour" describing coverage over the contig
+
+ ..note:: Naively incrementing values in an array is too slow and takes
+ too much memory. Sorting tuples by starts and ends and iterating
+ through them and the reference (O(nlogn + nlogn + n + n + m)) takes too
+ much memory and time. Iterating over the reference, using numpy
+ conditional indexing at each base on tStart and tEnd columns uses no
+ memory, but is too slow (O(nm), but in numpy (C, hopefully)). Building
+ a delta list via sorted tStarts and tEnds one at a time saves memory
+ and is ~5x faster than the second method above (O(nlogn + nlogn + m)).
+
+ """
+ log.debug("Generating coverage summary")
+ index = self._indexReadsInReference(rname)
+ # indexing issue. Doesn't really matter (just for split). Shifted:
+ coverage = [0] * (self.refLengths[rname] + 1)
+ starts = sorted(index.tStart)
+ for i in starts:
+ coverage[i] += 1
+ del starts
+ ends = sorted(index.tEnd)
+ for i in ends:
+ coverage[i] -= 1
+ del ends
+ curCov = 0
+ for i, delta in enumerate(coverage):
+ curCov += delta
+ coverage[i] = curCov
+ return coverage
+
+ def _splitContour(self, contour, splits):
+ """Take a contour and a number of splits, return the location of each
+ coverage mediated split with the first at 0"""
+ log.debug("Splitting coverage summary")
+ totalCoverage = sum(contour)
+ splitSize = totalCoverage/splits
+ tbr = [0]
+ for _ in range(splits - 1):
+ size = 0
+ # Start where the last one ended, so we append the current endpoint
+ tbr.append(tbr[-1])
+ while (size < splitSize and
+ tbr[-1] < (len(contour) - 1)):
+ # iterate the endpoint
+ tbr[-1] += 1
+ # track the size
+ size += contour[tbr[-1]]
+ assert len(tbr) == splits
+ return tbr
+
+ def _shiftAtoms(self, atoms):
+ shiftedAtoms = []
+ rnames = defaultdict(list)
+ for atom in atoms:
+ rnames[atom[0]].append(atom)
+ for rname, rAtoms in rnames.iteritems():
+ if len(rAtoms) > 1:
+ contour = self._intervalContour(rname)
+ splits = self._splitContour(contour, len(rAtoms))
+ ends = splits[1:] + [self.refLengths[rname]]
+ for start, end in zip(splits, ends):
+ newAtom = (rname, start, end)
+ shiftedAtoms.append(newAtom)
+ else:
+ shiftedAtoms.append(rAtoms[0])
+ return shiftedAtoms
+
+ def _split_contigs(self, chunks, maxChunks=0, breakContigs=False,
+ targetSize=5000, byRecords=True, updateCounts=True):
+ """Split a dataset into reference windows based on contigs.
Args:
- key: a key for the referenceInfoTable of each resource
- Returns:
- A list of tuples of refrence name, key_result pairs
+ chunks: The number of chunks to emit. If chunks < # contigs,
+ contigs are grouped by size. If chunks == contigs, one
+ contig is assigned to each dataset regardless of size. If
+ chunks >= contigs, contigs are split into roughly equal
+ chunks (<= 1.0 contig per file).
"""
- log.debug("Sampling references")
- names = self.referenceInfoTable['Name']
- infos = self.referenceInfoTable[key]
+ # removed the non-trivial case so that it is still filtered to just
+ # contigs with associated records
- log.debug("Removing duplicate reference entries")
- sampled = zip(names, infos)
- sampled = set(sampled)
+ # The format is rID, start, end, for a reference window
+ log.debug("Fetching reference names and lengths")
+ # pull both at once so you only have to mess with the
+ # referenceInfoTable once.
+ refLens = self.refLengths
+ refNames = refLens.keys()
+ log.debug("{i} references found".format(i=len(refNames)))
+
+ log.debug("Finding contigs")
+ # FIXME: this mess:
+ if len(refNames) < 100 and len(refNames) > 1:
+ if byRecords:
+ log.debug("Counting records...")
+ atoms = [(rn, 0, 0, self.countRecords(rn))
+ for rn in refNames
+ if len(self._indexReadsInReference(rn)) != 0]
+ else:
+ atoms = [(rn, 0, 0) for rn in refNames if
+ len(self._indexReadsInReference(rn)) != 0]
+ else:
+ log.debug("Skipping records for each reference check")
+ atoms = [(rn, 0, 0) for rn in refNames]
+ if byRecords:
+ log.debug("Counting records...")
+ # This is getting out of hand, but the number of references
+ # determines the best read counting algorithm:
+ if len(refNames) < 100:
+ atoms = [(rn, 0, 0, self.countRecords(rn))
+ for rn in refNames]
+ else:
+ counts = self._countMappedReads()
+ atoms = [(rn, 0, 0, counts[rn]) for rn in refNames]
+ log.debug("{i} contigs found".format(i=len(atoms)))
+
+ if byRecords:
+ balanceKey = lambda x: self.countRecords(*x)
+ else:
+ # The window length is used for balancing
+ balanceKey = lambda x: x[2] - x[1]
+
+ # By providing maxChunks and not chunks, this combination will set
+ # chunks down to < len(atoms) < maxChunks
+ if not chunks:
+ log.debug("Chunks not set, splitting to len(atoms): {i}"
+ .format(i=len(atoms)))
+ chunks = len(atoms)
+ if maxChunks and chunks > maxChunks:
+ log.debug("maxChunks trumps chunks")
+ chunks = maxChunks
+
+ # Decide whether to intelligently limit chunk count:
+ if maxChunks and breakContigs:
+ # The bounds:
+ minNum = 2
+ maxNum = maxChunks
+ # Adjust
+ log.debug("Target numRecords per chunk: {i}".format(i=targetSize))
+ dataSize = self.numRecords
+ log.debug("numRecords in dataset: {i}".format(i=dataSize))
+ chunks = int(dataSize/targetSize)
+ # Respect bounds:
+ chunks = minNum if chunks < minNum else chunks
+ chunks = maxNum if chunks > maxNum else chunks
+ log.debug("Resulting number of chunks: {i}".format(i=chunks))
+
+ # refwindow format: rId, start, end
+ if chunks > len(atoms):
+ # splitting atom format is slightly different (but more compatible
+ # going forward with countRecords): (rId, size, segments)
+
+ # Lets do a rough split, counting reads once and assuming uniform
+ # coverage (reads span, therefore can't split by specific reads)
+ if byRecords:
+ atoms = [[rn, size, 1] for rn, _, _, size in atoms]
+ else:
+ atoms = [[rn, refLens[rn], 1] for rn, _, _ in atoms]
+ log.debug("Splitting atoms")
+ atoms = self._split_atoms(atoms, chunks)
+
+ # convert back to window format:
+ segments = []
+ for atom in atoms:
+ segment_size = atom[1]/atom[2]
+ if byRecords:
+ segment_size = refLens[atom[0]]/atom[2]
+ sub_segments = [(atom[0], segment_size * i, segment_size *
+ (i + 1)) for i in range(atom[2])]
+ # if you can't divide it evenly you may have some messiness
+ # with the last window. Fix it:
+ tmp = sub_segments.pop()
+ tmp = (tmp[0], tmp[1], refLens[tmp[0]])
+ sub_segments.append(tmp)
+ segments.extend(sub_segments)
+ atoms = segments
+
+ log.debug("Done defining {n} chunks".format(n=chunks))
+ # duplicate
+ log.debug("Making copies")
+ results = [self.copy() for _ in range(chunks)]
+
+ if byRecords:
+ log.debug("Respacing chunks by records")
+ atoms = self._shiftAtoms(atoms)
+ # indicates byRecords with no sub atom splits: (the fourth spot is
+ # countrecords in that window)
+ if len(atoms[0]) == 4:
+ balanceKey = lambda x: x[3]
+ log.debug("Distributing chunks")
+ # if we didn't have to split atoms and are doing it byRecords, the
+ # original counts are still valid:
+ # Now well have to count records again to recombine atoms
+ chunks = self._chunkList(atoms, chunks, balanceKey)
+
+ log.debug("Done chunking")
+ log.debug("Modifying filters or resources")
+ for result, chunk in zip(results, chunks):
+ if atoms[0][2]:
+ result.filters.addRequirement(
+ rname=[('=', c[0]) for c in chunk],
+ tStart=[('>', c[1]) for c in chunk],
+ tEnd=[('<', c[2]) for c in chunk])
+ else:
+ result.filters.addRequirement(
+ rname=[('=', c[0]) for c in chunk])
+
+ # UniqueId was regenerated when the ExternalResource list was
+ # whole, therefore we need to regenerate it again here
+ log.debug("Generating new UUID")
+ # At this point the ID's should be corrected, so the namemap should be
+ # here:
+ for result in results:
+ result.newUuid()
+ if updateCounts:
+ result._openReaders = self._openReaders
+ passes = result._filters.filterIndexRecords(self.index,
+ self.refIds)
+ result._index = self.index[passes]
+ result.updateCounts()
+ del result._index
+ del passes
+ result._index = None
- log.debug("Filtering reference entries")
- if not self.noFiltering or not self._filters:
- sampled = [(name, info) for name, info in sampled
- if self._filters.testParam('rname', name)]
- return sampled
+ # Update the basic metadata for the new DataSets from external
+ # resources, or at least mark as dirty
+ # TODO
+ return results
- def _indexReadsInReference(self, refName):
- if isinstance(refName, np.int64):
- refName = str(refName)
- if refName.isdigit():
- if (not refName in self.refNames
- and not refName in self.fullRefNames):
- try:
- refName = self._idToRname(int(refName))
- except AttributeError:
- raise StopIteration
+ def _indexReadsInRange(self, refName, start, end, justIndices=False):
+ """Return the index (pbi) records within a range.
- # I would love to use readsInRange(refName, None, None), but
- # IndexedBamReader breaks this (works for regular BamReader).
- # So I have to do a little hacking...
- refLen = 0
- for resource in self.resourceReaders():
- if (refName in resource.referenceInfoTable['Name'] or
- refName in resource.referenceInfoTable['FullName']):
- refLen = resource.referenceInfo(refName).Length
- break
- if refLen:
- for read in self._indexReadsInRange(refName, 0, refLen):
- yield read
+ ..note:: Not sorted by genomic location!
- @filtered
- def readsInReference(self, refName):
- """A generator of (usually) BamAlignment objects for the
- reads in one or more Bam files pointed to by the ExternalResources in
- this DataSet that are mapped to the specified reference genome.
+ """
+ desiredTid = self.refIds[refName]
+ passes = ((self.index.tId == desiredTid) &
+ (self.index.tStart < end) &
+ (self.index.tEnd > start))
+ if justIndices:
+ return passes
+ return self.index[passes]
+
+ def _pbiReadsInRange(self, refName, start, end, longest=False):
+ """Return the reads in range for a file, but use the index in this
+ object to get the order of the (reader, read) index tuples, instead of
+ using the pbi rangeQuery for each file and merging the actual reads.
+ This also opens up the ability to sort the reads by length in the
+ window, and yield in that order (much much faster for quiver)
Args:
- refName: the name of the reference that we are sampling.
+ refName: The reference name to sample
+ start: The start of the target window
+ end: The end of the target window
+ longest: (False) yield the longest reads first
Yields:
- BamAlignment objects
+ reads in the range, potentially longest first
- Doctest:
- >>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet
- >>> ds = DataSet(data.getBam())
- >>> for read in ds.readsInReference(ds.refNames[15]):
- ... print 'hn: %i' % read.holeNumber # doctest:+ELLIPSIS
- hn: ...
"""
+ if not refName in self.refNames:
+ raise StopIteration
+ # get pass indices
+ passes = self._indexReadsInRange(refName, start, end, justIndices=True)
+ mapPasses = self._indexMap[passes]
+ if longest:
+ def lengthInWindow(hits):
+ ends = hits.tEnd
+ post = ends > end
+ ends[post] = end
+ starts = hits.tStart
+ pre = starts < start
+ starts[pre] = start
+ return ends - starts
+ lens = lengthInWindow(self.index[passes])
+ # reverse the keys here, so the descending sort is stable
+ lens = (end - start) - lens
+ sort_order = lens.argsort(kind='mergesort')
+ mapPasses = mapPasses[sort_order]
+ elif len(self.toExternalFiles()) > 1:
+ # sort the pooled passes and indices using a stable algorithm
+ sort_order = self.index[passes].tStart.argsort(kind='mergesort')
+ # pull out indexMap using those passes
+ mapPasses = mapPasses[sort_order]
+ return self._getRecords(mapPasses)
+
+ def _getRecords(self, indexList, buffsize=1):
+ """Get the records corresponding to indexList
- if isinstance(refName, np.int64):
- refName = str(refName)
- if refName.isdigit():
- if (not refName in self.refNames
- and not refName in self.fullRefNames):
- try:
- refName = self._idToRname(int(refName))
- except AttributeError:
- raise StopIteration
-
- # I would love to use readsInRange(refName, None, None), but
- # IndexedBamReader breaks this (works for regular BamReader).
- # So I have to do a little hacking...
- refLen = 0
- for resource in self.resourceReaders():
- if (refName in resource.referenceInfoTable['Name'] or
- refName in resource.referenceInfoTable['FullName']):
- refLen = resource.referenceInfo(refName).Length
- break
- if refLen:
- for read in self.readsInRange(refName, 0, refLen):
- yield read
-
+ Args:
+ indexList: A list of (reader, read) index tuples
+ buffsize: The number of reads to buffer (coalesced file reads)
- def _indexReadsInRange(self, refName, start, end):
+ Yields:
+ reads from all files
+
+ """
+ # yield in order of sorted indexMap
+ if buffsize == 1:
+ for indexTuple in indexList:
+ yield self.resourceReaders()[indexTuple[0]].atRowNumber(
+ indexTuple[1])
+ else:
+ def debuf():
+ # This will store the progress through the buffer for each
+ # reader
+ reqCacheI = [0] * len(self.resourceReaders())
+ # fill the record cache
+ for rrNum, rr in enumerate(self.resourceReaders()):
+ for req in reqCache[rrNum]:
+ recCache[rrNum].append(rr.atRowNumber(req))
+ # empty cache
+ for i in range(cacheFill):
+ rrNum = fromCache[i]
+ curI = reqCacheI[rrNum]
+ reqCacheI[rrNum] += 1
+ yield recCache[rrNum][curI]
+
+ def cleanBuffs():
+ # This will buffer the records being pulled from each reader
+ recCache = [[] for _ in self.resourceReaders()]
+ # This will buffer the indicies being pulled from each reader
+ reqCache = [[] for _ in self.resourceReaders()]
+ # This will store the order in which reads are consumed, which
+ # here can be specified by the reader number (read index order
+ # is cached in the reqCache buffer)
+ fromCache = [None] * buffsize
+ return recCache, reqCache, fromCache, 0
+
+ # The algorithm:
+ recCache, reqCache, fromCache, cacheFill = cleanBuffs()
+ for indexTuple in indexList:
+ # segregate the requests by reader into ordered lists of read
+ # indices
+ reqCache[indexTuple[0]].append(indexTuple[1])
+ # keep track of the order in which readers should be sampled,
+ # which will maintain the overall read order
+ fromCache[cacheFill] = indexTuple[0]
+ cacheFill += 1
+ if cacheFill >= buffsize:
+ for rec in debuf():
+ yield rec
+ recCache, reqCache, fromCache, cacheFill = cleanBuffs()
+ if cacheFill > 0:
+ for rec in debuf():
+ yield rec
+
+ def guaranteeName(self, nameOrId):
+ refName = nameOrId
if isinstance(refName, np.int64):
refName = str(refName)
if refName.isdigit():
@@ -1525,23 +2654,11 @@ class DataSet(object):
# we need the real refName, which may be hidden behind a
# mapping to resolve duplicate refIds between resources...
refName = self._idToRname(int(refName))
- for reader in self.resourceReaders():
- tIdMap = {n: name
- for n, name in enumerate(
- reader.referenceInfoTable['Name'])}
- filts = self._filters.tests(readType='pbi', tIdMap=tIdMap)
- index = reader.index
- winId = reader.referenceInfo(refName).ID
- for rec_i in index.rangeQuery(winId, start, end):
- read = index[rec_i]
- if filts:
- if any([filt(read) for filt in filts]):
- yield read
- else:
- yield read
+ return refName
@filtered
- def readsInRange(self, refName, start, end, buffsize=50):
+ def readsInRange(self, refName, start, end, buffsize=50, usePbi=True,
+ longest=False):
"""A generator of (usually) BamAlignment objects for the reads in one
or more Bam files pointed to by the ExternalResources in this DataSet
that have at least one coordinate within the specified range in the
@@ -1562,26 +2679,25 @@ class DataSet(object):
Doctest:
>>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet
- >>> ds = DataSet(data.getBam())
+ >>> from pbcore.io import AlignmentSet
+ >>> ds = AlignmentSet(data.getBam())
>>> for read in ds.readsInRange(ds.refNames[15], 100, 150):
... print 'hn: %i' % read.holeNumber # doctest:+ELLIPSIS
hn: ...
"""
- if isinstance(refName, np.int64):
- refName = str(refName)
- if refName.isdigit():
- if (not refName in self.refNames and
- not refName in self.fullRefNames):
- # we need the real refName, which may be hidden behind a
- # mapping to resolve duplicate refIds between resources...
- refName = self._idToRname(int(refName))
+ refName = self.guaranteeName(refName)
# correct the cmp.h5 reference names before reads go out the door
if self.isCmpH5:
for res in self.resourceReaders():
for row in res.referenceInfoTable:
- row.FullName = row.FullName.split(' ')[0]
+ row.FullName = self._cleanCmpName(row.FullName)
+
+ if self.hasPbi and usePbi:
+ for rec in self._pbiReadsInRange(refName, start, end,
+ longest=longest):
+ yield rec
+ raise StopIteration
# merge sort before yield
if self.numExternalResources > 1:
@@ -1624,261 +2740,93 @@ class DataSet(object):
del deep_buf[first_i]
del buf_indices[first_i]
else:
- tStarts[first_i] = deep_buf[first_i][buf_index].tStart
- yield first
- else:
- read_its = [iter(rr.readsInRange(refName, start, end))
- for rr in self.resourceReaders()]
- # buffer one element from each generator
- currents = [next(its, None) for its in read_its]
- # remove empty iterators
- read_its = [it for it, cur in zip(read_its, currents) if cur]
- currents = [cur for cur in currents if cur]
- tStarts = [cur.tStart for cur in currents]
- while len(read_its) != 0:
- # pick the first one to yield
- # this should be a bit faster than taking the min of an
- # enumeration of currents with a key function accessing a
- # field...
- first = min(tStarts)
- first_i = tStarts.index(first)
- first = currents[first_i]
- # update the buffers
- try:
- currents[first_i] = next(read_its[first_i])
- tStarts[first_i] = currents[first_i].tStart
- except StopIteration:
- del read_its[first_i]
- del currents[first_i]
- del tStarts[first_i]
- yield first
- else:
- # the above will work in either case, but this might be ever so
- # slightly faster
- for resource in self.resourceReaders():
- for read in resource.readsInRange(refName, start, end):
- yield read
-
- def _idToRname(self, rId):
- """Map the DataSet.referenceInfoTable.ID to the superior unique
- reference identifier: referenceInfoTable.Name
-
- Args:
- rId: The DataSet.referenceInfoTable.ID of interest
-
- Returns:
- The referenceInfoTable.Name corresponding to rId
- """
- resNo, rId = self._referenceIdMap[rId]
- if self.isCmpH5:
- rId -= 1
- if self.isCmpH5:
- # This is what CmpIO recognizes as the 'shortname'
- refName = self.resourceReaders()[
- resNo].referenceInfoTable[rId]['FullName']
- else:
- refName = self.resourceReaders()[
- resNo].referenceInfoTable[rId]['Name']
- return refName
-
- def toFofn(self, outfn=None, uri=False, relative=False):
- """Return a list of resource filenames (and write to optional outfile)
-
- Args:
- outfn: (None) the file to which the resouce filenames are to be
- written. If None, the only emission is a returned list of
- file names.
- uri: (t/F) write the resource filenames as URIs.
- relative: (t/F) emit paths relative to outfofn or '.' if no
- outfofn
-
- Returns:
- A list of filenames or uris
-
- Writes:
- (Optional) A file containing a list of filenames or uris
-
- Doctest:
- >>> from pbcore.io import DataSet
- >>> DataSet("bam1.bam", "bam2.bam", strict=False).toFofn(uri=False)
- ['bam1.bam', 'bam2.bam']
- """
- lines = [er.resourceId for er in self.externalResources]
- if not uri:
- lines = [urlparse(line).path for line in lines]
- if relative is True:
- # make it relative to the fofn location
- if outfn:
- lines = [os.path.relpath(line, os.path.dirname(outfn))
- for line in lines]
- # or current location
- else:
- lines = [os.path.relpath(line) for line in lines]
- if outfn:
- with open(outfn, 'w') as outFile:
- outFile.writelines(line + '\n' for line in lines)
- return lines
-
- def toExternalFiles(self):
- """Returns a list of top level external resources (no indices)."""
- files = self.externalResources.resourceIds
- tbr = []
- for fname in files:
- tbr.append(resolveLocation(fname, '.'))
- return tbr
-
- @property
- def _castableDataSetTypes(self):
- if isinstance(self.datasetType, tuple):
- return self.datasetType
- else:
- return (_toDsId('DataSet'), self.datasetType)
-
- @classmethod
- def castableTypes(cls):
- """The types to which this DataSet type may be cast. This is a property
- instead of a member variable as we can enforce casting limits here (and
- modify if needed by overriding them in subclasses).
-
- Returns:
- A dictionary of MetaType->Class mappings, e.g. 'DataSet': DataSet
- """
- if cls.__name__ != 'DataSet':
- return {'DataSet': DataSet,
- cls.__name__: cls}
- return {'DataSet': DataSet,
- 'SubreadSet': SubreadSet,
- 'HdfSubreadSet': HdfSubreadSet,
- 'AlignmentSet': AlignmentSet,
- 'ContigSet': ContigSet,
- 'ConsensusReadSet': ConsensusReadSet,
- 'ReferenceSet': ReferenceSet,
- 'BarcodeSet': BarcodeSet}
- @property
- def metadata(self):
- """Return the DataSet metadata as a DataSetMetadata object. Attributes
- should be populated intuitively, but see DataSetMetadata documentation
- for more detail."""
- return self._metadata
-
- @metadata.setter
- def metadata(self, newDict):
- """Set the metadata for this object. This is reasonably dangerous, as
- the argument must be a properly formated data structure, as specified
- in the DataSetMetadata documentation. This setter is primarily used
- by other DataSet objects, rather than users or API consumers."""
- if isinstance(newDict, DataSetMetadata):
- self._metadata = newDict
- else:
- self._metadata = self._metadata.__class__(newDict)
-
- @property
- def filters(self):
- """Limit setting to ensure cache hygiene and filter compatibility"""
- self._filters.registerCallback(lambda x=self: x.reFilter())
- return self._filters
-
- @filters.setter
- def filters(self, value):
- """Limit setting to ensure cache hygiene and filter compatibility"""
- self._filters = value
-
- def reFilter(self):
- """
- The filters on this dataset have changed, update DataSet state as
- needed
- """
- self._cachedFilters = []
- self.metadata.totalLength = -1
- self.metadata.numRecords = -1
- if self.metadata.summaryStats:
- self.metadata.removeChildren('SummaryStats')
-
- @property
- def numRecords(self):
- """The number of records in this DataSet (from the metadata)"""
- return self._metadata.numRecords
-
- def countRecords(self, rname=None, window=None):
- """Count the number of records mapped to 'rname' that overlap with
- 'window'
- """
- def count(iterable):
- count = 0
- for _ in iterable:
- count += 1
- return count
-
- if window:
- return count(self.readsInRange(rname, *window))
- if rname:
- return count(self.readsInReference(rname))
+ tStarts[first_i] = deep_buf[first_i][buf_index].tStart
+ yield first
+ else:
+ read_its = [iter(rr.readsInRange(refName, start, end))
+ for rr in self.resourceReaders()]
+ # buffer one element from each generator
+ currents = [next(its, None) for its in read_its]
+ # remove empty iterators
+ read_its = [it for it, cur in zip(read_its, currents) if cur]
+ currents = [cur for cur in currents if cur]
+ tStarts = [cur.tStart for cur in currents]
+ while len(read_its) != 0:
+ # pick the first one to yield
+ # this should be a bit faster than taking the min of an
+ # enumeration of currents with a key function accessing a
+ # field...
+ first = min(tStarts)
+ first_i = tStarts.index(first)
+ first = currents[first_i]
+ # update the buffers
+ try:
+ currents[first_i] = next(read_its[first_i])
+ tStarts[first_i] = currents[first_i].tStart
+ except StopIteration:
+ del read_its[first_i]
+ del currents[first_i]
+ del tStarts[first_i]
+ yield first
else:
- count(self.records)
+ # the above will work in either case, but this might be ever so
+ # slightly faster
+ for resource in self.resourceReaders():
+ for read in resource.readsInRange(refName, start, end):
+ yield read
@property
- def totalLength(self):
- """The total length of this DataSet"""
- return self._metadata.totalLength
+ def isSorted(self):
+ return self._checkIdentical('isSorted')
@property
- def uuid(self):
- """The UniqueId of this DataSet"""
- return self.objMetadata.get('UniqueId')
+ def tStart(self):
+ return self._checkIdentical('tStart')
@property
- def name(self):
- """The name of this DataSet"""
- return self.objMetadata.get('Name', '')
-
- @name.setter
- def name(self, value):
- """The name of this DataSet"""
- self.objMetadata['Name'] = value
+ def tEnd(self):
+ return self._checkIdentical('tEnd')
@property
- def numExternalResources(self):
- """The number of ExternalResources in this DataSet"""
- return len(self.externalResources)
+ def _length(self):
+ """Used to populate metadata in updateCounts. We're using the pbi here,
+ which is necessary and sufficient for both subreadsets and
+ alignmentsets, but doesn't work for hdfsubreadsets. Rather than
+ duplicate code, we'll implement the hdf specific _length as an
+ overriding function where needed.
- def _pollResources(self, func, refName=None):
- """Collect the responses to func on each resource (or those with reads
- mapping to refName)."""
- return [func(resource) for resource in self.resourceReaders(refName)]
+ ..note:: Both mapped and unmapped bams can be either indexed or
+ unindexed. This makes life more difficult, but we should
+ expect a pbi for both subreadsets and alignmentsets
- def _unifyResponses(self, responses, keyFunc=lambda x: x):
- """Make sure all of the responses from resources are the same."""
- if len(responses) > 1:
- # Check the rest against the first:
- for res in responses[1:]:
- if keyFunc(responses[0]) != keyFunc(res):
- raise ResourceMismatchError(responses)
- return responses[0]
+ """
+ if self.isCmpH5:
+ log.info("Correct counts not supported for cmp.h5 alignmentsets")
+ return -1, -1
+ count = len(self.index)
+ length = sum(self.index.aEnd - self.index.aStart)
+ return count, length
@property
- def isCmpH5(self):
- """Test whether all resources are cmp.h5 files"""
- res = self._pollResources(lambda x: isinstance(x, CmpH5Reader))
- return self._unifyResponses(res)
+ def _referenceFile(self):
+ responses = [res.reference for res in self.externalResources]
+ return self._unifyResponses(responses)
@property
- def hasPbi(self):
- """Test whether all resources are opened as IndexedBamReader objects"""
- try:
- res = self._pollResources(lambda x: isinstance(x,
- IndexedBamReader))
- return self._unifyResponses(res)
- except ResourceMismatchError:
- if not self._strict:
- log.error("Resources inconsistently indexed")
- return False
- else:
- raise
+ def recordsByReference(self):
+ """The records in this AlignmentSet, sorted by tStart."""
+ # we only care about aligned sequences here, so we can make this a
+ # chain of readsInReferences to add pre-filtering by rname, instead of
+ # going through every record and performing downstream filtering.
+ # This will make certain operations, like len(), potentially faster
+ for rname in self.refNames:
+ for read in self.readsInReference(rname):
+ yield read
def referenceInfo(self, refName):
"""Select a row from the DataSet.referenceInfoTable using the reference
name as a unique key"""
- # TODO: upgrade to use _referenceDict
+ # TODO: upgrade to use _referenceDict if needed
if not self.isCmpH5:
for row in self.referenceInfoTable:
if row.Name == refName:
@@ -1894,33 +2842,48 @@ class DataSet(object):
Record.ID is remapped to a unique integer key (though using record.Name
is preferred). Record.Names are remapped for cmp.h5 files to be
consistent with bam files.
+
"""
if self._referenceInfoTable is None:
# This isn't really right for cmp.h5 files (rowStart, rowEnd, for
# instance). Use the resource readers directly instead.
responses = self._pollResources(lambda x: x.referenceInfoTable)
+ table = []
if len(responses) > 1:
assert not self.isCmpH5 # see above
- tbr = np.concatenate(responses)
- tbr = np.unique(tbr)
- for i, rec in enumerate(tbr):
- rec.ID = i
- self._referenceInfoTable = tbr
+ try:
+ table = self._unifyResponses(
+ responses,
+ eqFunc=np.array_equal)
+ except ResourceMismatchError:
+ table = np.concatenate(responses)
+ table = np.unique(table)
+ for i, rec in enumerate(table):
+ rec.ID = i
+ self._stackedReferenceInfoTable = True
else:
table = responses[0]
if self.isCmpH5:
for rec in table:
rec.Name = self._cleanCmpName(rec.FullName)
- self._referenceInfoTable = table
- #TODO: Turn on when needed
+ log.debug("Filtering reference entries")
+ if not self.noFiltering and self._filters:
+ passes = []
+ for i, reference in enumerate(table):
+ if self._filters.testParam('rname', reference.Name):
+ passes.append(i)
+ table = table[passes]
+ self._referenceInfoTable = table
+ #TODO: Turn on when needed (expensive)
#self._referenceDict.update(zip(self.refIds.values(),
- #self._referenceInfoTable))
+ # self._referenceInfoTable))
return self._referenceInfoTable
@property
def _referenceIdMap(self):
"""Map the dataset shifted refIds to the [resource, refId] they came
from.
+
"""
# This isn't really possible for cmp.h5 files (rowStart, rowEnd, for
# instance). Use the resource readers directly instead.
@@ -1938,260 +2901,81 @@ class DataSet(object):
else:
return {i: [0, i] for i in responses[0]['ID']}
- @property
- def readGroupTable(self):
- """Combine the readGroupTables of each external resource"""
- responses = self._pollResources(lambda x: x.readGroupTable)
- if len(responses) > 1:
- tbr = reduce(np.append, responses)
- return tbr
- else:
- return responses[0]
-
- def hasPulseFeature(self, featureName):
- responses = self._pollResources(
- lambda x: x.hasPulseFeature(featureName))
- return self._unifyResponses(responses)
-
- def pulseFeaturesAvailable(self):
- responses = self._pollResources(lambda x: x.pulseFeaturesAvailable())
- return self._unifyResponses(responses)
-
- @property
- def sequencingChemistry(self):
- return self._checkIdentical('sequencingChemistry')
-
- @property
- def isSorted(self):
- return self._checkIdentical('isSorted')
-
- @property
- def isEmpty(self):
- return self._checkIdentical('isEmpty')
-
- @property
- def readType(self):
- return self._checkIdentical('readType')
+ def _cleanCmpName(self, name):
+ return splitFastaHeader(name)[0]
@property
- def tStart(self):
- return self._checkIdentical('tStart')
+ def refLengths(self):
+ """A dict of refName: refLength"""
+ return {name: length for name, length in self.refInfo('Length')}
@property
- def tEnd(self):
- return self._checkIdentical('tEnd')
-
- def _checkIdentical(self, key):
- responses = self._pollResources(lambda x: getattr(x, key))
- return self._unifyResponses(responses)
-
- def _chunkList(self, inlist, chunknum, balanceKey=len):
- """Divide <inlist> members into <chunknum> chunks roughly evenly using
- a round-robin binning system, return list of lists.
-
- This is a method so that balanceKey functions can access self."""
- chunks = [[] for _ in range(chunknum)]
- # a lightweight accounting of how big (entry 0) each sublist (numbered
- # by entry 1) is getting
- chunkSizes = [[0, i] for i in range(chunknum)]
- for i, item in enumerate(sorted(inlist, key=balanceKey, reverse=True)):
- # Refresh measure of bin fullness
- chunkSizes.sort()
- # Add one to the emptiest bin
- chunks[chunkSizes[0][1]].append(item)
- mass = balanceKey(item)
- if mass == 0:
- mass += 1
- chunkSizes[0][0] += mass
- return chunks
-
-class InvalidDataSetIOError(Exception):
- """The base class for all DataSetIO related custom exceptions (hopefully)
- """
-
-class ResourceMismatchError(InvalidDataSetIOError):
-
- def __init__(self, responses):
- super(ResourceMismatchError, self).__init__()
- self.responses = responses
-
- def __str__(self):
- return "Resources responded differently: " + ', '.join(
- map(str, self.responses))
-
-
-class ReadSet(DataSet):
- """Base type for read sets, should probably never be used as a concrete
- class"""
-
- def __init__(self, *files, **kwargs):
- super(ReadSet, self).__init__(*files, **kwargs)
- self._metadata = SubreadSetMetadata(self._metadata)
-
- def _openFiles(self):
- """Open the files (assert they exist, assert they are of the proper
- type before accessing any file)
- """
- if self._openReaders:
- log.debug("Closing old readers...")
- self.close()
- log.debug("Opening SubreadSet resources")
- for extRes in self.externalResources:
- refFile = extRes.reference
- log.debug("Using reference: {r}".format(r=refFile))
- location = urlparse(extRes.resourceId).path
- try:
- resource = openIndexedAlignmentFile(
- location,
- referenceFastaFname=refFile)
- except (IOError, ValueError):
- if not self._strict:
- log.info("pbi file missing for {f}, operating with "
- "reduced speed and functionality".format(
- f=location))
- resource = openAlignmentFile(
- location, referenceFastaFname=refFile)
- else:
- raise
- if not resource:
- raise IOError(errno.EIO,
- "{f} fails to open".format(f=location),
- location)
- self._openReaders.append(resource)
- log.debug("Done opening resources")
-
- def addMetadata(self, newMetadata, **kwargs):
- """Add metadata specific to this subtype, while leaning on the
- superclass method for generic metadata. Also enforce metadata type
- correctness."""
- # Validate, clean and prep input data
- if newMetadata:
- if isinstance(newMetadata, dict):
- newMetadata = SubreadSetMetadata(newMetadata)
- elif isinstance(newMetadata, SubreadSetMetadata) or (
- type(newMetadata).__name__ == 'DataSetMetadata'):
- newMetadata = SubreadSetMetadata(newMetadata.record)
- else:
- raise TypeError("Cannot extend SubreadSetMetadata with "
- "{t}".format(t=type(newMetadata).__name__))
+ def refIds(self):
+ """A dict of refName: refId for the joined referenceInfoTable"""
+ return {name: rId for name, rId in self.refInfo('ID')}
- # Pull generic values, kwargs, general treatment in super
- super(ReadSet, self).addMetadata(newMetadata, **kwargs)
+ def refLength(self, rname):
+ """The length of reference 'rname'. This is expensive, so if you're
+ going to do many lookups cache self.refLengths locally and use that."""
+ lut = self.refLengths
+ return lut[rname]
@property
- def _length(self):
- """Used to populate metadata in updateCounts"""
- length = -1
- count = -1
- return count, length
-
- def __len__(self):
- if self.numRecords == -1:
- if self._filters:
- self.updateCounts()
- else:
- count = 0
- for reader in self.resourceReaders():
- count += len(reader)
- self.numRecords = count
- return self.numRecords
-
-class HdfSubreadSet(ReadSet):
+ def fullRefNames(self):
+ """A list of reference full names (full header)."""
+ return [name for _, name in self.refInfo('FullName')]
- datasetType = DataSetMetaTypes.HDF_SUBREAD
+ def refInfo(self, key):
+ """The reference names present in the referenceInfoTable of the
+ ExtResources.
- def __init__(self, *files, **kwargs):
- log.debug("Opening HdfSubreadSet")
- kwargs['skipCounts'] = True
- super(HdfSubreadSet, self).__init__(*files, **kwargs)
+ Args:
+ key: a key for the referenceInfoTable of each resource
+ Returns:
+ A list of tuples of refrence name, key_result pairs
- def _openFiles(self):
- """Open the files (assert they exist, assert they are of the proper
- type before accessing any file)
"""
- if self._openReaders:
- log.debug("Closing old readers...")
- self.close()
- log.debug("Opening resources")
- for extRes in self.externalResources:
- location = urlparse(extRes.resourceId).path
- resource = BaxH5Reader(location)
- self._openReaders.append(resource)
- log.debug("Done opening resources")
-
- @staticmethod
- def _metaTypeMapping():
- return {'bax.h5':'PacBio.SubreadFile.SubreadBaxFile', }
-
+ #log.debug("Sampling references")
+ names = self.referenceInfoTable['Name']
+ infos = self.referenceInfoTable[key]
-class SubreadSet(ReadSet):
- """DataSet type specific to Subreads
+ #log.debug("Removing duplicate reference entries")
+ sampled = zip(names, infos)
+ sampled = set(sampled)
- DocTest:
+ return sampled
- >>> from pbcore.io import SubreadSet
- >>> from pbcore.io.dataset.DataSetMembers import ExternalResources
- >>> import pbcore.data.datasets as data
- >>> ds1 = SubreadSet(data.getXml(no=5))
- >>> ds2 = SubreadSet(data.getXml(no=5))
- >>> # So they don't conflict:
- >>> ds2.externalResources = ExternalResources()
- >>> ds1 # doctest:+ELLIPSIS
- <SubreadSet...
- >>> ds1._metadata # doctest:+ELLIPSIS
- <SubreadSetMetadata...
- >>> ds1._metadata # doctest:+ELLIPSIS
- <SubreadSetMetadata...
- >>> ds1.metadata # doctest:+ELLIPSIS
- <SubreadSetMetadata...
- >>> len(ds1.metadata.collections)
- 1
- >>> len(ds2.metadata.collections)
- 1
- >>> ds3 = ds1 + ds2
- >>> len(ds3.metadata.collections)
- 2
- >>> ds4 = SubreadSet(data.getSubreadSet())
- >>> ds4 # doctest:+ELLIPSIS
- <SubreadSet...
- >>> ds4._metadata # doctest:+ELLIPSIS
- <SubreadSetMetadata...
- >>> len(ds4.metadata.collections)
- 1
- """
+ def _idToRname(self, rId):
+ """Map the DataSet.referenceInfoTable.ID to the superior unique
+ reference identifier: referenceInfoTable.Name
- datasetType = DataSetMetaTypes.SUBREAD
+ Args:
+ rId: The DataSet.referenceInfoTable.ID of interest
- def __init__(self, *files, **kwargs):
- log.debug("Opening SubreadSet")
- super(SubreadSet, self).__init__(*files, **kwargs)
+ Returns:
+ The referenceInfoTable.Name corresponding to rId
- @property
- def _length(self):
- """Used to populate metadata in updateCounts"""
- length = 0
- count = 0
- endkey = 'qEnd'
- startkey = 'qStart'
- for rec in self.indexRecords:
- if isinstance(rec, np.ndarray):
- count += len(rec)
- length += sum(rec[endkey] - rec[startkey])
- elif isinstance(rec, PacBioBamIndex):
- count += len(rec)
- length += sum(rec.aEnd - rec.aStart)
- else:
- count += 1
- length += rec.aEnd - rec.aStart
- return count, length
+ """
+ resNo, rId = self._referenceIdMap[rId]
+ if self.isCmpH5:
+ rId -= 1
+ if self.isCmpH5:
+ # This is what CmpIO recognizes as the 'shortname'
+ refName = self.resourceReaders()[
+ resNo].referenceInfoTable[rId]['FullName']
+ else:
+ refName = self.resourceReaders()[
+ resNo].referenceInfoTable[rId]['Name']
+ return refName
@staticmethod
def _metaTypeMapping():
# This doesn't work for scraps.bam, whenever that is implemented
- return {'bam':'PacBio.SubreadFile.SubreadBamFile',
+ return {'bam':'PacBio.AlignmentFile.AlignmentBamFile',
'bai':'PacBio.Index.BamIndex',
'pbi':'PacBio.Index.PacBioIndex',
- }
+ 'cmp.h5':'PacBio.AlignmentFile.AlignmentCmpH5File',
+ }
class ConsensusReadSet(ReadSet):
@@ -2211,123 +2995,29 @@ class ConsensusReadSet(ReadSet):
datasetType = DataSetMetaTypes.CCS
-class AlignmentSet(ReadSet):
- """DataSet type specific to Alignments. No type specific Metadata exists,
- so the base class version is OK (this just ensures type representation on
- output and expandability"""
-
- datasetType = DataSetMetaTypes.ALIGNMENT
-
- def __init__(self, *files, **kwargs):
- """ An AlignmentSet
-
- Args:
- *files: handled by super
- referenceFastaFname=None: the reference fasta filename for this
- alignment.
- strict=False: see base class
- skipCounts=False: see base class
- """
- log.debug("Opening AlignmentSet with {f}".format(f=files))
- super(AlignmentSet, self).__init__(*files, **kwargs)
- fname = kwargs.get('referenceFastaFname', None)
- if fname:
- self.addReference(fname)
-
- def addReference(self, fname):
- if isinstance(fname, ReferenceSet):
- reference = fname.externalResources.resourceIds
- else:
- reference = ReferenceSet(fname).externalResources.resourceIds
- if len(reference) > 1:
- if len(reference) != self.numExternalResources:
- raise ResourceMismatchError(
- "More than one reference found, but not enough for one "
- "per resource")
- for res, ref in zip(self.externalResources, reference):
- res.reference = ref
- else:
- for res in self.externalResources:
- res.reference = reference[0]
- self._openFiles()
-
- @property
- def _referenceFile(self):
- responses = [res.reference for res in self.externalResources]
- return self._unifyResponses(responses)
-
- def updateCounts(self):
- if self._skipCounts:
- log.debug("SkipCounts is true, skipping updateCounts()")
- self.metadata.totalLength = -1
- self.metadata.numRecords = -1
- return
- try:
- self.assertIndexed()
- log.debug('Updating counts')
- numRecords, totalLength = self._length
- self.metadata.totalLength = totalLength
- self.metadata.numRecords = numRecords
- # I would prefer to just catch IOError and UnavailableFeature
- except (IOError, UnavailableFeature):
- if not self._strict:
- log.debug("File problem, metadata not populated")
- self.metadata.totalLength = -1
- self.metadata.numRecords = -1
- else:
- raise
-
- @property
- def _length(self):
- """Used to populate metadata in updateCounts"""
- length = 0
- count = 0
- endkey = 'aEnd'
- startkey = 'aStart'
- if self.isCmpH5:
- endkey = 'rEnd'
- startkey = 'rStart'
- for rec in self.indexRecords:
- if isinstance(rec, np.ndarray):
- count += len(rec)
- length += sum(rec[endkey] - rec[startkey])
- elif isinstance(rec, PacBioBamIndex):
- count += len(rec)
- length += sum(rec.aEnd - rec.aStart)
- else:
- count += 1
- length += rec.aEnd - rec.aStart
- return count, length
+ @staticmethod
+ def _metaTypeMapping():
+ # This doesn't work for scraps.bam, whenever that is implemented
+ return {'bam':'PacBio.ConsensusReadFile.ConsensusReadBamFile',
+ 'bai':'PacBio.Index.BamIndex',
+ 'pbi':'PacBio.Index.PacBioIndex',
+ }
- def __len__(self):
- if self.numRecords == -1:
- if self._filters:
- self.updateCounts()
- else:
- count = 0
- for reader in self.resourceReaders():
- count += len(reader)
- self.numRecords = count
- return self.numRecords
- @property
- def recordsByReference(self):
- """ The records in this AlignmentSet, sorted by tStart. """
- # we only care about aligned sequences here, so we can make this a
- # chain of readsInReferences to add pre-filtering by rname, instead of
- # going through every record and performing downstream filtering.
- # This will make certain operations, like len(), potentially faster
- for rname in self.refNames:
- for read in self.readsInReference(rname):
- yield read
+class ConsensusAlignmentSet(AlignmentSet):
+ """
+ Dataset type for aligned CCS reads. Essentially identical to AlignmentSet
+ aside from the contents of the underlying BAM files.
+ """
+ datasetType = DataSetMetaTypes.CCS_ALIGNMENT
@staticmethod
def _metaTypeMapping():
# This doesn't work for scraps.bam, whenever that is implemented
- return {'bam':'PacBio.SubreadFile.SubreadBamFile',
+ return {'bam':'PacBio.ConsensusReadFile.ConsensusReadBamFile',
'bai':'PacBio.Index.BamIndex',
'pbi':'PacBio.Index.PacBioIndex',
- }
+ }
class ContigSet(DataSet):
@@ -2341,10 +3031,14 @@ class ContigSet(DataSet):
self._metadata = ContigSetMetadata(self._metadata)
self._updateMetadata()
- def consolidate(self, outfn=None):
+ def consolidate(self, outfn=None, numFiles=1):
"""Consolidation should be implemented for window text in names and
for filters in ContigSets"""
+ if numFiles != 1:
+ raise NotImplementedError(
+ "Only one output file implemented so far.")
+
# In general "name" here refers to the contig.id only, which is why we
# also have to keep track of comments.
log.debug("Beginning consolidation")
@@ -2408,7 +3102,7 @@ class ContigSet(DataSet):
log.debug("Writing to a temp directory as no path given")
outdir = tempfile.mkdtemp(suffix="consolidated-contigset")
outfn = os.path.join(outdir,
- 'consolidated.contigset.xml')
+ 'consolidated_contigs.fasta')
with FastaWriter(outfn) as outfile:
log.debug("Writing new resource {o}".format(o=outfn))
for name, seq in writeMatches.items():
@@ -2425,6 +3119,9 @@ class ContigSet(DataSet):
self._populateContigMetadata()
def _popSuffix(self, name):
+ """Chunking and quivering adds suffixes to contig names, after the
+ normal ID and window. This complicates our dewindowing and
+ consolidation, so we'll remove them for now"""
observedSuffixes = ['|quiver']
for suff in observedSuffixes:
if name.endswith(suff):
@@ -2433,12 +3130,17 @@ class ContigSet(DataSet):
return name, ''
def _removeWindow(self, name):
+ """Chunking and quivering appends a window to the contig ID, which
+ allows us to consolidate the contig chunks but also gets in the way of
+ contig identification by ID. Remove it temporarily"""
if isinstance(self._parseWindow(name), np.ndarray):
name, suff = self._popSuffix(name)
return '_'.join(name.split('_')[:-2]) + suff
return name
def _parseWindow(self, name):
+ """Chunking and quivering appends a window to the contig ID, which
+ allows us to consolidate the contig chunks."""
name, _ = self._popSuffix(name)
possibilities = name.split('_')[-2:]
for pos in possibilities:
@@ -2504,7 +3206,19 @@ class ContigSet(DataSet):
# Pull subtype specific values where important
if newMetadata:
if newMetadata.contigs:
- self._metadata.contigs.extend(newMetadata.contigs)
+ self.metadata.contigs.extend(newMetadata.contigs)
+
+ @property
+ def metadata(self):
+ if not isinstance(self._metadata, ContigSetMetadata):
+ self._metadata = ContigSetMetadata(self._metadata)
+ return self._metadata
+
+ @metadata.setter
+ def metadata(self, value):
+ if not isinstance(value, ContigSetMetadata):
+ value = ContigSetMetadata(value)
+ self._metadata = value
def _openFiles(self):
"""Open the files (assert they exist, assert they are of the proper
@@ -2527,6 +3241,8 @@ class ContigSet(DataSet):
else:
raise
self._openReaders.append(resource)
+ if len(self._openReaders) == 0 and len(self.toExternalFiles()) != 0:
+ raise IOError("No files were openable or reads found")
log.debug("Done opening resources")
def resourceReaders(self, refName=None):
@@ -2535,15 +3251,7 @@ class ContigSet(DataSet):
Yields:
An open fasta file
- Doctest:
- >>> # Either way:
- >>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet
- >>> ds = DataSet(data.getBam())
- >>> for seqFile in ds.resourceReaders():
- ... for row in seqFile:
- ... print 'hn: %i' % row.holeNumber # doctest:+ELLIPSIS
- hn: ...
+
"""
if refName:
log.error("Specifying a contig name not yet implemented")
@@ -2559,15 +3267,6 @@ class ContigSet(DataSet):
Yields:
A fasta file entry
- Doctest:
- >>> # Either way:
- >>> import pbcore.data.datasets as data
- >>> from pbcore.io import DataSet
- >>> ds = DataSet(data.getBam())
- >>> for seqFile in ds.resourceReaders():
- ... for row in seqFile:
- ... print 'hn: %i' % row.holeNumber # doctest:+ELLIPSIS
- hn: ...
"""
for resource in self.resourceReaders():
for contig in resource:
@@ -2581,8 +3280,11 @@ class ContigSet(DataSet):
return contig
def assertIndexed(self):
- self._strict = True
- self._openFiles()
+ # I would prefer to use _assertIndexed, but want to pass up the
+ # original error
+ if not self.isIndexed:
+ self._strict = True
+ self._openFiles()
return True
@property
@@ -2612,10 +3314,48 @@ class ContigSet(DataSet):
@staticmethod
def _metaTypeMapping():
return {'fasta':'PacBio.ContigFile.ContigFastaFile',
+ 'fa':'PacBio.ContigFile.ContigFastaFile',
+ 'fas':'PacBio.ContigFile.ContigFastaFile',
'fai':'PacBio.Index.SamIndex',
'sa':'PacBio.Index.SaWriterIndex',
}
+ def _indexRecords(self):
+ """Returns index records summarizing all of the records in all of
+ the resources that conform to those filters addressing parameters
+ cached in the pbi.
+
+ """
+ recArrays = []
+ self._indexMap = []
+ for rrNum, rr in enumerate(self.resourceReaders()):
+ indices = rr.fai
+ indices = np.rec.fromrecords(
+ indices,
+ dtype=[('id', 'O'), ('comment', 'O'), ('header', 'O'),
+ ('length', '<i8'), ('offset', '<i8'),
+ ('lineWidth', '<i8'), ('stride', '<i8')])
+
+ if not self._filters or self.noFiltering:
+ recArrays.append(indices)
+ self._indexMap.extend([(rrNum, i) for i in
+ range(len(indices))])
+ else:
+ # Filtration will be necessary:
+ # dummy map, the id is the name in fasta space
+ nameMap = {name: name for name in indices.id}
+
+ passes = self._filters.filterIndexRecords(indices, nameMap)
+ newInds = indices[passes]
+ recArrays.append(newInds)
+ self._indexMap.extend([(rrNum, i) for i in
+ np.nonzero(passes)[0]])
+ self._indexMap = np.array(self._indexMap)
+ return _stackRecArrays(recArrays)
+
+ def _filterType(self):
+ return 'fasta'
+
class ReferenceSet(ContigSet):
"""DataSet type specific to References"""
@@ -2623,35 +3363,20 @@ class ReferenceSet(ContigSet):
datasetType = DataSetMetaTypes.REFERENCE
def __init__(self, *files, **kwargs):
- log.debug("Opening ReferenceSet")
+ log.debug("Opening ReferenceSet with {f}".format(f=files))
super(ReferenceSet, self).__init__(*files, **kwargs)
- def processFilters(self):
- # Allows us to not process all of the filters each time. This is marked
- # as dirty (= []) by addFilters etc. Filtration can be turned off by
- # setting this to [lambda x: True], which can be reversed by marking
- # the cache dirty. See disableFilters/enableFilters
- if self._cachedFilters:
- return self._cachedFilters
- filters = self.filters.tests(readType="fasta")
- # Having no filters means no opportunity to pass. Fix by filling with
- # always-true (e.g. disableFilters())
- if not filters:
- self._cachedFilters = [lambda x: True]
- return self._cachedFilters
- self._cachedFilters = filters
- return filters
-
@property
def refNames(self):
"""The reference names assigned to the External Resources, or contigs
if no name assigned."""
return self.contigNames
-
@staticmethod
def _metaTypeMapping():
- return {'fasta':'PacBio.ReferenceFile.ReferenceFastaFile',
+ return {'fasta':'PacBio.ContigFile.ContigFastaFile',
+ 'fa':'PacBio.ContigFile.ContigFastaFile',
+ 'fas':'PacBio.ContigFile.ContigFastaFile',
'fai':'PacBio.Index.SamIndex',
'sa':'PacBio.Index.SaWriterIndex',
}
@@ -2687,3 +3412,12 @@ class BarcodeSet(DataSet):
# Pull subtype specific values where important
# -> No type specific merging necessary, for now
+
+ @staticmethod
+ def _metaTypeMapping():
+ return {'fasta':'PacBio.BarcodeFile.BarcodeFastaFile',
+ 'fai':'PacBio.Index.SamIndex',
+ 'sa':'PacBio.Index.SaWriterIndex',
+ }
+
+
diff --git a/pbcore/io/dataset/DataSetMembers.py b/pbcore/io/dataset/DataSetMembers.py
index 4a1f891..fb79d29 100755
--- a/pbcore/io/dataset/DataSetMembers.py
+++ b/pbcore/io/dataset/DataSetMembers.py
@@ -46,15 +46,36 @@ serve two pruposes:
note: Assuming __getitem__ is implemented for the 'children' list
"""
+#import hashlib
+import uuid
+import datetime
import copy
import operator as OP
-import re
import numpy as np
import logging
from functools import partial as P
+from pbcore.io.dataset.DataSetWriter import namespaces
log = logging.getLogger(__name__)
+def newUuid(record):
+ # At some point the uuid may need to be a digest
+ #newId = str(hashlib.md5(str(record)).hexdigest())
+
+ # Group appropriately
+ #newId = '-'.join([newId[:8], newId[8:12], newId[12:16], newId[16:20],
+ # newId[20:]])
+ #return newId
+
+ # Today is not that day
+ return str(uuid.uuid4())
+
+def getTime():
+ return datetime.datetime.utcnow().strftime("%y%m%d_%H%M%S")
+
+def getTimeStampedName(mType):
+ return "{m}-{t}".format(m=mType, t=getTime())
+
class RecordWrapper(object):
"""The base functionality of a metadata element.
@@ -67,6 +88,8 @@ class RecordWrapper(object):
"""Here, record is any element in the Metadata Element tree and a
dictionary with four members: 'tag', 'attrib', 'text', and 'children'.
+ Now with a new member! 'namespace'
+
Do not deepcopy, we rely on side effects for all persistent
modifications.
"""
@@ -114,7 +137,6 @@ class RecordWrapper(object):
children will not be wrapped in a special wrapper object)"""
for child in self.record['children']:
yield RecordWrapper(child)
- #yield child['text']
def __repr__(self):
"""Return a pretty string represenation of this object:
@@ -123,9 +145,10 @@ class RecordWrapper(object):
"""
c_tags = [c.record['tag'] for c in self]
repr_d = dict(k=self.__class__.__name__, t=self.record['tag'],
+ n=self.record['namespace'],
x=self.record['text'], a=self.record['attrib'],
c=c_tags)
- rep = '<{k} tag:{t} text:{x} attribs:{a} children:{c}>'.format(
+ rep = '<{k} tag:{{{n}}}{t} text:{x} attribs:{a} children:{c}>'.format(
**repr_d)
return rep
@@ -203,6 +226,18 @@ class RecordWrapper(object):
return [child['tag'] for child in self.record['children']]
@property
+ def namespace(self):
+ return self.record['namespace']
+
+ @namespace.setter
+ def namespace(self, value):
+ self.record['namespace'] = value
+
+ @property
+ def attrib(self):
+ return self.record['attrib']
+
+ @property
def metaname(self):
"""Cleaner accessor for this node's tag"""
return self.record['tag']
@@ -377,9 +412,9 @@ class Filters(RecordWrapper):
def opMap(self, op):
ops = {'>=': OP.le,
- '>=': OP.le,
+ '>=': OP.ge,
'<=': OP.ge,
- '<=': OP.ge,
+ '<=': OP.le,
'==': OP.eq,
'!=': OP.ne,
'=': OP.eq,
@@ -399,12 +434,13 @@ class Filters(RecordWrapper):
return {'rname': (lambda x: x.referenceName),
'length': (lambda x: int(x.readLength)),
'qname': (lambda x: x.qNameA),
+ 'movie': (lambda x: x.movieName),
'zm': (lambda x: int(x.HoleNumber)),
'bc': (lambda x: x.barcode),
'qs': (lambda x: int(x.qStart)),
'rq': (lambda x: int(x.MapQV)),
'pos': (lambda x: int(x.tStart)),
- 'accuracy': (lambda x: int(x.identity)),
+ 'accuracy': (lambda x: float(x.identity)),
'readstart': (lambda x: int(x.aStart)),
'tstart': (lambda x: int(x.tEnd)), # see above
'tend': (lambda x: int(x.tStart)), # see above
@@ -445,6 +481,7 @@ class Filters(RecordWrapper):
return {'rname': str,
'length': int,
'qname': str,
+ 'movie': str,
'zm': int,
'bc': str,
'qs': int,
@@ -452,7 +489,7 @@ class Filters(RecordWrapper):
'pos': int,
'tstart': int,
'tend': int,
- 'accuracy': int,
+ 'accuracy': float,
'readstart': int,
}
@@ -489,25 +526,33 @@ class Filters(RecordWrapper):
return tests
def filterIndexRecords(self, indexRecords, nameMap):
- filterResultList = []
typeMap = self._bamTypeMap
accMap = self._pbiVecAccMap({})
accMap['rname'] = lambda x: x.tId
+ filterLastResult = None
for filt in self:
- thisFilterResultList = []
+ lastResult = None
for req in filt:
param = req.name
- value = typeMap[param](req.value)
- if param == 'rname':
- value = nameMap[value]
- operator = self.opMap(req.operator)
- reqResultsForRecords = operator(accMap[param](indexRecords),
- value)
- thisFilterResultList.append(reqResultsForRecords)
- thisFilterResultList = np.logical_and.reduce(thisFilterResultList)
- filterResultList.append(thisFilterResultList)
- filterResultList = np.logical_or.reduce(filterResultList)
- return filterResultList
+ if param in accMap.keys():
+ value = typeMap[param](req.value)
+ if param == 'rname':
+ value = nameMap[value]
+ operator = self.opMap(req.operator)
+ reqResultsForRecords = operator(accMap[param](indexRecords),
+ value)
+ if lastResult is None:
+ lastResult = reqResultsForRecords
+ else:
+ lastResult = np.logical_and(lastResult,
+ reqResultsForRecords)
+ del reqResultsForRecords
+ if filterLastResult is None:
+ filterLastResult = lastResult
+ else:
+ filterLastResult = np.logical_or(filterLastResult, lastResult)
+ del lastResult
+ return filterLastResult
def addRequirement(self, **kwargs):
"""Use this to add requirements. Members of the list will be considered
@@ -573,7 +618,7 @@ class Filter(RecordWrapper):
self.record['children'][0]['children'].pop(index)
def addRequirement(self, name, operator, value):
- param = Parameter()
+ param = Property()
param.name = name
param.operator = operator
param.value = value
@@ -591,9 +636,9 @@ class Filter(RecordWrapper):
@property
def plist(self):
if self.record['children']:
- return Parameters(self.record['children'][0])
+ return Properties(self.record['children'][0])
else:
- temp = Parameters()
+ temp = Properties()
self.append(temp)
return temp
@@ -601,24 +646,24 @@ class Filter(RecordWrapper):
pass
-class Parameters(RecordWrapper):
+class Properties(RecordWrapper):
def __init__(self, record=None):
super(self.__class__, self).__init__(record)
self.record['tag'] = self.__class__.__name__
def __getitem__(self, index):
- return Parameter(self.record['children'][index])
+ return Property(self.record['children'][index])
def __iter__(self):
for child in self.record['children']:
- yield Parameter(child)
+ yield Property(child)
def merge(self, other):
pass
-class Parameter(RecordWrapper):
+class Property(RecordWrapper):
def __init__(self, record=None):
super(self.__class__, self).__init__(record)
@@ -655,6 +700,7 @@ class Parameter(RecordWrapper):
class ExternalResources(RecordWrapper):
+
def __init__(self, record=None):
super(self.__class__, self).__init__(record)
self.record['tag'] = self.__class__.__name__
@@ -680,6 +726,24 @@ class ExternalResources(RecordWrapper):
for child in self.record['children']:
yield ExternalResource(child)
+ def merge(self, other):
+ # make sure we don't add dupes
+ curIds = [res.resourceId for res in self]
+
+ for newRes in other:
+ # merge instead
+ if newRes.resourceId in curIds:
+ indexof = curIds.index(newRes.resourceId)
+ self[indexof].merge(newRes)
+ else:
+ self.append(newRes)
+ curIds.append(newRes.resourceId)
+ # we may be missing some metadata
+ if not self.namespace:
+ self.namespace = other.namespace
+ self.attrib.update(other.attrib)
+
+
def addResources(self, resourceIds):
"""Add a new external reference with the given uris. If you're looking
to add ExternalResource objects, append() or extend() them instead.
@@ -688,11 +752,14 @@ class ExternalResources(RecordWrapper):
resourceIds: a list of uris as strings
"""
templist = []
- for ref in resourceIds:
- temp = ExternalResource()
- temp.resourceId = ref
- self.append(temp)
- templist.append(temp)
+ for res in resourceIds:
+ toAdd = res
+ if not isinstance(res, ExternalResource):
+ temp = ExternalResource()
+ temp.resourceId = res
+ toAdd = temp
+ self.append(toAdd)
+ templist.append(toAdd)
return templist
@property
@@ -718,9 +785,12 @@ class ExternalResources(RecordWrapper):
class ExternalResource(RecordWrapper):
+
def __init__(self, record=None):
super(self.__class__, self).__init__(record)
self.record['tag'] = self.__class__.__name__
+ self.attrib.setdefault('UniqueId', newUuid(self.record))
+ self.attrib.setdefault('TimeStampedName', '')
def __eq__(self, other):
if self.resourceId == other.resourceId:
@@ -744,6 +814,14 @@ class ExternalResource(RecordWrapper):
return self.setV(value, 'attrib', 'MetaType')
@property
+ def timeStampedName(self):
+ return self.getV('attrib', 'TimeStampedName')
+
+ @timeStampedName.setter
+ def timeStampedName(self, value):
+ return self.setV(value, 'attrib', 'TimeStampedName')
+
+ @property
def resourceId(self):
return self.getV('attrib', 'ResourceId')
@@ -805,6 +883,7 @@ class ExternalResource(RecordWrapper):
tmp = ExternalResource()
tmp.resourceId = value
tmp.metaType = mType
+ tmp.timeStampedName = getTimeStampedName(mType)
resources = self.externalResources
# externalresources objects have a tag by default, which means their
# truthiness is true. Perhaps a truthiness change is in order
@@ -855,6 +934,7 @@ class ExternalResource(RecordWrapper):
class FileIndices(RecordWrapper):
+
def __init__(self, record=None):
super(self.__class__, self).__init__(record)
self.record['tag'] = self.__class__.__name__
@@ -869,9 +949,12 @@ class FileIndices(RecordWrapper):
class FileIndex(RecordWrapper):
+
def __init__(self, record=None):
super(self.__class__, self).__init__(record)
self.record['tag'] = self.__class__.__name__
+ self.attrib.setdefault('UniqueId', newUuid(self.record))
+ self.attrib.setdefault('TimeStampedName', '')
@property
def resourceId(self):
@@ -889,6 +972,14 @@ class FileIndex(RecordWrapper):
def metaType(self, value):
return self.setV(value, 'attrib', 'MetaType')
+ @property
+ def timeStampedName(self):
+ return self.getV('attrib', 'TimeStampedName')
+
+ @timeStampedName.setter
+ def timeStampedName(self, value):
+ return self.setV(value, 'attrib', 'TimeStampedName')
+
class DataSetMetadata(RecordWrapper):
"""The root of the DataSetMetadata element tree, used as base for subtype
@@ -898,6 +989,7 @@ class DataSetMetadata(RecordWrapper):
def __init__(self, record=None):
"""Here, record is the root element of the Metadata Element tree"""
super(DataSetMetadata, self).__init__(record)
+ self.record['tag'] = 'DataSetMetadata'
def merge(self, other):
self.numRecords += other.numRecords
@@ -907,6 +999,10 @@ class DataSetMetadata(RecordWrapper):
self.summaryStats.merge(other.summaryStats)
else:
self.append(other.summaryStats)
+ if not self.namespace:
+ print "HERE"
+ self.namespace = other.namespace
+ self.attrib.update(other.attrib)
@property
def numRecords(self):
@@ -1004,7 +1100,10 @@ class ContigSetMetadata(DataSetMetadata):
def merge(self, other):
super(self.__class__, self).merge(other)
- self.contigs.merge(other.contigs)
+ if self.contigs:
+ self.contigs.merge(other.contigs)
+ else:
+ self.contigs = other.contigs
@property
def organism(self):
@@ -1037,9 +1136,11 @@ class ContigSetMetadata(DataSetMetadata):
@contigs.setter
def contigs(self, value):
+ self.removeChildren('Contigs')
if not value:
- self.removeChildren('Contigs')
self.append(ContigsMetadata())
+ else:
+ self.append(value)
def addContig(self, newContig):
if not self.contigs:
@@ -1600,17 +1701,17 @@ class PrimaryMetadata(RecordWrapper):
>>> from pbcore.io import SubreadSet
>>> import pbcore.data.datasets as data
>>> ds1 = SubreadSet(data.getXml(5))
- >>> ds1.metadata.collections[0].primary.resultsFolder
+ >>> ds1.metadata.collections[0].primary.outputOptions.resultsFolder
'Analysis_Results'
- >>> ds1.metadata.collections[0].primary.resultsFolder = (
+ >>> ds1.metadata.collections[0].primary.outputOptions.resultsFolder = (
... 'BetterAnalysis_Results')
- >>> ds1.metadata.collections[0].primary.resultsFolder
+ >>> ds1.metadata.collections[0].primary.outputOptions.resultsFolder
'BetterAnalysis_Results'
>>> outdir = tempfile.mkdtemp(suffix="dataset-doctest")
>>> outXml = 'xml:' + os.path.join(outdir, 'tempfile.xml')
>>> ds1.write(outXml, validate=False)
>>> ds2 = SubreadSet(outXml)
- >>> ds2.metadata.collections[0].primary.resultsFolder
+ >>> ds2.metadata.collections[0].primary.outputOptions.resultsFolder
'BetterAnalysis_Results'
"""
@@ -1627,6 +1728,12 @@ class PrimaryMetadata(RecordWrapper):
return self.getMemberV('SequencingCondition')
@property
+ def outputOptions(self):
+ return OutputOptions(self.getV('children', 'OutputOptions'))
+
+
+class OutputOptions(RecordWrapper):
+ @property
def resultsFolder(self):
return self.getMemberV('ResultsFolder')
@@ -1695,14 +1802,18 @@ class BioSampleMetadata(RecordWrapper):
return self.getV('attrib', 'CreatedAt')
-def _emptyMember(tag=None, text=None, attrib=None, children=None):
+def _emptyMember(tag=None, text=None, attrib=None, children=None,
+ namespace=None):
"""Return an empty stock Element representation"""
if not tag:
tag = ''
+ if not namespace:
+ namespace = ''
if not text:
text = ''
if not attrib:
attrib = {}
if not children:
children = []
- return {'tag': tag, 'text': text, 'attrib': attrib, 'children': children}
+ return {'tag': tag, 'text': text, 'attrib': attrib, 'children': children,
+ 'namespace': namespace}
diff --git a/pbcore/io/dataset/DataSetReader.py b/pbcore/io/dataset/DataSetReader.py
index 1031935..3c932db 100755
--- a/pbcore/io/dataset/DataSetReader.py
+++ b/pbcore/io/dataset/DataSetReader.py
@@ -12,8 +12,6 @@ from pbcore.io.dataset.DataSetMembers import (ExternalResource,
StatsMetadata)
from pbcore.io.dataset.DataSetWriter import _eleFromDictList
-XMLNS = "http://pacificbiosciences.com/PacBioDataModel.xsd"
-
log = logging.getLogger(__name__)
def resolveLocation(fname, possibleRelStart='.'):
@@ -36,7 +34,7 @@ def xmlRootType(fname):
with open(fname, 'rb') as xml_file:
tree = ET.parse(xml_file)
root = tree.getroot()
- return _tagCleaner(root.tag)
+ return _splitTag(root.tag)[-1]
def _addFile(dset, filename):
handledTypes = {'xml': _addXmlFile,
@@ -57,21 +55,26 @@ def _addXmlFile(dset, path):
with open(path, 'rb') as xml_file:
tree = ET.parse(xml_file)
root = tree.getroot()
- tmp = _parseXml(dset, root)
+ tmp = _parseXml(type(dset), root)
tmp.makePathsAbsolute(curStart=os.path.dirname(path))
dset.merge(tmp, copyOnMerge=False)
-def _addFofnFile(dset, path):
- """Open a fofn file by calling parseFiles on the new filename list"""
+def openFofnFile(path):
with open(path, 'r') as fofnFile:
files = []
for infn in fofnFile:
+ infn = infn.strip()
tmp = os.path.abspath(infn)
if os.path.exists(tmp):
files.append(tmp)
else:
files.append(os.path.join(os.path.dirname(path), infn))
- populateDataSet(dset, files)
+ return files
+
+def _addFofnFile(dset, path):
+ """Open a fofn file by calling parseFiles on the new filename list"""
+ files = openFofnFile(path)
+ populateDataSet(dset, files)
def _addUnknownFile(dset, path):
"""Open non-uri files
@@ -85,6 +88,7 @@ def _addUnknownFile(dset, path):
else:
return _addGenericFile(dset, path)
+# TODO needs namespace
def _addGenericFile(dset, path):
"""Create and populate an Element object, put it in an available members
dictionary, return"""
@@ -94,6 +98,7 @@ def _addGenericFile(dset, path):
# We'll update them all at the end, skip updating counts for now
dset.addExternalResources(extRess, updateCount=False)
+# TODO needs namespace
def wrapNewResource(path):
possible_indices = ['.fai', '.pbi', '.bai', '.metadata.xml']
for ext in possible_indices:
@@ -111,7 +116,7 @@ def wrapNewResource(path):
return extRes
-def _parseXml(dset, element):
+def _parseXml(dsetType, element):
"""Parse an XML DataSet tag, or the root tag of a DataSet XML file (they
should be equivalent)
@@ -121,62 +126,30 @@ def _parseXml(dset, element):
>>> type(ds).__name__
'SubreadSet'
"""
- result = type(dset)()
+ result = dsetType()
result.objMetadata = element.attrib
- namer = functools.partial(_namespaceTag, XMLNS)
- element = _updateDataset(element)
for child in element:
- if child.tag == namer('ExternalResources'):
+ if child.tag.endswith('ExternalResources'):
result.externalResources = _parseXmlExtResources(child)
- elif child.tag == namer('DataSets'):
- result.subdatasets = _parseXmls(dset, child)
- elif child.tag == namer('Filters'):
+ elif child.tag.endswith('DataSets'):
+ result.subdatasets = _parseXmls(dsetType, child)
+ elif child.tag.endswith('Filters'):
result.filters = _parseXmlFilters(child)
- elif child.tag == namer('DataSetMetadata'):
+ elif child.tag.endswith('DataSetMetadata'):
result.metadata = _parseXmlDataSetMetadata(child)
else:
# Unknown tag found in XML
pass
return result
-def _parseXmls(dset, element):
+def _parseXmls(dsetType, element):
"""DataSets can exist as elements in other datasets, representing subsets.
Pull these datasets, parse them, and return a list of them."""
result = []
for child in element:
- result.append(_parseXml(dset, child))
+ result.append(_parseXml(dsetType, child))
return result
-def _updateDataset(element):
- namer = functools.partial(_namespaceTag, XMLNS)
- updateMap = {
- './/' + namer('ExternalDataReferences'): 'ExternalResources',
- './/' + namer('ExternalReference'): 'ExternalResource',
- './/' + namer('BioSampleReferences'): 'BioSamplePointers',
- './/' + namer('BioSampleReference'): 'BioSamplePointer',
- './/' + namer('PacBioIndex'): 'FileIndex',
- './/' + namer('CCSreadSet'): 'ConsensusReadSet',
- }
- for old, new in updateMap.items():
- #while element.find('.//' + namer(old)) is not None:
- while element.find(old) is not None:
- log.error("Outdated XML received: {t}".format(
- t=old.split('}')[-1]))
- element.find(old).tag = namer(new)
-
- auton = ('.//' + namer('CollectionMetadata') + '/' +
- namer('AutomationName'))
- if element.find(auton) is not None:
- log.error("Outdated XML received: AutomationName")
- autonele = element.find(auton)
- autonele.tag = namer('Automation')
- val = autonele.text
- autonele.text = None
- newParams = AutomationParameters()
- newParams.addParameter(None, None)
- autonele.append(_eleFromDictList(newParams.record))
- return element
-
def _updateStats(element):
namer = functools.partial(
_namespaceTag,
@@ -226,9 +199,9 @@ def _namespaceTag(xmlns, tagName):
"""Preface an XML tag name with the provided namespace"""
return ''.join(["{", xmlns, "}", tagName])
-def _tagCleaner(tagName):
- """Remove the namespace prefix from a tag name"""
- return tagName.split('}')[-1]
+def _splitTag(tag):
+ """Split the namespace and tag name"""
+ return [part.strip('{') for part in tag.split('}')]
def _parseXmlExtResources(element):
"""Parse the ExternalResources tag, populating a list of
@@ -238,16 +211,11 @@ def _parseXmlExtResources(element):
def _parseXmlDataSetMetadata(element):
"""Parse the DataSetMetadata field of XML inputs. This data can be
extremely extensive."""
- result = []
- for child in element:
- result.append(_eleToDictList(child))
- tbr = DataSetMetadata()
- tbr.extend(result)
- return tbr.record
+ return DataSetMetadata(_eleToDictList(element))
def _eleToDictList(element):
"""A last ditch capture method for uknown Elements"""
- tag = _tagCleaner(element.tag)
+ namespace, tag = _splitTag(element.tag)
text = element.text
if text:
text = text.strip()
@@ -256,7 +224,7 @@ def _eleToDictList(element):
for child in element:
children.append(_eleToDictList(child))
return {'tag': tag, 'text': text, 'attrib': attrib,
- 'children': children}
+ 'children': children, 'namespace': namespace}
def _parseXmlFilters(element):
"""Pull filters from XML file, put them in a list of dictionaries, where
@@ -272,20 +240,6 @@ def _parseXmlFilters(element):
>>> str(_parseXmlFilters(filters))
'( rq > 0.75 ) OR ( qname == 100/0/0_100 )'
"""
- """
- namer = functools.partial(_namespaceTag, XMLNS)
- result = []
- for filtTag in filters:
- #filt = Filter()
- filt = {}
- # This is essentially to skip the <Parameters> level
- for child in filtTag:
- if child.tag == namer('Parameters'):
- for param in child:
- filt[param.attrib['Name'].lower()] = param.attrib['Value']
- result.append(filt)
- return result
- """
return Filters(_eleToDictList(element))
def parseStats(filename):
diff --git a/pbcore/io/dataset/DataSetValidator.py b/pbcore/io/dataset/DataSetValidator.py
index 58441b3..d0f9980 100755
--- a/pbcore/io/dataset/DataSetValidator.py
+++ b/pbcore/io/dataset/DataSetValidator.py
@@ -65,6 +65,8 @@ def validateXml(xmlroot, skipResources=False):
log.debug('Validating with PyXb')
fixedString = re.sub('UniqueId="[0-9]', 'UniqueId="f',
ET.tostring(xmlroot))
+ fixedString = re.sub('Pointer>[0-9]', 'Pointer>f',
+ fixedString)
DataSetXsd.CreateFromDocument(fixedString)
except ImportError:
log.debug('PyXb not found, validation disabled')
diff --git a/pbcore/io/dataset/DataSetWriter.py b/pbcore/io/dataset/DataSetWriter.py
index 85f7bb8..976572d 100755
--- a/pbcore/io/dataset/DataSetWriter.py
+++ b/pbcore/io/dataset/DataSetWriter.py
@@ -3,7 +3,9 @@
import copy, time
import xml.etree.ElementTree as ET
+# TODO add in other namespaces
XMLNS = "http://pacificbiosciences.com/PacBioDataModel.xsd"
+
# Not actually sure what this should be:
XMLVERSION = '3.0.0'
@@ -25,6 +27,113 @@ def toXml(dataset, core=False):
root = _toElementTree(dataset, root=None, core=core)
return ET.tostring(root, encoding="UTF-8")
+def namespaces():
+ return {
+ 'pbbase': 'http://pacificbiosciences.com/PacBioBaseDataModel.xsd',
+ 'pbsample': 'http://pacificbiosciences.com/PacBioSampleInfo.xsd',
+ 'pbstats': 'http://pacificbiosciences.com/PipelineStats/PipeStats.xsd',
+ 'pbmeta': 'http://pacificbiosciences.com/PacBioCollectionMetadata.xsd',
+ 'pbds': 'http://pacificbiosciences.com/PacBioDatasets.xsd'}
+
+TAGS = [
+ "pbbase:AutomationParameter",
+ "pbbase:AutomationParameters",
+ "pbbase:BinCount",
+ "pbbase:BinCounts",
+ "pbbase:BinLabel",
+ "pbbase:BinLabels",
+ "pbbase:BinWidth",
+ "pbbase:ExternalResource",
+ "pbbase:ExternalResources",
+ "pbbase:FileIndex",
+ "pbbase:FileIndices",
+ "pbbase:MaxBinValue",
+ "pbbase:MaxOutlierValue",
+ "pbbase:MetricDescription",
+ "pbbase:MinBinValue",
+ "pbbase:MinOutlierValue",
+ "pbbase:NumBins",
+ "pbbase:Properties",
+ "pbbase:Property",
+ "pbbase:Sample95thPct",
+ "pbbase:SampleMean",
+ "pbbase:SampleMed",
+ "pbbase:SampleSize",
+ "pbbase:SampleStd",
+ "pbds:AdapterDimerFraction",
+ "pbds:BarcodeConstruction",
+ "pbds:ControlReadLenDist",
+ "pbds:ControlReadQualDist",
+ "pbds:DataSetMetadata",
+ "pbds:DataSet",
+ "pbds:DataSets",
+ "pbds:Filter",
+ "pbds:Filters",
+ "pbds:Provenance",
+ "pbds:ParentTool",
+ "pbds:InsertReadLenDist",
+ "pbds:InsertReadQualDist",
+ "pbds:MedianInsertDist",
+ "pbds:NumRecords",
+ "pbds:NumSequencingZmws",
+ "pbds:ProdDist",
+ "pbds:ReadLenDist",
+ "pbds:ReadQualDist",
+ "pbds:ReadTypeDist",
+ "pbds:ShortInsertFraction",
+ "pbds:HdfSubreadSet",
+ "pbds:SubreadSet",
+ "pbds:SummaryStats",
+ "pbds:TotalLength",
+ "pbmeta:Automation",
+ "pbmeta:AutomationName",
+ "pbmeta:CellIndex",
+ "pbmeta:CellPac",
+ "pbmeta:CollectionFileCopy",
+ "pbmeta:CollectionMetadata",
+ "pbmeta:CollectionNumber",
+ "pbmeta:CollectionPathUri",
+ "pbmeta:Collections",
+ "pbmeta:Concentration",
+ "pbmeta:ConfigFileName",
+ "pbmeta:CopyFiles",
+ "pbmeta:InstCtrlVer",
+ "pbmeta:MetricsVerbosity",
+ "pbmeta:Name",
+ "pbmeta:OutputOptions",
+ "pbmeta:PlateId",
+ "pbmeta:Primary",
+ "pbmeta:Readout",
+ "pbmeta:ResultsFolder",
+ "pbmeta:RunDetails",
+ "pbmeta:RunId",
+ "pbmeta:SampleReuseEnabled",
+ "pbmeta:SequencingCondition",
+ "pbmeta:SigProcVer",
+ "pbmeta:SizeSelectionEnabled",
+ "pbmeta:StageHotstartEnabled",
+ "pbmeta:UseCount",
+ "pbmeta:WellName",
+ "pbmeta:WellSample",
+ "pbsample:BioSample",
+ "pbsample:BioSamplePointer",
+ "pbsample:BioSamplePointers",
+ "pbsample:BioSamples",
+ "pbds:AlignmentSet",
+ "pbds:BarcodeSet",
+ "pbds:ConsensusReadSet",
+ "pbds:ContigSet",
+ "pbds:ReferenceSet",
+ "pbds:Ploidy",
+ "pbds:Organism",
+ "pbds:Contig",
+ "pbds:Contigs"
+]
+
+def register_namespaces():
+ for prefix, uri in namespaces().items():
+ ET.register_namespace(prefix, uri)
+
def _toElementTree(dataSet, root=None, core=False):
"""Generate an ElementTree representation of this object. This is a
function independent of "write" and "toXml" so that it can also be used
@@ -40,7 +149,9 @@ def _toElementTree(dataSet, root=None, core=False):
"""
# 'if not root:' would conflict with testing root for children
if root is None:
- rootType = type(dataSet).__name__
+ register_namespaces()
+ rootType = '{{{n}}}{t}'.format(n=namespaces()['pbds'],
+ t=type(dataSet).__name__)
attribs = dataSet.objMetadata
if core:
attribs = _coreClean(attribs)
@@ -98,9 +209,7 @@ def _addExternalResourcesElement(dataSet, root, core=False):
core=False: T/F strip out user editable attributes
"""
if dataSet.externalResources:
- dsmd = ET.SubElement(root, 'ExternalResources')
- for child in dataSet.externalResources.record['children']:
- dsmd.append(_eleFromDictList(child, core))
+ root.append(_eleFromDictList(dataSet.externalResources.record, core))
def _addDataSetMetadataElement(dataSet, root):
"""Add DataSetMetadata Elements to the root ElementTree object. Full
@@ -110,27 +219,31 @@ def _addDataSetMetadataElement(dataSet, root):
root: The root ElementTree object. Extended here using SubElement
"""
if dataSet.metadata:
- dsmd = ET.SubElement(root, 'DataSetMetadata')
- for child in dataSet.metadata.record['children']:
- dsmd.append(_eleFromDictList(child))
+ root.append(_eleFromDictList(dataSet.metadata.record))
+ # Metadata order matters....
#tl = dsmd.find('TotalLength')
#tl = dsmd.remove(tl)
#dsmd.insert(0, tl)
-def _eleFromDict(tag, eleAsDict):
- """A last ditch capture method for uknown Elements"""
- ele = ET.Element(tag, eleAsDict['attrib'])
- ele.text = eleAsDict['text']
- for childTag, childDict in eleAsDict['children'].items():
- ele.append(_eleFromDict(childTag, childDict))
- return ele
+def _guessNs(tag):
+ for option in TAGS:
+ nsprefix, nstag = option.split(':')
+ if nstag == tag:
+ return namespaces()[nsprefix]
+ return ''
def _eleFromDictList(eleAsDict, core=False):
"""A last ditch capture method for uknown Elements"""
+ if not eleAsDict['namespace']:
+ eleAsDict['namespace'] = _guessNs(eleAsDict['tag'])
if core:
- ele = ET.Element(eleAsDict['tag'], _coreClean(eleAsDict['attrib']))
+ ele = ET.Element("{{{n}}}{t}".format(n=eleAsDict['namespace'],
+ t=eleAsDict['tag']),
+ _coreClean(eleAsDict['attrib']))
else:
- ele = ET.Element(eleAsDict['tag'], eleAsDict['attrib'])
+ ele = ET.Element("{{{n}}}{t}".format(n=eleAsDict['namespace'],
+ t=eleAsDict['tag']),
+ eleAsDict['attrib'])
ele.text = eleAsDict['text']
for child in eleAsDict['children']:
ele.append(_eleFromDictList(child))
diff --git a/pbcore/io/dataset/DataSetXsd.py b/pbcore/io/dataset/DataSetXsd.py
index e8b1330..c6e1f02 100755
--- a/pbcore/io/dataset/DataSetXsd.py
+++ b/pbcore/io/dataset/DataSetXsd.py
@@ -1,7 +1,7 @@
-# ./DataSetXsd.py
+# ./DataSetXsd/py.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:3c1eccef1b156ac43379b476cb78e3eecd9f5c97
-# Generated 2015-06-23 13:50:43.883039 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Generated 2015-08-04 20:41:05.098928 by PyXB version 1.2.4 using Python 2.7.6.final.0
# Namespace http://pacificbiosciences.com/PacBioDataModel.xsd
from __future__ import unicode_literals
@@ -15,7 +15,7 @@ import sys
import pyxb.utils.six as _six
# Unique identifier for bindings created at the same time
-_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:83991eee-19e9-11e5-8315-001a4acb6b14')
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
# Version of PyXB used to generate the bindings
_PyXBVersion = '1.2.4'
@@ -24,11 +24,22 @@ if pyxb.__version__ != _PyXBVersion:
raise pyxb.PyXBVersionError(_PyXBVersion)
# Import bindings for namespaces imported into schema
+import _pbds as _ImportedBinding__pbds
import pyxb.binding.datatypes
+import _pbrk as _ImportedBinding__pbrk
+import _pbbase as _ImportedBinding__pbbase
+import _pbpn as _ImportedBinding__pbpn
+import _pbsample as _ImportedBinding__pbsample
# NOTE: All namespace declarations are reserved within the binding
Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioDataModel.xsd', create_if_missing=True)
Namespace.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbpn = _ImportedBinding__pbpn.Namespace
+_Namespace_pbpn.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbds = _ImportedBinding__pbds.Namespace
+_Namespace_pbds.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbbase = _ImportedBinding__pbbase.Namespace
+_Namespace_pbbase.configureCategories(['typeBinding', 'elementBinding'])
def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
"""Parse the given XML and use the document element to create a
@@ -74,126 +85,26 @@ def CreateFromDOM (node, default_namespace=None):
# Atomic simple type: [anonymous]
-class STD_ANON (pyxb.binding.datatypes.ID):
+class STD_ANON (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
"""An atomic simple type."""
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 69, 3)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 76, 4)
_Documentation = None
-STD_ANON._CF_pattern = pyxb.binding.facets.CF_pattern()
-STD_ANON._CF_pattern.addPattern(pattern='[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}')
-STD_ANON._InitializeFacetMap(STD_ANON._CF_pattern)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}SupportedAcquisitionStates
-class SupportedAcquisitionStates (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedAcquisitionStates')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 555, 1)
- _Documentation = None
-SupportedAcquisitionStates._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedAcquisitionStates, enum_prefix=None)
-SupportedAcquisitionStates.Ready = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Ready', tag='Ready')
-SupportedAcquisitionStates.Initializing = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Initializing', tag='Initializing')
-SupportedAcquisitionStates.Acquiring = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Acquiring', tag='Acquiring')
-SupportedAcquisitionStates.Aligning = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aligning', tag='Aligning')
-SupportedAcquisitionStates.Aligned = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aligned', tag='Aligned')
-SupportedAcquisitionStates.Aborting = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aborting', tag='Aborting')
-SupportedAcquisitionStates.Aborted = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aborted', tag='Aborted')
-SupportedAcquisitionStates.Failed = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Failed', tag='Failed')
-SupportedAcquisitionStates.Completing = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Completing', tag='Completing')
-SupportedAcquisitionStates.Complete = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Complete', tag='Complete')
-SupportedAcquisitionStates.Calibrating = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Calibrating', tag='Calibrating')
-SupportedAcquisitionStates.Unknown = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Unknown', tag='Unknown')
-SupportedAcquisitionStates._InitializeFacetMap(SupportedAcquisitionStates._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'SupportedAcquisitionStates', SupportedAcquisitionStates)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}SupportedDataTypes
-class SupportedDataTypes (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedDataTypes')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 571, 1)
- _Documentation = None
-SupportedDataTypes._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedDataTypes, enum_prefix=None)
-SupportedDataTypes.Int16 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int16', tag='Int16')
-SupportedDataTypes.Int32 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int32', tag='Int32')
-SupportedDataTypes.Int64 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int64', tag='Int64')
-SupportedDataTypes.UInt16 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt16', tag='UInt16')
-SupportedDataTypes.UInt32 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt32', tag='UInt32')
-SupportedDataTypes.UInt64 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt64', tag='UInt64')
-SupportedDataTypes.Single = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Single', tag='Single')
-SupportedDataTypes.Double = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Double', tag='Double')
-SupportedDataTypes.String = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='String', tag='String')
-SupportedDataTypes.DateTime = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='DateTime', tag='DateTime')
-SupportedDataTypes.Int16_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int16_1D', tag='Int16_1D')
-SupportedDataTypes.Int32_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int32_1D', tag='Int32_1D')
-SupportedDataTypes.Int64_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int64_1D', tag='Int64_1D')
-SupportedDataTypes.UInt16_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt16_1D', tag='UInt16_1D')
-SupportedDataTypes.UInt32_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt32_1D', tag='UInt32_1D')
-SupportedDataTypes.UInt64_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt64_1D', tag='UInt64_1D')
-SupportedDataTypes.Single_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Single_1D', tag='Single_1D')
-SupportedDataTypes.Double_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Double_1D', tag='Double_1D')
-SupportedDataTypes.String_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='String_1D', tag='String_1D')
-SupportedDataTypes.DateTime_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='DateTime_1D', tag='DateTime_1D')
-SupportedDataTypes.Int16_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int16_2D', tag='Int16_2D')
-SupportedDataTypes.Int32_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int32_2D', tag='Int32_2D')
-SupportedDataTypes.Int64_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int64_2D', tag='Int64_2D')
-SupportedDataTypes.UInt16_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt16_2D', tag='UInt16_2D')
-SupportedDataTypes.UInt32_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt32_2D', tag='UInt32_2D')
-SupportedDataTypes.UInt64_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt64_2D', tag='UInt64_2D')
-SupportedDataTypes.Single_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Single_2D', tag='Single_2D')
-SupportedDataTypes.Double_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Double_2D', tag='Double_2D')
-SupportedDataTypes.String_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='String_2D', tag='String_2D')
-SupportedDataTypes.DateTime_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='DateTime_2D', tag='DateTime_2D')
-SupportedDataTypes.XML = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='XML', tag='XML')
-SupportedDataTypes.JSON = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='JSON', tag='JSON')
-SupportedDataTypes.Object = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Object', tag='Object')
-SupportedDataTypes.Other = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Other', tag='Other')
-SupportedDataTypes.Unknown = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Unknown', tag='Unknown')
-SupportedDataTypes._InitializeFacetMap(SupportedDataTypes._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'SupportedDataTypes', SupportedDataTypes)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}SupportedNucleotides
-class SupportedNucleotides (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedNucleotides')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 610, 1)
- _Documentation = None
-SupportedNucleotides._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedNucleotides, enum_prefix=None)
-SupportedNucleotides.A = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='A', tag='A')
-SupportedNucleotides.C = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='C', tag='C')
-SupportedNucleotides.T = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='T', tag='T')
-SupportedNucleotides.G = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='G', tag='G')
-SupportedNucleotides._InitializeFacetMap(SupportedNucleotides._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'SupportedNucleotides', SupportedNucleotides)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}SupportedRunStates
-class SupportedRunStates (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedRunStates')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 618, 1)
- _Documentation = None
-SupportedRunStates._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedRunStates, enum_prefix=None)
-SupportedRunStates.Ready = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Ready', tag='Ready')
-SupportedRunStates.Idle = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Idle', tag='Idle')
-SupportedRunStates.System_Test = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='System Test', tag='System_Test')
-SupportedRunStates.Starting = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Starting', tag='Starting')
-SupportedRunStates.Running = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Running', tag='Running')
-SupportedRunStates.Aborting = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Aborting', tag='Aborting')
-SupportedRunStates.Aborted = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Aborted', tag='Aborted')
-SupportedRunStates.Terminated = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Terminated', tag='Terminated')
-SupportedRunStates.Completing = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Completing', tag='Completing')
-SupportedRunStates.Complete = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Complete', tag='Complete')
-SupportedRunStates.Unknown = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Unknown', tag='Unknown')
-SupportedRunStates._InitializeFacetMap(SupportedRunStates._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'SupportedRunStates', SupportedRunStates)
+STD_ANON._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON, enum_prefix=None)
+STD_ANON.AverageReadLength = STD_ANON._CF_enumeration.addEnumeration(unicode_value='AverageReadLength', tag='AverageReadLength')
+STD_ANON.AcquisitionTime = STD_ANON._CF_enumeration.addEnumeration(unicode_value='AcquisitionTime', tag='AcquisitionTime')
+STD_ANON.InsertSize = STD_ANON._CF_enumeration.addEnumeration(unicode_value='InsertSize', tag='InsertSize')
+STD_ANON.ReuseComplex = STD_ANON._CF_enumeration.addEnumeration(unicode_value='ReuseComplex', tag='ReuseComplex')
+STD_ANON.StageHS = STD_ANON._CF_enumeration.addEnumeration(unicode_value='StageHS', tag='StageHS')
+STD_ANON.JobId = STD_ANON._CF_enumeration.addEnumeration(unicode_value='JobId', tag='JobId')
+STD_ANON.JobName = STD_ANON._CF_enumeration.addEnumeration(unicode_value='JobName', tag='JobName')
+STD_ANON.NumberOfCollections = STD_ANON._CF_enumeration.addEnumeration(unicode_value='NumberOfCollections', tag='NumberOfCollections')
+STD_ANON.StrobeByTime = STD_ANON._CF_enumeration.addEnumeration(unicode_value='StrobeByTime', tag='StrobeByTime')
+STD_ANON.UsedControl = STD_ANON._CF_enumeration.addEnumeration(unicode_value='UsedControl', tag='UsedControl')
+STD_ANON.Use2ndLook = STD_ANON._CF_enumeration.addEnumeration(unicode_value='Use2ndLook', tag='Use2ndLook')
+STD_ANON._InitializeFacetMap(STD_ANON._CF_enumeration)
# Atomic simple type: [anonymous]
class STD_ANON_ (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
@@ -201,208 +112,136 @@ class STD_ANON_ (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_m
"""An atomic simple type."""
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 47, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 186, 4)
_Documentation = None
STD_ANON_._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON_, enum_prefix=None)
-STD_ANON_.Instrument = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Instrument', tag='Instrument')
-STD_ANON_.User = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='User', tag='User')
-STD_ANON_.AnalysisJob = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='AnalysisJob', tag='AnalysisJob')
+STD_ANON_.PlateId = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='PlateId', tag='PlateId')
+STD_ANON_.PlateDefinition = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='PlateDefinition', tag='PlateDefinition')
+STD_ANON_.SchemaVersion = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='SchemaVersion', tag='SchemaVersion')
+STD_ANON_.DefType = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='DefType', tag='DefType')
+STD_ANON_.Owner = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Owner', tag='Owner')
+STD_ANON_.CreatedBy = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='CreatedBy', tag='CreatedBy')
+STD_ANON_.Comments = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Comments', tag='Comments')
+STD_ANON_.OutputPath = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='OutputPath', tag='OutputPath')
+STD_ANON_.Collections = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Collections', tag='Collections')
+STD_ANON_.Collection = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Collection', tag='Collection')
+STD_ANON_.DNATemplatePrepKitDefinition = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='DNATemplatePrepKitDefinition', tag='DNATemplatePrepKitDefinition')
+STD_ANON_.BindingKitDefinition = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='BindingKitDefinition', tag='BindingKitDefinition')
+STD_ANON_.RunResources = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='RunResources', tag='RunResources')
+STD_ANON_.CompatibleChipLayouts = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='CompatibleChipLayouts', tag='CompatibleChipLayouts')
+STD_ANON_.ChipLayout = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='ChipLayout', tag='ChipLayout')
+STD_ANON_.CompatibleSequencingKits = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='CompatibleSequencingKits', tag='CompatibleSequencingKits')
+STD_ANON_.SequencingKit = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='SequencingKit', tag='SequencingKit')
+STD_ANON_.RequiredTips = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='RequiredTips', tag='RequiredTips')
+STD_ANON_.EstimatedTotalRunTime = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='EstimatedTotalRunTime', tag='EstimatedTotalRunTime')
+STD_ANON_.RequiredSMRTCells = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='RequiredSMRTCells', tag='RequiredSMRTCells')
+STD_ANON_.CollectionAutomation = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='CollectionAutomation', tag='CollectionAutomation')
+STD_ANON_.Basecaller = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Basecaller', tag='Basecaller')
+STD_ANON_.SecondaryAnalysisAutomation = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='SecondaryAnalysisAutomation', tag='SecondaryAnalysisAutomation')
+STD_ANON_.WellNo = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='WellNo', tag='WellNo')
+STD_ANON_.SampleName = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='SampleName', tag='SampleName')
+STD_ANON_.Barcode = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Barcode', tag='Barcode')
+STD_ANON_.AcquisitionTime = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='AcquisitionTime', tag='AcquisitionTime')
+STD_ANON_.InsertSize = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='InsertSize', tag='InsertSize')
+STD_ANON_.ReuseComplex = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='ReuseComplex', tag='ReuseComplex')
+STD_ANON_.StageHS = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='StageHS', tag='StageHS')
+STD_ANON_.NumberOfCollections = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='NumberOfCollections', tag='NumberOfCollections')
+STD_ANON_.Confidence = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Confidence', tag='Confidence')
+STD_ANON_.SampleComment = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='SampleComment', tag='SampleComment')
+STD_ANON_.StrobeByTime = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='StrobeByTime', tag='StrobeByTime')
STD_ANON_._InitializeFacetMap(STD_ANON_._CF_enumeration)
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}PapOutputFile
-class PapOutputFile (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """Defines a list of available file output types from primary output that can be copied out to the CollectionPathUri. The types Pulse, Base, Fasta, and Fastq are for legacy use only."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'PapOutputFile')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 624, 1)
- _Documentation = 'Defines a list of available file output types from primary output that can be copied out to the CollectionPathUri. The types Pulse, Base, Fasta, and Fastq are for legacy use only.'
-PapOutputFile._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=PapOutputFile, enum_prefix=None)
-PapOutputFile.Movie = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Movie', tag='Movie')
-PapOutputFile.Trace = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Trace', tag='Trace')
-PapOutputFile.Pulse = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Pulse', tag='Pulse')
-PapOutputFile.Base = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Base', tag='Base')
-PapOutputFile.Baz = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Baz', tag='Baz')
-PapOutputFile.Bam = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Bam', tag='Bam')
-PapOutputFile.Fasta = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Fasta', tag='Fasta')
-PapOutputFile.Bam_ = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Bam', tag='Bam_')
-PapOutputFile._InitializeFacetMap(PapOutputFile._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'PapOutputFile', PapOutputFile)
-
-# Atomic simple type: [anonymous]
-class STD_ANON_2 (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 72, 4)
- _Documentation = None
-STD_ANON_2._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON_2, enum_prefix=None)
-STD_ANON_2.AverageReadLength = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='AverageReadLength', tag='AverageReadLength')
-STD_ANON_2.AcquisitionTime = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='AcquisitionTime', tag='AcquisitionTime')
-STD_ANON_2.InsertSize = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='InsertSize', tag='InsertSize')
-STD_ANON_2.ReuseComplex = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='ReuseComplex', tag='ReuseComplex')
-STD_ANON_2.StageHS = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='StageHS', tag='StageHS')
-STD_ANON_2.JobId = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='JobId', tag='JobId')
-STD_ANON_2.JobName = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='JobName', tag='JobName')
-STD_ANON_2.NumberOfCollections = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='NumberOfCollections', tag='NumberOfCollections')
-STD_ANON_2.StrobeByTime = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='StrobeByTime', tag='StrobeByTime')
-STD_ANON_2.UsedControl = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='UsedControl', tag='UsedControl')
-STD_ANON_2.Use2ndLook = STD_ANON_2._CF_enumeration.addEnumeration(unicode_value='Use2ndLook', tag='Use2ndLook')
-STD_ANON_2._InitializeFacetMap(STD_ANON_2._CF_enumeration)
-
# Atomic simple type: [anonymous]
-class STD_ANON_3 (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+class STD_ANON_2 (pyxb.binding.datatypes.dateTime):
"""An atomic simple type."""
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 182, 4)
- _Documentation = None
-STD_ANON_3._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON_3, enum_prefix=None)
-STD_ANON_3.PlateId = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='PlateId', tag='PlateId')
-STD_ANON_3.PlateDefinition = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='PlateDefinition', tag='PlateDefinition')
-STD_ANON_3.SchemaVersion = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='SchemaVersion', tag='SchemaVersion')
-STD_ANON_3.DefType = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='DefType', tag='DefType')
-STD_ANON_3.Owner = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Owner', tag='Owner')
-STD_ANON_3.CreatedBy = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='CreatedBy', tag='CreatedBy')
-STD_ANON_3.Comments = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Comments', tag='Comments')
-STD_ANON_3.OutputPath = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='OutputPath', tag='OutputPath')
-STD_ANON_3.Collections = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Collections', tag='Collections')
-STD_ANON_3.Collection = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Collection', tag='Collection')
-STD_ANON_3.DNATemplatePrepKitDefinition = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='DNATemplatePrepKitDefinition', tag='DNATemplatePrepKitDefinition')
-STD_ANON_3.BindingKitDefinition = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='BindingKitDefinition', tag='BindingKitDefinition')
-STD_ANON_3.RunResources = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='RunResources', tag='RunResources')
-STD_ANON_3.CompatibleChipLayouts = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='CompatibleChipLayouts', tag='CompatibleChipLayouts')
-STD_ANON_3.ChipLayout = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='ChipLayout', tag='ChipLayout')
-STD_ANON_3.CompatibleSequencingKits = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='CompatibleSequencingKits', tag='CompatibleSequencingKits')
-STD_ANON_3.SequencingKit = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='SequencingKit', tag='SequencingKit')
-STD_ANON_3.RequiredTips = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='RequiredTips', tag='RequiredTips')
-STD_ANON_3.EstimatedTotalRunTime = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='EstimatedTotalRunTime', tag='EstimatedTotalRunTime')
-STD_ANON_3.RequiredSMRTCells = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='RequiredSMRTCells', tag='RequiredSMRTCells')
-STD_ANON_3.CollectionAutomation = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='CollectionAutomation', tag='CollectionAutomation')
-STD_ANON_3.Basecaller = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Basecaller', tag='Basecaller')
-STD_ANON_3.SecondaryAnalysisAutomation = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='SecondaryAnalysisAutomation', tag='SecondaryAnalysisAutomation')
-STD_ANON_3.WellNo = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='WellNo', tag='WellNo')
-STD_ANON_3.SampleName = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='SampleName', tag='SampleName')
-STD_ANON_3.Barcode = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Barcode', tag='Barcode')
-STD_ANON_3.AcquisitionTime = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='AcquisitionTime', tag='AcquisitionTime')
-STD_ANON_3.InsertSize = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='InsertSize', tag='InsertSize')
-STD_ANON_3.ReuseComplex = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='ReuseComplex', tag='ReuseComplex')
-STD_ANON_3.StageHS = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='StageHS', tag='StageHS')
-STD_ANON_3.NumberOfCollections = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='NumberOfCollections', tag='NumberOfCollections')
-STD_ANON_3.Confidence = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='Confidence', tag='Confidence')
-STD_ANON_3.SampleComment = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='SampleComment', tag='SampleComment')
-STD_ANON_3.StrobeByTime = STD_ANON_3._CF_enumeration.addEnumeration(unicode_value='StrobeByTime', tag='StrobeByTime')
-STD_ANON_3._InitializeFacetMap(STD_ANON_3._CF_enumeration)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}TubeLocation
-class TubeLocation (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'TubeLocation')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 128, 1)
- _Documentation = None
-TubeLocation._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=TubeLocation, enum_prefix=None)
-TubeLocation.ReagentTube0 = TubeLocation._CF_enumeration.addEnumeration(unicode_value='ReagentTube0', tag='ReagentTube0')
-TubeLocation.ReagentTube1 = TubeLocation._CF_enumeration.addEnumeration(unicode_value='ReagentTube1', tag='ReagentTube1')
-TubeLocation._InitializeFacetMap(TubeLocation._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'TubeLocation', TubeLocation)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}TubeSize
-class TubeSize (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'TubeSize')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 134, 1)
- _Documentation = None
-TubeSize._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=TubeSize, enum_prefix=None)
-TubeSize.DeepTube = TubeSize._CF_enumeration.addEnumeration(unicode_value='DeepTube', tag='DeepTube')
-TubeSize.ShallowTube = TubeSize._CF_enumeration.addEnumeration(unicode_value='ShallowTube', tag='ShallowTube')
-TubeSize._InitializeFacetMap(TubeSize._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'TubeSize', TubeSize)
-
-# Atomic simple type: {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentKey
-class ReagentKey (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
-
- """An atomic simple type."""
-
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentKey')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 140, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 393, 5)
_Documentation = None
-ReagentKey._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=ReagentKey, enum_prefix=None)
-ReagentKey.Base = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Base', tag='Base')
-ReagentKey.DTT = ReagentKey._CF_enumeration.addEnumeration(unicode_value='DTT', tag='DTT')
-ReagentKey.DilBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='DilBuffer', tag='DilBuffer')
-ReagentKey.MineralOil = ReagentKey._CF_enumeration.addEnumeration(unicode_value='MineralOil', tag='MineralOil')
-ReagentKey.MIXED_DilBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='MIXED_DilBuffer', tag='MIXED_DilBuffer')
-ReagentKey.MIXED_OS = ReagentKey._CF_enumeration.addEnumeration(unicode_value='MIXED_OS', tag='MIXED_OS')
-ReagentKey.OSbuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='OSbuffer', tag='OSbuffer')
-ReagentKey.OSenzyme = ReagentKey._CF_enumeration.addEnumeration(unicode_value='OSenzyme', tag='OSenzyme')
-ReagentKey.PhospholinkedNT = ReagentKey._CF_enumeration.addEnumeration(unicode_value='PhospholinkedNT', tag='PhospholinkedNT')
-ReagentKey.SABuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='SABuffer', tag='SABuffer')
-ReagentKey.Spike = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Spike', tag='Spike')
-ReagentKey.Streptavidin = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Streptavidin', tag='Streptavidin')
-ReagentKey.SubstrateOS = ReagentKey._CF_enumeration.addEnumeration(unicode_value='SubstrateOS', tag='SubstrateOS')
-ReagentKey.TSQ = ReagentKey._CF_enumeration.addEnumeration(unicode_value='TSQ', tag='TSQ')
-ReagentKey.WashBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='WashBuffer', tag='WashBuffer')
-ReagentKey.WettingBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='WettingBuffer', tag='WettingBuffer')
-ReagentKey.PCA = ReagentKey._CF_enumeration.addEnumeration(unicode_value='PCA', tag='PCA')
-ReagentKey.PCD = ReagentKey._CF_enumeration.addEnumeration(unicode_value='PCD', tag='PCD')
-ReagentKey.Analog = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Analog', tag='Analog')
-ReagentKey.Sample = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Sample', tag='Sample')
-ReagentKey._InitializeFacetMap(ReagentKey._CF_enumeration)
-Namespace.addCategoryObject('typeBinding', 'ReagentKey', ReagentKey)
+STD_ANON_2._InitializeFacetMap()
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
- """The root element of the Automation Constraints """
+ """Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 13, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 16, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationConstraints uses Python identifier AutomationConstraints
- __AutomationConstraints = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraints'), 'AutomationConstraints', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_httppacificbiosciences_comPacBioDataModel_xsdAutomationConstraints', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 19, 1), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
+
+
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
+
+
+ # Attribute Name uses Python identifier Name
+ __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_Name', pyxb.binding.datatypes.string, required=True)
+ __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 20, 3)
+ __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 20, 3)
+
+ Name = property(__Name.value, __Name.set, None, None)
+
+
+ # Attribute PartNumber uses Python identifier PartNumber
+ __PartNumber = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PartNumber'), 'PartNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_PartNumber', pyxb.binding.datatypes.string, required=True)
+ __PartNumber._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 21, 3)
+ __PartNumber._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 21, 3)
+
+ PartNumber = property(__PartNumber.value, __PartNumber.set, None, None)
- AutomationConstraints = property(__AutomationConstraints.value, __AutomationConstraints.set, None, None)
+ # Attribute Quantity uses Python identifier Quantity
+ __Quantity = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Quantity'), 'Quantity', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_Quantity', pyxb.binding.datatypes.anySimpleType)
+ __Quantity._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 22, 3)
+ __Quantity._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 22, 3)
+
+ Quantity = property(__Quantity.value, __Quantity.set, None, 'The number of cells required, of a particular part number')
_ElementMap.update({
- __AutomationConstraints.name() : __AutomationConstraints
+ __Validation.name() : __Validation
})
_AttributeMap.update({
-
+ __Name.name() : __Name,
+ __PartNumber.name() : __PartNumber,
+ __Quantity.name() : __Quantity
})
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ """A set of Chip Layouts deemed compatible with the current plate"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 20, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 33, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationConstraint uses Python identifier AutomationConstraint
- __AutomationConstraint = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraint'), 'AutomationConstraint', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON__httppacificbiosciences_comPacBioDataModel_xsdAutomationConstraint', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 26, 1), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ChipLayout uses Python identifier ChipLayout
+ __ChipLayout = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), 'ChipLayout', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON__httppacificbiosciences_comPacBioDataModel_xsdChipLayout', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 12, 1), )
+
+
+ ChipLayout = property(__ChipLayout.value, __ChipLayout.set, None, 'Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate')
- AutomationConstraint = property(__AutomationConstraint.value, __AutomationConstraint.set, None, None)
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON__httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
+
+
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
_ElementMap.update({
- __AutomationConstraint.name() : __AutomationConstraint
+ __ChipLayout.name() : __ChipLayout,
+ __Validation.name() : __Validation
})
_AttributeMap.update({
@@ -412,24 +251,40 @@ class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
- """Names of automations that are all similarly constrained"""
+ """A set of reagent kits deemed compatible with the current plate"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 38, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 44, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Automation uses Python identifier Automation
- __Automation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automation'), 'Automation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDataModel_xsdAutomation', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 40, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}EstimatedTotalRunTime uses Python identifier EstimatedTotalRunTime
+ __EstimatedTotalRunTime = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime'), 'EstimatedTotalRunTime', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDataModel_xsdEstimatedTotalRunTime', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 52, 1), )
+
+
+ EstimatedTotalRunTime = property(__EstimatedTotalRunTime.value, __EstimatedTotalRunTime.set, None, 'The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RequiredTips uses Python identifier RequiredTips
+ __RequiredTips = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips'), 'RequiredTips', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDataModel_xsdRequiredTips', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 121, 1), )
+
+
+ RequiredTips = property(__RequiredTips.value, __RequiredTips.set, None, 'Part of the RunResources; specifies the required number of tips via two attributes, Left and Right')
+
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}SequencingKit uses Python identifier SequencingKit
+ __SequencingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbpn, 'SequencingKit'), 'SequencingKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioPartNumbers_xsdSequencingKit', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 67, 1), )
- Automation = property(__Automation.value, __Automation.set, None, None)
+ SequencingKit = property(__SequencingKit.value, __SequencingKit.set, None, None)
_ElementMap.update({
- __Automation.name() : __Automation
+ __EstimatedTotalRunTime.name() : __EstimatedTotalRunTime,
+ __RequiredTips.name() : __RequiredTips,
+ __SequencingKit.name() : __SequencingKit
})
_AttributeMap.update({
@@ -439,51 +294,69 @@ class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
- """A list of insert sizes (buckets) recommended for use"""
+ """The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 48, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 56, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InsertSize uses Python identifier InsertSize
- __InsertSize = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertSize'), 'InsertSize', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioDataModel_xsdInsertSize', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 50, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
+
+
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
+
+
+ # Attribute Value uses Python identifier Value
+ __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_3_Value', pyxb.binding.datatypes.string, required=True)
+ __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 60, 3)
+ __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 60, 3)
+
+ Value = property(__Value.value, __Value.set, None, None)
- InsertSize = property(__InsertSize.value, __InsertSize.set, None, None)
+ # Attribute Confidence uses Python identifier Confidence
+ __Confidence = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Confidence'), 'Confidence', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_3_Confidence', pyxb.binding.datatypes.int, required=True)
+ __Confidence._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 61, 3)
+ __Confidence._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 61, 3)
+
+ Confidence = property(__Confidence.value, __Confidence.set, None, None)
_ElementMap.update({
- __InsertSize.name() : __InsertSize
+ __Validation.name() : __Validation
})
_AttributeMap.update({
-
+ __Value.name() : __Value,
+ __Confidence.name() : __Confidence
})
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ """PacBio Data Model root element"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 58, 4)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 99, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExtensionElement uses Python identifier ExtensionElement
- __ExtensionElement = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement'), 'ExtensionElement', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioDataModel_xsdExtensionElement', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 640, 1), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExperimentContainer uses Python identifier ExperimentContainer
+ __ExperimentContainer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainer'), 'ExperimentContainer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioDataModel_xsdExperimentContainer', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 101, 4), )
- ExtensionElement = property(__ExtensionElement.value, __ExtensionElement.set, None, 'A generic element whose contents are undefined at the schema level. This is used to extend the data model.')
+ ExperimentContainer = property(__ExperimentContainer.value, __ExperimentContainer.set, None, None)
+ _HasWildcardElement = True
_ElementMap.update({
- __ExtensionElement.name() : __ExtensionElement
+ __ExperimentContainer.name() : __ExperimentContainer
})
_AttributeMap.update({
@@ -493,78 +366,119 @@ class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_5 (pyxb.binding.basis.complexTypeDefinition):
- """Pointer to Run/Outputs/Output/@UniqueId"""
+ """Part of the RunResources; specifies the required number of SMRT cells"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 172, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 114, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataPointer uses Python identifier DataPointer
- __DataPointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataPointer'), 'DataPointer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioDataModel_xsdDataPointer', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 174, 4), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
+
+
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
- DataPointer = property(__DataPointer.value, __DataPointer.set, None, None)
+ # Attribute Quantity uses Python identifier Quantity
+ __Quantity = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Quantity'), 'Quantity', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_5_Quantity', pyxb.binding.datatypes.int, required=True)
+ __Quantity._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 118, 3)
+ __Quantity._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 118, 3)
+
+ Quantity = property(__Quantity.value, __Quantity.set, None, None)
_ElementMap.update({
- __DataPointer.name() : __DataPointer
+ __Validation.name() : __Validation
})
_AttributeMap.update({
-
+ __Quantity.name() : __Quantity
})
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_6 (pyxb.binding.basis.complexTypeDefinition):
- """Pointers to data that do not reside inside the parent structure"""
+ """Part of the RunResources; specifies the required number of tips via two attributes, Left and Right"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 206, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 125, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResource uses Python identifier ExternalResource
- __ExternalResource = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource'), 'ExternalResource', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_6_httppacificbiosciences_comPacBioDataModel_xsdExternalResource', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 662, 1), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_6_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
+
+
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
+
+
+ # Attribute Left uses Python identifier Left
+ __Left = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Left'), 'Left', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_6_Left', pyxb.binding.datatypes.int, required=True)
+ __Left._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 129, 3)
+ __Left._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 129, 3)
+
+ Left = property(__Left.value, __Left.set, None, None)
- ExternalResource = property(__ExternalResource.value, __ExternalResource.set, None, 'for example, an output file could be the BAM file, which could be associated with multiple indices into it.')
+ # Attribute Right uses Python identifier Right
+ __Right = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Right'), 'Right', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_6_Right', pyxb.binding.datatypes.int, required=True)
+ __Right._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 130, 3)
+ __Right._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 130, 3)
+
+ Right = property(__Right.value, __Right.set, None, None)
_ElementMap.update({
- __ExternalResource.name() : __ExternalResource
+ __Validation.name() : __Validation
})
_AttributeMap.update({
-
+ __Left.name() : __Left,
+ __Right.name() : __Right
})
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_7 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ """This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc."""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 222, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 137, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}FileIndex uses Python identifier FileIndex
- __FileIndex = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'FileIndex'), 'FileIndex', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioDataModel_xsdFileIndex', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 224, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CompatibleChipLayouts uses Python identifier CompatibleChipLayouts
+ __CompatibleChipLayouts = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts'), 'CompatibleChipLayouts', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioDataModel_xsdCompatibleChipLayouts', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 29, 1), )
+
+
+ CompatibleChipLayouts = property(__CompatibleChipLayouts.value, __CompatibleChipLayouts.set, None, 'A set of Chip Layouts deemed compatible with the current plate')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CompatibleSequencingKits uses Python identifier CompatibleSequencingKits
+ __CompatibleSequencingKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits'), 'CompatibleSequencingKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioDataModel_xsdCompatibleSequencingKits', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 40, 1), )
+
+
+ CompatibleSequencingKits = property(__CompatibleSequencingKits.value, __CompatibleSequencingKits.set, None, 'A set of reagent kits deemed compatible with the current plate')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
- FileIndex = property(__FileIndex.value, __FileIndex.set, None, 'e.g. index for output files, allowing one to find information in the output file')
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
_ElementMap.update({
- __FileIndex.name() : __FileIndex
+ __CompatibleChipLayouts.name() : __CompatibleChipLayouts,
+ __CompatibleSequencingKits.name() : __CompatibleSequencingKits,
+ __Validation.name() : __Validation
})
_AttributeMap.update({
@@ -572,53 +486,61 @@ class CTD_ANON_7 (pyxb.binding.basis.complexTypeDefinition):
-# Complex type [anonymous] with content type ELEMENT_ONLY
+# Complex type [anonymous] with content type MIXED
class CTD_ANON_8 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ """A general sample description"""
_TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_MIXED
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 242, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 149, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationParameter uses Python identifier AutomationParameter
- __AutomationParameter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), 'AutomationParameter', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_8_httppacificbiosciences_comPacBioDataModel_xsdAutomationParameter', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 253, 1), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_8_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
+
+
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
- AutomationParameter = property(__AutomationParameter.value, __AutomationParameter.set, None, 'One or more collection parameters, such as MovieLength, InsertSize, UseStageStart, IsControl, etc..')
+ # Attribute Value uses Python identifier Value
+ __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_8_Value', pyxb.binding.datatypes.string)
+ __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 153, 3)
+ __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 153, 3)
+
+ Value = property(__Value.value, __Value.set, None, None)
_ElementMap.update({
- __AutomationParameter.name() : __AutomationParameter
+ __Validation.name() : __Validation
})
_AttributeMap.update({
-
+ __Value.name() : __Value
})
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_9 (pyxb.binding.basis.complexTypeDefinition):
- """By default, a PN is compatible for use with other PNs in the system. In order to exclude the usage of one or more PNs with this one, the incompatible PNs are listed here."""
+ """Multiple acquisitions from different instrument runs"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 271, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 275, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumber uses Python identifier IncompatiblePartNumber
- __IncompatiblePartNumber = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumber'), 'IncompatiblePartNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_9_httppacificbiosciences_comPacBioDataModel_xsdIncompatiblePartNumber', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 273, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Run uses Python identifier Run
+ __Run = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Run'), 'Run', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_9_httppacificbiosciences_comPacBioDataModel_xsdRun', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 277, 8), )
- IncompatiblePartNumber = property(__IncompatiblePartNumber.value, __IncompatiblePartNumber.set, None, 'A reference to the incompatible part number UID')
+ Run = property(__Run.value, __Run.set, None, None)
_ElementMap.update({
- __IncompatiblePartNumber.name() : __IncompatiblePartNumber
+ __Run.name() : __Run
})
_AttributeMap.update({
@@ -628,24 +550,24 @@ class CTD_ANON_9 (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_10 (pyxb.binding.basis.complexTypeDefinition):
- """By default, a PN is compatible for use with all automations in the system. In order to exclude the usage of automations with this PN, the incompatible automation names are listed here."""
+ """Pointers to various data elements associated with the acquisitions"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 285, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 285, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomation uses Python identifier IncompatibleAutomation
- __IncompatibleAutomation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomation'), 'IncompatibleAutomation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_10_httppacificbiosciences_comPacBioDataModel_xsdIncompatibleAutomation', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 287, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSet uses Python identifier DataSet
+ __DataSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbds, 'DataSet'), 'DataSet', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_10_httppacificbiosciences_comPacBioDatasets_xsdDataSet', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 34, 1), )
- IncompatibleAutomation = property(__IncompatibleAutomation.value, __IncompatibleAutomation.set, None, 'A reference to the incompatible automation type UID')
+ DataSet = property(__DataSet.value, __DataSet.set, None, None)
_ElementMap.update({
- __IncompatibleAutomation.name() : __IncompatibleAutomation
+ __DataSet.name() : __DataSet
})
_AttributeMap.update({
@@ -655,24 +577,24 @@ class CTD_ANON_10 (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_11 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ """Journal of metrics, system events, or alarms that were generated during this container's lifetime"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 347, 11)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 295, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Analog uses Python identifier Analog
- __Analog = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analog'), 'Analog', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_11_httppacificbiosciences_comPacBioDataModel_xsdAnalog', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 349, 13), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvent uses Python identifier RecordedEvent
+ __RecordedEvent = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), 'RecordedEvent', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_11_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvent', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 297, 8), )
- Analog = property(__Analog.value, __Analog.set, None, None)
+ RecordedEvent = property(__RecordedEvent.value, __RecordedEvent.set, None, "Journal of metrics, system events, or alarms that were generated during this container's lifetime")
_ElementMap.update({
- __Analog.name() : __Analog
+ __RecordedEvent.name() : __RecordedEvent
})
_AttributeMap.update({
@@ -682,24 +604,24 @@ class CTD_ANON_11 (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_12 (pyxb.binding.basis.complexTypeDefinition):
- """Root element for document containing the container of analog set, SequencingChemistryConfig"""
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 366, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 306, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ChemistryConfig uses Python identifier ChemistryConfig
- __ChemistryConfig = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfig'), 'ChemistryConfig', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioDataModel_xsdChemistryConfig', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 368, 4), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSample uses Python identifier BioSample
+ __BioSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), 'BioSample', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioDataModel_xsdBioSample', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 308, 8), )
- ChemistryConfig = property(__ChemistryConfig.value, __ChemistryConfig.set, None, None)
+ BioSample = property(__BioSample.value, __BioSample.set, None, None)
_ElementMap.update({
- __ChemistryConfig.name() : __ChemistryConfig
+ __BioSample.name() : __BioSample
})
_AttributeMap.update({
@@ -714,19 +636,27 @@ class CTD_ANON_13 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 380, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 326, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Analog uses Python identifier Analog
- __Analog = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analog'), 'Analog', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioDataModel_xsdAnalog', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 382, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Output uses Python identifier Output
+ __Output = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Output'), 'Output', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioDataModel_xsdOutput', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 66, 1), )
+
+
+ Output = property(__Output.value, __Output.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSets uses Python identifier SubreadSets
+ __SubreadSets = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets'), 'SubreadSets', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioDataModel_xsdSubreadSets', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 407, 1), )
- Analog = property(__Analog.value, __Analog.set, None, None)
+ SubreadSets = property(__SubreadSets.value, __SubreadSets.set, None, None)
_ElementMap.update({
- __Analog.name() : __Analog
+ __Output.name() : __Output,
+ __SubreadSets.name() : __SubreadSets
})
_AttributeMap.update({
@@ -741,19 +671,19 @@ class CTD_ANON_14 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 404, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 340, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinCount uses Python identifier BinCount
- __BinCount = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), 'BinCount', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_14_httppacificbiosciences_comPacBioDataModel_xsdBinCount', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 406, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Input uses Python identifier Input
+ __Input = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Input'), 'Input', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_14_httppacificbiosciences_comPacBioDataModel_xsdInput', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 65, 1), )
- BinCount = property(__BinCount.value, __BinCount.set, None, None)
+ Input = property(__Input.value, __Input.set, None, None)
_ElementMap.update({
- __BinCount.name() : __BinCount
+ __Input.name() : __Input
})
_AttributeMap.update({
@@ -763,24 +693,24 @@ class CTD_ANON_14 (pyxb.binding.basis.complexTypeDefinition):
# Complex type [anonymous] with content type ELEMENT_ONLY
class CTD_ANON_15 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ """Journal of metrics, system events, or alarms that were generated during this run's lifetime"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 430, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 356, 6)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinCount uses Python identifier BinCount
- __BinCount = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), 'BinCount', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_15_httppacificbiosciences_comPacBioDataModel_xsdBinCount', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 432, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvent uses Python identifier RecordedEvent
+ __RecordedEvent = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), 'RecordedEvent', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_15_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvent', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 358, 8), )
- BinCount = property(__BinCount.value, __BinCount.set, None, None)
+ RecordedEvent = property(__RecordedEvent.value, __RecordedEvent.set, None, "Journal of metrics, system events, or alarms that were generated during this run's lifetime.\nIn the case of Primary generating the DataSet containing the sts.xml, this RecordedEvent object should be a pointer to the DataSet object generated.")
_ElementMap.update({
- __BinCount.name() : __BinCount
+ __RecordedEvent.name() : __RecordedEvent
})
_AttributeMap.update({
@@ -795,19 +725,19 @@ class CTD_ANON_16 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 438, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 401, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinLabel uses Python identifier BinLabel
- __BinLabel = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinLabel'), 'BinLabel', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_16_httppacificbiosciences_comPacBioDataModel_xsdBinLabel', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 440, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionMetadataRef uses Python identifier CollectionMetadataRef
+ __CollectionMetadataRef = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadataRef'), 'CollectionMetadataRef', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_16_httppacificbiosciences_comPacBioDataModel_xsdCollectionMetadataRef', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 403, 4), )
- BinLabel = property(__BinLabel.value, __BinLabel.set, None, None)
+ CollectionMetadataRef = property(__CollectionMetadataRef.value, __CollectionMetadataRef.set, None, None)
_ElementMap.update({
- __BinLabel.name() : __BinLabel
+ __CollectionMetadataRef.name() : __CollectionMetadataRef
})
_AttributeMap.update({
@@ -822,19 +752,19 @@ class CTD_ANON_17 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 460, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 408, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Val uses Python identifier Val
- __Val = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Val'), 'Val', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_17_httppacificbiosciences_comPacBioDataModel_xsdVal', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 462, 8), )
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}SubreadSet uses Python identifier SubreadSet
+ __SubreadSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbds, 'SubreadSet'), 'SubreadSet', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_17_httppacificbiosciences_comPacBioDatasets_xsdSubreadSet', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 137, 1), )
- Val = property(__Val.value, __Val.set, None, None)
+ SubreadSet = property(__SubreadSet.value, __SubreadSet.set, None, None)
_ElementMap.update({
- __Val.name() : __Val
+ __SubreadSet.name() : __SubreadSet
})
_AttributeMap.update({
@@ -842,13080 +772,1328 @@ class CTD_ANON_17 (pyxb.binding.basis.complexTypeDefinition):
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}UserDefinedFieldsType with content type ELEMENT_ONLY
-class UserDefinedFieldsType (pyxb.binding.basis.complexTypeDefinition):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}UserDefinedFieldsType with content type ELEMENT_ONLY"""
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_18 (pyxb.binding.basis.complexTypeDefinition):
+ """A variable, as a name/value pair, associated with a protocol (one of Collection, Primary, and Secondary)"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFieldsType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 633, 1)
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 71, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntities uses Python identifier DataEntities
- __DataEntities = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataEntities'), 'DataEntities', '__httppacificbiosciences_comPacBioDataModel_xsd_UserDefinedFieldsType_httppacificbiosciences_comPacBioDataModel_xsdDataEntities', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 635, 3), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
+ __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_18_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1), )
- DataEntities = property(__DataEntities.value, __DataEntities.set, None, None)
-
- _ElementMap.update({
- __DataEntities.name() : __DataEntities
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'UserDefinedFieldsType', UserDefinedFieldsType)
-
+ Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}FilterType with content type ELEMENT_ONLY
-class FilterType (pyxb.binding.basis.complexTypeDefinition):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}FilterType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'FilterType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 645, 1)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Properties uses Python identifier Properties
- __Properties = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Properties'), 'Properties', '__httppacificbiosciences_comPacBioDataModel_xsd_FilterType_httppacificbiosciences_comPacBioDataModel_xsdProperties', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 647, 3), )
+ # Attribute Name uses Python identifier Name
+ __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_18_Name', STD_ANON, required=True)
+ __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 75, 3)
+ __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 75, 3)
+
+ Name = property(__Name.value, __Name.set, None, None)
- Properties = property(__Properties.value, __Properties.set, None, None)
+ # Attribute Value uses Python identifier Value
+ __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_18_Value', pyxb.binding.datatypes.string, required=True)
+ __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 92, 3)
+ __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 92, 3)
+
+ Value = property(__Value.value, __Value.set, None, None)
_ElementMap.update({
- __Properties.name() : __Properties
+ __Validation.name() : __Validation
})
_AttributeMap.update({
-
+ __Name.name() : __Name,
+ __Value.name() : __Value
})
-Namespace.addCategoryObject('typeBinding', 'FilterType', FilterType)
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_18 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+
+# Complex type [anonymous] with content type EMPTY
+class CTD_ANON_19 (pyxb.binding.basis.complexTypeDefinition):
+ """
+ A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.
+ """
_TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_EMPTY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 648, 4)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 162, 2)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Property uses Python identifier Property
- __Property = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Property'), 'Property', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_18_httppacificbiosciences_comPacBioDataModel_xsdProperty', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 650, 6), )
-
+ # Attribute IsValid uses Python identifier IsValid
+ __IsValid = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'IsValid'), 'IsValid', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_IsValid', pyxb.binding.datatypes.boolean, required=True)
+ __IsValid._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 163, 3)
+ __IsValid._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 163, 3)
- Property = property(__Property.value, __Property.set, None, None)
-
- _ElementMap.update({
- __Property.name() : __Property
- })
- _AttributeMap.update({
-
- })
-
+ IsValid = property(__IsValid.value, __IsValid.set, None, '\n Indicates whether or not the element is valid. The assumption is that the\n Validation element is omitted unless the element is invalid, in which case,\n the Validation element would describe the problem.\n ')
+
+ # Attribute ID uses Python identifier ID
+ __ID = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ID'), 'ID', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_ID', pyxb.binding.datatypes.string, required=True)
+ __ID._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 172, 3)
+ __ID._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 172, 3)
+
+ ID = property(__ID.value, __ID.set, None, '\n An identifier which can be used by client applications to translate/map\n to a human decipherable message.\n ')
-# Complex type [anonymous] with content type EMPTY
-class CTD_ANON_19 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type EMPTY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_EMPTY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 651, 7)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
- # Attribute Name uses Python identifier Name
- __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_Name', pyxb.binding.datatypes.string, required=True)
- __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 652, 8)
- __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 652, 8)
+ # Attribute Source uses Python identifier Source
+ __Source = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Source'), 'Source', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_Source', STD_ANON_, required=True)
+ __Source._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 180, 3)
+ __Source._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 180, 3)
- Name = property(__Name.value, __Name.set, None, None)
+ Source = property(__Source.value, __Source.set, None, '\n This is the element which has experienced a validation issue.\n ')
- # Attribute Value uses Python identifier Value
- __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_Value', pyxb.binding.datatypes.string, required=True)
- __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 653, 8)
- __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 653, 8)
+ # Attribute ElementPath uses Python identifier ElementPath
+ __ElementPath = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ElementPath'), 'ElementPath', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_ElementPath', pyxb.binding.datatypes.string)
+ __ElementPath._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 225, 3)
+ __ElementPath._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 225, 3)
- Value = property(__Value.value, __Value.set, None, None)
+ ElementPath = property(__ElementPath.value, __ElementPath.set, None, '\n An optional string attribute which holds the path to the offending element.\n ')
- # Attribute Operator uses Python identifier Operator
- __Operator = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Operator'), 'Operator', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_Operator', pyxb.binding.datatypes.string, required=True)
- __Operator._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 654, 8)
- __Operator._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 654, 8)
+ # Attribute SupplementalInfo uses Python identifier SupplementalInfo
+ __SupplementalInfo = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SupplementalInfo'), 'SupplementalInfo', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_19_SupplementalInfo', pyxb.binding.datatypes.string)
+ __SupplementalInfo._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 232, 3)
+ __SupplementalInfo._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 232, 3)
- Operator = property(__Operator.value, __Operator.set, None, None)
+ SupplementalInfo = property(__SupplementalInfo.value, __SupplementalInfo.set, None, '\n An optional string attribute which holds extraneous information.\n ')
_ElementMap.update({
})
_AttributeMap.update({
- __Name.name() : __Name,
- __Value.name() : __Value,
- __Operator.name() : __Operator
+ __IsValid.name() : __IsValid,
+ __ID.name() : __ID,
+ __Source.name() : __Source,
+ __ElementPath.name() : __ElementPath,
+ __SupplementalInfo.name() : __SupplementalInfo
})
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_20 (pyxb.binding.basis.complexTypeDefinition):
- """Root element of a standalone CollectionMetadata file."""
+# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ExperimentContainerType with content type ELEMENT_ONLY
+class ExperimentContainerType (_ImportedBinding__pbbase.BaseEntityType):
+ """A composite object type that can encompass multiple runs, possibly across multiple instruments.
+
+One use case may be that a user may have a large genome they'd like to sequence, and it may take multiple runs on multiple instruments, to get enough data. Another use case may be that a user has multiple samples of the same phenotype which they would like to analyze in a similar fashion/automation, and as such these samples are run as part of one experiment.
+
+The experiment object is intended to be packagable, such that the metadata of all acquisitions within is contained."""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 13, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainerType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 250, 1)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionMetadata uses Python identifier CollectionMetadata
- __CollectionMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), 'CollectionMetadata', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_20_httppacificbiosciences_comPacBioDataModel_xsdCollectionMetadata', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 136, 1), )
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InvestigatorName uses Python identifier InvestigatorName
+ __InvestigatorName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InvestigatorName'), 'InvestigatorName', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdInvestigatorName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 261, 5), )
- CollectionMetadata = property(__CollectionMetadata.value, __CollectionMetadata.set, None, 'Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ')
+ InvestigatorName = property(__InvestigatorName.value, __InvestigatorName.set, None, 'An optional PI name')
- _ElementMap.update({
- __CollectionMetadata.name() : __CollectionMetadata
- })
- _AttributeMap.update({
-
- })
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CreatedDate uses Python identifier CreatedDate
+ __CreatedDate = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CreatedDate'), 'CreatedDate', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdCreatedDate', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 266, 5), )
+
+ CreatedDate = property(__CreatedDate.value, __CreatedDate.set, None, 'Automatically generated creation date')
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Runs uses Python identifier Runs
+ __Runs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Runs'), 'Runs', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdRuns', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 271, 5), )
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType with content type ELEMENT_ONLY
-class DataSetMetadataType (pyxb.binding.basis.complexTypeDefinition):
- """Extend this type to provide DataSetMetadata element in each DataSet."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 31, 1)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}TotalLength uses Python identifier TotalLength
- __TotalLength = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TotalLength'), 'TotalLength', '__httppacificbiosciences_comPacBioDataModel_xsd_DataSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdTotalLength', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3), )
+ Runs = property(__Runs.value, __Runs.set, None, 'Multiple acquisitions from different instrument runs')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets uses Python identifier DataSets
+ __DataSets = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), 'DataSets', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdDataSets', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 281, 5), )
- TotalLength = property(__TotalLength.value, __TotalLength.set, None, None)
+ DataSets = property(__DataSets.value, __DataSets.set, None, 'Pointers to various data elements associated with the acquisitions')
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}NumRecords uses Python identifier NumRecords
- __NumRecords = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumRecords'), 'NumRecords', '__httppacificbiosciences_comPacBioDataModel_xsd_DataSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdNumRecords', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvents uses Python identifier RecordedEvents
+ __RecordedEvents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), 'RecordedEvents', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvents', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 291, 5), )
- NumRecords = property(__NumRecords.value, __NumRecords.set, None, None)
+ RecordedEvents = property(__RecordedEvents.value, __RecordedEvents.set, None, "Journal of metrics, system events, or alarms that were generated during this container's lifetime")
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Provenance uses Python identifier Provenance
- __Provenance = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Provenance'), 'Provenance', '__httppacificbiosciences_comPacBioDataModel_xsd_DataSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdProvenance', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3), )
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamples uses Python identifier BioSamples
+ __BioSamples = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), 'BioSamples', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdBioSamples', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 305, 5), )
- Provenance = property(__Provenance.value, __Provenance.set, None, None)
+ BioSamples = property(__BioSamples.value, __BioSamples.set, None, None)
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
_ElementMap.update({
- __TotalLength.name() : __TotalLength,
- __NumRecords.name() : __NumRecords,
- __Provenance.name() : __Provenance
+ __InvestigatorName.name() : __InvestigatorName,
+ __CreatedDate.name() : __CreatedDate,
+ __Runs.name() : __Runs,
+ __DataSets.name() : __DataSets,
+ __RecordedEvents.name() : __RecordedEvents,
+ __BioSamples.name() : __BioSamples
})
_AttributeMap.update({
})
-Namespace.addCategoryObject('typeBinding', 'DataSetMetadataType', DataSetMetadataType)
+Namespace.addCategoryObject('typeBinding', 'ExperimentContainerType', ExperimentContainerType)
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_21 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AssayType with content type ELEMENT_ONLY
+class AssayType (_ImportedBinding__pbbase.DataEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AssayType with content type ELEMENT_ONLY"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 66, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AdapterDimerFraction uses Python identifier AdapterDimerFraction
- __AdapterDimerFraction = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AdapterDimerFraction'), 'AdapterDimerFraction', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdAdapterDimerFraction', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 68, 8), )
-
-
- AdapterDimerFraction = property(__AdapterDimerFraction.value, __AdapterDimerFraction.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ShortInsertFraction uses Python identifier ShortInsertFraction
- __ShortInsertFraction = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ShortInsertFraction'), 'ShortInsertFraction', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdShortInsertFraction', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 69, 8), )
-
-
- ShortInsertFraction = property(__ShortInsertFraction.value, __ShortInsertFraction.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}NumSequencingZmws uses Python identifier NumSequencingZmws
- __NumSequencingZmws = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumSequencingZmws'), 'NumSequencingZmws', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdNumSequencingZmws', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 70, 8), )
-
-
- NumSequencingZmws = property(__NumSequencingZmws.value, __NumSequencingZmws.set, None, None)
-
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AssayType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 241, 1)
+ _ElementMap = _ImportedBinding__pbbase.DataEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.DataEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.DataEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ProdDist uses Python identifier ProdDist
- __ProdDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ProdDist'), 'ProdDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdProdDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 71, 8), )
-
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- ProdDist = property(__ProdDist.value, __ProdDist.set, None, None)
-
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadTypeDist uses Python identifier ReadTypeDist
- __ReadTypeDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReadTypeDist'), 'ReadTypeDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdReadTypeDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 72, 8), )
-
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
- ReadTypeDist = property(__ReadTypeDist.value, __ReadTypeDist.set, None, None)
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSets uses Python identifier SubreadSets
+ __SubreadSets = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets'), 'SubreadSets', '__httppacificbiosciences_comPacBioDataModel_xsd_AssayType_httppacificbiosciences_comPacBioDataModel_xsdSubreadSets', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 407, 1), )
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadLenDist uses Python identifier ReadLenDist
- __ReadLenDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReadLenDist'), 'ReadLenDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdReadLenDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 73, 8), )
+ SubreadSets = property(__SubreadSets.value, __SubreadSets.set, None, None)
- ReadLenDist = property(__ReadLenDist.value, __ReadLenDist.set, None, None)
-
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadQualDist uses Python identifier ReadQualDist
- __ReadQualDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReadQualDist'), 'ReadQualDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdReadQualDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 74, 8), )
-
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- ReadQualDist = property(__ReadQualDist.value, __ReadQualDist.set, None, None)
-
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ControlReadLenDist uses Python identifier ControlReadLenDist
- __ControlReadLenDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlReadLenDist'), 'ControlReadLenDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdControlReadLenDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 75, 8), )
-
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- ControlReadLenDist = property(__ControlReadLenDist.value, __ControlReadLenDist.set, None, None)
-
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ControlReadQualDist uses Python identifier ControlReadQualDist
- __ControlReadQualDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlReadQualDist'), 'ControlReadQualDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdControlReadQualDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 76, 8), )
-
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- ControlReadQualDist = property(__ControlReadQualDist.value, __ControlReadQualDist.set, None, None)
-
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MedianInsertDist uses Python identifier MedianInsertDist
- __MedianInsertDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MedianInsertDist'), 'MedianInsertDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdMedianInsertDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 77, 8), )
-
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- MedianInsertDist = property(__MedianInsertDist.value, __MedianInsertDist.set, None, None)
-
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InsertReadLenDist uses Python identifier InsertReadLenDist
- __InsertReadLenDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertReadLenDist'), 'InsertReadLenDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdInsertReadLenDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 78, 8), )
-
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
- InsertReadLenDist = property(__InsertReadLenDist.value, __InsertReadLenDist.set, None, None)
-
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InsertReadQualDist uses Python identifier InsertReadQualDist
- __InsertReadQualDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertReadQualDist'), 'InsertReadQualDist', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_21_httppacificbiosciences_comPacBioDataModel_xsdInsertReadQualDist', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 79, 8), )
-
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
- InsertReadQualDist = property(__InsertReadQualDist.value, __InsertReadQualDist.set, None, None)
-
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
_ElementMap.update({
- __AdapterDimerFraction.name() : __AdapterDimerFraction,
- __ShortInsertFraction.name() : __ShortInsertFraction,
- __NumSequencingZmws.name() : __NumSequencingZmws,
- __ProdDist.name() : __ProdDist,
- __ReadTypeDist.name() : __ReadTypeDist,
- __ReadLenDist.name() : __ReadLenDist,
- __ReadQualDist.name() : __ReadQualDist,
- __ControlReadLenDist.name() : __ControlReadLenDist,
- __ControlReadQualDist.name() : __ControlReadQualDist,
- __MedianInsertDist.name() : __MedianInsertDist,
- __InsertReadLenDist.name() : __InsertReadLenDist,
- __InsertReadQualDist.name() : __InsertReadQualDist
+ __SubreadSets.name() : __SubreadSets
})
_AttributeMap.update({
})
+Namespace.addCategoryObject('typeBinding', 'AssayType', AssayType)
+# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}RunType with content type ELEMENT_ONLY
+class RunType (_ImportedBinding__pbbase.StrictEntityType):
+ """A run is defined as a set of one or more data collections acquired in sequence on an instrument. A run specifies the wells and SMRT Cells to include in the sequencing run, along with the collection and analysis automation to use for the selected wells and cells.
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_22 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
+"""
_TypeDefinition = None
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 108, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'RunType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 316, 1)
+ _ElementMap = _ImportedBinding__pbbase.StrictEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.StrictEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.StrictEntityType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Filter uses Python identifier Filter
- __Filter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Filter'), 'Filter', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_22_httppacificbiosciences_comPacBioDataModel_xsdFilter', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 110, 8), )
-
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
- Filter = property(__Filter.value, __Filter.set, None, None)
-
- _ElementMap.update({
- __Filter.name() : __Filter
- })
- _AttributeMap.update({
-
- })
-
-
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Assay uses Python identifier Assay
+ __Assay = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Assay'), 'Assay', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdAssay', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 11, 1), )
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_23 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 115, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSet uses Python identifier DataSet
- __DataSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), 'DataSet', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_23_httppacificbiosciences_comPacBioDataModel_xsdDataSet', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 135, 1), )
+ Assay = property(__Assay.value, __Assay.set, None, None)
- DataSet = property(__DataSet.value, __DataSet.set, None, None)
-
- _ElementMap.update({
- __DataSet.name() : __DataSet
- })
- _AttributeMap.update({
-
- })
-
-
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RunResources uses Python identifier RunResources
+ __RunResources = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RunResources'), 'RunResources', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdRunResources', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 133, 1), )
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_24 (pyxb.binding.basis.complexTypeDefinition):
- """A set of acquisition definitions"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 129, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionMetadata uses Python identifier CollectionMetadata
- __CollectionMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), 'CollectionMetadata', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_24_httppacificbiosciences_comPacBioDataModel_xsdCollectionMetadata', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 136, 1), )
+ RunResources = property(__RunResources.value, __RunResources.set, None, 'This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc.')
- CollectionMetadata = property(__CollectionMetadata.value, __CollectionMetadata.set, None, 'Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ')
-
- _ElementMap.update({
- __CollectionMetadata.name() : __CollectionMetadata
- })
- _AttributeMap.update({
-
- })
-
-
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Outputs uses Python identifier Outputs
+ __Outputs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Outputs'), 'Outputs', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdOutputs', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 325, 5), )
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_25 (pyxb.binding.basis.complexTypeDefinition):
- """Information related to an instrument run. A run can contain multiple chips, wells, and movies. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 252, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RunId uses Python identifier RunId
- __RunId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RunId'), 'RunId', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_25_httppacificbiosciences_comPacBioDataModel_xsdRunId', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 254, 4), )
+ Outputs = property(__Outputs.value, __Outputs.set, None, None)
- RunId = property(__RunId.value, __RunId.set, None, 'A unique identifier for this run. Format is r[sid]_[iname]_[ts]. Where [id] is a system generated id and [iname] is the instrument name and [ts] is a timestamp YYMMDD Example: r000123_00117_100713 ')
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Inputs uses Python identifier Inputs
+ __Inputs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Inputs'), 'Inputs', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdInputs', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 339, 5), )
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Name uses Python identifier Name
- __Name = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_25_httppacificbiosciences_comPacBioDataModel_xsdName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 259, 4), )
+ Inputs = property(__Inputs.value, __Inputs.set, None, None)
- Name = property(__Name.value, __Name.set, None, 'Assigned name for a run, which consists of multiple wells. There is no constraint on the uniqueness of this data. ')
+ # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvents uses Python identifier RecordedEvents
+ __RecordedEvents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), 'RecordedEvents', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvents', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 352, 5), )
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CreatedBy uses Python identifier CreatedBy
- __CreatedBy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CreatedBy'), 'CreatedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_25_httppacificbiosciences_comPacBioDataModel_xsdCreatedBy', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 264, 4), )
+ RecordedEvents = property(__RecordedEvents.value, __RecordedEvents.set, None, "Journal of metrics, system events, or alarms that were generated during this run's lifetime")
- CreatedBy = property(__CreatedBy.value, __CreatedBy.set, None, 'Who created the run. ')
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute Status uses Python identifier Status
+ __Status = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Status'), 'Status', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_Status', _ImportedBinding__pbbase.SupportedRunStates)
+ __Status._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 368, 4)
+ __Status._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 368, 4)
+
+ Status = property(__Status.value, __Status.set, None, None)
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}WhenCreated uses Python identifier WhenCreated
- __WhenCreated = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WhenCreated'), 'WhenCreated', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_25_httppacificbiosciences_comPacBioDataModel_xsdWhenCreated', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 269, 4), )
+ # Attribute InstrumentId uses Python identifier InstrumentId
+ __InstrumentId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentId'), 'InstrumentId', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_InstrumentId', pyxb.binding.datatypes.string)
+ __InstrumentId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 369, 4)
+ __InstrumentId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 369, 4)
+
+ InstrumentId = property(__InstrumentId.value, __InstrumentId.set, None, 'World unique id assigned by PacBio. ')
- WhenCreated = property(__WhenCreated.value, __WhenCreated.set, None, 'Date and time of when the overall run was created in the system. ')
+ # Attribute InstrumentName uses Python identifier InstrumentName
+ __InstrumentName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentName'), 'InstrumentName', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_InstrumentName', pyxb.binding.datatypes.string)
+ __InstrumentName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 374, 4)
+ __InstrumentName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 374, 4)
+
+ InstrumentName = property(__InstrumentName.value, __InstrumentName.set, None, 'Friendly name assigned by customer')
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}StartedBy uses Python identifier StartedBy
- __StartedBy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'StartedBy'), 'StartedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_25_httppacificbiosciences_comPacBioDataModel_xsdStartedBy', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 274, 4), )
+ # Attribute CreatedBy uses Python identifier CreatedBy
+ __CreatedBy = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CreatedBy'), 'CreatedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_CreatedBy', pyxb.binding.datatypes.string)
+ __CreatedBy._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 379, 4)
+ __CreatedBy._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 379, 4)
+
+ CreatedBy = property(__CreatedBy.value, __CreatedBy.set, None, 'Who created the run. ')
+ # Attribute StartedBy uses Python identifier StartedBy
+ __StartedBy = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'StartedBy'), 'StartedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_StartedBy', pyxb.binding.datatypes.string)
+ __StartedBy._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 384, 4)
+ __StartedBy._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 384, 4)
+
StartedBy = property(__StartedBy.value, __StartedBy.set, None, 'Who started the run. Could be different from who created it. ')
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}WhenStarted uses Python identifier WhenStarted
- __WhenStarted = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), 'WhenStarted', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_25_httppacificbiosciences_comPacBioDataModel_xsdWhenStarted', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 279, 4), )
-
+ # Attribute WhenStarted uses Python identifier WhenStarted
+ __WhenStarted = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'WhenStarted'), 'WhenStarted', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_WhenStarted', STD_ANON_2)
+ __WhenStarted._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 389, 4)
+ __WhenStarted._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 389, 4)
WhenStarted = property(__WhenStarted.value, __WhenStarted.set, None, 'Date and time of when the overall run was started. ')
_ElementMap.update({
- __RunId.name() : __RunId,
- __Name.name() : __Name,
+ __Assay.name() : __Assay,
+ __RunResources.name() : __RunResources,
+ __Outputs.name() : __Outputs,
+ __Inputs.name() : __Inputs,
+ __RecordedEvents.name() : __RecordedEvents
+ })
+ _AttributeMap.update({
+ __Status.name() : __Status,
+ __InstrumentId.name() : __InstrumentId,
+ __InstrumentName.name() : __InstrumentName,
__CreatedBy.name() : __CreatedBy,
- __WhenCreated.name() : __WhenCreated,
__StartedBy.name() : __StartedBy,
__WhenStarted.name() : __WhenStarted
})
- _AttributeMap.update({
-
- })
+Namespace.addCategoryObject('typeBinding', 'RunType', RunType)
+ChipLayout = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), CTD_ANON, documentation='Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 12, 1))
+Namespace.addCategoryObject('elementBinding', ChipLayout.name().localName(), ChipLayout)
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_26 (pyxb.binding.basis.complexTypeDefinition):
- """A movie corresponds to one acquisition for a chip, one set (look) and one strobe. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 291, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}WhenStarted uses Python identifier WhenStarted
- __WhenStarted = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), 'WhenStarted', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_26_httppacificbiosciences_comPacBioDataModel_xsdWhenStarted', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 293, 4), )
-
-
- WhenStarted = property(__WhenStarted.value, __WhenStarted.set, None, 'Date and time of when this movie acquisition started. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DurationInSec uses Python identifier DurationInSec
- __DurationInSec = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DurationInSec'), 'DurationInSec', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_26_httppacificbiosciences_comPacBioDataModel_xsdDurationInSec', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 298, 4), )
-
-
- DurationInSec = property(__DurationInSec.value, __DurationInSec.set, None, 'The actual length of the movie acquisition (in seconds), irrespective of the movie duration specified by an automation parameter. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Number uses Python identifier Number
- __Number = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Number'), 'Number', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_26_httppacificbiosciences_comPacBioDataModel_xsdNumber', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 303, 4), )
-
-
- Number = property(__Number.value, __Number.set, None, "The number of this movie within the set (i.e., look). This is unique when combined with the 'SetNumber'. ")
-
- _ElementMap.update({
- __WhenStarted.name() : __WhenStarted,
- __DurationInSec.name() : __DurationInSec,
- __Number.name() : __Number
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_27 (pyxb.binding.basis.complexTypeDefinition):
- """Container for the expired consumable data. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 315, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}EightPacPastExpiration uses Python identifier EightPacPastExpiration
- __EightPacPastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'EightPacPastExpiration'), 'EightPacPastExpiration', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_27_httppacificbiosciences_comPacBioDataModel_xsdEightPacPastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 317, 4), )
-
-
- EightPacPastExpiration = property(__EightPacPastExpiration.value, __EightPacPastExpiration.set, None, 'Number of days past expiration the eight pac was (if at all). ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentKitPastExpiration uses Python identifier ReagentKitPastExpiration
- __ReagentKitPastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentKitPastExpiration'), 'ReagentKitPastExpiration', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_27_httppacificbiosciences_comPacBioDataModel_xsdReagentKitPastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 322, 4), )
-
-
- ReagentKitPastExpiration = property(__ReagentKitPastExpiration.value, __ReagentKitPastExpiration.set, None, 'Number of days past expiration the reagent kit was (if at all). ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTube0PastExpiration uses Python identifier ReagentTube0PastExpiration
- __ReagentTube0PastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube0PastExpiration'), 'ReagentTube0PastExpiration', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_27_httppacificbiosciences_comPacBioDataModel_xsdReagentTube0PastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 327, 4), )
-
-
- ReagentTube0PastExpiration = property(__ReagentTube0PastExpiration.value, __ReagentTube0PastExpiration.set, None, 'Number of days past expiration the reagent tube 0 was (if at all). ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTube1PastExpiration uses Python identifier ReagentTube1PastExpiration
- __ReagentTube1PastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube1PastExpiration'), 'ReagentTube1PastExpiration', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_27_httppacificbiosciences_comPacBioDataModel_xsdReagentTube1PastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 332, 4), )
-
-
- ReagentTube1PastExpiration = property(__ReagentTube1PastExpiration.value, __ReagentTube1PastExpiration.set, None, 'Number of days past expiration the reagent tube 1 was (if at all). ')
-
- _ElementMap.update({
- __EightPacPastExpiration.name() : __EightPacPastExpiration,
- __ReagentKitPastExpiration.name() : __ReagentKitPastExpiration,
- __ReagentTube0PastExpiration.name() : __ReagentTube0PastExpiration,
- __ReagentTube1PastExpiration.name() : __ReagentTube1PastExpiration
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_28 (pyxb.binding.basis.complexTypeDefinition):
- """A list of barcodes associated with the biological sample"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 351, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Barcode uses Python identifier Barcode
- __Barcode = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Barcode'), 'Barcode', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_28_httppacificbiosciences_comPacBioDataModel_xsdBarcode', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 353, 8), )
-
-
- Barcode = property(__Barcode.value, __Barcode.set, None, 'A sequence of barcodes associated with the biological sample')
-
- _ElementMap.update({
- __Barcode.name() : __Barcode
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_29 (pyxb.binding.basis.complexTypeDefinition):
- """Container for the primary analysis related data. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 507, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleTrace uses Python identifier SampleTrace
- __SampleTrace = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleTrace'), 'SampleTrace', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdSampleTrace', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 509, 4), )
-
-
- SampleTrace = property(__SampleTrace.value, __SampleTrace.set, None, 'Tag to indicate that the trace file will be sampled. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationName uses Python identifier AutomationName
- __AutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), 'AutomationName', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 528, 4), )
-
-
- AutomationName = property(__AutomationName.value, __AutomationName.set, None, 'Name of primary analysis protocol. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ConfigFileName uses Python identifier ConfigFileName
- __ConfigFileName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ConfigFileName'), 'ConfigFileName', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdConfigFileName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 533, 4), )
-
-
- ConfigFileName = property(__ConfigFileName.value, __ConfigFileName.set, None, 'Name of primary analysis config file. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingCondition uses Python identifier SequencingCondition
- __SequencingCondition = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingCondition'), 'SequencingCondition', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdSequencingCondition', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 538, 4), )
-
-
- SequencingCondition = property(__SequencingCondition.value, __SequencingCondition.set, None, 'A sequencing condition tag to be used by primary analysis, e.g., to select basecaller calibration or training parameters. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ResultsFolder uses Python identifier ResultsFolder
- __ResultsFolder = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ResultsFolder'), 'ResultsFolder', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdResultsFolder', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 543, 4), )
-
-
- ResultsFolder = property(__ResultsFolder.value, __ResultsFolder.set, None, "NOTE: not for customers. A sub-folder under the CollectionPath created by Primary Analysis. This is a field that will be updated by the primary analysis pipeline. The default (as created by homer) should be set to 'Reports_Sms' for now. Consumers of the data should be aware that they will find collection metadata (and trace files if acquisition is so-configured) at the CollectionPathUri, and all primary ana [...]
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionPathUri uses Python identifier CollectionPathUri
- __CollectionPathUri = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionPathUri'), 'CollectionPathUri', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdCollectionPathUri', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 548, 4), )
-
-
- CollectionPathUri = property(__CollectionPathUri.value, __CollectionPathUri.set, None, 'User-specified location of where the results should be copied after an analysis has been completed. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CopyFiles uses Python identifier CopyFiles
- __CopyFiles = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CopyFiles'), 'CopyFiles', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_29_httppacificbiosciences_comPacBioDataModel_xsdCopyFiles', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 553, 4), )
-
-
- CopyFiles = property(__CopyFiles.value, __CopyFiles.set, None, None)
-
- _ElementMap.update({
- __SampleTrace.name() : __SampleTrace,
- __AutomationName.name() : __AutomationName,
- __ConfigFileName.name() : __ConfigFileName,
- __SequencingCondition.name() : __SequencingCondition,
- __ResultsFolder.name() : __ResultsFolder,
- __CollectionPathUri.name() : __CollectionPathUri,
- __CopyFiles.name() : __CopyFiles
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_30 (pyxb.binding.basis.complexTypeDefinition):
- """Tag to indicate that the trace file will be sampled. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 513, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}TraceSamplingFactor uses Python identifier TraceSamplingFactor
- __TraceSamplingFactor = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TraceSamplingFactor'), 'TraceSamplingFactor', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_30_httppacificbiosciences_comPacBioDataModel_xsdTraceSamplingFactor', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 515, 7), )
-
-
- TraceSamplingFactor = property(__TraceSamplingFactor.value, __TraceSamplingFactor.set, None, 'Percentage of traces to sample. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}FullPulseFile uses Python identifier FullPulseFile
- __FullPulseFile = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'FullPulseFile'), 'FullPulseFile', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_30_httppacificbiosciences_comPacBioDataModel_xsdFullPulseFile', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 520, 7), )
-
-
- FullPulseFile = property(__FullPulseFile.value, __FullPulseFile.set, None, 'Whether full or sampled pulse file is transferred if requested. ')
-
- _ElementMap.update({
- __TraceSamplingFactor.name() : __TraceSamplingFactor,
- __FullPulseFile.name() : __FullPulseFile
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_31 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 554, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionFileCopy uses Python identifier CollectionFileCopy
- __CollectionFileCopy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionFileCopy'), 'CollectionFileCopy', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_31_httppacificbiosciences_comPacBioDataModel_xsdCollectionFileCopy', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 556, 7), )
-
-
- CollectionFileCopy = property(__CollectionFileCopy.value, __CollectionFileCopy.set, None, 'Defines the set of files to be copied to the CollectionPathUri. 1 or more. ')
-
- _ElementMap.update({
- __CollectionFileCopy.name() : __CollectionFileCopy
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_32 (pyxb.binding.basis.complexTypeDefinition):
- """Container for the primary analysis related data. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 572, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationName uses Python identifier AutomationName
- __AutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), 'AutomationName', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_32_httppacificbiosciences_comPacBioDataModel_xsdAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 574, 4), )
-
-
- AutomationName = property(__AutomationName.value, __AutomationName.set, None, 'The secondary analysis protocol name specified in the sample sheet. Ignored by secondary. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationParameters uses Python identifier AutomationParameters
- __AutomationParameters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), 'AutomationParameters', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_32_httppacificbiosciences_comPacBioDataModel_xsdAutomationParameters', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 579, 4), )
-
-
- AutomationParameters = property(__AutomationParameters.value, __AutomationParameters.set, None, 'The parameters for secondary analysis specified in the sample sheet. Ignored by secondary. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CellCountInJob uses Python identifier CellCountInJob
- __CellCountInJob = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellCountInJob'), 'CellCountInJob', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_32_httppacificbiosciences_comPacBioDataModel_xsdCellCountInJob', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 593, 4), )
-
-
- CellCountInJob = property(__CellCountInJob.value, __CellCountInJob.set, None, "The number of cells in this secondary analysis job, identified by the secondary analysis parameter 'JobName'. Supports automated secondary analysis. ")
-
- _ElementMap.update({
- __AutomationName.name() : __AutomationName,
- __AutomationParameters.name() : __AutomationParameters,
- __CellCountInJob.name() : __CellCountInJob
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_33 (pyxb.binding.basis.complexTypeDefinition):
- """The parameters for secondary analysis specified in the sample sheet. Ignored by secondary. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 583, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationParameter uses Python identifier AutomationParameter
- __AutomationParameter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), 'AutomationParameter', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_33_httppacificbiosciences_comPacBioDataModel_xsdAutomationParameter', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 585, 7), )
-
-
- AutomationParameter = property(__AutomationParameter.value, __AutomationParameter.set, None, 'One or more secondary analysis parameters, such as JobName, Workflow, etc..')
-
- _ElementMap.update({
- __AutomationParameter.name() : __AutomationParameter
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type SIMPLE
-class CTD_ANON_34 (pyxb.binding.basis.complexTypeDefinition):
- """One custom, possibly non-unique, key-value pair. """
- _TypeDefinition = pyxb.binding.datatypes.string
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_SIMPLE
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 611, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.string
-
- # Attribute key uses Python identifier key
- __key = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'key'), 'key', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_34_key', pyxb.binding.datatypes.string, required=True)
- __key._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 614, 5)
- __key._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 614, 5)
-
- key = property(__key.value, __key.set, None, 'Key (attribute) and Value (element content). ')
-
-
- # Attribute label uses Python identifier label
- __label = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'label'), 'label', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_34_label', pyxb.binding.datatypes.string)
- __label._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 619, 5)
- __label._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 619, 5)
-
- label = property(__label.value, __label.set, None, None)
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __key.name() : __key,
- __label.name() : __label
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_35 (pyxb.binding.basis.complexTypeDefinition):
- """Back references to other BarcodedSampleType object UniqueIds which utilize this sample"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 643, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamplePointer uses Python identifier BioSamplePointer
- __BioSamplePointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer'), 'BioSamplePointer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_35_httppacificbiosciences_comPacBioDataModel_xsdBioSamplePointer', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 650, 5), )
-
-
- BioSamplePointer = property(__BioSamplePointer.value, __BioSamplePointer.set, None, 'Pointer to a single biological sample')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodedSamplePointers uses Python identifier BarcodedSamplePointers
- __BarcodedSamplePointers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), 'BarcodedSamplePointers', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_35_httppacificbiosciences_comPacBioDataModel_xsdBarcodedSamplePointers', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 659, 1), )
-
-
- BarcodedSamplePointers = property(__BarcodedSamplePointers.value, __BarcodedSamplePointers.set, None, 'Back references to other BarcodedSampleType object UniqueIds which utilize this sample')
-
- _ElementMap.update({
- __BioSamplePointer.name() : __BioSamplePointer,
- __BarcodedSamplePointers.name() : __BarcodedSamplePointers
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_36 (pyxb.binding.basis.complexTypeDefinition):
- """Back references to other BarcodedSampleType object UniqueIds which utilize this sample"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 663, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodedSamplePointer uses Python identifier BarcodedSamplePointer
- __BarcodedSamplePointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), 'BarcodedSamplePointer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_36_httppacificbiosciences_comPacBioDataModel_xsdBarcodedSamplePointer', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 665, 4), )
-
-
- BarcodedSamplePointer = property(__BarcodedSamplePointer.value, __BarcodedSamplePointer.set, None, 'Pointer to a group of barcoded samples')
-
- _ElementMap.update({
- __BarcodedSamplePointer.name() : __BarcodedSamplePointer
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_37 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 674, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSample uses Python identifier BioSample
- __BioSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), 'BioSample', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_37_httppacificbiosciences_comPacBioDataModel_xsdBioSample', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 680, 1), )
-
-
- BioSample = property(__BioSample.value, __BioSample.set, None, None)
-
- _ElementMap.update({
- __BioSample.name() : __BioSample
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_38 (pyxb.binding.basis.complexTypeDefinition):
- """Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 16, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_38_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
-
- # Attribute Name uses Python identifier Name
- __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_38_Name', pyxb.binding.datatypes.string, required=True)
- __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 20, 3)
- __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 20, 3)
-
- Name = property(__Name.value, __Name.set, None, None)
-
-
- # Attribute PartNumber uses Python identifier PartNumber
- __PartNumber = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PartNumber'), 'PartNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_38_PartNumber', pyxb.binding.datatypes.string, required=True)
- __PartNumber._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 21, 3)
- __PartNumber._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 21, 3)
-
- PartNumber = property(__PartNumber.value, __PartNumber.set, None, None)
-
- _ElementMap.update({
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
- __Name.name() : __Name,
- __PartNumber.name() : __PartNumber
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_39 (pyxb.binding.basis.complexTypeDefinition):
- """A set of Chip Layouts deemed compatible with the current plate"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 28, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ChipLayout uses Python identifier ChipLayout
- __ChipLayout = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), 'ChipLayout', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_39_httppacificbiosciences_comPacBioDataModel_xsdChipLayout', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 12, 1), )
-
-
- ChipLayout = property(__ChipLayout.value, __ChipLayout.set, None, 'Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RequiredSMRTCells uses Python identifier RequiredSMRTCells
- __RequiredSMRTCells = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RequiredSMRTCells'), 'RequiredSMRTCells', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_39_httppacificbiosciences_comPacBioDataModel_xsdRequiredSMRTCells', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 106, 1), )
-
-
- RequiredSMRTCells = property(__RequiredSMRTCells.value, __RequiredSMRTCells.set, None, 'Part of the RunResources; specifies the required number of SMRT cells')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_39_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
- _ElementMap.update({
- __ChipLayout.name() : __ChipLayout,
- __RequiredSMRTCells.name() : __RequiredSMRTCells,
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_40 (pyxb.binding.basis.complexTypeDefinition):
- """A set of reagent kits deemed compatible with the current plate"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 40, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}EstimatedTotalRunTime uses Python identifier EstimatedTotalRunTime
- __EstimatedTotalRunTime = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime'), 'EstimatedTotalRunTime', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_40_httppacificbiosciences_comPacBioDataModel_xsdEstimatedTotalRunTime', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 48, 1), )
-
-
- EstimatedTotalRunTime = property(__EstimatedTotalRunTime.value, __EstimatedTotalRunTime.set, None, 'The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RequiredTips uses Python identifier RequiredTips
- __RequiredTips = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips'), 'RequiredTips', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_40_httppacificbiosciences_comPacBioDataModel_xsdRequiredTips', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 117, 1), )
-
-
- RequiredTips = property(__RequiredTips.value, __RequiredTips.set, None, 'Part of the RunResources; specifies the required number of tips via two attributes, Left and Right')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingKit uses Python identifier SequencingKit
- __SequencingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), 'SequencingKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_40_httppacificbiosciences_comPacBioDataModel_xsdSequencingKit', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 67, 1), )
-
-
- SequencingKit = property(__SequencingKit.value, __SequencingKit.set, None, None)
-
- _ElementMap.update({
- __EstimatedTotalRunTime.name() : __EstimatedTotalRunTime,
- __RequiredTips.name() : __RequiredTips,
- __SequencingKit.name() : __SequencingKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_41 (pyxb.binding.basis.complexTypeDefinition):
- """The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 52, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_41_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
-
- # Attribute Value uses Python identifier Value
- __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_41_Value', pyxb.binding.datatypes.string, required=True)
- __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 56, 3)
- __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 56, 3)
-
- Value = property(__Value.value, __Value.set, None, None)
-
-
- # Attribute Confidence uses Python identifier Confidence
- __Confidence = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Confidence'), 'Confidence', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_41_Confidence', pyxb.binding.datatypes.int, required=True)
- __Confidence._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 57, 3)
- __Confidence._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 57, 3)
-
- Confidence = property(__Confidence.value, __Confidence.set, None, None)
-
- _ElementMap.update({
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
- __Value.name() : __Value,
- __Confidence.name() : __Confidence
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_42 (pyxb.binding.basis.complexTypeDefinition):
- """PacBio Data Model root element"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 95, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExperimentContainer uses Python identifier ExperimentContainer
- __ExperimentContainer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainer'), 'ExperimentContainer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_42_httppacificbiosciences_comPacBioDataModel_xsdExperimentContainer', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 97, 4), )
-
-
- ExperimentContainer = property(__ExperimentContainer.value, __ExperimentContainer.set, None, None)
-
- _HasWildcardElement = True
- _ElementMap.update({
- __ExperimentContainer.name() : __ExperimentContainer
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_43 (pyxb.binding.basis.complexTypeDefinition):
- """Part of the RunResources; specifies the required number of SMRT cells"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 110, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_43_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
-
- # Attribute Quantity uses Python identifier Quantity
- __Quantity = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Quantity'), 'Quantity', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_43_Quantity', pyxb.binding.datatypes.int, required=True)
- __Quantity._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 114, 3)
- __Quantity._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 114, 3)
-
- Quantity = property(__Quantity.value, __Quantity.set, None, None)
-
- _ElementMap.update({
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
- __Quantity.name() : __Quantity
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_44 (pyxb.binding.basis.complexTypeDefinition):
- """Part of the RunResources; specifies the required number of tips via two attributes, Left and Right"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 121, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_44_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
-
- # Attribute Left uses Python identifier Left
- __Left = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Left'), 'Left', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_44_Left', pyxb.binding.datatypes.int, required=True)
- __Left._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 125, 3)
- __Left._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 125, 3)
-
- Left = property(__Left.value, __Left.set, None, None)
-
-
- # Attribute Right uses Python identifier Right
- __Right = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Right'), 'Right', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_44_Right', pyxb.binding.datatypes.int, required=True)
- __Right._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 126, 3)
- __Right._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 126, 3)
-
- Right = property(__Right.value, __Right.set, None, None)
-
- _ElementMap.update({
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
- __Left.name() : __Left,
- __Right.name() : __Right
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_45 (pyxb.binding.basis.complexTypeDefinition):
- """This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 133, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CompatibleChipLayouts uses Python identifier CompatibleChipLayouts
- __CompatibleChipLayouts = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts'), 'CompatibleChipLayouts', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_45_httppacificbiosciences_comPacBioDataModel_xsdCompatibleChipLayouts', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 24, 1), )
-
-
- CompatibleChipLayouts = property(__CompatibleChipLayouts.value, __CompatibleChipLayouts.set, None, 'A set of Chip Layouts deemed compatible with the current plate')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CompatibleSequencingKits uses Python identifier CompatibleSequencingKits
- __CompatibleSequencingKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits'), 'CompatibleSequencingKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_45_httppacificbiosciences_comPacBioDataModel_xsdCompatibleSequencingKits', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 36, 1), )
-
-
- CompatibleSequencingKits = property(__CompatibleSequencingKits.value, __CompatibleSequencingKits.set, None, 'A set of reagent kits deemed compatible with the current plate')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_45_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
- _ElementMap.update({
- __CompatibleChipLayouts.name() : __CompatibleChipLayouts,
- __CompatibleSequencingKits.name() : __CompatibleSequencingKits,
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type MIXED
-class CTD_ANON_46 (pyxb.binding.basis.complexTypeDefinition):
- """A general sample description"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_MIXED
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 145, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_46_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
-
- # Attribute Value uses Python identifier Value
- __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_46_Value', pyxb.binding.datatypes.string)
- __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 149, 3)
- __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 149, 3)
-
- Value = property(__Value.value, __Value.set, None, None)
-
- _ElementMap.update({
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
- __Value.name() : __Value
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_47 (pyxb.binding.basis.complexTypeDefinition):
- """Multiple acquisitions from different instrument runs"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 271, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Run uses Python identifier Run
- __Run = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Run'), 'Run', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_47_httppacificbiosciences_comPacBioDataModel_xsdRun', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 273, 8), )
-
-
- Run = property(__Run.value, __Run.set, None, None)
-
- _ElementMap.update({
- __Run.name() : __Run
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_48 (pyxb.binding.basis.complexTypeDefinition):
- """Pointers to various data elements associated with the acquisitions"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 281, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSet uses Python identifier DataSet
- __DataSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), 'DataSet', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_48_httppacificbiosciences_comPacBioDataModel_xsdDataSet', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 135, 1), )
-
-
- DataSet = property(__DataSet.value, __DataSet.set, None, None)
-
- _ElementMap.update({
- __DataSet.name() : __DataSet
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_49 (pyxb.binding.basis.complexTypeDefinition):
- """Journal of metrics, system events, or alarms that were generated during this container's lifetime"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 291, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvent uses Python identifier RecordedEvent
- __RecordedEvent = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), 'RecordedEvent', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_49_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvent', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 293, 8), )
-
-
- RecordedEvent = property(__RecordedEvent.value, __RecordedEvent.set, None, "Journal of metrics, system events, or alarms that were generated during this container's lifetime")
-
- _ElementMap.update({
- __RecordedEvent.name() : __RecordedEvent
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_50 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 302, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSample uses Python identifier BioSample
- __BioSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), 'BioSample', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_50_httppacificbiosciences_comPacBioDataModel_xsdBioSample', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 304, 8), )
-
-
- BioSample = property(__BioSample.value, __BioSample.set, None, None)
-
- _ElementMap.update({
- __BioSample.name() : __BioSample
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_51 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 322, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Input uses Python identifier Input
- __Input = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Input'), 'Input', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_51_httppacificbiosciences_comPacBioDataModel_xsdInput', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 61, 1), )
-
-
- Input = property(__Input.value, __Input.set, None, None)
-
- _ElementMap.update({
- __Input.name() : __Input
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_52 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 329, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Output uses Python identifier Output
- __Output = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Output'), 'Output', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_52_httppacificbiosciences_comPacBioDataModel_xsdOutput', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 62, 1), )
-
-
- Output = property(__Output.value, __Output.set, None, None)
-
- _ElementMap.update({
- __Output.name() : __Output
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_53 (pyxb.binding.basis.complexTypeDefinition):
- """Journal of metrics, system events, or alarms that were generated during this run's lifetime"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 345, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvent uses Python identifier RecordedEvent
- __RecordedEvent = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), 'RecordedEvent', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_53_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvent', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 347, 8), )
-
-
- RecordedEvent = property(__RecordedEvent.value, __RecordedEvent.set, None, "Journal of metrics, system events, or alarms that were generated during this run's lifetime.\nIn the case of Primary generating the DataSet containing the sts.xml, this RecordedEvent object should be a pointer to the DataSet object generated.")
-
- _ElementMap.update({
- __RecordedEvent.name() : __RecordedEvent
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_54 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 388, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionMetadataRef uses Python identifier CollectionMetadataRef
- __CollectionMetadataRef = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadataRef'), 'CollectionMetadataRef', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_54_httppacificbiosciences_comPacBioDataModel_xsdCollectionMetadataRef', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 390, 4), )
-
-
- CollectionMetadataRef = property(__CollectionMetadataRef.value, __CollectionMetadataRef.set, None, None)
-
- _ElementMap.update({
- __CollectionMetadataRef.name() : __CollectionMetadataRef
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_55 (pyxb.binding.basis.complexTypeDefinition):
- """The root element of the Part Numbers """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 12, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingKits uses Python identifier SequencingKits
- __SequencingKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKits'), 'SequencingKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_55_httppacificbiosciences_comPacBioDataModel_xsdSequencingKits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 14, 4), )
-
-
- SequencingKits = property(__SequencingKits.value, __SequencingKits.set, None, 'List the sequencing kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BindingKits uses Python identifier BindingKits
- __BindingKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BindingKits'), 'BindingKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_55_httppacificbiosciences_comPacBioDataModel_xsdBindingKits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 24, 4), )
-
-
- BindingKits = property(__BindingKits.value, __BindingKits.set, None, 'List the binding kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}TemplatePrepKits uses Python identifier TemplatePrepKits
- __TemplatePrepKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKits'), 'TemplatePrepKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_55_httppacificbiosciences_comPacBioDataModel_xsdTemplatePrepKits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 34, 4), )
-
-
- TemplatePrepKits = property(__TemplatePrepKits.value, __TemplatePrepKits.set, None, 'List the sample prep kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ControlKits uses Python identifier ControlKits
- __ControlKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlKits'), 'ControlKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_55_httppacificbiosciences_comPacBioDataModel_xsdControlKits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 44, 4), )
-
-
- ControlKits = property(__ControlKits.value, __ControlKits.set, None, 'List the DNA control complex part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CellPackKits uses Python identifier CellPackKits
- __CellPackKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellPackKits'), 'CellPackKits', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_55_httppacificbiosciences_comPacBioDataModel_xsdCellPackKits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 54, 4), )
-
-
- CellPackKits = property(__CellPackKits.value, __CellPackKits.set, None, 'List the cell tray part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
-
- _ElementMap.update({
- __SequencingKits.name() : __SequencingKits,
- __BindingKits.name() : __BindingKits,
- __TemplatePrepKits.name() : __TemplatePrepKits,
- __ControlKits.name() : __ControlKits,
- __CellPackKits.name() : __CellPackKits
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_56 (pyxb.binding.basis.complexTypeDefinition):
- """List the sequencing kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 18, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingKit uses Python identifier SequencingKit
- __SequencingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), 'SequencingKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_56_httppacificbiosciences_comPacBioDataModel_xsdSequencingKit', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 67, 1), )
-
-
- SequencingKit = property(__SequencingKit.value, __SequencingKit.set, None, None)
-
- _ElementMap.update({
- __SequencingKit.name() : __SequencingKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_57 (pyxb.binding.basis.complexTypeDefinition):
- """List the binding kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 28, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BindingKit uses Python identifier BindingKit
- __BindingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), 'BindingKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_57_httppacificbiosciences_comPacBioDataModel_xsdBindingKit', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 68, 1), )
-
-
- BindingKit = property(__BindingKit.value, __BindingKit.set, None, None)
-
- _ElementMap.update({
- __BindingKit.name() : __BindingKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_58 (pyxb.binding.basis.complexTypeDefinition):
- """List the sample prep kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 38, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}TemplatePrepKit uses Python identifier TemplatePrepKit
- __TemplatePrepKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), 'TemplatePrepKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_58_httppacificbiosciences_comPacBioDataModel_xsdTemplatePrepKit', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 69, 1), )
-
-
- TemplatePrepKit = property(__TemplatePrepKit.value, __TemplatePrepKit.set, None, None)
-
- _ElementMap.update({
- __TemplatePrepKit.name() : __TemplatePrepKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_59 (pyxb.binding.basis.complexTypeDefinition):
- """List the DNA control complex part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 48, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ControlKit uses Python identifier ControlKit
- __ControlKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlKit'), 'ControlKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_59_httppacificbiosciences_comPacBioDataModel_xsdControlKit', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 70, 1), )
-
-
- ControlKit = property(__ControlKit.value, __ControlKit.set, None, None)
-
- _ElementMap.update({
- __ControlKit.name() : __ControlKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_60 (pyxb.binding.basis.complexTypeDefinition):
- """List the cell tray part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 58, 5)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CellPackKit uses Python identifier CellPackKit
- __CellPackKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit'), 'CellPackKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_60_httppacificbiosciences_comPacBioDataModel_xsdCellPackKit', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 71, 1), )
-
-
- CellPackKit = property(__CellPackKit.value, __CellPackKit.set, None, None)
-
- _ElementMap.update({
- __CellPackKit.name() : __CellPackKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_61 (pyxb.binding.basis.complexTypeDefinition):
- """The root element of the reagent kit standalone file"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 11, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentKit uses Python identifier ReagentKit
- __ReagentKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), 'ReagentKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_61_httppacificbiosciences_comPacBioDataModel_xsdReagentKit', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 18, 1), )
-
-
- ReagentKit = property(__ReagentKit.value, __ReagentKit.set, None, None)
-
- _ElementMap.update({
- __ReagentKit.name() : __ReagentKit
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_62 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 70, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Reagent uses Python identifier Reagent
- __Reagent = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), 'Reagent', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_62_httppacificbiosciences_comPacBioDataModel_xsdReagent', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 17, 1), )
-
-
- Reagent = property(__Reagent.value, __Reagent.set, None, None)
-
- _ElementMap.update({
- __Reagent.name() : __Reagent
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_63 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 77, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTube uses Python identifier ReagentTube
- __ReagentTube = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), 'ReagentTube', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_63_httppacificbiosciences_comPacBioDataModel_xsdReagentTube', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 19, 1), )
-
-
- ReagentTube = property(__ReagentTube.value, __ReagentTube.set, None, None)
-
- _ElementMap.update({
- __ReagentTube.name() : __ReagentTube
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_64 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 84, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentPlateRow uses Python identifier ReagentPlateRow
- __ReagentPlateRow = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), 'ReagentPlateRow', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_64_httppacificbiosciences_comPacBioDataModel_xsdReagentPlateRow', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 20, 1), )
-
-
- ReagentPlateRow = property(__ReagentPlateRow.value, __ReagentPlateRow.set, None, None)
-
- _ElementMap.update({
- __ReagentPlateRow.name() : __ReagentPlateRow
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_65 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 91, 6)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CompatibleAutomation uses Python identifier CompatibleAutomation
- __CompatibleAutomation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomation'), 'CompatibleAutomation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_65_httppacificbiosciences_comPacBioDataModel_xsdCompatibleAutomation', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 93, 8), )
-
-
- CompatibleAutomation = property(__CompatibleAutomation.value, __CompatibleAutomation.set, None, None)
-
- _ElementMap.update({
- __CompatibleAutomation.name() : __CompatibleAutomation
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType with content type ELEMENT_ONLY
-class BaseEntityType (pyxb.binding.basis.complexTypeDefinition):
- """This is the base element type for all types in this data model"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BaseEntityType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 52, 1)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions uses Python identifier Extensions
- __Extensions = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Extensions'), 'Extensions', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_httppacificbiosciences_comPacBioDataModel_xsdExtensions', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3), )
-
-
- Extensions = property(__Extensions.value, __Extensions.set, None, None)
-
-
- # Attribute UniqueId uses Python identifier UniqueId
- __UniqueId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'UniqueId'), 'UniqueId', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_UniqueId', STD_ANON)
- __UniqueId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 65, 2)
- __UniqueId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 65, 2)
-
- UniqueId = property(__UniqueId.value, __UniqueId.set, None, 'A unique identifier, such as a GUID - likely autogenerated')
-
-
- # Attribute Name uses Python identifier Name
- __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_Name', pyxb.binding.datatypes.string)
- __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 75, 2)
- __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 75, 2)
-
- Name = property(__Name.value, __Name.set, None, 'A short text identifier; uniqueness not necessary')
-
-
- # Attribute TimeStampedName uses Python identifier TimeStampedName
- __TimeStampedName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TimeStampedName'), 'TimeStampedName', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_TimeStampedName', pyxb.binding.datatypes.string)
- __TimeStampedName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 80, 2)
- __TimeStampedName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 80, 2)
-
- TimeStampedName = property(__TimeStampedName.value, __TimeStampedName.set, None, 'This is NOT intended to be used as a unique field. For uniqueness, use UniqueId. In order to not utilize customer provided names, this attribute may be used as an alternative means of Human Readable ID, e.g. Run-20150304_231155')
-
-
- # Attribute Description uses Python identifier Description
- __Description = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Description'), 'Description', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_Description', pyxb.binding.datatypes.string)
- __Description._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 85, 2)
- __Description._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 85, 2)
-
- Description = property(__Description.value, __Description.set, None, 'A long text description of the object')
-
-
- # Attribute MetaType uses Python identifier MetaType
- __MetaType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MetaType'), 'MetaType', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_MetaType', pyxb.binding.datatypes.string)
- __MetaType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 90, 2)
- __MetaType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 90, 2)
-
- MetaType = property(__MetaType.value, __MetaType.set, None, 'Controlled Vocabulary, meant as a means to group similar entities; the type of the object, e.g. Instrument Run, Secondary Run, Assay, Sample, Barcode, Alignment File, Alarm, Exception, Metric, SystemEvent, etc.')
-
-
- # Attribute Tags uses Python identifier Tags
- __Tags = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Tags'), 'Tags', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_Tags', pyxb.binding.datatypes.string)
- __Tags._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 95, 2)
- __Tags._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 95, 2)
-
- Tags = property(__Tags.value, __Tags.set, None, 'A set of keywords assigned to the object to help describe it and allow it to be found via search')
-
-
- # Attribute ResourceId uses Python identifier ResourceId
- __ResourceId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ResourceId'), 'ResourceId', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_ResourceId', pyxb.binding.datatypes.anyURI)
- __ResourceId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 100, 2)
- __ResourceId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 100, 2)
-
- ResourceId = property(__ResourceId.value, __ResourceId.set, None, 'A uniform resource identifier used to identify a "web" resource. e.g. svc://run/acquisition/alignment/gridding')
-
-
- # Attribute Format uses Python identifier Format
- __Format = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Format'), 'Format', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_Format', pyxb.binding.datatypes.string)
- __Format._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 105, 2)
- __Format._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 105, 2)
-
- Format = property(__Format.value, __Format.set, None, 'Optional, but recommended. The MIME-Type of the referenced file. See http://www.iana.org/assignments/media-types/media-types.xhtml for examples')
-
-
- # Attribute Version uses Python identifier Version
- __Version = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Version'), 'Version', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_Version', pyxb.binding.datatypes.string)
- __Version._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 110, 2)
- __Version._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 110, 2)
-
- Version = property(__Version.value, __Version.set, None, 'An optional identifier denoting the revision of this particular entity')
-
-
- # Attribute CreatedAt uses Python identifier CreatedAt
- __CreatedAt = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CreatedAt'), 'CreatedAt', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_CreatedAt', pyxb.binding.datatypes.dateTime)
- __CreatedAt._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 115, 2)
- __CreatedAt._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 115, 2)
-
- CreatedAt = property(__CreatedAt.value, __CreatedAt.set, None, 'Timestamp designating the creation of this object, relative to UTC; millisecond precision is expected.')
-
-
- # Attribute ModifiedAt uses Python identifier ModifiedAt
- __ModifiedAt = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ModifiedAt'), 'ModifiedAt', '__httppacificbiosciences_comPacBioDataModel_xsd_BaseEntityType_ModifiedAt', pyxb.binding.datatypes.dateTime)
- __ModifiedAt._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 120, 2)
- __ModifiedAt._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 120, 2)
-
- ModifiedAt = property(__ModifiedAt.value, __ModifiedAt.set, None, 'Timestamp designating the modification of this object, relative to UTC; millisecond precision is expected.')
-
- _ElementMap.update({
- __Extensions.name() : __Extensions
- })
- _AttributeMap.update({
- __UniqueId.name() : __UniqueId,
- __Name.name() : __Name,
- __TimeStampedName.name() : __TimeStampedName,
- __Description.name() : __Description,
- __MetaType.name() : __MetaType,
- __Tags.name() : __Tags,
- __ResourceId.name() : __ResourceId,
- __Format.name() : __Format,
- __Version.name() : __Version,
- __CreatedAt.name() : __CreatedAt,
- __ModifiedAt.name() : __ModifiedAt
- })
-Namespace.addCategoryObject('typeBinding', 'BaseEntityType', BaseEntityType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_66 (pyxb.binding.basis.complexTypeDefinition):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 39, 4)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CommonServicesInstanceId uses Python identifier CommonServicesInstanceId
- __CommonServicesInstanceId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CommonServicesInstanceId'), 'CommonServicesInstanceId', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_66_httppacificbiosciences_comPacBioDataModel_xsdCommonServicesInstanceId', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 41, 6), )
-
-
- CommonServicesInstanceId = property(__CommonServicesInstanceId.value, __CommonServicesInstanceId.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CreatorUserId uses Python identifier CreatorUserId
- __CreatorUserId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CreatorUserId'), 'CreatorUserId', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_66_httppacificbiosciences_comPacBioDataModel_xsdCreatorUserId', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 42, 6), )
-
-
- CreatorUserId = property(__CreatorUserId.value, __CreatorUserId.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ParentJobId uses Python identifier ParentJobId
- __ParentJobId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ParentJobId'), 'ParentJobId', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_66_httppacificbiosciences_comPacBioDataModel_xsdParentJobId', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 43, 6), )
-
-
- ParentJobId = property(__ParentJobId.value, __ParentJobId.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ParentTool uses Python identifier ParentTool
- __ParentTool = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ParentTool'), 'ParentTool', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_66_httppacificbiosciences_comPacBioDataModel_xsdParentTool', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 44, 6), )
-
-
- ParentTool = property(__ParentTool.value, __ParentTool.set, None, None)
-
-
- # Attribute CreatedBy uses Python identifier CreatedBy
- __CreatedBy = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CreatedBy'), 'CreatedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_66_CreatedBy', STD_ANON_, required=True)
- __CreatedBy._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 46, 5)
- __CreatedBy._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 46, 5)
-
- CreatedBy = property(__CreatedBy.value, __CreatedBy.set, None, None)
-
- _ElementMap.update({
- __CommonServicesInstanceId.name() : __CommonServicesInstanceId,
- __CreatorUserId.name() : __CreatorUserId,
- __ParentJobId.name() : __ParentJobId,
- __ParentTool.name() : __ParentTool
- })
- _AttributeMap.update({
- __CreatedBy.name() : __CreatedBy
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadSetMetadataType with content type ELEMENT_ONLY
-class ReadSetMetadataType (DataSetMetadataType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadSetMetadataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReadSetMetadataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 59, 1)
- _ElementMap = DataSetMetadataType._ElementMap.copy()
- _AttributeMap = DataSetMetadataType._AttributeMap.copy()
- # Base type is DataSetMetadataType
-
- # Element TotalLength ({http://pacificbiosciences.com/PacBioDataModel.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element NumRecords ({http://pacificbiosciences.com/PacBioDataModel.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element Provenance ({http://pacificbiosciences.com/PacBioDataModel.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SummaryStats uses Python identifier SummaryStats
- __SummaryStats = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SummaryStats'), 'SummaryStats', '__httppacificbiosciences_comPacBioDataModel_xsd_ReadSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdSummaryStats', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 65, 5), )
-
-
- SummaryStats = property(__SummaryStats.value, __SummaryStats.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Collections uses Python identifier Collections
- __Collections = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Collections'), 'Collections', '__httppacificbiosciences_comPacBioDataModel_xsd_ReadSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdCollections', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 125, 1), )
-
-
- Collections = property(__Collections.value, __Collections.set, None, 'A set of acquisition definitions')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamples uses Python identifier BioSamples
- __BioSamples = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), 'BioSamples', '__httppacificbiosciences_comPacBioDataModel_xsd_ReadSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdBioSamples', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 673, 1), )
-
-
- BioSamples = property(__BioSamples.value, __BioSamples.set, None, None)
-
- _ElementMap.update({
- __SummaryStats.name() : __SummaryStats,
- __Collections.name() : __Collections,
- __BioSamples.name() : __BioSamples
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'ReadSetMetadataType', ReadSetMetadataType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSetMetadataType with content type ELEMENT_ONLY
-class SubreadSetMetadataType (DataSetMetadataType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSetMetadataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SubreadSetMetadataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 87, 1)
- _ElementMap = DataSetMetadataType._ElementMap.copy()
- _AttributeMap = DataSetMetadataType._AttributeMap.copy()
- # Base type is DataSetMetadataType
-
- # Element TotalLength ({http://pacificbiosciences.com/PacBioDataModel.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element NumRecords ({http://pacificbiosciences.com/PacBioDataModel.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element Provenance ({http://pacificbiosciences.com/PacBioDataModel.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AverageSubreadLength uses Python identifier AverageSubreadLength
- __AverageSubreadLength = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadLength'), 'AverageSubreadLength', '__httppacificbiosciences_comPacBioDataModel_xsd_SubreadSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdAverageSubreadLength', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 91, 5), )
-
-
- AverageSubreadLength = property(__AverageSubreadLength.value, __AverageSubreadLength.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AverageSubreadQuality uses Python identifier AverageSubreadQuality
- __AverageSubreadQuality = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadQuality'), 'AverageSubreadQuality', '__httppacificbiosciences_comPacBioDataModel_xsd_SubreadSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdAverageSubreadQuality', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 92, 5), )
-
-
- AverageSubreadQuality = property(__AverageSubreadQuality.value, __AverageSubreadQuality.set, None, None)
-
- _ElementMap.update({
- __AverageSubreadLength.name() : __AverageSubreadLength,
- __AverageSubreadQuality.name() : __AverageSubreadQuality
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SubreadSetMetadataType', SubreadSetMetadataType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_67 (pyxb.binding.basis.complexTypeDefinition):
- """A variable, as a name/value pair, associated with a protocol (one of Collection, Primary, and Secondary)"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 67, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Validation uses Python identifier Validation
- __Validation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Validation'), 'Validation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_67_httppacificbiosciences_comPacBioDataModel_xsdValidation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1), )
-
-
- Validation = property(__Validation.value, __Validation.set, None, '\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ')
-
-
- # Attribute Name uses Python identifier Name
- __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_67_Name', STD_ANON_2, required=True)
- __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 71, 3)
- __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 71, 3)
-
- Name = property(__Name.value, __Name.set, None, None)
-
-
- # Attribute Value uses Python identifier Value
- __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_67_Value', pyxb.binding.datatypes.string, required=True)
- __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 88, 3)
- __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 88, 3)
-
- Value = property(__Value.value, __Value.set, None, None)
-
- _ElementMap.update({
- __Validation.name() : __Validation
- })
- _AttributeMap.update({
- __Name.name() : __Name,
- __Value.name() : __Value
- })
-
-
-
-# Complex type [anonymous] with content type EMPTY
-class CTD_ANON_68 (pyxb.binding.basis.complexTypeDefinition):
- """
- A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.
- """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_EMPTY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 158, 2)
- _ElementMap = {}
- _AttributeMap = {}
- # Base type is pyxb.binding.datatypes.anyType
-
- # Attribute IsValid uses Python identifier IsValid
- __IsValid = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'IsValid'), 'IsValid', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_68_IsValid', pyxb.binding.datatypes.boolean, required=True)
- __IsValid._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 159, 3)
- __IsValid._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 159, 3)
-
- IsValid = property(__IsValid.value, __IsValid.set, None, '\n Indicates whether or not the element is valid. The assumption is that the\n Validation element is omitted unless the element is invalid, in which case,\n the Validation element would describe the problem.\n ')
-
-
- # Attribute ID uses Python identifier ID
- __ID = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ID'), 'ID', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_68_ID', pyxb.binding.datatypes.string, required=True)
- __ID._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 168, 3)
- __ID._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 168, 3)
-
- ID = property(__ID.value, __ID.set, None, '\n An identifier which can be used by client applications to translate/map\n to a human decipherable message.\n ')
-
-
- # Attribute Source uses Python identifier Source
- __Source = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Source'), 'Source', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_68_Source', STD_ANON_3, required=True)
- __Source._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 176, 3)
- __Source._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 176, 3)
-
- Source = property(__Source.value, __Source.set, None, '\n This is the element which has experienced a validation issue.\n ')
-
-
- # Attribute ElementPath uses Python identifier ElementPath
- __ElementPath = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ElementPath'), 'ElementPath', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_68_ElementPath', pyxb.binding.datatypes.string)
- __ElementPath._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 221, 3)
- __ElementPath._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 221, 3)
-
- ElementPath = property(__ElementPath.value, __ElementPath.set, None, '\n An optional string attribute which holds the path to the offending element.\n ')
-
-
- # Attribute SupplementalInfo uses Python identifier SupplementalInfo
- __SupplementalInfo = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SupplementalInfo'), 'SupplementalInfo', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_68_SupplementalInfo', pyxb.binding.datatypes.string)
- __SupplementalInfo._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 228, 3)
- __SupplementalInfo._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 228, 3)
-
- SupplementalInfo = property(__SupplementalInfo.value, __SupplementalInfo.set, None, '\n An optional string attribute which holds extraneous information.\n ')
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __IsValid.name() : __IsValid,
- __ID.name() : __ID,
- __Source.name() : __Source,
- __ElementPath.name() : __ElementPath,
- __SupplementalInfo.name() : __SupplementalInfo
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AlignmentSetMetadataType with content type ELEMENT_ONLY
-class AlignmentSetMetadataType (DataSetMetadataType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AlignmentSetMetadataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AlignmentSetMetadataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 137, 1)
- _ElementMap = DataSetMetadataType._ElementMap.copy()
- _AttributeMap = DataSetMetadataType._AttributeMap.copy()
- # Base type is DataSetMetadataType
-
- # Element TotalLength ({http://pacificbiosciences.com/PacBioDataModel.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element NumRecords ({http://pacificbiosciences.com/PacBioDataModel.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element Provenance ({http://pacificbiosciences.com/PacBioDataModel.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Aligner uses Python identifier Aligner
- __Aligner = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Aligner'), 'Aligner', '__httppacificbiosciences_comPacBioDataModel_xsd_AlignmentSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdAligner', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 141, 5), )
-
-
- Aligner = property(__Aligner.value, __Aligner.set, None, None)
-
- _ElementMap.update({
- __Aligner.name() : __Aligner
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'AlignmentSetMetadataType', AlignmentSetMetadataType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ContigSetMetadataType with content type ELEMENT_ONLY
-class ContigSetMetadataType (DataSetMetadataType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ContigSetMetadataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ContigSetMetadataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 146, 1)
- _ElementMap = DataSetMetadataType._ElementMap.copy()
- _AttributeMap = DataSetMetadataType._AttributeMap.copy()
- # Base type is DataSetMetadataType
-
- # Element TotalLength ({http://pacificbiosciences.com/PacBioDataModel.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element NumRecords ({http://pacificbiosciences.com/PacBioDataModel.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element Provenance ({http://pacificbiosciences.com/PacBioDataModel.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Contigs uses Python identifier Contigs
- __Contigs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Contigs'), 'Contigs', '__httppacificbiosciences_comPacBioDataModel_xsd_ContigSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdContigs', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 114, 1), )
-
-
- Contigs = property(__Contigs.value, __Contigs.set, None, 'List of contigs in a ContigSet')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Organism uses Python identifier Organism
- __Organism = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Organism'), 'Organism', '__httppacificbiosciences_comPacBioDataModel_xsd_ContigSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdOrganism', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 150, 5), )
-
-
- Organism = property(__Organism.value, __Organism.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Ploidy uses Python identifier Ploidy
- __Ploidy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Ploidy'), 'Ploidy', '__httppacificbiosciences_comPacBioDataModel_xsd_ContigSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdPloidy', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 151, 5), )
-
-
- Ploidy = property(__Ploidy.value, __Ploidy.set, None, None)
-
- _ElementMap.update({
- __Contigs.name() : __Contigs,
- __Organism.name() : __Organism,
- __Ploidy.name() : __Ploidy
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'ContigSetMetadataType', ContigSetMetadataType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodeSetMetadataType with content type ELEMENT_ONLY
-class BarcodeSetMetadataType (DataSetMetadataType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodeSetMetadataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BarcodeSetMetadataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 157, 1)
- _ElementMap = DataSetMetadataType._ElementMap.copy()
- _AttributeMap = DataSetMetadataType._AttributeMap.copy()
- # Base type is DataSetMetadataType
-
- # Element TotalLength ({http://pacificbiosciences.com/PacBioDataModel.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element NumRecords ({http://pacificbiosciences.com/PacBioDataModel.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element Provenance ({http://pacificbiosciences.com/PacBioDataModel.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadataType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodeConstruction uses Python identifier BarcodeConstruction
- __BarcodeConstruction = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodeConstruction'), 'BarcodeConstruction', '__httppacificbiosciences_comPacBioDataModel_xsd_BarcodeSetMetadataType_httppacificbiosciences_comPacBioDataModel_xsdBarcodeConstruction', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 161, 5), )
-
-
- BarcodeConstruction = property(__BarcodeConstruction.value, __BarcodeConstruction.set, None, None)
-
- _ElementMap.update({
- __BarcodeConstruction.name() : __BarcodeConstruction
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'BarcodeSetMetadataType', BarcodeSetMetadataType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationConstraintType with content type ELEMENT_ONLY
-class AutomationConstraintType (BaseEntityType):
- """This data type defines constraints that an automation has. The information here, along with the availability of an exclusionary list of automations in the PartNumberType, allows for defining a robust compatibility matrix."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraintType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 27, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Automations uses Python identifier Automations
- __Automations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automations'), 'Automations', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationConstraintType_httppacificbiosciences_comPacBioDataModel_xsdAutomations', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 34, 5), )
-
-
- Automations = property(__Automations.value, __Automations.set, None, 'Names of automations that are all similarly constrained')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InsertSizes uses Python identifier InsertSizes
- __InsertSizes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertSizes'), 'InsertSizes', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationConstraintType_httppacificbiosciences_comPacBioDataModel_xsdInsertSizes', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 44, 5), )
-
-
- InsertSizes = property(__InsertSizes.value, __InsertSizes.set, None, 'A list of insert sizes (buckets) recommended for use')
-
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute SupportsCellReuse uses Python identifier SupportsCellReuse
- __SupportsCellReuse = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SupportsCellReuse'), 'SupportsCellReuse', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationConstraintType_SupportsCellReuse', pyxb.binding.datatypes.boolean)
- __SupportsCellReuse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 55, 4)
- __SupportsCellReuse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 55, 4)
-
- SupportsCellReuse = property(__SupportsCellReuse.value, __SupportsCellReuse.set, None, 'Does this automation support cell reuse?')
-
-
- # Attribute MaxCollectionsPerCell uses Python identifier MaxCollectionsPerCell
- __MaxCollectionsPerCell = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MaxCollectionsPerCell'), 'MaxCollectionsPerCell', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationConstraintType_MaxCollectionsPerCell', pyxb.binding.datatypes.int)
- __MaxCollectionsPerCell._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 60, 4)
- __MaxCollectionsPerCell._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 60, 4)
-
- MaxCollectionsPerCell = property(__MaxCollectionsPerCell.value, __MaxCollectionsPerCell.set, None, 'If cell reuse is supported (i.e. above attribute is true) how many times can the cell be reused?')
-
-
- # Attribute MinMovieLength uses Python identifier MinMovieLength
- __MinMovieLength = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MinMovieLength'), 'MinMovieLength', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationConstraintType_MinMovieLength', pyxb.binding.datatypes.int)
- __MinMovieLength._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 65, 4)
- __MinMovieLength._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 65, 4)
-
- MinMovieLength = property(__MinMovieLength.value, __MinMovieLength.set, None, 'Minimum length of movie acquisition')
-
-
- # Attribute MaxMovieLength uses Python identifier MaxMovieLength
- __MaxMovieLength = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MaxMovieLength'), 'MaxMovieLength', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationConstraintType_MaxMovieLength', pyxb.binding.datatypes.int)
- __MaxMovieLength._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 70, 4)
- __MaxMovieLength._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 70, 4)
-
- MaxMovieLength = property(__MaxMovieLength.value, __MaxMovieLength.set, None, 'Maximum length of movie acquisition')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __Automations.name() : __Automations,
- __InsertSizes.name() : __InsertSizes
- })
- _AttributeMap.update({
- __SupportsCellReuse.name() : __SupportsCellReuse,
- __MaxCollectionsPerCell.name() : __MaxCollectionsPerCell,
- __MinMovieLength.name() : __MinMovieLength,
- __MaxMovieLength.name() : __MaxMovieLength
- })
-Namespace.addCategoryObject('typeBinding', 'AutomationConstraintType', AutomationConstraintType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType with content type ELEMENT_ONLY
-class AnalogType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AnalogType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 6, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Base uses Python identifier Base
- __Base = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Base'), 'Base', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_Base', SupportedNucleotides)
- __Base._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 9, 4)
- __Base._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 9, 4)
-
- Base = property(__Base.value, __Base.set, None, 'The base label, A, C, T, or G')
-
-
- # Attribute SpectralAngle uses Python identifier SpectralAngle
- __SpectralAngle = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SpectralAngle'), 'SpectralAngle', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_SpectralAngle', pyxb.binding.datatypes.float)
- __SpectralAngle._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 14, 4)
- __SpectralAngle._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 14, 4)
-
- SpectralAngle = property(__SpectralAngle.value, __SpectralAngle.set, None, 'In radians (0 \u2264 \u03b1 \u2264 \u03c0/2), it is the estimate of arctan(red_pixel / green_pixel), where red[green]_pixel is the relative amplitude, as measured by the instrument\u2019s detector, of emitted light that is collected in the red[green] pixel channel.')
-
-
- # Attribute RelativeAmplitude uses Python identifier RelativeAmplitude
- __RelativeAmplitude = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'RelativeAmplitude'), 'RelativeAmplitude', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_RelativeAmplitude', pyxb.binding.datatypes.float)
- __RelativeAmplitude._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 19, 4)
- __RelativeAmplitude._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 19, 4)
-
- RelativeAmplitude = property(__RelativeAmplitude.value, __RelativeAmplitude.set, None, 'Relative intensity vs. a specific molecule used as a baseline measure. The expected relative amplitude (DWS-normalized) of the analog label relative to 542 as measured on Astro.')
-
-
- # Attribute Label uses Python identifier Label
- __Label = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Label'), 'Label', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_Label', pyxb.binding.datatypes.string)
- __Label._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 24, 4)
- __Label._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 24, 4)
-
- Label = property(__Label.value, __Label.set, None, 'Identifier of the acceptor dye which determines the emission spectrum')
-
-
- # Attribute Nucleotide uses Python identifier Nucleotide
- __Nucleotide = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Nucleotide'), 'Nucleotide', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_Nucleotide', pyxb.binding.datatypes.string)
- __Nucleotide._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 29, 4)
- __Nucleotide._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 29, 4)
-
- Nucleotide = property(__Nucleotide.value, __Nucleotide.set, None, 'The type and number of nucleotides on a given analog. e.g. (dT6P)6')
-
-
- # Attribute Wavelength uses Python identifier Wavelength
- __Wavelength = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Wavelength'), 'Wavelength', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_Wavelength', pyxb.binding.datatypes.float)
- __Wavelength._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 34, 4)
- __Wavelength._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 34, 4)
-
- Wavelength = property(__Wavelength.value, __Wavelength.set, None, 'The peak emission wavelength associated with the dye label in nm.')
-
-
- # Attribute CompoundID uses Python identifier CompoundID
- __CompoundID = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CompoundID'), 'CompoundID', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_CompoundID', pyxb.binding.datatypes.string)
- __CompoundID._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 39, 4)
- __CompoundID._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 39, 4)
-
- CompoundID = property(__CompoundID.value, __CompoundID.set, None, 'Identification code of the final compound. The suffix \u2018N\u2019 should be used to distinguish these values from enzyme identifiers.\te.g. 5031N')
-
-
- # Attribute LotID uses Python identifier LotID
- __LotID = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'LotID'), 'LotID', '__httppacificbiosciences_comPacBioDataModel_xsd_AnalogType_LotID', pyxb.binding.datatypes.string)
- __LotID._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 44, 4)
- __LotID._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 44, 4)
-
- LotID = property(__LotID.value, __LotID.set, None, 'Identification code for the build of the final compound, written as initials/date, where date is written as YYYY-MM-DD.\te.g. js/2014-06-30')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __Base.name() : __Base,
- __SpectralAngle.name() : __SpectralAngle,
- __RelativeAmplitude.name() : __RelativeAmplitude,
- __Label.name() : __Label,
- __Nucleotide.name() : __Nucleotide,
- __Wavelength.name() : __Wavelength,
- __CompoundID.name() : __CompoundID,
- __LotID.name() : __LotID
- })
-Namespace.addCategoryObject('typeBinding', 'AnalogType', AnalogType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType with content type ELEMENT_ONLY
-class DataEntityType (BaseEntityType):
- """Extends BaseEntityType and adds a value element. The intent is to have only one of the value elements exist at any point in time; however, this is not enforced."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DataEntityType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 137, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue uses Python identifier EncodedValue
- __EncodedValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue'), 'EncodedValue', '__httppacificbiosciences_comPacBioDataModel_xsd_DataEntityType_httppacificbiosciences_comPacBioDataModel_xsdEncodedValue', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5), )
-
-
- EncodedValue = property(__EncodedValue.value, __EncodedValue.set, None, 'A complex data type element, such as an image, file, binary object, etc.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum uses Python identifier CheckSum
- __CheckSum = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CheckSum'), 'CheckSum', '__httppacificbiosciences_comPacBioDataModel_xsd_DataEntityType_httppacificbiosciences_comPacBioDataModel_xsdCheckSum', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5), )
-
-
- CheckSum = property(__CheckSum.value, __CheckSum.set, None, 'small-size datum of the attached value for the purpose of detecting errors or modification which may have been introduced during its transmission or storage')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType uses Python identifier ValueDataType
- __ValueDataType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ValueDataType'), 'ValueDataType', '__httppacificbiosciences_comPacBioDataModel_xsd_DataEntityType_ValueDataType', SupportedDataTypes, unicode_default='Object')
- __ValueDataType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 155, 4)
- __ValueDataType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 155, 4)
-
- ValueDataType = property(__ValueDataType.value, __ValueDataType.set, None, 'The datatype of the simple or encoded value. If not specified, a string is assumed.')
-
-
- # Attribute SimpleValue uses Python identifier SimpleValue
- __SimpleValue = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SimpleValue'), 'SimpleValue', '__httppacificbiosciences_comPacBioDataModel_xsd_DataEntityType_SimpleValue', pyxb.binding.datatypes.anySimpleType)
- __SimpleValue._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 160, 4)
- __SimpleValue._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 160, 4)
-
- SimpleValue = property(__SimpleValue.value, __SimpleValue.set, None, 'A simple data type element, such as a string, int, float, etc.')
-
- _ElementMap.update({
- __EncodedValue.name() : __EncodedValue,
- __CheckSum.name() : __CheckSum
- })
- _AttributeMap.update({
- __ValueDataType.name() : __ValueDataType,
- __SimpleValue.name() : __SimpleValue
- })
-Namespace.addCategoryObject('typeBinding', 'DataEntityType', DataEntityType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}DNABarcode with content type ELEMENT_ONLY
-class DNABarcode (BaseEntityType):
- """Composite of uuid, sequence, and name"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DNABarcode')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 178, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute DNASequence uses Python identifier DNASequence
- __DNASequence = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DNASequence'), 'DNASequence', '__httppacificbiosciences_comPacBioDataModel_xsd_DNABarcode_DNASequence', pyxb.binding.datatypes.anySimpleType)
- __DNASequence._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 184, 4)
- __DNASequence._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 184, 4)
-
- DNASequence = property(__DNASequence.value, __DNASequence.set, None, "This is the sample's DNA barcode")
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __DNASequence.name() : __DNASequence
- })
-Namespace.addCategoryObject('typeBinding', 'DNABarcode', DNABarcode)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationType with content type ELEMENT_ONLY
-class AutomationType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AutomationType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 237, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}AutomationParameters uses Python identifier AutomationParameters
- __AutomationParameters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), 'AutomationParameters', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationType_httppacificbiosciences_comPacBioDataModel_xsdAutomationParameters', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 241, 5), )
-
-
- AutomationParameters = property(__AutomationParameters.value, __AutomationParameters.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute IsObsolete uses Python identifier IsObsolete
- __IsObsolete = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'IsObsolete'), 'IsObsolete', '__httppacificbiosciences_comPacBioDataModel_xsd_AutomationType_IsObsolete', pyxb.binding.datatypes.boolean)
- __IsObsolete._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 249, 4)
- __IsObsolete._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 249, 4)
-
- IsObsolete = property(__IsObsolete.value, __IsObsolete.set, None, None)
-
- _ElementMap.update({
- __AutomationParameters.name() : __AutomationParameters
- })
- _AttributeMap.update({
- __IsObsolete.name() : __IsObsolete
- })
-Namespace.addCategoryObject('typeBinding', 'AutomationType', AutomationType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_69 (BaseEntityType):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 342, 6)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Analogs uses Python identifier Analogs
- __Analogs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), 'Analogs', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_69_httppacificbiosciences_comPacBioDataModel_xsdAnalogs', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 346, 10), )
-
-
- Analogs = property(__Analogs.value, __Analogs.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __Analogs.name() : __Analogs
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingChemistryConfig with content type ELEMENT_ONLY
-class SequencingChemistryConfig (BaseEntityType):
- """A container for a set of analogs"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistryConfig')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 372, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Analogs uses Python identifier Analogs
- __Analogs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), 'Analogs', '__httppacificbiosciences_comPacBioDataModel_xsd_SequencingChemistryConfig_httppacificbiosciences_comPacBioDataModel_xsdAnalogs', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 379, 5), )
-
-
- Analogs = property(__Analogs.value, __Analogs.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __Analogs.name() : __Analogs
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SequencingChemistryConfig', SequencingChemistryConfig)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}StatsContinuousDistType with content type ELEMENT_ONLY
-class StatsContinuousDistType (BaseEntityType):
- """Continuous distribution class"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StatsContinuousDistType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 390, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleSize uses Python identifier SampleSize
- __SampleSize = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleSize'), 'SampleSize', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdSampleSize', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 397, 5), )
-
-
- SampleSize = property(__SampleSize.value, __SampleSize.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleMean uses Python identifier SampleMean
- __SampleMean = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleMean'), 'SampleMean', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdSampleMean', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 398, 5), )
-
-
- SampleMean = property(__SampleMean.value, __SampleMean.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleMed uses Python identifier SampleMed
- __SampleMed = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleMed'), 'SampleMed', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdSampleMed', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 399, 5), )
-
-
- SampleMed = property(__SampleMed.value, __SampleMed.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleStd uses Python identifier SampleStd
- __SampleStd = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleStd'), 'SampleStd', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdSampleStd', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 400, 5), )
-
-
- SampleStd = property(__SampleStd.value, __SampleStd.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Sample95thPct uses Python identifier Sample95thPct
- __Sample95thPct = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Sample95thPct'), 'Sample95thPct', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdSample95thPct', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 401, 5), )
-
-
- Sample95thPct = property(__Sample95thPct.value, __Sample95thPct.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}NumBins uses Python identifier NumBins
- __NumBins = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), 'NumBins', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdNumBins', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 402, 5), )
-
-
- NumBins = property(__NumBins.value, __NumBins.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinCounts uses Python identifier BinCounts
- __BinCounts = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), 'BinCounts', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdBinCounts', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 403, 5), )
-
-
- BinCounts = property(__BinCounts.value, __BinCounts.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinWidth uses Python identifier BinWidth
- __BinWidth = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinWidth'), 'BinWidth', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdBinWidth', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 410, 5), )
-
-
- BinWidth = property(__BinWidth.value, __BinWidth.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MinOutlierValue uses Python identifier MinOutlierValue
- __MinOutlierValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MinOutlierValue'), 'MinOutlierValue', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdMinOutlierValue', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 411, 5), )
-
-
- MinOutlierValue = property(__MinOutlierValue.value, __MinOutlierValue.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MinBinValue uses Python identifier MinBinValue
- __MinBinValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MinBinValue'), 'MinBinValue', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdMinBinValue', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 412, 5), )
-
-
- MinBinValue = property(__MinBinValue.value, __MinBinValue.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MaxBinValue uses Python identifier MaxBinValue
- __MaxBinValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MaxBinValue'), 'MaxBinValue', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdMaxBinValue', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 413, 5), )
-
-
- MaxBinValue = property(__MaxBinValue.value, __MaxBinValue.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MaxOutlierValue uses Python identifier MaxOutlierValue
- __MaxOutlierValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MaxOutlierValue'), 'MaxOutlierValue', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdMaxOutlierValue', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 414, 5), )
-
-
- MaxOutlierValue = property(__MaxOutlierValue.value, __MaxOutlierValue.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MetricDescription uses Python identifier MetricDescription
- __MetricDescription = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), 'MetricDescription', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioDataModel_xsdMetricDescription', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 415, 5), )
-
-
- MetricDescription = property(__MetricDescription.value, __MetricDescription.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Channel uses Python identifier Channel
- __Channel = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Channel'), 'Channel', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsContinuousDistType_Channel', pyxb.binding.datatypes.string)
- __Channel._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 417, 4)
- __Channel._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 417, 4)
-
- Channel = property(__Channel.value, __Channel.set, None, None)
-
- _ElementMap.update({
- __SampleSize.name() : __SampleSize,
- __SampleMean.name() : __SampleMean,
- __SampleMed.name() : __SampleMed,
- __SampleStd.name() : __SampleStd,
- __Sample95thPct.name() : __Sample95thPct,
- __NumBins.name() : __NumBins,
- __BinCounts.name() : __BinCounts,
- __BinWidth.name() : __BinWidth,
- __MinOutlierValue.name() : __MinOutlierValue,
- __MinBinValue.name() : __MinBinValue,
- __MaxBinValue.name() : __MaxBinValue,
- __MaxOutlierValue.name() : __MaxOutlierValue,
- __MetricDescription.name() : __MetricDescription
- })
- _AttributeMap.update({
- __Channel.name() : __Channel
- })
-Namespace.addCategoryObject('typeBinding', 'StatsContinuousDistType', StatsContinuousDistType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}StatsDiscreteDistType with content type ELEMENT_ONLY
-class StatsDiscreteDistType (BaseEntityType):
- """Discrete distribution class"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StatsDiscreteDistType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 421, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}NumBins uses Python identifier NumBins
- __NumBins = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), 'NumBins', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioDataModel_xsdNumBins', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 428, 5), )
-
-
- NumBins = property(__NumBins.value, __NumBins.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinCounts uses Python identifier BinCounts
- __BinCounts = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), 'BinCounts', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioDataModel_xsdBinCounts', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 429, 5), )
-
-
- BinCounts = property(__BinCounts.value, __BinCounts.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MetricDescription uses Python identifier MetricDescription
- __MetricDescription = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), 'MetricDescription', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioDataModel_xsdMetricDescription', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 436, 5), )
-
-
- MetricDescription = property(__MetricDescription.value, __MetricDescription.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BinLabels uses Python identifier BinLabels
- __BinLabels = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinLabels'), 'BinLabels', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioDataModel_xsdBinLabels', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 437, 5), )
-
-
- BinLabels = property(__BinLabels.value, __BinLabels.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __NumBins.name() : __NumBins,
- __BinCounts.name() : __BinCounts,
- __MetricDescription.name() : __MetricDescription,
- __BinLabels.name() : __BinLabels
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'StatsDiscreteDistType', StatsDiscreteDistType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}StatsTimeSeriesType with content type ELEMENT_ONLY
-class StatsTimeSeriesType (BaseEntityType):
- """Time series (for time-dependent metrics)"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StatsTimeSeriesType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 448, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}TimeUnits uses Python identifier TimeUnits
- __TimeUnits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TimeUnits'), 'TimeUnits', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioDataModel_xsdTimeUnits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 455, 5), )
-
-
- TimeUnits = property(__TimeUnits.value, __TimeUnits.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ValueUnits uses Python identifier ValueUnits
- __ValueUnits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ValueUnits'), 'ValueUnits', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioDataModel_xsdValueUnits', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 456, 5), )
-
-
- ValueUnits = property(__ValueUnits.value, __ValueUnits.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}StartTime uses Python identifier StartTime
- __StartTime = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'StartTime'), 'StartTime', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioDataModel_xsdStartTime', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 457, 5), )
-
-
- StartTime = property(__StartTime.value, __StartTime.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}MeasInterval uses Python identifier MeasInterval
- __MeasInterval = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MeasInterval'), 'MeasInterval', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioDataModel_xsdMeasInterval', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 458, 5), )
-
-
- MeasInterval = property(__MeasInterval.value, __MeasInterval.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Values uses Python identifier Values
- __Values = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Values'), 'Values', '__httppacificbiosciences_comPacBioDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioDataModel_xsdValues', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 459, 5), )
-
-
- Values = property(__Values.value, __Values.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __TimeUnits.name() : __TimeUnits,
- __ValueUnits.name() : __ValueUnits,
- __StartTime.name() : __StartTime,
- __MeasInterval.name() : __MeasInterval,
- __Values.name() : __Values
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'StatsTimeSeriesType', StatsTimeSeriesType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType with content type ELEMENT_ONLY
-class DataSetType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DataSetType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 102, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources uses Python identifier ExternalResources
- __ExternalResources = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), 'ExternalResources', '__httppacificbiosciences_comPacBioDataModel_xsd_DataSetType_httppacificbiosciences_comPacBioDataModel_xsdExternalResources', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 202, 1), )
-
-
- ExternalResources = property(__ExternalResources.value, __ExternalResources.set, None, 'Pointers to data that do not reside inside the parent structure')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Filters uses Python identifier Filters
- __Filters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Filters'), 'Filters', '__httppacificbiosciences_comPacBioDataModel_xsd_DataSetType_httppacificbiosciences_comPacBioDataModel_xsdFilters', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5), )
-
-
- Filters = property(__Filters.value, __Filters.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets uses Python identifier DataSets
- __DataSets = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), 'DataSets', '__httppacificbiosciences_comPacBioDataModel_xsd_DataSetType_httppacificbiosciences_comPacBioDataModel_xsdDataSets', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5), )
-
-
- DataSets = property(__DataSets.value, __DataSets.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __ExternalResources.name() : __ExternalResources,
- __Filters.name() : __Filters,
- __DataSets.name() : __DataSets
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'DataSetType', DataSetType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_70 (BaseEntityType):
- """Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 140, 2)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InstCtrlVer uses Python identifier InstCtrlVer
- __InstCtrlVer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InstCtrlVer'), 'InstCtrlVer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdInstCtrlVer', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 144, 6), )
-
-
- InstCtrlVer = property(__InstCtrlVer.value, __InstCtrlVer.set, None, 'Instrument control software version. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SigProcVer uses Python identifier SigProcVer
- __SigProcVer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SigProcVer'), 'SigProcVer', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdSigProcVer', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 149, 6), )
-
-
- SigProcVer = property(__SigProcVer.value, __SigProcVer.set, None, 'Signal processing software version. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Automation uses Python identifier Automation
- __Automation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automation'), 'Automation', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdAutomation', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 171, 6), )
-
-
- Automation = property(__Automation.value, __Automation.set, None, 'Defines the collection workflow (e.g., robotic movement, movie acquisition) for a particular cell. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CollectionNumber uses Python identifier CollectionNumber
- __CollectionNumber = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionNumber'), 'CollectionNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdCollectionNumber', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 176, 6), )
-
-
- CollectionNumber = property(__CollectionNumber.value, __CollectionNumber.set, None, 'Collection number for this plate well. Sample from one plate well or tube can be distributed to more than one cell. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CellIndex uses Python identifier CellIndex
- __CellIndex = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellIndex'), 'CellIndex', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdCellIndex', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 181, 6), )
-
-
- CellIndex = property(__CellIndex.value, __CellIndex.set, None, 'The zero-based index of this particular cell within the cell tray. Likely to be in the range of [0-3]')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SetNumber uses Python identifier SetNumber
- __SetNumber = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SetNumber'), 'SetNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdSetNumber', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 186, 6), )
-
-
- SetNumber = property(__SetNumber.value, __SetNumber.set, None, 'Formerly known as the look number. 1 - N. Defaults to 1. 0 if the look is unknown. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CellPac uses Python identifier CellPac
- __CellPac = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellPac'), 'CellPac', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdCellPac', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 191, 6), )
-
-
- CellPac = property(__CellPac.value, __CellPac.set, None, 'The SMRT cell packaging supply information. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}TemplatePrepKit uses Python identifier TemplatePrepKit
- __TemplatePrepKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), 'TemplatePrepKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdTemplatePrepKit', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 196, 6), )
-
-
- TemplatePrepKit = property(__TemplatePrepKit.value, __TemplatePrepKit.set, None, 'Defines the template (sample) prep kit used for this experiment. Can be used to get back to the primary and adapter used. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BindingKit uses Python identifier BindingKit
- __BindingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), 'BindingKit', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdBindingKit', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 201, 6), )
-
-
- BindingKit = property(__BindingKit.value, __BindingKit.set, None, 'The binding kit supply information. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingKitPlate uses Python identifier SequencingKitPlate
- __SequencingKitPlate = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitPlate'), 'SequencingKitPlate', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdSequencingKitPlate', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 206, 6), )
-
-
- SequencingKitPlate = property(__SequencingKitPlate.value, __SequencingKitPlate.set, None, 'The sequencing kit supply information. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RunDetails uses Python identifier RunDetails
- __RunDetails = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RunDetails'), 'RunDetails', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdRunDetails', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 248, 1), )
-
-
- RunDetails = property(__RunDetails.value, __RunDetails.set, None, 'Information related to an instrument run. A run can contain multiple chips, wells, and movies. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Movie uses Python identifier Movie
- __Movie = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Movie'), 'Movie', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdMovie', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 287, 1), )
-
-
- Movie = property(__Movie.value, __Movie.set, None, 'A movie corresponds to one acquisition for a chip, one set (look) and one strobe. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExpirationData uses Python identifier ExpirationData
- __ExpirationData = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData'), 'ExpirationData', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdExpirationData', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 311, 1), )
-
-
- ExpirationData = property(__ExpirationData.value, __ExpirationData.set, None, 'Container for the expired consumable data. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}WellSample uses Python identifier WellSample
- __WellSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WellSample'), 'WellSample', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdWellSample', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 432, 1), )
-
-
- WellSample = property(__WellSample.value, __WellSample.set, None, 'Container for the sample related data. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Primary uses Python identifier Primary
- __Primary = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Primary'), 'Primary', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdPrimary', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 503, 1), )
-
-
- Primary = property(__Primary.value, __Primary.set, None, 'Container for the primary analysis related data. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Secondary uses Python identifier Secondary
- __Secondary = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Secondary'), 'Secondary', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdSecondary', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 568, 1), )
-
-
- Secondary = property(__Secondary.value, __Secondary.set, None, 'Container for the primary analysis related data. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}UserDefinedFields uses Python identifier UserDefinedFields
- __UserDefinedFields = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields'), 'UserDefinedFields', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_httppacificbiosciences_comPacBioDataModel_xsdUserDefinedFields', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 602, 1), )
-
-
- UserDefinedFields = property(__UserDefinedFields.value, __UserDefinedFields.set, None, 'A set of key-value pairs specified by a user via the run input mechanism. Note that uniqueness of keys is not enforced here and so may contain duplicate keys. ')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Context uses Python identifier Context
- __Context = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Context'), 'Context', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_Context', pyxb.binding.datatypes.string)
- __Context._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 232, 5)
- __Context._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 232, 5)
-
- Context = property(__Context.value, __Context.set, None, None)
-
-
- # Attribute Status uses Python identifier Status
- __Status = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Status'), 'Status', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_Status', SupportedAcquisitionStates)
- __Status._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 233, 5)
- __Status._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 233, 5)
-
- Status = property(__Status.value, __Status.set, None, None)
-
-
- # Attribute InstrumentId uses Python identifier InstrumentId
- __InstrumentId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentId'), 'InstrumentId', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_InstrumentId', pyxb.binding.datatypes.string)
- __InstrumentId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 234, 5)
- __InstrumentId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 234, 5)
-
- InstrumentId = property(__InstrumentId.value, __InstrumentId.set, None, 'World unique id assigned by PacBio. ')
-
-
- # Attribute InstrumentName uses Python identifier InstrumentName
- __InstrumentName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentName'), 'InstrumentName', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_70_InstrumentName', pyxb.binding.datatypes.string)
- __InstrumentName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 239, 5)
- __InstrumentName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 239, 5)
-
- InstrumentName = property(__InstrumentName.value, __InstrumentName.set, None, 'Friendly name assigned by customer')
-
- _ElementMap.update({
- __InstCtrlVer.name() : __InstCtrlVer,
- __SigProcVer.name() : __SigProcVer,
- __Automation.name() : __Automation,
- __CollectionNumber.name() : __CollectionNumber,
- __CellIndex.name() : __CellIndex,
- __SetNumber.name() : __SetNumber,
- __CellPac.name() : __CellPac,
- __TemplatePrepKit.name() : __TemplatePrepKit,
- __BindingKit.name() : __BindingKit,
- __SequencingKitPlate.name() : __SequencingKitPlate,
- __RunDetails.name() : __RunDetails,
- __Movie.name() : __Movie,
- __ExpirationData.name() : __ExpirationData,
- __WellSample.name() : __WellSample,
- __Primary.name() : __Primary,
- __Secondary.name() : __Secondary,
- __UserDefinedFields.name() : __UserDefinedFields
- })
- _AttributeMap.update({
- __Context.name() : __Context,
- __Status.name() : __Status,
- __InstrumentId.name() : __InstrumentId,
- __InstrumentName.name() : __InstrumentName
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType with content type ELEMENT_ONLY
-class BioSampleType (BaseEntityType):
- """The actual biological sample; this could be prep'd, or in original form; could be bound, or annealed..."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BioSampleType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 365, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamples uses Python identifier BioSamples
- __BioSamples = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), 'BioSamples', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_httppacificbiosciences_comPacBioDataModel_xsdBioSamples', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 673, 1), )
-
-
- BioSamples = property(__BioSamples.value, __BioSamples.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute DateReceived uses Python identifier DateReceived
- __DateReceived = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DateReceived'), 'DateReceived', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_DateReceived', pyxb.binding.datatypes.dateTime)
- __DateReceived._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 374, 4)
- __DateReceived._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 374, 4)
-
- DateReceived = property(__DateReceived.value, __DateReceived.set, None, 'Date the sample was received by the lab')
-
-
- # Attribute Organism uses Python identifier Organism
- __Organism = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Organism'), 'Organism', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_Organism', pyxb.binding.datatypes.string)
- __Organism._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 379, 4)
- __Organism._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 379, 4)
-
- Organism = property(__Organism.value, __Organism.set, None, 'e.g. HIV, E.coli')
-
-
- # Attribute Reference uses Python identifier Reference
- __Reference = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Reference'), 'Reference', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_Reference', pyxb.binding.datatypes.string)
- __Reference._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 384, 4)
- __Reference._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 384, 4)
-
- Reference = property(__Reference.value, __Reference.set, None, 'Name of reference, or pointer to one at e.g. NCBI RefSeq')
-
-
- # Attribute DNAType uses Python identifier DNAType
- __DNAType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DNAType'), 'DNAType', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_DNAType', pyxb.binding.datatypes.string)
- __DNAType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 389, 4)
- __DNAType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 389, 4)
-
- DNAType = property(__DNAType.value, __DNAType.set, None, 'shotgun library, amplicon, etc.')
-
-
- # Attribute Concentration uses Python identifier Concentration
- __Concentration = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Concentration'), 'Concentration', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_Concentration', pyxb.binding.datatypes.float)
- __Concentration._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 394, 4)
- __Concentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 394, 4)
-
- Concentration = property(__Concentration.value, __Concentration.set, None, 'in ng/uL, e.g. 250')
-
-
- # Attribute QuantificationMethod uses Python identifier QuantificationMethod
- __QuantificationMethod = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'QuantificationMethod'), 'QuantificationMethod', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_QuantificationMethod', pyxb.binding.datatypes.string)
- __QuantificationMethod._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 399, 4)
- __QuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 399, 4)
-
- QuantificationMethod = property(__QuantificationMethod.value, __QuantificationMethod.set, None, 'e.g. Qubit')
-
-
- # Attribute SMRTBellConcentration uses Python identifier SMRTBellConcentration
- __SMRTBellConcentration = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SMRTBellConcentration'), 'SMRTBellConcentration', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_SMRTBellConcentration', pyxb.binding.datatypes.float)
- __SMRTBellConcentration._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 404, 4)
- __SMRTBellConcentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 404, 4)
-
- SMRTBellConcentration = property(__SMRTBellConcentration.value, __SMRTBellConcentration.set, None, 'in ng/uL, e.g. 4.5')
-
-
- # Attribute SMRTBellQuantificationMethod uses Python identifier SMRTBellQuantificationMethod
- __SMRTBellQuantificationMethod = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SMRTBellQuantificationMethod'), 'SMRTBellQuantificationMethod', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_SMRTBellQuantificationMethod', pyxb.binding.datatypes.string)
- __SMRTBellQuantificationMethod._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 409, 4)
- __SMRTBellQuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 409, 4)
-
- SMRTBellQuantificationMethod = property(__SMRTBellQuantificationMethod.value, __SMRTBellQuantificationMethod.set, None, 'e.g. Qubit')
-
-
- # Attribute BufferName uses Python identifier BufferName
- __BufferName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'BufferName'), 'BufferName', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_BufferName', pyxb.binding.datatypes.string)
- __BufferName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 414, 4)
- __BufferName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 414, 4)
-
- BufferName = property(__BufferName.value, __BufferName.set, None, 'e.g. Tris HCl')
-
-
- # Attribute SamplePrepKit uses Python identifier SamplePrepKit
- __SamplePrepKit = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SamplePrepKit'), 'SamplePrepKit', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_SamplePrepKit', pyxb.binding.datatypes.string)
- __SamplePrepKit._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 419, 4)
- __SamplePrepKit._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 419, 4)
-
- SamplePrepKit = property(__SamplePrepKit.value, __SamplePrepKit.set, None, 'e.g. SMRTbell Template Prep Kit')
-
-
- # Attribute TargetLibrarySize uses Python identifier TargetLibrarySize
- __TargetLibrarySize = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TargetLibrarySize'), 'TargetLibrarySize', '__httppacificbiosciences_comPacBioDataModel_xsd_BioSampleType_TargetLibrarySize', pyxb.binding.datatypes.string)
- __TargetLibrarySize._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 424, 4)
- __TargetLibrarySize._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 424, 4)
-
- TargetLibrarySize = property(__TargetLibrarySize.value, __TargetLibrarySize.set, None, '2000, 10000, 20000')
-
- _ElementMap.update({
- __BioSamples.name() : __BioSamples
- })
- _AttributeMap.update({
- __DateReceived.name() : __DateReceived,
- __Organism.name() : __Organism,
- __Reference.name() : __Reference,
- __DNAType.name() : __DNAType,
- __Concentration.name() : __Concentration,
- __QuantificationMethod.name() : __QuantificationMethod,
- __SMRTBellConcentration.name() : __SMRTBellConcentration,
- __SMRTBellQuantificationMethod.name() : __SMRTBellQuantificationMethod,
- __BufferName.name() : __BufferName,
- __SamplePrepKit.name() : __SamplePrepKit,
- __TargetLibrarySize.name() : __TargetLibrarySize
- })
-Namespace.addCategoryObject('typeBinding', 'BioSampleType', BioSampleType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_71 (BaseEntityType):
- """Container for the sample related data. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 436, 2)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}PlateId uses Python identifier PlateId
- __PlateId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'PlateId'), 'PlateId', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdPlateId', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 440, 6), )
-
-
- PlateId = property(__PlateId.value, __PlateId.set, None, 'The ID of the sample plate. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}WellName uses Python identifier WellName
- __WellName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WellName'), 'WellName', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdWellName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 445, 6), )
-
-
- WellName = property(__WellName.value, __WellName.set, None, 'Identifies which well this sample came from (e.g., coordinate on a plate). ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Concentration uses Python identifier Concentration
- __Concentration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Concentration'), 'Concentration', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdConcentration', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 450, 6), )
-
-
- Concentration = property(__Concentration.value, __Concentration.set, None, 'Sample input concentration. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleReuseEnabled uses Python identifier SampleReuseEnabled
- __SampleReuseEnabled = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleReuseEnabled'), 'SampleReuseEnabled', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdSampleReuseEnabled', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 455, 6), )
-
-
- SampleReuseEnabled = property(__SampleReuseEnabled.value, __SampleReuseEnabled.set, None, 'Whether or not complex reuse is enabled for this well. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}StageHotstartEnabled uses Python identifier StageHotstartEnabled
- __StageHotstartEnabled = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'StageHotstartEnabled'), 'StageHotstartEnabled', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdStageHotstartEnabled', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 460, 6), )
-
-
- StageHotstartEnabled = property(__StageHotstartEnabled.value, __StageHotstartEnabled.set, None, 'Whether or not hotstart at the stage is enabled for this well. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SizeSelectionEnabled uses Python identifier SizeSelectionEnabled
- __SizeSelectionEnabled = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SizeSelectionEnabled'), 'SizeSelectionEnabled', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdSizeSelectionEnabled', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 465, 6), )
-
-
- SizeSelectionEnabled = property(__SizeSelectionEnabled.value, __SizeSelectionEnabled.set, None, 'Whether or not size selection is enabled for this well. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}UseCount uses Python identifier UseCount
- __UseCount = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'UseCount'), 'UseCount', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdUseCount', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 470, 6), )
-
-
- UseCount = property(__UseCount.value, __UseCount.set, None, 'Count of usages for this batch of complex. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Comments uses Python identifier Comments
- __Comments = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Comments'), 'Comments', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdComments', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 475, 6), )
-
-
- Comments = property(__Comments.value, __Comments.set, None, 'User-supplied comments about the sample. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DNAControlComplex uses Python identifier DNAControlComplex
- __DNAControlComplex = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DNAControlComplex'), 'DNAControlComplex', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdDNAControlComplex', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 480, 6), )
-
-
- DNAControlComplex = property(__DNAControlComplex.value, __DNAControlComplex.set, None, 'Indicating what kind (if any) control was used. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SampleBarcodeInfo uses Python identifier SampleBarcodeInfo
- __SampleBarcodeInfo = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleBarcodeInfo'), 'SampleBarcodeInfo', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdSampleBarcodeInfo', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 485, 6), )
-
-
- SampleBarcodeInfo = property(__SampleBarcodeInfo.value, __SampleBarcodeInfo.set, None, 'When utilizing DNA barcoding, store the list of smaple barcodes in this element.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamplePointers uses Python identifier BioSamplePointers
- __BioSamplePointers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointers'), 'BioSamplePointers', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_71_httppacificbiosciences_comPacBioDataModel_xsdBioSamplePointers', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 639, 1), )
-
-
- BioSamplePointers = property(__BioSamplePointers.value, __BioSamplePointers.set, None, 'Back references to other BarcodedSampleType object UniqueIds which utilize this sample')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __PlateId.name() : __PlateId,
- __WellName.name() : __WellName,
- __Concentration.name() : __Concentration,
- __SampleReuseEnabled.name() : __SampleReuseEnabled,
- __StageHotstartEnabled.name() : __StageHotstartEnabled,
- __SizeSelectionEnabled.name() : __SizeSelectionEnabled,
- __UseCount.name() : __UseCount,
- __Comments.name() : __Comments,
- __DNAControlComplex.name() : __DNAControlComplex,
- __SampleBarcodeInfo.name() : __SampleBarcodeInfo,
- __BioSamplePointers.name() : __BioSamplePointers
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentType with content type ELEMENT_ONLY
-class ReagentType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 54, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ReagentKey uses Python identifier ReagentKey
- __ReagentKey = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentKey'), 'ReagentKey', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentType_ReagentKey', ReagentKey, required=True)
- __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 57, 4)
- __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 57, 4)
-
- ReagentKey = property(__ReagentKey.value, __ReagentKey.set, None, None)
-
-
- # Attribute PlateColumn uses Python identifier PlateColumn
- __PlateColumn = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PlateColumn'), 'PlateColumn', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentType_PlateColumn', pyxb.binding.datatypes.string, required=True)
- __PlateColumn._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 58, 4)
- __PlateColumn._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 58, 4)
-
- PlateColumn = property(__PlateColumn.value, __PlateColumn.set, None, None)
-
-
- # Attribute Volume uses Python identifier Volume
- __Volume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Volume'), 'Volume', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentType_Volume', pyxb.binding.datatypes.int, required=True)
- __Volume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 59, 4)
- __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 59, 4)
-
- Volume = property(__Volume.value, __Volume.set, None, None)
-
-
- # Attribute DeadVolume uses Python identifier DeadVolume
- __DeadVolume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DeadVolume'), 'DeadVolume', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentType_DeadVolume', pyxb.binding.datatypes.int, required=True)
- __DeadVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 60, 4)
- __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 60, 4)
-
- DeadVolume = property(__DeadVolume.value, __DeadVolume.set, None, None)
-
-
- # Attribute ActiveInHour uses Python identifier ActiveInHour
- __ActiveInHour = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveInHour'), 'ActiveInHour', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentType_ActiveInHour', pyxb.binding.datatypes.int, required=True)
- __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 61, 4)
- __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 61, 4)
-
- ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __ReagentKey.name() : __ReagentKey,
- __PlateColumn.name() : __PlateColumn,
- __Volume.name() : __Volume,
- __DeadVolume.name() : __DeadVolume,
- __ActiveInHour.name() : __ActiveInHour
- })
-Namespace.addCategoryObject('typeBinding', 'ReagentType', ReagentType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentKitType with content type ELEMENT_ONLY
-class ReagentKitType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentKitType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentKitType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 65, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Reagents uses Python identifier Reagents
- __Reagents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), 'Reagents', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_httppacificbiosciences_comPacBioDataModel_xsdReagents', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 69, 5), )
-
-
- Reagents = property(__Reagents.value, __Reagents.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTubes uses Python identifier ReagentTubes
- __ReagentTubes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), 'ReagentTubes', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_httppacificbiosciences_comPacBioDataModel_xsdReagentTubes', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 76, 5), )
-
-
- ReagentTubes = property(__ReagentTubes.value, __ReagentTubes.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentPlateRows uses Python identifier ReagentPlateRows
- __ReagentPlateRows = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), 'ReagentPlateRows', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_httppacificbiosciences_comPacBioDataModel_xsdReagentPlateRows', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 83, 5), )
-
-
- ReagentPlateRows = property(__ReagentPlateRows.value, __ReagentPlateRows.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CompatibleAutomations uses Python identifier CompatibleAutomations
- __CompatibleAutomations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomations'), 'CompatibleAutomations', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_httppacificbiosciences_comPacBioDataModel_xsdCompatibleAutomations', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 90, 5), )
-
-
- CompatibleAutomations = property(__CompatibleAutomations.value, __CompatibleAutomations.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ProductCode uses Python identifier ProductCode
- __ProductCode = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ProductCode'), 'ProductCode', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_ProductCode', pyxb.binding.datatypes.string)
- __ProductCode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 98, 4)
- __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 98, 4)
-
- ProductCode = property(__ProductCode.value, __ProductCode.set, None, None)
-
-
- # Attribute PlateType uses Python identifier PlateType
- __PlateType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PlateType'), 'PlateType', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_PlateType', pyxb.binding.datatypes.string)
- __PlateType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 99, 4)
- __PlateType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 99, 4)
-
- PlateType = property(__PlateType.value, __PlateType.set, None, None)
-
-
- # Attribute ActiveInHour uses Python identifier ActiveInHour
- __ActiveInHour = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveInHour'), 'ActiveInHour', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_ActiveInHour', pyxb.binding.datatypes.int)
- __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 100, 4)
- __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 100, 4)
-
- ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
-
-
- # Attribute BasesPerSecond uses Python identifier BasesPerSecond
- __BasesPerSecond = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'BasesPerSecond'), 'BasesPerSecond', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_BasesPerSecond', pyxb.binding.datatypes.decimal)
- __BasesPerSecond._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 101, 4)
- __BasesPerSecond._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 101, 4)
-
- BasesPerSecond = property(__BasesPerSecond.value, __BasesPerSecond.set, None, None)
-
-
- # Attribute AcquisitionCount uses Python identifier AcquisitionCount
- __AcquisitionCount = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'AcquisitionCount'), 'AcquisitionCount', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentKitType_AcquisitionCount', pyxb.binding.datatypes.int)
- __AcquisitionCount._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 102, 4)
- __AcquisitionCount._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 102, 4)
-
- AcquisitionCount = property(__AcquisitionCount.value, __AcquisitionCount.set, None, None)
-
- _ElementMap.update({
- __Reagents.name() : __Reagents,
- __ReagentTubes.name() : __ReagentTubes,
- __ReagentPlateRows.name() : __ReagentPlateRows,
- __CompatibleAutomations.name() : __CompatibleAutomations
- })
- _AttributeMap.update({
- __ProductCode.name() : __ProductCode,
- __PlateType.name() : __PlateType,
- __ActiveInHour.name() : __ActiveInHour,
- __BasesPerSecond.name() : __BasesPerSecond,
- __AcquisitionCount.name() : __AcquisitionCount
- })
-Namespace.addCategoryObject('typeBinding', 'ReagentKitType', ReagentKitType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTubeType with content type ELEMENT_ONLY
-class ReagentTubeType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTubeType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentTubeType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 106, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ProductCode uses Python identifier ProductCode
- __ProductCode = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ProductCode'), 'ProductCode', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_ProductCode', pyxb.binding.datatypes.string, required=True)
- __ProductCode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 109, 4)
- __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 109, 4)
-
- ProductCode = property(__ProductCode.value, __ProductCode.set, None, None)
-
-
- # Attribute ReagentKey uses Python identifier ReagentKey
- __ReagentKey = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentKey'), 'ReagentKey', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_ReagentKey', ReagentKey, required=True)
- __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 110, 4)
- __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 110, 4)
-
- ReagentKey = property(__ReagentKey.value, __ReagentKey.set, None, None)
-
-
- # Attribute Volume uses Python identifier Volume
- __Volume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Volume'), 'Volume', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_Volume', pyxb.binding.datatypes.short, required=True)
- __Volume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 111, 4)
- __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 111, 4)
-
- Volume = property(__Volume.value, __Volume.set, None, None)
-
-
- # Attribute DeadVolume uses Python identifier DeadVolume
- __DeadVolume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DeadVolume'), 'DeadVolume', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_DeadVolume', pyxb.binding.datatypes.short, required=True)
- __DeadVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 112, 4)
- __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 112, 4)
-
- DeadVolume = property(__DeadVolume.value, __DeadVolume.set, None, None)
-
-
- # Attribute ActiveInHour uses Python identifier ActiveInHour
- __ActiveInHour = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveInHour'), 'ActiveInHour', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_ActiveInHour', pyxb.binding.datatypes.int, required=True)
- __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 113, 4)
- __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 113, 4)
-
- ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
-
-
- # Attribute TubeWellType uses Python identifier TubeWellType
- __TubeWellType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TubeWellType'), 'TubeWellType', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_TubeWellType', TubeSize, required=True)
- __TubeWellType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 114, 4)
- __TubeWellType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 114, 4)
-
- TubeWellType = property(__TubeWellType.value, __TubeWellType.set, None, None)
-
-
- # Attribute ReagentTubeType uses Python identifier ReagentTubeType
- __ReagentTubeType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentTubeType'), 'ReagentTubeType', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_ReagentTubeType', TubeLocation, required=True)
- __ReagentTubeType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 115, 4)
- __ReagentTubeType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 115, 4)
-
- ReagentTubeType = property(__ReagentTubeType.value, __ReagentTubeType.set, None, None)
-
-
- # Attribute InitialUse uses Python identifier InitialUse
- __InitialUse = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InitialUse'), 'InitialUse', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentTubeType_InitialUse', pyxb.binding.datatypes.dateTime)
- __InitialUse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 116, 4)
- __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 116, 4)
-
- InitialUse = property(__InitialUse.value, __InitialUse.set, None, None)
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __ProductCode.name() : __ProductCode,
- __ReagentKey.name() : __ReagentKey,
- __Volume.name() : __Volume,
- __DeadVolume.name() : __DeadVolume,
- __ActiveInHour.name() : __ActiveInHour,
- __TubeWellType.name() : __TubeWellType,
- __ReagentTubeType.name() : __ReagentTubeType,
- __InitialUse.name() : __InitialUse
- })
-Namespace.addCategoryObject('typeBinding', 'ReagentTubeType', ReagentTubeType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentPlateRowType with content type ELEMENT_ONLY
-class ReagentPlateRowType (BaseEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentPlateRowType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRowType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 120, 1)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute PlateRow uses Python identifier PlateRow
- __PlateRow = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PlateRow'), 'PlateRow', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentPlateRowType_PlateRow', pyxb.binding.datatypes.string, required=True)
- __PlateRow._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 123, 4)
- __PlateRow._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 123, 4)
-
- PlateRow = property(__PlateRow.value, __PlateRow.set, None, None)
-
-
- # Attribute InitialUse uses Python identifier InitialUse
- __InitialUse = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InitialUse'), 'InitialUse', '__httppacificbiosciences_comPacBioDataModel_xsd_ReagentPlateRowType_InitialUse', pyxb.binding.datatypes.dateTime)
- __InitialUse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 124, 4)
- __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 124, 4)
-
- InitialUse = property(__InitialUse.value, __InitialUse.set, None, None)
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __PlateRow.name() : __PlateRow,
- __InitialUse.name() : __InitialUse
- })
-Namespace.addCategoryObject('typeBinding', 'ReagentPlateRowType', ReagentPlateRowType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_72 (BaseEntityType):
- """List of contigs in a ContigSet"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 118, 2)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Contig uses Python identifier Contig
- __Contig = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Contig'), 'Contig', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_72_httppacificbiosciences_comPacBioDataModel_xsdContig', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 122, 6), )
-
-
- Contig = property(__Contig.value, __Contig.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __Contig.name() : __Contig
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_73 (BaseEntityType):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 123, 7)
- _ElementMap = BaseEntityType._ElementMap.copy()
- _AttributeMap = BaseEntityType._AttributeMap.copy()
- # Base type is BaseEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Length uses Python identifier Length
- __Length = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Length'), 'Length', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_73_Length', pyxb.binding.datatypes.anySimpleType, required=True)
- __Length._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 126, 10)
- __Length._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 126, 10)
-
- Length = property(__Length.value, __Length.set, None, None)
-
-
- # Attribute Digest uses Python identifier Digest
- __Digest = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Digest'), 'Digest', '__httppacificbiosciences_comPacBioDataModel_xsd_CTD_ANON_73_Digest', pyxb.binding.datatypes.anySimpleType, required=True)
- __Digest._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 127, 10)
- __Digest._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 127, 10)
-
- Digest = property(__Digest.value, __Digest.set, None, None)
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __Length.name() : __Length,
- __Digest.name() : __Digest
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_74 (AnalogType):
- """An unlimited number of analogs listed for the purposes of hosting in a configuration file. e.g. a list of all possible analogs on the system"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 130, 2)
- _ElementMap = AnalogType._ElementMap.copy()
- _AttributeMap = AnalogType._AttributeMap.copy()
- # Base type is AnalogType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Base inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute SpectralAngle inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute RelativeAmplitude inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute Label inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute Nucleotide inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute Wavelength inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute CompoundID inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute LotID inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_75 (AnalogType):
- """A set of four analogs, one for each of the nucleotides, grouped together for the purposes of a single experiment."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 196, 2)
- _ElementMap = AnalogType._ElementMap.copy()
- _AttributeMap = AnalogType._AttributeMap.copy()
- # Base type is AnalogType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Base inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute SpectralAngle inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute RelativeAmplitude inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute Label inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute Nucleotide inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute Wavelength inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute CompoundID inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute LotID inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AnalogType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}InputOutputDataType with content type ELEMENT_ONLY
-class InputOutputDataType (DataEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}InputOutputDataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'InputOutputDataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 212, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'InputOutputDataType', InputOutputDataType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType with content type ELEMENT_ONLY
-class PartNumberType (DataEntityType):
- """Generic representation of a supply kit.
-
-If the part number has an NFC associated with it, the contents of the NFC may be encoded here."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'PartNumberType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 258, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumbers uses Python identifier IncompatiblePartNumbers
- __IncompatiblePartNumbers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers'), 'IncompatiblePartNumbers', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_httppacificbiosciences_comPacBioDataModel_xsdIncompatiblePartNumbers', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5), )
-
-
- IncompatiblePartNumbers = property(__IncompatiblePartNumbers.value, __IncompatiblePartNumbers.set, None, 'By default, a PN is compatible for use with other PNs in the system. In order to exclude the usage of one or more PNs with this one, the incompatible PNs are listed here.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomations uses Python identifier IncompatibleAutomations
- __IncompatibleAutomations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations'), 'IncompatibleAutomations', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_httppacificbiosciences_comPacBioDataModel_xsdIncompatibleAutomations', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5), )
-
-
- IncompatibleAutomations = property(__IncompatibleAutomations.value, __IncompatibleAutomations.set, None, 'By default, a PN is compatible for use with all automations in the system. In order to exclude the usage of automations with this PN, the incompatible automation names are listed here.')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute PartNumber uses Python identifier PartNumber
- __PartNumber = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PartNumber'), 'PartNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_PartNumber', pyxb.binding.datatypes.string)
- __PartNumber._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 296, 4)
- __PartNumber._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 296, 4)
-
- PartNumber = property(__PartNumber.value, __PartNumber.set, None, 'The kit part number')
-
-
- # Attribute LotNumber uses Python identifier LotNumber
- __LotNumber = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'LotNumber'), 'LotNumber', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_LotNumber', pyxb.binding.datatypes.string)
- __LotNumber._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 301, 4)
- __LotNumber._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 301, 4)
-
- LotNumber = property(__LotNumber.value, __LotNumber.set, None, 'The kit lot number')
-
-
- # Attribute Barcode uses Python identifier Barcode
- __Barcode = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Barcode'), 'Barcode', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_Barcode', pyxb.binding.datatypes.string)
- __Barcode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 306, 4)
- __Barcode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 306, 4)
-
- Barcode = property(__Barcode.value, __Barcode.set, None, 'The kit barcode; used for tracking purposes.')
-
-
- # Attribute ExpirationDate uses Python identifier ExpirationDate
- __ExpirationDate = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ExpirationDate'), 'ExpirationDate', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_ExpirationDate', pyxb.binding.datatypes.date)
- __ExpirationDate._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 311, 4)
- __ExpirationDate._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 311, 4)
-
- ExpirationDate = property(__ExpirationDate.value, __ExpirationDate.set, None, "The kit's shelf life")
-
-
- # Attribute IsObsolete uses Python identifier IsObsolete
- __IsObsolete = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'IsObsolete'), 'IsObsolete', '__httppacificbiosciences_comPacBioDataModel_xsd_PartNumberType_IsObsolete', pyxb.binding.datatypes.boolean, unicode_default='false')
- __IsObsolete._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 316, 4)
- __IsObsolete._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 316, 4)
-
- IsObsolete = property(__IsObsolete.value, __IsObsolete.set, None, None)
-
- _ElementMap.update({
- __IncompatiblePartNumbers.name() : __IncompatiblePartNumbers,
- __IncompatibleAutomations.name() : __IncompatibleAutomations
- })
- _AttributeMap.update({
- __PartNumber.name() : __PartNumber,
- __LotNumber.name() : __LotNumber,
- __Barcode.name() : __Barcode,
- __ExpirationDate.name() : __ExpirationDate,
- __IsObsolete.name() : __IsObsolete
- })
-Namespace.addCategoryObject('typeBinding', 'PartNumberType', PartNumberType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEventType with content type ELEMENT_ONLY
-class RecordedEventType (DataEntityType):
- """Metrics, system events, alarms, and logs may utilize this type"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'RecordedEventType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 320, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute Context uses Python identifier Context
- __Context = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Context'), 'Context', '__httppacificbiosciences_comPacBioDataModel_xsd_RecordedEventType_Context', pyxb.binding.datatypes.string)
- __Context._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 326, 4)
- __Context._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 326, 4)
-
- Context = property(__Context.value, __Context.set, None, 'The part of the system in effect when the event was recorded')
-
- _ElementMap.update({
-
- })
- _AttributeMap.update({
- __Context.name() : __Context
- })
-Namespace.addCategoryObject('typeBinding', 'RecordedEventType', RecordedEventType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingChemistry with content type ELEMENT_ONLY
-class SequencingChemistry (DataEntityType):
- """A container for a set of analogs"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 334, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DyeSet uses Python identifier DyeSet
- __DyeSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DyeSet'), 'DyeSet', '__httppacificbiosciences_comPacBioDataModel_xsd_SequencingChemistry_httppacificbiosciences_comPacBioDataModel_xsdDyeSet', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 341, 5), )
-
-
- DyeSet = property(__DyeSet.value, __DyeSet.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
- _ElementMap.update({
- __DyeSet.name() : __DyeSet
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SequencingChemistry', SequencingChemistry)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadSetType with content type ELEMENT_ONLY
-class ReadSetType (DataSetType):
- """Type for DataSets consisting of unaligned subreads and CCS reads DataSets"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReadSetType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 19, 1)
- _ElementMap = DataSetType._ElementMap.copy()
- _AttributeMap = DataSetType._AttributeMap.copy()
- # Base type is DataSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata uses Python identifier DataSetMetadata
- __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDataModel_xsd_ReadSetType_httppacificbiosciences_comPacBioDataModel_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5), )
-
-
- DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
-
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __DataSetMetadata.name() : __DataSetMetadata
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'ReadSetType', ReadSetType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodedSampleType with content type ELEMENT_ONLY
-class BarcodedSampleType (BioSampleType):
- """This is a data type to hold a barcoded biological sample, or a raw biological sample - so, barcode is optional."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BarcodedSampleType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 340, 1)
- _ElementMap = BioSampleType._ElementMap.copy()
- _AttributeMap = BioSampleType._AttributeMap.copy()
- # Base type is BioSampleType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Barcodes uses Python identifier Barcodes
- __Barcodes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Barcodes'), 'Barcodes', '__httppacificbiosciences_comPacBioDataModel_xsd_BarcodedSampleType_httppacificbiosciences_comPacBioDataModel_xsdBarcodes', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 347, 5), )
-
-
- Barcodes = property(__Barcodes.value, __Barcodes.set, None, 'A list of barcodes associated with the biological sample')
-
-
- # Element BioSamples ({http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamples) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute DateReceived inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute Organism inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute Reference inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute DNAType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute Concentration inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute QuantificationMethod inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute SMRTBellConcentration inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute SMRTBellQuantificationMethod inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute BufferName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute SamplePrepKit inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
-
- # Attribute TargetLibrarySize inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSampleType
- _ElementMap.update({
- __Barcodes.name() : __Barcodes
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'BarcodedSampleType', BarcodedSampleType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AssayType with content type ELEMENT_ONLY
-class AssayType (DataEntityType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AssayType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AssayType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 237, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSet uses Python identifier SubreadSet
- __SubreadSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet'), 'SubreadSet', '__httppacificbiosciences_comPacBioDataModel_xsd_AssayType_httppacificbiosciences_comPacBioDataModel_xsdSubreadSet', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 681, 1), )
-
-
- SubreadSet = property(__SubreadSet.value, __SubreadSet.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
- _ElementMap.update({
- __SubreadSet.name() : __SubreadSet
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'AssayType', AssayType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ExperimentContainerType with content type ELEMENT_ONLY
-class ExperimentContainerType (DataEntityType):
- """A composite object type that can encompass multiple runs, possibly across multiple instruments.
-
-One use case may be that a user may have a large genome they'd like to sequence, and it may take multiple runs on multiple instruments, to get enough data. Another use case may be that a user has multiple samples of the same phenotype which they would like to analyze in a similar fashion/automation, and as such these samples are run as part of one experiment.
-
-The experiment object is intended to be packagable, such that the metadata of all acquisitions within is contained."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainerType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 246, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InvestigatorName uses Python identifier InvestigatorName
- __InvestigatorName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InvestigatorName'), 'InvestigatorName', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdInvestigatorName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 257, 5), )
-
-
- InvestigatorName = property(__InvestigatorName.value, __InvestigatorName.set, None, 'An optional PI name')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}CreatedDate uses Python identifier CreatedDate
- __CreatedDate = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CreatedDate'), 'CreatedDate', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdCreatedDate', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 262, 5), )
-
-
- CreatedDate = property(__CreatedDate.value, __CreatedDate.set, None, 'Automatically generated creation date')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Runs uses Python identifier Runs
- __Runs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Runs'), 'Runs', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdRuns', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 267, 5), )
-
-
- Runs = property(__Runs.value, __Runs.set, None, 'Multiple acquisitions from different instrument runs')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets uses Python identifier DataSets
- __DataSets = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), 'DataSets', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdDataSets', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 277, 5), )
-
-
- DataSets = property(__DataSets.value, __DataSets.set, None, 'Pointers to various data elements associated with the acquisitions')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvents uses Python identifier RecordedEvents
- __RecordedEvents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), 'RecordedEvents', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvents', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 287, 5), )
-
-
- RecordedEvents = property(__RecordedEvents.value, __RecordedEvents.set, None, "Journal of metrics, system events, or alarms that were generated during this container's lifetime")
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}BioSamples uses Python identifier BioSamples
- __BioSamples = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), 'BioSamples', '__httppacificbiosciences_comPacBioDataModel_xsd_ExperimentContainerType_httppacificbiosciences_comPacBioDataModel_xsdBioSamples', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 301, 5), )
-
-
- BioSamples = property(__BioSamples.value, __BioSamples.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
- _ElementMap.update({
- __InvestigatorName.name() : __InvestigatorName,
- __CreatedDate.name() : __CreatedDate,
- __Runs.name() : __Runs,
- __DataSets.name() : __DataSets,
- __RecordedEvents.name() : __RecordedEvents,
- __BioSamples.name() : __BioSamples
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'ExperimentContainerType', ExperimentContainerType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}RunType with content type ELEMENT_ONLY
-class RunType (DataEntityType):
- """A run is defined as a set of one or more data collections acquired in sequence on an instrument. A run specifies the wells and SMRT Cells to include in the sequencing run, along with the collection and analysis automation to use for the selected wells and cells.
-
-"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'RunType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 312, 1)
- _ElementMap = DataEntityType._ElementMap.copy()
- _AttributeMap = DataEntityType._AttributeMap.copy()
- # Base type is DataEntityType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSet uses Python identifier SubreadSet
- __SubreadSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet'), 'SubreadSet', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdSubreadSet', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 681, 1), )
-
-
- SubreadSet = property(__SubreadSet.value, __SubreadSet.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Assay uses Python identifier Assay
- __Assay = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Assay'), 'Assay', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdAssay', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 11, 1), )
-
-
- Assay = property(__Assay.value, __Assay.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RunResources uses Python identifier RunResources
- __RunResources = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RunResources'), 'RunResources', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdRunResources', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 129, 1), )
-
-
- RunResources = property(__RunResources.value, __RunResources.set, None, 'This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Inputs uses Python identifier Inputs
- __Inputs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Inputs'), 'Inputs', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdInputs', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 321, 5), )
-
-
- Inputs = property(__Inputs.value, __Inputs.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Outputs uses Python identifier Outputs
- __Outputs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Outputs'), 'Outputs', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdOutputs', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 328, 5), )
-
-
- Outputs = property(__Outputs.value, __Outputs.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RecordedEvents uses Python identifier RecordedEvents
- __RecordedEvents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), 'RecordedEvents', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_httppacificbiosciences_comPacBioDataModel_xsdRecordedEvents', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 341, 5), )
-
-
- RecordedEvents = property(__RecordedEvents.value, __RecordedEvents.set, None, "Journal of metrics, system events, or alarms that were generated during this run's lifetime")
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute Status uses Python identifier Status
- __Status = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Status'), 'Status', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_Status', SupportedRunStates)
- __Status._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 358, 4)
- __Status._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 358, 4)
-
- Status = property(__Status.value, __Status.set, None, None)
-
-
- # Attribute InstrumentId uses Python identifier InstrumentId
- __InstrumentId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentId'), 'InstrumentId', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_InstrumentId', pyxb.binding.datatypes.string)
- __InstrumentId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 359, 4)
- __InstrumentId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 359, 4)
-
- InstrumentId = property(__InstrumentId.value, __InstrumentId.set, None, 'World unique id assigned by PacBio. ')
-
-
- # Attribute InstrumentName uses Python identifier InstrumentName
- __InstrumentName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentName'), 'InstrumentName', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_InstrumentName', pyxb.binding.datatypes.string)
- __InstrumentName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 364, 4)
- __InstrumentName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 364, 4)
-
- InstrumentName = property(__InstrumentName.value, __InstrumentName.set, None, 'Friendly name assigned by customer')
-
-
- # Attribute CreatedBy uses Python identifier CreatedBy
- __CreatedBy = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CreatedBy'), 'CreatedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_CreatedBy', pyxb.binding.datatypes.string)
- __CreatedBy._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 369, 4)
- __CreatedBy._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 369, 4)
-
- CreatedBy = property(__CreatedBy.value, __CreatedBy.set, None, 'Who created the run. ')
-
-
- # Attribute StartedBy uses Python identifier StartedBy
- __StartedBy = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'StartedBy'), 'StartedBy', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_StartedBy', pyxb.binding.datatypes.string)
- __StartedBy._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 374, 4)
- __StartedBy._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 374, 4)
-
- StartedBy = property(__StartedBy.value, __StartedBy.set, None, 'Who started the run. Could be different from who created it. ')
-
-
- # Attribute WhenStarted uses Python identifier WhenStarted
- __WhenStarted = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'WhenStarted'), 'WhenStarted', '__httppacificbiosciences_comPacBioDataModel_xsd_RunType_WhenStarted', pyxb.binding.datatypes.dateTime)
- __WhenStarted._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 379, 4)
- __WhenStarted._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 379, 4)
-
- WhenStarted = property(__WhenStarted.value, __WhenStarted.set, None, 'Date and time of when the overall run was started. ')
-
- _ElementMap.update({
- __SubreadSet.name() : __SubreadSet,
- __Assay.name() : __Assay,
- __RunResources.name() : __RunResources,
- __Inputs.name() : __Inputs,
- __Outputs.name() : __Outputs,
- __RecordedEvents.name() : __RecordedEvents
- })
- _AttributeMap.update({
- __Status.name() : __Status,
- __InstrumentId.name() : __InstrumentId,
- __InstrumentName.name() : __InstrumentName,
- __CreatedBy.name() : __CreatedBy,
- __StartedBy.name() : __StartedBy,
- __WhenStarted.name() : __WhenStarted
- })
-Namespace.addCategoryObject('typeBinding', 'RunType', RunType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodeSetType with content type ELEMENT_ONLY
-class BarcodeSetType (DataSetType):
- """Type for the Barcode DataSet."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BarcodeSetType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 28, 1)
- _ElementMap = DataSetType._ElementMap.copy()
- _AttributeMap = DataSetType._AttributeMap.copy()
- # Base type is DataSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata uses Python identifier DataSetMetadata
- __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDataModel_xsd_BarcodeSetType_httppacificbiosciences_comPacBioDataModel_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 35, 5), )
-
-
- DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __DataSetMetadata.name() : __DataSetMetadata
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'BarcodeSetType', BarcodeSetType)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_76 (DataSetType):
- """DataSets of CCS reads (typically in unaligned BAM format)."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 54, 2)
- _ElementMap = DataSetType._ElementMap.copy()
- _AttributeMap = DataSetType._AttributeMap.copy()
- # Base type is DataSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}AlignmentSetType with content type ELEMENT_ONLY
-class AlignmentSetType (DataSetType):
- """Type for DataSets consisting of aligned subreads and CCS reads."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AlignmentSetType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 60, 1)
- _ElementMap = DataSetType._ElementMap.copy()
- _AttributeMap = DataSetType._AttributeMap.copy()
- # Base type is DataSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata uses Python identifier DataSetMetadata
- __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDataModel_xsd_AlignmentSetType_httppacificbiosciences_comPacBioDataModel_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5), )
-
-
- DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __DataSetMetadata.name() : __DataSetMetadata
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'AlignmentSetType', AlignmentSetType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}ContigSetType with content type ELEMENT_ONLY
-class ContigSetType (DataSetType):
- """Type for a Contig DataSet."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ContigSetType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 92, 1)
- _ElementMap = DataSetType._ElementMap.copy()
- _AttributeMap = DataSetType._AttributeMap.copy()
- # Base type is DataSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata uses Python identifier DataSetMetadata
- __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDataModel_xsd_ContigSetType_httppacificbiosciences_comPacBioDataModel_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 99, 5), )
-
-
- DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
- __DataSetMetadata.name() : __DataSetMetadata
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'ContigSetType', ContigSetType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}IndexedDataType with content type ELEMENT_ONLY
-class IndexedDataType (InputOutputDataType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}IndexedDataType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'IndexedDataType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 217, 1)
- _ElementMap = InputOutputDataType._ElementMap.copy()
- _AttributeMap = InputOutputDataType._AttributeMap.copy()
- # Base type is InputOutputDataType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources uses Python identifier ExternalResources
- __ExternalResources = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), 'ExternalResources', '__httppacificbiosciences_comPacBioDataModel_xsd_IndexedDataType_httppacificbiosciences_comPacBioDataModel_xsdExternalResources', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 202, 1), )
-
-
- ExternalResources = property(__ExternalResources.value, __ExternalResources.set, None, 'Pointers to data that do not reside inside the parent structure')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}FileIndices uses Python identifier FileIndices
- __FileIndices = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'FileIndices'), 'FileIndices', '__httppacificbiosciences_comPacBioDataModel_xsd_IndexedDataType_httppacificbiosciences_comPacBioDataModel_xsdFileIndices', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 221, 5), )
-
-
- FileIndices = property(__FileIndices.value, __FileIndices.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
- _ElementMap.update({
- __ExternalResources.name() : __ExternalResources,
- __FileIndices.name() : __FileIndices
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'IndexedDataType', IndexedDataType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SupplyKitBinding with content type ELEMENT_ONLY
-class SupplyKitBinding (PartNumberType):
- """A more specific binding kit representation (includes SupplyKit fields). """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitBinding')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 470, 1)
- _ElementMap = PartNumberType._ElementMap.copy()
- _AttributeMap = PartNumberType._AttributeMap.copy()
- # Base type is PartNumberType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}Control uses Python identifier Control
- __Control = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Control'), 'Control', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitBinding_httppacificbiosciences_comPacBioDataModel_xsdControl', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 477, 5), )
-
-
- Control = property(__Control.value, __Control.set, None, 'Defines the binding kit internal control name. Present when used, otherwise not used if not defined. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}IsControlUsed uses Python identifier IsControlUsed
- __IsControlUsed = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IsControlUsed'), 'IsControlUsed', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitBinding_httppacificbiosciences_comPacBioDataModel_xsdIsControlUsed', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 482, 5), )
-
-
- IsControlUsed = property(__IsControlUsed.value, __IsControlUsed.set, None, 'True if the control was used during run, otherwise false. ')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
- _ElementMap.update({
- __Control.name() : __Control,
- __IsControlUsed.name() : __IsControlUsed
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SupplyKitBinding', SupplyKitBinding)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SupplyKitCellPack with content type ELEMENT_ONLY
-class SupplyKitCellPack (PartNumberType):
- """Represents the package of cells. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitCellPack')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 491, 1)
- _ElementMap = PartNumberType._ElementMap.copy()
- _AttributeMap = PartNumberType._AttributeMap.copy()
- # Base type is PartNumberType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ChipLayout uses Python identifier ChipLayout
- __ChipLayout = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), 'ChipLayout', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitCellPack_httppacificbiosciences_comPacBioDataModel_xsdChipLayout', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 498, 5), )
-
-
- ChipLayout = property(__ChipLayout.value, __ChipLayout.set, None, 'Defines the internal chip layout name, if any. ')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
- _ElementMap.update({
- __ChipLayout.name() : __ChipLayout
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SupplyKitCellPack', SupplyKitCellPack)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SupplyKitControl with content type ELEMENT_ONLY
-class SupplyKitControl (PartNumberType):
- """Represents the DNA control complex. """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitControl')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 507, 1)
- _ElementMap = PartNumberType._ElementMap.copy()
- _AttributeMap = PartNumberType._AttributeMap.copy()
- # Base type is PartNumberType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InternalControlName uses Python identifier InternalControlName
- __InternalControlName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InternalControlName'), 'InternalControlName', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitControl_httppacificbiosciences_comPacBioDataModel_xsdInternalControlName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 514, 5), )
-
-
- InternalControlName = property(__InternalControlName.value, __InternalControlName.set, None, 'Defines the internal control name, if any. ')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
- _ElementMap.update({
- __InternalControlName.name() : __InternalControlName
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SupplyKitControl', SupplyKitControl)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SupplyKitTemplate with content type ELEMENT_ONLY
-class SupplyKitTemplate (PartNumberType):
- """A more specific template kit representation (includes SupplyKit fields). """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitTemplate')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 523, 1)
- _ElementMap = PartNumberType._ElementMap.copy()
- _AttributeMap = PartNumberType._AttributeMap.copy()
- # Base type is PartNumberType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}LeftAdaptorSequence uses Python identifier LeftAdaptorSequence
- __LeftAdaptorSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'LeftAdaptorSequence'), 'LeftAdaptorSequence', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioDataModel_xsdLeftAdaptorSequence', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 530, 5), )
-
-
- LeftAdaptorSequence = property(__LeftAdaptorSequence.value, __LeftAdaptorSequence.set, None, 'Left adapter DNA sequence.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}LeftPrimerSequence uses Python identifier LeftPrimerSequence
- __LeftPrimerSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'LeftPrimerSequence'), 'LeftPrimerSequence', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioDataModel_xsdLeftPrimerSequence', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 535, 5), )
-
-
- LeftPrimerSequence = property(__LeftPrimerSequence.value, __LeftPrimerSequence.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RightAdaptorSequence uses Python identifier RightAdaptorSequence
- __RightAdaptorSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RightAdaptorSequence'), 'RightAdaptorSequence', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioDataModel_xsdRightAdaptorSequence', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 536, 5), )
-
-
- RightAdaptorSequence = property(__RightAdaptorSequence.value, __RightAdaptorSequence.set, None, 'Right adapter DNA sequence. If not specified, a symmetric adapter model is inferred, where the left adapter sequence is used wherever needed.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}RightPrimerSequence uses Python identifier RightPrimerSequence
- __RightPrimerSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RightPrimerSequence'), 'RightPrimerSequence', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioDataModel_xsdRightPrimerSequence', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 541, 5), )
-
-
- RightPrimerSequence = property(__RightPrimerSequence.value, __RightPrimerSequence.set, None, 'Right primaer sequence. If not specified, a symmetric model is inferred, where the left primer sequence is used wherever needed.')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}InsertSize uses Python identifier InsertSize
- __InsertSize = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertSize'), 'InsertSize', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioDataModel_xsdInsertSize', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 546, 5), )
-
-
- InsertSize = property(__InsertSize.value, __InsertSize.set, None, 'Approximate size of insert. ')
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
- _ElementMap.update({
- __LeftAdaptorSequence.name() : __LeftAdaptorSequence,
- __LeftPrimerSequence.name() : __LeftPrimerSequence,
- __RightAdaptorSequence.name() : __RightAdaptorSequence,
- __RightPrimerSequence.name() : __RightPrimerSequence,
- __InsertSize.name() : __InsertSize
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SupplyKitTemplate', SupplyKitTemplate)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSetType with content type ELEMENT_ONLY
-class SubreadSetType (ReadSetType):
- """Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SubreadSetType with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SubreadSetType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 97, 1)
- _ElementMap = ReadSetType._ElementMap.copy()
- _AttributeMap = ReadSetType._AttributeMap.copy()
- # Base type is ReadSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-Namespace.addCategoryObject('typeBinding', 'SubreadSetType', SubreadSetType)
-
-
-# Complex type {http://pacificbiosciences.com/PacBioDataModel.xsd}SupplyKitSequencing with content type ELEMENT_ONLY
-class SupplyKitSequencing (PartNumberType):
- """A more specific template kit representation (includes SupplyKit fields). """
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitSequencing')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 21, 1)
- _ElementMap = PartNumberType._ElementMap.copy()
- _AttributeMap = PartNumberType._AttributeMap.copy()
- # Base type is PartNumberType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element EncodedValue ({http://pacificbiosciences.com/PacBioDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element CheckSum ({http://pacificbiosciences.com/PacBioDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentAutomationName uses Python identifier ReagentAutomationName
- __ReagentAutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName'), 'ReagentAutomationName', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioDataModel_xsdReagentAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 28, 5), )
-
-
- ReagentAutomationName = property(__ReagentAutomationName.value, __ReagentAutomationName.set, None, 'The reagent-mixing protocol used. ')
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}ReagentTubes uses Python identifier ReagentTubes
- __ReagentTubes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), 'ReagentTubes', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioDataModel_xsdReagentTubes', True, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 33, 5), )
-
-
- ReagentTubes = property(__ReagentTubes.value, __ReagentTubes.set, None, "Tubes associated with the reagent kit - can have up to two; don't forget to set the location, 0 or 1")
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingChemistry uses Python identifier SequencingChemistry
- __SequencingChemistry = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), 'SequencingChemistry', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioDataModel_xsdSequencingChemistry', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 38, 5), )
-
-
- SequencingChemistry = property(__SequencingChemistry.value, __SequencingChemistry.set, None, None)
-
-
- # Element {http://pacificbiosciences.com/PacBioDataModel.xsd}SequencingKitDefinition uses Python identifier SequencingKitDefinition
- __SequencingKitDefinition = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), 'SequencingKitDefinition', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioDataModel_xsdSequencingKitDefinition', False, pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 39, 5), )
-
-
- SequencingKitDefinition = property(__SequencingKitDefinition.value, __SequencingKitDefinition.set, None, None)
-
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataEntityType
-
- # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}PartNumberType
-
- # Attribute Location uses Python identifier Location
- __Location = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Location'), 'Location', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitSequencing_Location', pyxb.binding.datatypes.int, unicode_default='0')
- __Location._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 41, 4)
- __Location._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 41, 4)
-
- Location = property(__Location.value, __Location.set, None, 'The location of the supply kit - for a reagent plate, it could be 0 or 1, and for a tube it could be 0 or 1')
-
-
- # Attribute MaxCollections uses Python identifier MaxCollections
- __MaxCollections = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MaxCollections'), 'MaxCollections', '__httppacificbiosciences_comPacBioDataModel_xsd_SupplyKitSequencing_MaxCollections', pyxb.binding.datatypes.int, unicode_default='8')
- __MaxCollections._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 46, 4)
- __MaxCollections._UseLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 46, 4)
-
- MaxCollections = property(__MaxCollections.value, __MaxCollections.set, None, 'The number of collections this supply kit is capable of')
-
- _ElementMap.update({
- __ReagentAutomationName.name() : __ReagentAutomationName,
- __ReagentTubes.name() : __ReagentTubes,
- __SequencingChemistry.name() : __SequencingChemistry,
- __SequencingKitDefinition.name() : __SequencingKitDefinition
- })
- _AttributeMap.update({
- __Location.name() : __Location,
- __MaxCollections.name() : __MaxCollections
- })
-Namespace.addCategoryObject('typeBinding', 'SupplyKitSequencing', SupplyKitSequencing)
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_77 (AlignmentSetType):
- """DataSets for aligned subreads and CCS reads."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 12, 2)
- _ElementMap = AlignmentSetType._ElementMap.copy()
- _AttributeMap = AlignmentSetType._AttributeMap.copy()
- # Base type is AlignmentSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AlignmentSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_78 (BarcodeSetType):
- """DataSets of Barcodes. Basically a thin metadata layer on top of the barcode FASTA."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 22, 2)
- _ElementMap = BarcodeSetType._ElementMap.copy()
- _AttributeMap = BarcodeSetType._AttributeMap.copy()
- # Base type is BarcodeSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BarcodeSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_79 (AlignmentSetType):
- """DataSets of aligned CCS reads."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 44, 2)
- _ElementMap = AlignmentSetType._ElementMap.copy()
- _AttributeMap = AlignmentSetType._AttributeMap.copy()
- # Base type is AlignmentSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}AlignmentSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_80 (ContigSetType):
- """DataSets of reference sequences. Replaces the reference.info.xml"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 76, 2)
- _ElementMap = ContigSetType._ElementMap.copy()
- _AttributeMap = ContigSetType._AttributeMap.copy()
- # Base type is ContigSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}ContigSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_81 (ContigSetType):
- """DataSets of contigs sequences. Basically a thin metadata layer on top of a contigs FASTA (e.g. from HGAP)."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 86, 2)
- _ElementMap = ContigSetType._ElementMap.copy()
- _AttributeMap = ContigSetType._AttributeMap.copy()
- # Base type is ContigSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}ContigSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_82 (ReadSetType):
- """DataSets of subreads in bax.h5 or bas.h5 format."""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 108, 2)
- _ElementMap = ReadSetType._ElementMap.copy()
- _AttributeMap = ReadSetType._AttributeMap.copy()
- # Base type is ReadSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-# Complex type [anonymous] with content type ELEMENT_ONLY
-class CTD_ANON_83 (SubreadSetType):
- """Complex type [anonymous] with content type ELEMENT_ONLY"""
- _TypeDefinition = None
- _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
- _Abstract = False
- _ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 682, 2)
- _ElementMap = SubreadSetType._ElementMap.copy()
- _AttributeMap = SubreadSetType._AttributeMap.copy()
- # Base type is SubreadSetType
-
- # Element Extensions ({http://pacificbiosciences.com/PacBioDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Element ExternalResources ({http://pacificbiosciences.com/PacBioDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}ReadSetType
-
- # Element Filters ({http://pacificbiosciences.com/PacBioDataModel.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Element DataSets ({http://pacificbiosciences.com/PacBioDataModel.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}DataSetType
-
- # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Name inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Description inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Format inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute Version inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
-
- # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioDataModel.xsd}BaseEntityType
- _ElementMap.update({
-
- })
- _AttributeMap.update({
-
- })
-
-
-
-ExtensionElement = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement'), pyxb.binding.datatypes.anyType, documentation='A generic element whose contents are undefined at the schema level. This is used to extend the data model.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 640, 1))
-Namespace.addCategoryObject('elementBinding', ExtensionElement.name().localName(), ExtensionElement)
-
-PacBioAutomationConstraints = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioAutomationConstraints'), CTD_ANON, documentation='The root element of the Automation Constraints ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 9, 1))
-Namespace.addCategoryObject('elementBinding', PacBioAutomationConstraints.name().localName(), PacBioAutomationConstraints)
-
-AutomationConstraints = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraints'), CTD_ANON_, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 19, 1))
-Namespace.addCategoryObject('elementBinding', AutomationConstraints.name().localName(), AutomationConstraints)
-
-DataPointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataPointers'), CTD_ANON_5, documentation='Pointer to Run/Outputs/Output/@UniqueId', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 168, 1))
-Namespace.addCategoryObject('elementBinding', DataPointers.name().localName(), DataPointers)
-
-ExternalResources = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), CTD_ANON_6, documentation='Pointers to data that do not reside inside the parent structure', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 202, 1))
-Namespace.addCategoryObject('elementBinding', ExternalResources.name().localName(), ExternalResources)
-
-PacBioSequencingChemistry = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioSequencingChemistry'), CTD_ANON_12, documentation='Root element for document containing the container of analog set, SequencingChemistryConfig', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 362, 1))
-Namespace.addCategoryObject('elementBinding', PacBioSequencingChemistry.name().localName(), PacBioSequencingChemistry)
-
-ValueDataType = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ValueDataType'), SupportedDataTypes, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 638, 1))
-Namespace.addCategoryObject('elementBinding', ValueDataType.name().localName(), ValueDataType)
-
-PacBioCollectionMetadata = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioCollectionMetadata'), CTD_ANON_20, documentation='Root element of a standalone CollectionMetadata file.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 9, 1))
-Namespace.addCategoryObject('elementBinding', PacBioCollectionMetadata.name().localName(), PacBioCollectionMetadata)
-
-Collections = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Collections'), CTD_ANON_24, documentation='A set of acquisition definitions', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 125, 1))
-Namespace.addCategoryObject('elementBinding', Collections.name().localName(), Collections)
-
-RunDetails = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunDetails'), CTD_ANON_25, documentation='Information related to an instrument run. A run can contain multiple chips, wells, and movies. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 248, 1))
-Namespace.addCategoryObject('elementBinding', RunDetails.name().localName(), RunDetails)
-
-Movie = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Movie'), CTD_ANON_26, documentation='A movie corresponds to one acquisition for a chip, one set (look) and one strobe. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 287, 1))
-Namespace.addCategoryObject('elementBinding', Movie.name().localName(), Movie)
-
-ExpirationData = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData'), CTD_ANON_27, documentation='Container for the expired consumable data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 311, 1))
-Namespace.addCategoryObject('elementBinding', ExpirationData.name().localName(), ExpirationData)
-
-Primary = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Primary'), CTD_ANON_29, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 503, 1))
-Namespace.addCategoryObject('elementBinding', Primary.name().localName(), Primary)
-
-Secondary = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Secondary'), CTD_ANON_32, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 568, 1))
-Namespace.addCategoryObject('elementBinding', Secondary.name().localName(), Secondary)
-
-UserDefinedFields = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields'), UserDefinedFieldsType, documentation='A set of key-value pairs specified by a user via the run input mechanism. Note that uniqueness of keys is not enforced here and so may contain duplicate keys. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 602, 1))
-Namespace.addCategoryObject('elementBinding', UserDefinedFields.name().localName(), UserDefinedFields)
-
-KeyValue = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'KeyValue'), CTD_ANON_34, documentation='One custom, possibly non-unique, key-value pair. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 607, 1))
-Namespace.addCategoryObject('elementBinding', KeyValue.name().localName(), KeyValue)
-
-BioSamplePointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointers'), CTD_ANON_35, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 639, 1))
-Namespace.addCategoryObject('elementBinding', BioSamplePointers.name().localName(), BioSamplePointers)
-
-BarcodedSamplePointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_36, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 659, 1))
-Namespace.addCategoryObject('elementBinding', BarcodedSamplePointers.name().localName(), BarcodedSamplePointers)
-
-BioSamples = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_37, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 673, 1))
-Namespace.addCategoryObject('elementBinding', BioSamples.name().localName(), BioSamples)
-
-ChipLayout = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), CTD_ANON_38, documentation='Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 12, 1))
-Namespace.addCategoryObject('elementBinding', ChipLayout.name().localName(), ChipLayout)
-
-CompatibleChipLayouts = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts'), CTD_ANON_39, documentation='A set of Chip Layouts deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 24, 1))
-Namespace.addCategoryObject('elementBinding', CompatibleChipLayouts.name().localName(), CompatibleChipLayouts)
-
-CompatibleSequencingKits = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits'), CTD_ANON_40, documentation='A set of reagent kits deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 36, 1))
-Namespace.addCategoryObject('elementBinding', CompatibleSequencingKits.name().localName(), CompatibleSequencingKits)
-
-EstimatedTotalRunTime = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime'), CTD_ANON_41, documentation='The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 48, 1))
-Namespace.addCategoryObject('elementBinding', EstimatedTotalRunTime.name().localName(), EstimatedTotalRunTime)
-
-PacBioDataModel = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioDataModel'), CTD_ANON_42, documentation='PacBio Data Model root element', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 91, 1))
-Namespace.addCategoryObject('elementBinding', PacBioDataModel.name().localName(), PacBioDataModel)
-
-RequiredSMRTCells = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredSMRTCells'), CTD_ANON_43, documentation='Part of the RunResources; specifies the required number of SMRT cells', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 106, 1))
-Namespace.addCategoryObject('elementBinding', RequiredSMRTCells.name().localName(), RequiredSMRTCells)
-
-RequiredTips = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips'), CTD_ANON_44, documentation='Part of the RunResources; specifies the required number of tips via two attributes, Left and Right', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 117, 1))
-Namespace.addCategoryObject('elementBinding', RequiredTips.name().localName(), RequiredTips)
-
-RunResources = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunResources'), CTD_ANON_45, documentation='This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 129, 1))
-Namespace.addCategoryObject('elementBinding', RunResources.name().localName(), RunResources)
-
-SampleComment = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleComment'), CTD_ANON_46, documentation='A general sample description', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 141, 1))
-Namespace.addCategoryObject('elementBinding', SampleComment.name().localName(), SampleComment)
-
-CollectionReferences = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionReferences'), CTD_ANON_54, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 387, 1))
-Namespace.addCategoryObject('elementBinding', CollectionReferences.name().localName(), CollectionReferences)
-
-PacBioPartNumbers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioPartNumbers'), CTD_ANON_55, documentation='The root element of the Part Numbers ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 8, 1))
-Namespace.addCategoryObject('elementBinding', PacBioPartNumbers.name().localName(), PacBioPartNumbers)
-
-PacBioReagentKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioReagentKit'), CTD_ANON_61, documentation='The root element of the reagent kit standalone file', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 7, 1))
-Namespace.addCategoryObject('elementBinding', PacBioReagentKit.name().localName(), PacBioReagentKit)
-
-Parameter = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Parameter'), CTD_ANON_67, documentation='A variable, as a name/value pair, associated with a protocol (one of Collection, Primary, and Secondary)', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 63, 1))
-Namespace.addCategoryObject('elementBinding', Parameter.name().localName(), Parameter)
-
-Validation = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1))
-Namespace.addCategoryObject('elementBinding', Validation.name().localName(), Validation)
-
-AutomationConstraint = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraint'), AutomationConstraintType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 26, 1))
-Namespace.addCategoryObject('elementBinding', AutomationConstraint.name().localName(), AutomationConstraint)
-
-DataEntity = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataEntity'), DataEntityType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 136, 1))
-Namespace.addCategoryObject('elementBinding', DataEntity.name().localName(), DataEntity)
-
-AutomationParameter = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), DataEntityType, documentation='One or more collection parameters, such as MovieLength, InsertSize, UseStageStart, IsControl, etc..', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 253, 1))
-Namespace.addCategoryObject('elementBinding', AutomationParameter.name().localName(), AutomationParameter)
-
-DataSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), DataSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 135, 1))
-Namespace.addCategoryObject('elementBinding', DataSet.name().localName(), DataSet)
-
-CollectionMetadata = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), CTD_ANON_70, documentation='Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ', location=pyxb.utils.utility.Location(' [...]
-Namespace.addCategoryObject('elementBinding', CollectionMetadata.name().localName(), CollectionMetadata)
-
-WellSample = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WellSample'), CTD_ANON_71, documentation='Container for the sample related data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 432, 1))
-Namespace.addCategoryObject('elementBinding', WellSample.name().localName(), WellSample)
-
-BioSample = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 680, 1))
-Namespace.addCategoryObject('elementBinding', BioSample.name().localName(), BioSample)
-
-Reagent = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 17, 1))
-Namespace.addCategoryObject('elementBinding', Reagent.name().localName(), Reagent)
-
-ReagentKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 18, 1))
-Namespace.addCategoryObject('elementBinding', ReagentKit.name().localName(), ReagentKit)
-
-ReagentTube = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 19, 1))
-Namespace.addCategoryObject('elementBinding', ReagentTube.name().localName(), ReagentTube)
-
-ReagentPlateRow = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 20, 1))
-Namespace.addCategoryObject('elementBinding', ReagentPlateRow.name().localName(), ReagentPlateRow)
-
-Contigs = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Contigs'), CTD_ANON_72, documentation='List of contigs in a ContigSet', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 114, 1))
-Namespace.addCategoryObject('elementBinding', Contigs.name().localName(), Contigs)
-
-ConfigSetAnalog = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConfigSetAnalog'), CTD_ANON_74, documentation='An unlimited number of analogs listed for the purposes of hosting in a configuration file. e.g. a list of all possible analogs on the system', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 126, 1))
-Namespace.addCategoryObject('elementBinding', ConfigSetAnalog.name().localName(), ConfigSetAnalog)
-
-DyeSetAnalog = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DyeSetAnalog'), CTD_ANON_75, documentation='A set of four analogs, one for each of the nucleotides, grouped together for the purposes of a single experiment.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 192, 1))
-Namespace.addCategoryObject('elementBinding', DyeSetAnalog.name().localName(), DyeSetAnalog)
-
-Assay = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Assay'), AssayType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 11, 1))
-Namespace.addCategoryObject('elementBinding', Assay.name().localName(), Assay)
-
-Events = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Events'), RecordedEventType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 60, 1))
-Namespace.addCategoryObject('elementBinding', Events.name().localName(), Events)
-
-Input = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Input'), InputOutputDataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 61, 1))
-Namespace.addCategoryObject('elementBinding', Input.name().localName(), Input)
-
-Output = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Output'), InputOutputDataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 62, 1))
-Namespace.addCategoryObject('elementBinding', Output.name().localName(), Output)
-
-ConsensusReadSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConsensusReadSet'), CTD_ANON_76, documentation='DataSets of CCS reads (typically in unaligned BAM format).', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 50, 1))
-Namespace.addCategoryObject('elementBinding', ConsensusReadSet.name().localName(), ConsensusReadSet)
-
-ExternalResource = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource'), IndexedDataType, documentation='for example, an output file could be the BAM file, which could be associated with multiple indices into it.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 662, 1))
-Namespace.addCategoryObject('elementBinding', ExternalResource.name().localName(), ExternalResource)
-
-SequencingKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 67, 1))
-Namespace.addCategoryObject('elementBinding', SequencingKit.name().localName(), SequencingKit)
-
-BindingKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), SupplyKitBinding, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 68, 1))
-Namespace.addCategoryObject('elementBinding', BindingKit.name().localName(), BindingKit)
-
-TemplatePrepKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), SupplyKitTemplate, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 69, 1))
-Namespace.addCategoryObject('elementBinding', TemplatePrepKit.name().localName(), TemplatePrepKit)
-
-ControlKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlKit'), SupplyKitControl, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 70, 1))
-Namespace.addCategoryObject('elementBinding', ControlKit.name().localName(), ControlKit)
-
-CellPackKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit'), SupplyKitCellPack, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 71, 1))
-Namespace.addCategoryObject('elementBinding', CellPackKit.name().localName(), CellPackKit)
-
-AlignmentSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AlignmentSet'), CTD_ANON_77, documentation='DataSets for aligned subreads and CCS reads.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 8, 1))
-Namespace.addCategoryObject('elementBinding', AlignmentSet.name().localName(), AlignmentSet)
-
-BarcodeSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodeSet'), CTD_ANON_78, documentation='DataSets of Barcodes. Basically a thin metadata layer on top of the barcode FASTA.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 18, 1))
-Namespace.addCategoryObject('elementBinding', BarcodeSet.name().localName(), BarcodeSet)
-
-ConsensusAlignmentSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConsensusAlignmentSet'), CTD_ANON_79, documentation='DataSets of aligned CCS reads.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 40, 1))
-Namespace.addCategoryObject('elementBinding', ConsensusAlignmentSet.name().localName(), ConsensusAlignmentSet)
-
-ReferenceSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReferenceSet'), CTD_ANON_80, documentation='DataSets of reference sequences. Replaces the reference.info.xml', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 72, 1))
-Namespace.addCategoryObject('elementBinding', ReferenceSet.name().localName(), ReferenceSet)
-
-ContigSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ContigSet'), CTD_ANON_81, documentation='DataSets of contigs sequences. Basically a thin metadata layer on top of a contigs FASTA (e.g. from HGAP).', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 82, 1))
-Namespace.addCategoryObject('elementBinding', ContigSet.name().localName(), ContigSet)
-
-HdfSubreadSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'HdfSubreadSet'), CTD_ANON_82, documentation='DataSets of subreads in bax.h5 or bas.h5 format.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 104, 1))
-Namespace.addCategoryObject('elementBinding', HdfSubreadSet.name().localName(), HdfSubreadSet)
-
-SubreadSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet'), CTD_ANON_83, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 681, 1))
-Namespace.addCategoryObject('elementBinding', SubreadSet.name().localName(), SubreadSet)
-
-
-
-CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraints'), CTD_ANON_, scope=CTD_ANON, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 19, 1)))
-
-def _BuildAutomaton ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton
- del _BuildAutomaton
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraints')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 15, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON._Automaton = _BuildAutomaton()
-
-
-
-
-CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraint'), AutomationConstraintType, scope=CTD_ANON_, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 26, 1)))
-
-def _BuildAutomaton_ ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_
- del _BuildAutomaton_
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationConstraint')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 22, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_._Automaton = _BuildAutomaton_()
-
-
-
-
-CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automation'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 40, 8)))
-
-def _BuildAutomaton_2 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_2
- del _BuildAutomaton_2
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 40, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_2._Automaton = _BuildAutomaton_2()
-
-
-
-
-CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertSize'), pyxb.binding.datatypes.int, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 50, 8)))
-
-def _BuildAutomaton_3 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_3
- del _BuildAutomaton_3
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertSize')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 50, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_3._Automaton = _BuildAutomaton_3()
-
-
-
-
-CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement'), pyxb.binding.datatypes.anyType, scope=CTD_ANON_4, documentation='A generic element whose contents are undefined at the schema level. This is used to extend the data model.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 640, 1)))
-
-def _BuildAutomaton_4 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_4
- del _BuildAutomaton_4
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 60, 6))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 60, 6))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_4._Automaton = _BuildAutomaton_4()
-
-
-
-
-CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataPointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 174, 4)))
-
-def _BuildAutomaton_5 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_5
- del _BuildAutomaton_5
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 174, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataPointer')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 174, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_5._Automaton = _BuildAutomaton_5()
-
-
-
-
-CTD_ANON_6._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource'), IndexedDataType, scope=CTD_ANON_6, documentation='for example, an output file could be the BAM file, which could be associated with multiple indices into it.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 662, 1)))
-
-def _BuildAutomaton_6 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_6
- del _BuildAutomaton_6
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 208, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_6._Automaton = _BuildAutomaton_6()
-
-
-
-
-CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'FileIndex'), InputOutputDataType, scope=CTD_ANON_7, documentation='e.g. index for output files, allowing one to find information in the output file', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 224, 8)))
-
-def _BuildAutomaton_7 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_7
- del _BuildAutomaton_7
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'FileIndex')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 224, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_7._Automaton = _BuildAutomaton_7()
-
-
-
-
-CTD_ANON_8._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), DataEntityType, scope=CTD_ANON_8, documentation='One or more collection parameters, such as MovieLength, InsertSize, UseStageStart, IsControl, etc..', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 253, 1)))
-
-def _BuildAutomaton_8 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_8
- del _BuildAutomaton_8
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 244, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_8._Automaton = _BuildAutomaton_8()
-
-
-
-
-CTD_ANON_9._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumber'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_9, documentation='A reference to the incompatible part number UID', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 273, 8)))
-
-def _BuildAutomaton_9 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_9
- del _BuildAutomaton_9
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumber')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 273, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_9._Automaton = _BuildAutomaton_9()
-
-
-
-
-CTD_ANON_10._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomation'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_10, documentation='A reference to the incompatible automation type UID', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 287, 8)))
-
-def _BuildAutomaton_10 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_10
- del _BuildAutomaton_10
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 287, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_10._Automaton = _BuildAutomaton_10()
-
-
-
-
-CTD_ANON_11._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analog'), AnalogType, scope=CTD_ANON_11, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 349, 13)))
-
-def _BuildAutomaton_11 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_11
- del _BuildAutomaton_11
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=1, max=4, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 349, 13))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analog')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 349, 13))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_11._Automaton = _BuildAutomaton_11()
-
-
-
-
-CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfig'), SequencingChemistryConfig, scope=CTD_ANON_12, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 368, 4)))
-
-def _BuildAutomaton_12 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_12
- del _BuildAutomaton_12
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfig')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 368, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_12._Automaton = _BuildAutomaton_12()
-
-
-
-
-CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analog'), AnalogType, scope=CTD_ANON_13, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 382, 8)))
-
-def _BuildAutomaton_13 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_13
- del _BuildAutomaton_13
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=1, max=4, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 382, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analog')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 382, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_13._Automaton = _BuildAutomaton_13()
-
-
-
-
-CTD_ANON_14._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), pyxb.binding.datatypes.int, scope=CTD_ANON_14, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 406, 8)))
-
-def _BuildAutomaton_14 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_14
- del _BuildAutomaton_14
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCount')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 406, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_14._Automaton = _BuildAutomaton_14()
-
-
-
-
-CTD_ANON_15._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), pyxb.binding.datatypes.int, scope=CTD_ANON_15, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 432, 8)))
-
-def _BuildAutomaton_15 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_15
- del _BuildAutomaton_15
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCount')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 432, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_15._Automaton = _BuildAutomaton_15()
-
-
-
-
-CTD_ANON_16._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinLabel'), pyxb.binding.datatypes.string, scope=CTD_ANON_16, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 440, 8)))
-
-def _BuildAutomaton_16 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_16
- del _BuildAutomaton_16
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_16._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinLabel')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 440, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_16._Automaton = _BuildAutomaton_16()
-
-
-
-
-CTD_ANON_17._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Val'), pyxb.binding.datatypes.float, scope=CTD_ANON_17, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 462, 8)))
-
-def _BuildAutomaton_17 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_17
- del _BuildAutomaton_17
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 462, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_17._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Val')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 462, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_17._Automaton = _BuildAutomaton_17()
-
-
-
-
-UserDefinedFieldsType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataEntities'), DataEntityType, scope=UserDefinedFieldsType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 635, 3)))
-
-def _BuildAutomaton_18 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_18
- del _BuildAutomaton_18
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(UserDefinedFieldsType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataEntities')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 635, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-UserDefinedFieldsType._Automaton = _BuildAutomaton_18()
-
-
-
-
-FilterType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Properties'), CTD_ANON_18, scope=FilterType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 647, 3)))
-
-def _BuildAutomaton_19 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_19
- del _BuildAutomaton_19
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(FilterType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Properties')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 647, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-FilterType._Automaton = _BuildAutomaton_19()
-
-
-
-
-CTD_ANON_18._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Property'), CTD_ANON_19, scope=CTD_ANON_18, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 650, 6)))
-
-def _BuildAutomaton_20 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_20
- del _BuildAutomaton_20
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_18._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Property')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 650, 6))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_18._Automaton = _BuildAutomaton_20()
-
-
-
-
-CTD_ANON_20._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), CTD_ANON_70, scope=CTD_ANON_20, documentation='Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ', location=pyxb.ut [...]
-
-def _BuildAutomaton_21 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_21
- del _BuildAutomaton_21
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 15, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_20._Automaton = _BuildAutomaton_21()
-
-
-
-
-DataSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TotalLength'), pyxb.binding.datatypes.int, scope=DataSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3)))
-
-DataSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumRecords'), pyxb.binding.datatypes.int, scope=DataSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3)))
-
-DataSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Provenance'), CTD_ANON_66, scope=DataSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3)))
-
-def _BuildAutomaton_22 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_22
- del _BuildAutomaton_22
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(DataSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(DataSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(DataSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-DataSetMetadataType._Automaton = _BuildAutomaton_22()
-
-
-
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AdapterDimerFraction'), pyxb.binding.datatypes.float, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 68, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ShortInsertFraction'), pyxb.binding.datatypes.float, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 69, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumSequencingZmws'), pyxb.binding.datatypes.int, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 70, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ProdDist'), StatsDiscreteDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 71, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReadTypeDist'), StatsDiscreteDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 72, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReadLenDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 73, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReadQualDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 74, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlReadLenDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 75, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlReadQualDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 76, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MedianInsertDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 77, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertReadLenDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 78, 8)))
-
-CTD_ANON_21._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertReadQualDist'), StatsContinuousDistType, scope=CTD_ANON_21, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 79, 8)))
-
-def _BuildAutomaton_23 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_23
- del _BuildAutomaton_23
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AdapterDimerFraction')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 68, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ShortInsertFraction')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 69, 8))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumSequencingZmws')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 70, 8))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ProdDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 71, 8))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReadTypeDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 72, 8))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReadLenDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 73, 8))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReadQualDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 74, 8))
- st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlReadLenDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 75, 8))
- st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlReadQualDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 76, 8))
- st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MedianInsertDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 77, 8))
- st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_9)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertReadLenDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 78, 8))
- st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_10)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_21._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertReadQualDist')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 79, 8))
- st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_11)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_9, [
- ]))
- st_8._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_10, [
- ]))
- st_9._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_11, [
- ]))
- st_10._set_transitionSet(transitions)
- transitions = []
- st_11._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_21._Automaton = _BuildAutomaton_23()
-
-
-
-
-CTD_ANON_22._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Filter'), FilterType, scope=CTD_ANON_22, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 110, 8)))
-
-def _BuildAutomaton_24 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_24
- del _BuildAutomaton_24
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_22._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filter')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 110, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_22._Automaton = _BuildAutomaton_24()
-
-
-
-
-CTD_ANON_23._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), DataSetType, scope=CTD_ANON_23, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 135, 1)))
-
-def _BuildAutomaton_25 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_25
- del _BuildAutomaton_25
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 117, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_23._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSet')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 117, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_23._Automaton = _BuildAutomaton_25()
-
-
-
-
-CTD_ANON_24._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), CTD_ANON_70, scope=CTD_ANON_24, documentation='Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ', location=pyxb.ut [...]
-
-def _BuildAutomaton_26 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_26
- del _BuildAutomaton_26
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_24._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 131, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_24._Automaton = _BuildAutomaton_26()
-
-
-
-
-CTD_ANON_25._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunId'), pyxb.binding.datatypes.string, scope=CTD_ANON_25, documentation='A unique identifier for this run. Format is r[sid]_[iname]_[ts]. Where [id] is a system generated id and [iname] is the instrument name and [ts] is a timestamp YYMMDD Example: r000123_00117_100713 ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 254, 4)))
-
-CTD_ANON_25._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Name'), pyxb.binding.datatypes.string, scope=CTD_ANON_25, documentation='Assigned name for a run, which consists of multiple wells. There is no constraint on the uniqueness of this data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 259, 4)))
-
-CTD_ANON_25._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CreatedBy'), pyxb.binding.datatypes.string, scope=CTD_ANON_25, documentation='Who created the run. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 264, 4)))
-
-CTD_ANON_25._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WhenCreated'), pyxb.binding.datatypes.dateTime, scope=CTD_ANON_25, documentation='Date and time of when the overall run was created in the system. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 269, 4)))
-
-CTD_ANON_25._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'StartedBy'), pyxb.binding.datatypes.string, scope=CTD_ANON_25, documentation='Who started the run. Could be different from who created it. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 274, 4)))
-
-CTD_ANON_25._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), pyxb.binding.datatypes.dateTime, scope=CTD_ANON_25, documentation='Date and time of when the overall run was started. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 279, 4)))
-
-def _BuildAutomaton_27 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_27
- del _BuildAutomaton_27
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 259, 4))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 264, 4))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 269, 4))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 274, 4))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 279, 4))
- counters.add(cc_4)
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_25._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RunId')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 254, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_25._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Name')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 259, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_25._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CreatedBy')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 264, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_25._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WhenCreated')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 269, 4))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_25._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'StartedBy')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 274, 4))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_25._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 279, 4))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- transitions.append(fac.Transition(st_5, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, True) ]))
- st_5._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_25._Automaton = _BuildAutomaton_27()
-
-
-
-
-CTD_ANON_26._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), pyxb.binding.datatypes.dateTime, scope=CTD_ANON_26, documentation='Date and time of when this movie acquisition started. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 293, 4)))
-
-CTD_ANON_26._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DurationInSec'), pyxb.binding.datatypes.int, scope=CTD_ANON_26, documentation='The actual length of the movie acquisition (in seconds), irrespective of the movie duration specified by an automation parameter. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 298, 4), unicode_default='0'))
-
-CTD_ANON_26._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Number'), pyxb.binding.datatypes.int, scope=CTD_ANON_26, documentation="The number of this movie within the set (i.e., look). This is unique when combined with the 'SetNumber'. ", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 303, 4), unicode_default='0'))
-
-def _BuildAutomaton_28 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_28
- del _BuildAutomaton_28
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_26._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 293, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_26._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DurationInSec')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 298, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_26._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Number')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 303, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_26._Automaton = _BuildAutomaton_28()
-
-
-
-
-CTD_ANON_27._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EightPacPastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_27, documentation='Number of days past expiration the eight pac was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 317, 4)))
-
-CTD_ANON_27._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKitPastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_27, documentation='Number of days past expiration the reagent kit was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 322, 4)))
-
-CTD_ANON_27._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube0PastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_27, documentation='Number of days past expiration the reagent tube 0 was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 327, 4)))
-
-CTD_ANON_27._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube1PastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_27, documentation='Number of days past expiration the reagent tube 1 was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 332, 4)))
-
-def _BuildAutomaton_29 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_29
- del _BuildAutomaton_29
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_27._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EightPacPastExpiration')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 317, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_27._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentKitPastExpiration')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 322, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_27._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube0PastExpiration')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 327, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_27._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube1PastExpiration')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 332, 4))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_27._Automaton = _BuildAutomaton_29()
-
-
-
-
-CTD_ANON_28._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Barcode'), DNABarcode, scope=CTD_ANON_28, documentation='A sequence of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 353, 8)))
-
-def _BuildAutomaton_30 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_30
- del _BuildAutomaton_30
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 353, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_28._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Barcode')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 353, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_28._Automaton = _BuildAutomaton_30()
-
-
-
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleTrace'), CTD_ANON_30, scope=CTD_ANON_29, documentation='Tag to indicate that the trace file will be sampled. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 509, 4)))
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), pyxb.binding.datatypes.string, scope=CTD_ANON_29, documentation='Name of primary analysis protocol. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 528, 4)))
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConfigFileName'), pyxb.binding.datatypes.string, scope=CTD_ANON_29, documentation='Name of primary analysis config file. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 533, 4)))
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingCondition'), pyxb.binding.datatypes.string, scope=CTD_ANON_29, documentation='A sequencing condition tag to be used by primary analysis, e.g., to select basecaller calibration or training parameters. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 538, 4)))
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ResultsFolder'), pyxb.binding.datatypes.string, scope=CTD_ANON_29, documentation="NOTE: not for customers. A sub-folder under the CollectionPath created by Primary Analysis. This is a field that will be updated by the primary analysis pipeline. The default (as created by homer) should be set to 'Reports_Sms' for now. Consumers of the data should be aware that they will find collection metadata (a [...]
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionPathUri'), pyxb.binding.datatypes.anyURI, scope=CTD_ANON_29, documentation='User-specified location of where the results should be copied after an analysis has been completed. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 548, 4)))
-
-CTD_ANON_29._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CopyFiles'), CTD_ANON_31, scope=CTD_ANON_29, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 553, 4)))
-
-def _BuildAutomaton_31 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_31
- del _BuildAutomaton_31
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 509, 4))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleTrace')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 509, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 528, 4))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ConfigFileName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 533, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingCondition')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 538, 4))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ResultsFolder')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 543, 4))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionPathUri')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 548, 4))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_29._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CopyFiles')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 553, 4))
- st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- st_6._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_29._Automaton = _BuildAutomaton_31()
-
-
-
-
-CTD_ANON_30._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TraceSamplingFactor'), pyxb.binding.datatypes.float, scope=CTD_ANON_30, documentation='Percentage of traces to sample. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 515, 7)))
-
-CTD_ANON_30._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'FullPulseFile'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_30, documentation='Whether full or sampled pulse file is transferred if requested. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 520, 7)))
-
-def _BuildAutomaton_32 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_32
- del _BuildAutomaton_32
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_30._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TraceSamplingFactor')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 515, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_30._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'FullPulseFile')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 520, 7))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_30._Automaton = _BuildAutomaton_32()
-
-
-
-
-CTD_ANON_31._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionFileCopy'), PapOutputFile, scope=CTD_ANON_31, documentation='Defines the set of files to be copied to the CollectionPathUri. 1 or more. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 556, 7)))
-
-def _BuildAutomaton_33 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_33
- del _BuildAutomaton_33
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_31._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionFileCopy')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 556, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_31._Automaton = _BuildAutomaton_33()
-
-
-
-
-CTD_ANON_32._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), pyxb.binding.datatypes.string, scope=CTD_ANON_32, documentation='The secondary analysis protocol name specified in the sample sheet. Ignored by secondary. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 574, 4)))
-
-CTD_ANON_32._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), CTD_ANON_33, scope=CTD_ANON_32, documentation='The parameters for secondary analysis specified in the sample sheet. Ignored by secondary. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 579, 4)))
-
-CTD_ANON_32._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellCountInJob'), pyxb.binding.datatypes.int, scope=CTD_ANON_32, documentation="The number of cells in this secondary analysis job, identified by the secondary analysis parameter 'JobName'. Supports automated secondary analysis. ", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 593, 4)))
-
-def _BuildAutomaton_34 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_34
- del _BuildAutomaton_34
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 579, 4))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_32._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 574, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_32._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 579, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_32._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellCountInJob')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 593, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- transitions.append(fac.Transition(st_2, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_32._Automaton = _BuildAutomaton_34()
-
-
-
-
-CTD_ANON_33._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), DataEntityType, scope=CTD_ANON_33, documentation='One or more secondary analysis parameters, such as JobName, Workflow, etc..', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 585, 7)))
-
-def _BuildAutomaton_35 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_35
- del _BuildAutomaton_35
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 585, 7))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_33._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 585, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_33._Automaton = _BuildAutomaton_35()
-
-
-
-
-CTD_ANON_35._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_35, documentation='Pointer to a single biological sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 650, 5)))
-
-CTD_ANON_35._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_36, scope=CTD_ANON_35, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 659, 1)))
-
-def _BuildAutomaton_36 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_36
- del _BuildAutomaton_36
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_35._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 649, 5))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_35._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 650, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- st_0._set_transitionSet(transitions)
- transitions = []
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_35._Automaton = _BuildAutomaton_36()
-
-
-
-
-CTD_ANON_36._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_36, documentation='Pointer to a group of barcoded samples', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 665, 4)))
-
-def _BuildAutomaton_37 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_37
- del _BuildAutomaton_37
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_36._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 665, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_36._Automaton = _BuildAutomaton_37()
-
-
-
-
-CTD_ANON_37._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, scope=CTD_ANON_37, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 680, 1)))
-
-def _BuildAutomaton_38 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_38
- del _BuildAutomaton_38
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 676, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_37._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSample')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 676, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_37._Automaton = _BuildAutomaton_38()
-
-
-
-
-CTD_ANON_38._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_38, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_39 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_39
- del _BuildAutomaton_39
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 18, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_38._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 18, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_38._Automaton = _BuildAutomaton_39()
-
-
-
-
-CTD_ANON_39._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), CTD_ANON_38, scope=CTD_ANON_39, documentation='Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 12, 1)))
-
-CTD_ANON_39._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredSMRTCells'), CTD_ANON_43, scope=CTD_ANON_39, documentation='Part of the RunResources; specifies the required number of SMRT cells', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 106, 1)))
-
-CTD_ANON_39._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_39, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_40 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_40
- del _BuildAutomaton_40
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 32, 4))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_39._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 30, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_39._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RequiredSMRTCells')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 31, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_39._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 32, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_39._Automaton = _BuildAutomaton_40()
-
-
-
-
-CTD_ANON_40._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime'), CTD_ANON_41, scope=CTD_ANON_40, documentation='The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 48, 1)))
-
-CTD_ANON_40._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips'), CTD_ANON_44, scope=CTD_ANON_40, documentation='Part of the RunResources; specifies the required number of tips via two attributes, Left and Right', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 117, 1)))
-
-CTD_ANON_40._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), SupplyKitSequencing, scope=CTD_ANON_40, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 67, 1)))
-
-def _BuildAutomaton_41 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_41
- del _BuildAutomaton_41
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_40._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 42, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_40._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 43, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_40._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 44, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_40._Automaton = _BuildAutomaton_41()
-
-
-
-
-CTD_ANON_41._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_41, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_42 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_42
- del _BuildAutomaton_42
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 54, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_41._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 54, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_41._Automaton = _BuildAutomaton_42()
-
-
-
-
-CTD_ANON_42._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainer'), ExperimentContainerType, scope=CTD_ANON_42, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 97, 4)))
-
-def _BuildAutomaton_43 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_43
- del _BuildAutomaton_43
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 98, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_42._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainer')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 97, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.WildcardUse(pyxb.binding.content.Wildcard(process_contents=pyxb.binding.content.Wildcard.PC_strict, namespace_constraint=pyxb.binding.content.Wildcard.NC_any), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 98, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_42._Automaton = _BuildAutomaton_43()
-
-
-
-
-CTD_ANON_43._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_43, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_44 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_44
- del _BuildAutomaton_44
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 112, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_43._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 112, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_43._Automaton = _BuildAutomaton_44()
-
-
-
-
-CTD_ANON_44._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_44, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_45 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_45
- del _BuildAutomaton_45
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 123, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_44._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 123, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_44._Automaton = _BuildAutomaton_45()
-
-
-
-
-CTD_ANON_45._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts'), CTD_ANON_39, scope=CTD_ANON_45, documentation='A set of Chip Layouts deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 24, 1)))
-
-CTD_ANON_45._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits'), CTD_ANON_40, scope=CTD_ANON_45, documentation='A set of reagent kits deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 36, 1)))
-
-CTD_ANON_45._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_45, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_46 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_46
- del _BuildAutomaton_46
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 137, 4))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_45._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 135, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_45._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 136, 4))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_45._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 137, 4))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_45._Automaton = _BuildAutomaton_46()
-
-
-
-
-CTD_ANON_46._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_46, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_47 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_47
- del _BuildAutomaton_47
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 147, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_46._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 147, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_46._Automaton = _BuildAutomaton_47()
-
-
-
-
-CTD_ANON_47._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Run'), RunType, scope=CTD_ANON_47, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 273, 8)))
-
-def _BuildAutomaton_48 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_48
- del _BuildAutomaton_48
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_47._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Run')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 273, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_47._Automaton = _BuildAutomaton_48()
-
-
-
-
-CTD_ANON_48._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), DataSetType, scope=CTD_ANON_48, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 135, 1)))
-
-def _BuildAutomaton_49 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_49
- del _BuildAutomaton_49
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 283, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_48._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSet')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 283, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_48._Automaton = _BuildAutomaton_49()
-
-
-
-
-CTD_ANON_49._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), RecordedEventType, scope=CTD_ANON_49, documentation="Journal of metrics, system events, or alarms that were generated during this container's lifetime", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 293, 8)))
-
-def _BuildAutomaton_50 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_50
- del _BuildAutomaton_50
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 293, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_49._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 293, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_49._Automaton = _BuildAutomaton_50()
-
-
-
-
-CTD_ANON_50._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, scope=CTD_ANON_50, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 304, 8)))
-
-def _BuildAutomaton_51 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_51
- del _BuildAutomaton_51
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 304, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_50._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSample')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 304, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_50._Automaton = _BuildAutomaton_51()
-
-
-
-
-CTD_ANON_51._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Input'), InputOutputDataType, scope=CTD_ANON_51, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 61, 1)))
-
-def _BuildAutomaton_52 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_52
- del _BuildAutomaton_52
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_51._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Input')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 324, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_51._Automaton = _BuildAutomaton_52()
-
-
-
-
-CTD_ANON_52._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Output'), InputOutputDataType, scope=CTD_ANON_52, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 62, 1)))
-
-def _BuildAutomaton_53 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_53
- del _BuildAutomaton_53
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_52._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Output')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 331, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_52._Automaton = _BuildAutomaton_53()
-
-
-
-
-CTD_ANON_53._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), RecordedEventType, scope=CTD_ANON_53, documentation="Journal of metrics, system events, or alarms that were generated during this run's lifetime.\nIn the case of Primary generating the DataSet containing the sts.xml, this RecordedEvent object should be a pointer to the DataSet object generated.", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 347, 8)))
-
-def _BuildAutomaton_54 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_54
- del _BuildAutomaton_54
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 347, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_53._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 347, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_53._Automaton = _BuildAutomaton_54()
-
-
-
-
-CTD_ANON_54._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadataRef'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_54, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 390, 4)))
-
-def _BuildAutomaton_55 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_55
- del _BuildAutomaton_55
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_54._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadataRef')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 390, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_54._Automaton = _BuildAutomaton_55()
-
-
-
-
-CTD_ANON_55._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKits'), CTD_ANON_56, scope=CTD_ANON_55, documentation='List the sequencing kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 14, 4)))
-
-CTD_ANON_55._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKits'), CTD_ANON_57, scope=CTD_ANON_55, documentation='List the binding kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 24, 4)))
-
-CTD_ANON_55._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKits'), CTD_ANON_58, scope=CTD_ANON_55, documentation='List the sample prep kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 34, 4)))
-
-CTD_ANON_55._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlKits'), CTD_ANON_59, scope=CTD_ANON_55, documentation='List the DNA control complex part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 44, 4)))
-
-CTD_ANON_55._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPackKits'), CTD_ANON_60, scope=CTD_ANON_55, documentation='List the cell tray part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 54, 4)))
-
-def _BuildAutomaton_56 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_56
- del _BuildAutomaton_56
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 14, 4))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 24, 4))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 34, 4))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 44, 4))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 54, 4))
- counters.add(cc_4)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_55._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 14, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_55._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BindingKits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 24, 4))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_55._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 34, 4))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_55._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlKits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 44, 4))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_55._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellPackKits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 54, 4))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_55._Automaton = _BuildAutomaton_56()
-
-
-
-
-CTD_ANON_56._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), SupplyKitSequencing, scope=CTD_ANON_56, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 67, 1)))
-
-def _BuildAutomaton_57 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_57
- del _BuildAutomaton_57
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_56._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 20, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_56._Automaton = _BuildAutomaton_57()
-
-
-
-
-CTD_ANON_57._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), SupplyKitBinding, scope=CTD_ANON_57, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 68, 1)))
-
-def _BuildAutomaton_58 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_58
- del _BuildAutomaton_58
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_57._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BindingKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 30, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_57._Automaton = _BuildAutomaton_58()
-
-
-
-
-CTD_ANON_58._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), SupplyKitTemplate, scope=CTD_ANON_58, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 69, 1)))
-
-def _BuildAutomaton_59 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_59
- del _BuildAutomaton_59
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_58._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 40, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_58._Automaton = _BuildAutomaton_59()
-
-
-
-
-CTD_ANON_59._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlKit'), SupplyKitControl, scope=CTD_ANON_59, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 70, 1)))
-
-def _BuildAutomaton_60 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_60
- del _BuildAutomaton_60
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_59._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 50, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_59._Automaton = _BuildAutomaton_60()
-
-
-
-
-CTD_ANON_60._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit'), SupplyKitCellPack, scope=CTD_ANON_60, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 71, 1)))
-
-def _BuildAutomaton_61 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_61
- del _BuildAutomaton_61
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_60._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioPartNumbers.xsd', 60, 7))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_60._Automaton = _BuildAutomaton_61()
-
-
-
-
-CTD_ANON_61._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, scope=CTD_ANON_61, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 18, 1)))
-
-def _BuildAutomaton_62 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_62
- del _BuildAutomaton_62
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_61._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 13, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_61._Automaton = _BuildAutomaton_62()
-
-
-
-
-CTD_ANON_62._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, scope=CTD_ANON_62, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 17, 1)))
-
-def _BuildAutomaton_63 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_63
- del _BuildAutomaton_63
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_62._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagent')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 72, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_62._Automaton = _BuildAutomaton_63()
-
-
-
-
-CTD_ANON_63._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, scope=CTD_ANON_63, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 19, 1)))
-
-def _BuildAutomaton_64 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_64
- del _BuildAutomaton_64
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_63._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 79, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_63._Automaton = _BuildAutomaton_64()
-
-
-
-
-CTD_ANON_64._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, scope=CTD_ANON_64, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 20, 1)))
-
-def _BuildAutomaton_65 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_65
- del _BuildAutomaton_65
- import pyxb.utils.fac as fac
-
- counters = set()
- states = []
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_64._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 86, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_64._Automaton = _BuildAutomaton_65()
-
-
-
-
-CTD_ANON_65._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomation'), pyxb.binding.datatypes.string, scope=CTD_ANON_65, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 93, 8)))
-
-def _BuildAutomaton_66 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_66
- del _BuildAutomaton_66
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 93, 8))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_65._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 93, 8))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_65._Automaton = _BuildAutomaton_66()
-
-
-
-
-BaseEntityType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Extensions'), CTD_ANON_4, scope=BaseEntityType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3)))
-
-def _BuildAutomaton_67 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_67
- del _BuildAutomaton_67
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(BaseEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-BaseEntityType._Automaton = _BuildAutomaton_67()
-
-
-
-
-CTD_ANON_66._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CommonServicesInstanceId'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_66, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 41, 6)))
-
-CTD_ANON_66._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CreatorUserId'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_66, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 42, 6)))
-
-CTD_ANON_66._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ParentJobId'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_66, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 43, 6)))
-
-CTD_ANON_66._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ParentTool'), BaseEntityType, scope=CTD_ANON_66, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 44, 6)))
-
-def _BuildAutomaton_68 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_68
- del _BuildAutomaton_68
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 41, 6))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 42, 6))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 43, 6))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 44, 6))
- counters.add(cc_3)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_66._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CommonServicesInstanceId')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 41, 6))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_66._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CreatorUserId')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 42, 6))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_66._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ParentJobId')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 43, 6))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_66._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ParentTool')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 44, 6))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_66._Automaton = _BuildAutomaton_68()
-
-
-
-
-ReadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SummaryStats'), CTD_ANON_21, scope=ReadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 65, 5)))
-
-ReadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Collections'), CTD_ANON_24, scope=ReadSetMetadataType, documentation='A set of acquisition definitions', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 125, 1)))
-
-ReadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_37, scope=ReadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 673, 1)))
-
-def _BuildAutomaton_69 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_69
- del _BuildAutomaton_69
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 63, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 64, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 65, 5))
- counters.add(cc_3)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Collections')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 63, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 64, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SummaryStats')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 65, 5))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- transitions.append(fac.Transition(st_5, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_5._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-ReadSetMetadataType._Automaton = _BuildAutomaton_69()
-
-
-
-
-SubreadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadLength'), pyxb.binding.datatypes.int, scope=SubreadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 91, 5)))
-
-SubreadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadQuality'), pyxb.binding.datatypes.float, scope=SubreadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 92, 5)))
-
-def _BuildAutomaton_70 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_70
- del _BuildAutomaton_70
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 91, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadQuality')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 92, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-SubreadSetMetadataType._Automaton = _BuildAutomaton_70()
-
-
-
-
-CTD_ANON_67._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_68, scope=CTD_ANON_67, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 152, 1)))
-
-def _BuildAutomaton_71 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_71
- del _BuildAutomaton_71
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 69, 4))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_67._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 69, 4))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_67._Automaton = _BuildAutomaton_71()
-
-
-
-
-AlignmentSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Aligner'), pyxb.binding.datatypes.anyType, scope=AlignmentSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 141, 5)))
-
-def _BuildAutomaton_72 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_72
- del _BuildAutomaton_72
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 141, 5))
- counters.add(cc_1)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Aligner')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 141, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, True) ]))
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-AlignmentSetMetadataType._Automaton = _BuildAutomaton_72()
-
-
-
-
-ContigSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Contigs'), CTD_ANON_72, scope=ContigSetMetadataType, documentation='List of contigs in a ContigSet', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 114, 1)))
-
-ContigSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Organism'), pyxb.binding.datatypes.string, scope=ContigSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 150, 5)))
-
-ContigSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Ploidy'), pyxb.binding.datatypes.string, scope=ContigSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 151, 5)))
-
-def _BuildAutomaton_73 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_73
- del _BuildAutomaton_73
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 150, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 151, 5))
- counters.add(cc_2)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Organism')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 150, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Ploidy')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 151, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Contigs')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 152, 5))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- transitions.append(fac.Transition(st_5, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- st_5._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-ContigSetMetadataType._Automaton = _BuildAutomaton_73()
-
-
-
-
-BarcodeSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodeConstruction'), pyxb.binding.datatypes.string, scope=BarcodeSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 161, 5)))
-
-def _BuildAutomaton_74 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_74
- del _BuildAutomaton_74
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 36, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 37, 3))
- st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 38, 3))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodeConstruction')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 161, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-BarcodeSetMetadataType._Automaton = _BuildAutomaton_74()
-
-
-
-
-AutomationConstraintType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automations'), CTD_ANON_2, scope=AutomationConstraintType, documentation='Names of automations that are all similarly constrained', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 34, 5)))
-
-AutomationConstraintType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertSizes'), CTD_ANON_3, scope=AutomationConstraintType, documentation='A list of insert sizes (buckets) recommended for use', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 44, 5)))
-
-def _BuildAutomaton_75 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_75
- del _BuildAutomaton_75
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 34, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 44, 5))
- counters.add(cc_2)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(AutomationConstraintType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(AutomationConstraintType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 34, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(AutomationConstraintType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertSizes')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioAutomationConstraints.xsd', 44, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-AutomationConstraintType._Automaton = _BuildAutomaton_75()
-
-
-
-
-def _BuildAutomaton_76 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_76
- del _BuildAutomaton_76
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-AnalogType._Automaton = _BuildAutomaton_76()
-
-
-
-
-DataEntityType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue'), pyxb.binding.datatypes.base64Binary, scope=DataEntityType, documentation='A complex data type element, such as an image, file, binary object, etc.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5)))
-
-DataEntityType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CheckSum'), pyxb.binding.datatypes.string, scope=DataEntityType, documentation='small-size datum of the attached value for the purpose of detecting errors or modification which may have been introduced during its transmission or storage', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5)))
-
-def _BuildAutomaton_77 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_77
- del _BuildAutomaton_77
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(DataEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(DataEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(DataEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-DataEntityType._Automaton = _BuildAutomaton_77()
-
-
-
-
-def _BuildAutomaton_78 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_78
- del _BuildAutomaton_78
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(DNABarcode._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-DNABarcode._Automaton = _BuildAutomaton_78()
-
-
-
-
-AutomationType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), CTD_ANON_8, scope=AutomationType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 241, 5)))
-
-def _BuildAutomaton_79 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_79
- del _BuildAutomaton_79
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 241, 5))
- counters.add(cc_1)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(AutomationType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(AutomationType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 241, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-AutomationType._Automaton = _BuildAutomaton_79()
-
-
-
-
-CTD_ANON_69._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), CTD_ANON_11, scope=CTD_ANON_69, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 346, 10)))
-
-def _BuildAutomaton_80 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_80
- del _BuildAutomaton_80
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_69._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_69._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analogs')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 346, 10))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_69._Automaton = _BuildAutomaton_80()
-
-
-
-
-SequencingChemistryConfig._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), CTD_ANON_13, scope=SequencingChemistryConfig, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 379, 5)))
-
-def _BuildAutomaton_81 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_81
- del _BuildAutomaton_81
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SequencingChemistryConfig._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(SequencingChemistryConfig._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analogs')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 379, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-SequencingChemistryConfig._Automaton = _BuildAutomaton_81()
-
-
-
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleSize'), pyxb.binding.datatypes.int, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 397, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleMean'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 398, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleMed'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 399, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleStd'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 400, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Sample95thPct'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 401, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), pyxb.binding.datatypes.int, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 402, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), CTD_ANON_14, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 403, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinWidth'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 410, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MinOutlierValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 411, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MinBinValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 412, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MaxBinValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 413, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MaxOutlierValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 414, 5)))
-
-StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), pyxb.binding.datatypes.string, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 415, 5)))
-
-def _BuildAutomaton_82 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_82
- del _BuildAutomaton_82
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleSize')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 397, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleMean')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 398, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleMed')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 399, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleStd')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 400, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Sample95thPct')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 401, 5))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumBins')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 402, 5))
- st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCounts')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 403, 5))
- st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinWidth')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 410, 5))
- st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MinOutlierValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 411, 5))
- st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_9)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MinBinValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 412, 5))
- st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_10)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MaxBinValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 413, 5))
- st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_11)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MaxOutlierValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 414, 5))
- st_12 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_12)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 415, 5))
- st_13 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_13)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_9, [
- ]))
- st_8._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_10, [
- ]))
- st_9._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_11, [
- ]))
- st_10._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_12, [
- ]))
- st_11._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_13, [
- ]))
- st_12._set_transitionSet(transitions)
- transitions = []
- st_13._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-StatsContinuousDistType._Automaton = _BuildAutomaton_82()
-
-
-
-
-StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), pyxb.binding.datatypes.int, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 428, 5)))
-
-StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), CTD_ANON_15, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 429, 5)))
-
-StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), pyxb.binding.datatypes.string, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 436, 5)))
-
-StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinLabels'), CTD_ANON_16, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 437, 5)))
-
-def _BuildAutomaton_83 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_83
- del _BuildAutomaton_83
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumBins')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 428, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCounts')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 429, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 436, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinLabels')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 437, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-StatsDiscreteDistType._Automaton = _BuildAutomaton_83()
-
-
-
-
-StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TimeUnits'), pyxb.binding.datatypes.string, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 455, 5)))
-
-StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ValueUnits'), pyxb.binding.datatypes.string, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 456, 5)))
-
-StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'StartTime'), pyxb.binding.datatypes.float, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 457, 5)))
-
-StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MeasInterval'), pyxb.binding.datatypes.float, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 458, 5)))
-
-StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Values'), CTD_ANON_17, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 459, 5)))
-
-def _BuildAutomaton_84 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_84
- del _BuildAutomaton_84
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 459, 5))
- counters.add(cc_1)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TimeUnits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 455, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ValueUnits')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 456, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'StartTime')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 457, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MeasInterval')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 458, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Values')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 459, 5))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, True) ]))
- st_5._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-StatsTimeSeriesType._Automaton = _BuildAutomaton_84()
-
-
-
-
-DataSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), CTD_ANON_6, scope=DataSetType, documentation='Pointers to data that do not reside inside the parent structure', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 202, 1)))
-
-DataSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Filters'), CTD_ANON_22, scope=DataSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5)))
-
-DataSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), CTD_ANON_23, scope=DataSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5)))
-
-def _BuildAutomaton_85 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_85
- del _BuildAutomaton_85
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-DataSetType._Automaton = _BuildAutomaton_85()
-
-
-
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InstCtrlVer'), pyxb.binding.datatypes.string, scope=CTD_ANON_70, documentation='Instrument control software version. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 144, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SigProcVer'), pyxb.binding.datatypes.string, scope=CTD_ANON_70, documentation='Signal processing software version. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 149, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automation'), AutomationType, scope=CTD_ANON_70, documentation='Defines the collection workflow (e.g., robotic movement, movie acquisition) for a particular cell. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 171, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionNumber'), pyxb.binding.datatypes.int, scope=CTD_ANON_70, documentation='Collection number for this plate well. Sample from one plate well or tube can be distributed to more than one cell. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 176, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellIndex'), pyxb.binding.datatypes.int, scope=CTD_ANON_70, documentation='The zero-based index of this particular cell within the cell tray. Likely to be in the range of [0-3]', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 181, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SetNumber'), pyxb.binding.datatypes.unsignedShort, scope=CTD_ANON_70, documentation='Formerly known as the look number. 1 - N. Defaults to 1. 0 if the look is unknown. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 186, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPac'), SupplyKitCellPack, scope=CTD_ANON_70, documentation='The SMRT cell packaging supply information. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 191, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), SupplyKitTemplate, scope=CTD_ANON_70, documentation='Defines the template (sample) prep kit used for this experiment. Can be used to get back to the primary and adapter used. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 196, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), SupplyKitBinding, scope=CTD_ANON_70, documentation='The binding kit supply information. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 201, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitPlate'), SupplyKitSequencing, scope=CTD_ANON_70, documentation='The sequencing kit supply information. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 206, 6)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunDetails'), CTD_ANON_25, scope=CTD_ANON_70, documentation='Information related to an instrument run. A run can contain multiple chips, wells, and movies. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 248, 1)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Movie'), CTD_ANON_26, scope=CTD_ANON_70, documentation='A movie corresponds to one acquisition for a chip, one set (look) and one strobe. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 287, 1)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData'), CTD_ANON_27, scope=CTD_ANON_70, documentation='Container for the expired consumable data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 311, 1)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WellSample'), CTD_ANON_71, scope=CTD_ANON_70, documentation='Container for the sample related data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 432, 1)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Primary'), CTD_ANON_29, scope=CTD_ANON_70, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 503, 1)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Secondary'), CTD_ANON_32, scope=CTD_ANON_70, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 568, 1)))
-
-CTD_ANON_70._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields'), UserDefinedFieldsType, scope=CTD_ANON_70, documentation='A set of key-value pairs specified by a user via the run input mechanism. Note that uniqueness of keys is not enforced here and so may contain duplicate keys. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 602, 1)))
-
-def _BuildAutomaton_86 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_86
- del _BuildAutomaton_86
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 144, 6))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 149, 6))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 154, 6))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 159, 6))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 176, 6))
- counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 181, 6))
- counters.add(cc_6)
- cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 186, 6))
- counters.add(cc_7)
- cc_8 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 191, 6))
- counters.add(cc_8)
- cc_9 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 196, 6))
- counters.add(cc_9)
- cc_10 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 201, 6))
- counters.add(cc_10)
- cc_11 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 206, 6))
- counters.add(cc_11)
- cc_12 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 211, 6))
- counters.add(cc_12)
- cc_13 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 216, 6))
- counters.add(cc_13)
- cc_14 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 221, 6))
- counters.add(cc_14)
- cc_15 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 226, 6))
- counters.add(cc_15)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InstCtrlVer')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 144, 6))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SigProcVer')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 149, 6))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RunDetails')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 154, 6))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Movie')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 159, 6))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WellSample')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 164, 6))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automation')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 171, 6))
- st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionNumber')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 176, 6))
- st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_6, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellIndex')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 181, 6))
- st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_7, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SetNumber')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 186, 6))
- st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_9)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_8, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellPac')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 191, 6))
- st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_10)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_9, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 196, 6))
- st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_11)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_10, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BindingKit')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 201, 6))
- st_12 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_12)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_11, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitPlate')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 206, 6))
- st_13 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_13)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_12, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Primary')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 211, 6))
- st_14 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_14)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_13, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Secondary')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 216, 6))
- st_15 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_15)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_14, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 221, 6))
- st_16 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_16)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_15, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_70._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 226, 6))
- st_17 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_17)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- ]))
- transitions.append(fac.Transition(st_8, [
- ]))
- transitions.append(fac.Transition(st_9, [
- ]))
- transitions.append(fac.Transition(st_10, [
- ]))
- transitions.append(fac.Transition(st_11, [
- ]))
- transitions.append(fac.Transition(st_12, [
- ]))
- transitions.append(fac.Transition(st_13, [
- ]))
- transitions.append(fac.Transition(st_14, [
- ]))
- transitions.append(fac.Transition(st_15, [
- ]))
- transitions.append(fac.Transition(st_16, [
- ]))
- transitions.append(fac.Transition(st_17, [
- ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_5, True) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_10, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_12, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_5, False) ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_6, True) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_10, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_12, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_6, False) ]))
- st_8._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_7, True) ]))
- transitions.append(fac.Transition(st_10, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_12, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_7, False) ]))
- st_9._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_10, [
- fac.UpdateInstruction(cc_8, True) ]))
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_8, False) ]))
- transitions.append(fac.Transition(st_12, [
- fac.UpdateInstruction(cc_8, False) ]))
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_8, False) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_8, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_8, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_8, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_8, False) ]))
- st_10._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_9, True) ]))
- transitions.append(fac.Transition(st_12, [
- fac.UpdateInstruction(cc_9, False) ]))
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_9, False) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_9, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_9, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_9, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_9, False) ]))
- st_11._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_12, [
- fac.UpdateInstruction(cc_10, True) ]))
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_10, False) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_10, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_10, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_10, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_10, False) ]))
- st_12._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_13, [
- fac.UpdateInstruction(cc_11, True) ]))
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_11, False) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_11, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_11, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_11, False) ]))
- st_13._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_14, [
- fac.UpdateInstruction(cc_12, True) ]))
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_12, False) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_12, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_12, False) ]))
- st_14._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_15, [
- fac.UpdateInstruction(cc_13, True) ]))
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_13, False) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_13, False) ]))
- st_15._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_16, [
- fac.UpdateInstruction(cc_14, True) ]))
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_14, False) ]))
- st_16._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_17, [
- fac.UpdateInstruction(cc_15, True) ]))
- st_17._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_70._Automaton = _BuildAutomaton_86()
-
-
-
-
-BioSampleType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_37, scope=BioSampleType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 673, 1)))
-
-def _BuildAutomaton_87 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_87
- del _BuildAutomaton_87
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 372, 5))
- counters.add(cc_1)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 372, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-BioSampleType._Automaton = _BuildAutomaton_87()
-
-
-
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PlateId'), pyxb.binding.datatypes.string, scope=CTD_ANON_71, documentation='The ID of the sample plate. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 440, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WellName'), pyxb.binding.datatypes.string, scope=CTD_ANON_71, documentation='Identifies which well this sample came from (e.g., coordinate on a plate). ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 445, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Concentration'), pyxb.binding.datatypes.double, scope=CTD_ANON_71, documentation='Sample input concentration. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 450, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleReuseEnabled'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_71, documentation='Whether or not complex reuse is enabled for this well. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 455, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'StageHotstartEnabled'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_71, documentation='Whether or not hotstart at the stage is enabled for this well. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 460, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SizeSelectionEnabled'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_71, documentation='Whether or not size selection is enabled for this well. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 465, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'UseCount'), pyxb.binding.datatypes.int, scope=CTD_ANON_71, documentation='Count of usages for this batch of complex. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 470, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Comments'), pyxb.binding.datatypes.string, scope=CTD_ANON_71, documentation='User-supplied comments about the sample. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 475, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DNAControlComplex'), pyxb.binding.datatypes.string, scope=CTD_ANON_71, documentation='Indicating what kind (if any) control was used. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 480, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleBarcodeInfo'), DataEntityType, scope=CTD_ANON_71, documentation='When utilizing DNA barcoding, store the list of smaple barcodes in this element.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 485, 6)))
-
-CTD_ANON_71._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointers'), CTD_ANON_35, scope=CTD_ANON_71, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 639, 1)))
-
-def _BuildAutomaton_88 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_88
- del _BuildAutomaton_88
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 480, 6))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 485, 6))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 490, 6))
- counters.add(cc_3)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'PlateId')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 440, 6))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WellName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 445, 6))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Concentration')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 450, 6))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleReuseEnabled')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 455, 6))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'StageHotstartEnabled')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 460, 6))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SizeSelectionEnabled')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 465, 6))
- st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'UseCount')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 470, 6))
- st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Comments')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 475, 6))
- st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DNAControlComplex')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 480, 6))
- st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_9)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleBarcodeInfo')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 485, 6))
- st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_10)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_71._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 490, 6))
- st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_11)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_9, [
- ]))
- transitions.append(fac.Transition(st_10, [
- ]))
- transitions.append(fac.Transition(st_11, [
- ]))
- st_8._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_10, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_9._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_10, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_10._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_11, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_11._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_71._Automaton = _BuildAutomaton_88()
-
-
-
-
-def _BuildAutomaton_89 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_89
- del _BuildAutomaton_89
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(ReagentType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-ReagentType._Automaton = _BuildAutomaton_89()
-
-
-
-
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), CTD_ANON_62, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 69, 5)))
-
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), CTD_ANON_63, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 76, 5)))
-
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), CTD_ANON_64, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 83, 5)))
-
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomations'), CTD_ANON_65, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 90, 5)))
-
-def _BuildAutomaton_90 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_90
- del _BuildAutomaton_90
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 90, 5))
- counters.add(cc_1)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagents')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 69, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 76, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 83, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 90, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, True) ]))
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-ReagentKitType._Automaton = _BuildAutomaton_90()
-
-
-
-
-def _BuildAutomaton_91 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_91
- del _BuildAutomaton_91
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(ReagentTubeType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-ReagentTubeType._Automaton = _BuildAutomaton_91()
-
-
-
-
-def _BuildAutomaton_92 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_92
- del _BuildAutomaton_92
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(ReagentPlateRowType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-ReagentPlateRowType._Automaton = _BuildAutomaton_92()
-
-
-
-
-CTD_ANON_72._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Contig'), CTD_ANON_73, scope=CTD_ANON_72, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 122, 6)))
-
-def _BuildAutomaton_93 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_93
- del _BuildAutomaton_93
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_72._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_72._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Contig')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 122, 6))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- st_1._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_72._Automaton = _BuildAutomaton_93()
-
-
-
-
-def _BuildAutomaton_94 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_94
- del _BuildAutomaton_94
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_73._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_73._Automaton = _BuildAutomaton_94()
-
-
-
-
-def _BuildAutomaton_95 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_95
- del _BuildAutomaton_95
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_74._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_74._Automaton = _BuildAutomaton_95()
-
-
-
-
-def _BuildAutomaton_96 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_96
- del _BuildAutomaton_96
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_75._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- st_0._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-CTD_ANON_75._Automaton = _BuildAutomaton_96()
-
-
-
-
-def _BuildAutomaton_97 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_97
- del _BuildAutomaton_97
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(InputOutputDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(InputOutputDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(InputOutputDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-InputOutputDataType._Automaton = _BuildAutomaton_97()
-
-
-
-
-PartNumberType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers'), CTD_ANON_9, scope=PartNumberType, documentation='By default, a PN is compatible for use with other PNs in the system. In order to exclude the usage of one or more PNs with this one, the incompatible PNs are listed here.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5)))
-
-PartNumberType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations'), CTD_ANON_10, scope=PartNumberType, documentation='By default, a PN is compatible for use with all automations in the system. In order to exclude the usage of automations with this PN, the incompatible automation names are listed here.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5)))
-
-def _BuildAutomaton_98 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_98
- del _BuildAutomaton_98
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- counters.add(cc_4)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-PartNumberType._Automaton = _BuildAutomaton_98()
-
-
-
-
-def _BuildAutomaton_99 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_99
- del _BuildAutomaton_99
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(RecordedEventType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(RecordedEventType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(RecordedEventType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-RecordedEventType._Automaton = _BuildAutomaton_99()
-
-
-
-
-SequencingChemistry._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DyeSet'), CTD_ANON_69, scope=SequencingChemistry, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 341, 5)))
-
-def _BuildAutomaton_100 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_100
- del _BuildAutomaton_100
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DyeSet')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 341, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-SequencingChemistry._Automaton = _BuildAutomaton_100()
-
-
-
-
-ReadSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), ReadSetMetadataType, scope=ReadSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5)))
-
-def _BuildAutomaton_101 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_101
- del _BuildAutomaton_101
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- counters.add(cc_3)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-ReadSetType._Automaton = _BuildAutomaton_101()
-
-
-
-
-BarcodedSampleType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Barcodes'), CTD_ANON_28, scope=BarcodedSampleType, documentation='A list of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 347, 5)))
-
-def _BuildAutomaton_102 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_102
- del _BuildAutomaton_102
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 372, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 347, 5))
- counters.add(cc_2)
- states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(BarcodedSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(BarcodedSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 372, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(BarcodedSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Barcodes')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 347, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_2._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-BarcodedSampleType._Automaton = _BuildAutomaton_102()
-
-
-
-
-AssayType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet'), CTD_ANON_83, scope=AssayType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 681, 1)))
-
-def _BuildAutomaton_103 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_103
- del _BuildAutomaton_103
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 241, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- st_3._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-AssayType._Automaton = _BuildAutomaton_103()
-
-
-
-
-ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InvestigatorName'), pyxb.binding.datatypes.string, scope=ExperimentContainerType, documentation='An optional PI name', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 257, 5)))
-
-ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CreatedDate'), pyxb.binding.datatypes.date, scope=ExperimentContainerType, documentation='Automatically generated creation date', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 262, 5)))
-
-ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Runs'), CTD_ANON_47, scope=ExperimentContainerType, documentation='Multiple acquisitions from different instrument runs', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 267, 5)))
-
-ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), CTD_ANON_48, scope=ExperimentContainerType, documentation='Pointers to various data elements associated with the acquisitions', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 277, 5)))
-
-ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), CTD_ANON_49, scope=ExperimentContainerType, documentation="Journal of metrics, system events, or alarms that were generated during this container's lifetime", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 287, 5)))
-
-ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_50, scope=ExperimentContainerType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 301, 5)))
-
-def _BuildAutomaton_104 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_104
- del _BuildAutomaton_104
- import pyxb.utils.fac as fac
-
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 257, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 267, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 277, 5))
- counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 287, 5))
- counters.add(cc_6)
- cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 301, 5))
- counters.add(cc_7)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InvestigatorName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 257, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CreatedDate')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 262, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Runs')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 267, 5))
- st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 277, 5))
- st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_6, False))
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 287, 5))
- st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_7, False))
- symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 301, 5))
- st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- ]))
- transitions.append(fac.Transition(st_6, [
- ]))
- transitions.append(fac.Transition(st_7, [
- ]))
- transitions.append(fac.Transition(st_8, [
- ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_5, True) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_5, False) ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_6, True) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_6, False) ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_7, True) ]))
- st_8._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-ExperimentContainerType._Automaton = _BuildAutomaton_104()
-
+CompatibleChipLayouts = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts'), CTD_ANON_, documentation='A set of Chip Layouts deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 29, 1))
+Namespace.addCategoryObject('elementBinding', CompatibleChipLayouts.name().localName(), CompatibleChipLayouts)
+CompatibleSequencingKits = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits'), CTD_ANON_2, documentation='A set of reagent kits deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 40, 1))
+Namespace.addCategoryObject('elementBinding', CompatibleSequencingKits.name().localName(), CompatibleSequencingKits)
+EstimatedTotalRunTime = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime'), CTD_ANON_3, documentation='The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 52, 1))
+Namespace.addCategoryObject('elementBinding', EstimatedTotalRunTime.name().localName(), EstimatedTotalRunTime)
-RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet'), CTD_ANON_83, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 681, 1)))
+PacBioDataModel = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioDataModel'), CTD_ANON_4, documentation='PacBio Data Model root element', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 95, 1))
+Namespace.addCategoryObject('elementBinding', PacBioDataModel.name().localName(), PacBioDataModel)
-RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Assay'), AssayType, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 11, 1)))
+RequiredSMRTCells = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredSMRTCells'), CTD_ANON_5, documentation='Part of the RunResources; specifies the required number of SMRT cells', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 110, 1))
+Namespace.addCategoryObject('elementBinding', RequiredSMRTCells.name().localName(), RequiredSMRTCells)
-RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunResources'), CTD_ANON_45, scope=RunType, documentation='This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 129, 1)))
+RequiredTips = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips'), CTD_ANON_6, documentation='Part of the RunResources; specifies the required number of tips via two attributes, Left and Right', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 121, 1))
+Namespace.addCategoryObject('elementBinding', RequiredTips.name().localName(), RequiredTips)
-RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Inputs'), CTD_ANON_51, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 321, 5)))
+RunResources = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunResources'), CTD_ANON_7, documentation='This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 133, 1))
+Namespace.addCategoryObject('elementBinding', RunResources.name().localName(), RunResources)
-RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Outputs'), CTD_ANON_52, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 328, 5)))
+SampleComment = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleComment'), CTD_ANON_8, documentation='A general sample description', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 145, 1))
+Namespace.addCategoryObject('elementBinding', SampleComment.name().localName(), SampleComment)
-RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), CTD_ANON_53, scope=RunType, documentation="Journal of metrics, system events, or alarms that were generated during this run's lifetime", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 341, 5)))
+CollectionReferences = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionReferences'), CTD_ANON_16, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 400, 1))
+Namespace.addCategoryObject('elementBinding', CollectionReferences.name().localName(), CollectionReferences)
-def _BuildAutomaton_105 ():
- # Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_105
- del _BuildAutomaton_105
- import pyxb.utils.fac as fac
+SubreadSets = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets'), CTD_ANON_17, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 407, 1))
+Namespace.addCategoryObject('elementBinding', SubreadSets.name().localName(), SubreadSets)
- counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 321, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 328, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 335, 5))
- counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 340, 5))
- counters.add(cc_6)
- cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 341, 5))
- counters.add(cc_7)
- states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Inputs')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 321, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Outputs')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 328, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Assay')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 335, 5))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RunResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 340, 5))
- st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 341, 5))
- st_7 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioDataModel.xsd', 356, 5))
- st_8 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_5, True) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_5, False) ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_6, True) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_6, False) ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_7, True) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_7, False) ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- st_8._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-RunType._Automaton = _BuildAutomaton_105()
+Parameter = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Parameter'), CTD_ANON_18, documentation='A variable, as a name/value pair, associated with a protocol (one of Collection, Primary, and Secondary)', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 67, 1))
+Namespace.addCategoryObject('elementBinding', Parameter.name().localName(), Parameter)
+
+Validation = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1))
+Namespace.addCategoryObject('elementBinding', Validation.name().localName(), Validation)
+
+Assay = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Assay'), AssayType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 11, 1))
+Namespace.addCategoryObject('elementBinding', Assay.name().localName(), Assay)
+
+Events = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Events'), _ImportedBinding__pbbase.RecordedEventType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 64, 1))
+Namespace.addCategoryObject('elementBinding', Events.name().localName(), Events)
+
+Input = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Input'), _ImportedBinding__pbbase.InputOutputDataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 65, 1))
+Namespace.addCategoryObject('elementBinding', Input.name().localName(), Input)
+Output = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Output'), _ImportedBinding__pbbase.InputOutputDataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 66, 1))
+Namespace.addCategoryObject('elementBinding', Output.name().localName(), Output)
-BarcodeSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), BarcodeSetMetadataType, scope=BarcodeSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 35, 5)))
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
-def _BuildAutomaton_106 ():
+def _BuildAutomaton ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_106
- del _BuildAutomaton_106
+ global _BuildAutomaton
+ del _BuildAutomaton
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 18, 4))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 18, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 35, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-BarcodeSetType._Automaton = _BuildAutomaton_106()
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), CTD_ANON, scope=CTD_ANON_, documentation='Part of the RunResources; specifies a ChipLayout which is compatible with the collection protocols defined on the plate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 12, 1)))
-def _BuildAutomaton_107 ():
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
+
+def _BuildAutomaton_ ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_107
- del _BuildAutomaton_107
+ global _BuildAutomaton_
+ del _BuildAutomaton_
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 36, 4))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_76._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 35, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_76._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 36, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_76._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_76._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
transitions = []
transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
+ ]))
transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
+ ]))
st_0._set_transitionSet(transitions)
transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, True) ]))
st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- st_3._set_transitionSet(transitions)
return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_76._Automaton = _BuildAutomaton_107()
+CTD_ANON_._Automaton = _BuildAutomaton_()
-AlignmentSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), AlignmentSetMetadataType, scope=AlignmentSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5)))
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime'), CTD_ANON_3, scope=CTD_ANON_2, documentation='The total amount of time the run is estimated to require. A confidence value (defaulted to 90%) indicates the degree of certainty associated with the estimate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 52, 1)))
-def _BuildAutomaton_108 ():
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips'), CTD_ANON_6, scope=CTD_ANON_2, documentation='Part of the RunResources; specifies the required number of tips via two attributes, Left and Right', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 121, 1)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbpn, 'SequencingKit'), _ImportedBinding__pbrk.SupplyKitSequencing, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 67, 1)))
+
+def _BuildAutomaton_2 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_108
- del _BuildAutomaton_108
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5))
- counters.add(cc_3)
states = []
final_update = None
- symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbpn, 'SequencingKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 46, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RequiredTips')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 47, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EstimatedTotalRunTime')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 48, 4))
st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
- transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
+ ]))
st_0._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_2, [
]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
st_1._set_transitionSet(transitions)
transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_4._set_transitionSet(transitions)
return fac.Automaton(states, counters, False, containing_state=None)
-AlignmentSetType._Automaton = _BuildAutomaton_108()
+CTD_ANON_2._Automaton = _BuildAutomaton_2()
-ContigSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), ContigSetMetadataType, scope=ContigSetType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 99, 5)))
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_3, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
-def _BuildAutomaton_109 ():
+def _BuildAutomaton_3 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_109
- del _BuildAutomaton_109
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 58, 4))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 58, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 99, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_3()
+
+
+
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainer'), ExperimentContainerType, scope=CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 101, 4)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 102, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExperimentContainer')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 101, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.WildcardUse(pyxb.binding.content.Wildcard(process_contents=pyxb.binding.content.Wildcard.PC_strict, namespace_constraint=pyxb.binding.content.Wildcard.NC_any), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 102, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
+ transitions.append(fac.Transition(st_1, [
]))
- st_1._set_transitionSet(transitions)
+ st_0._set_transitionSet(transitions)
transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_4._Automaton = _BuildAutomaton_4()
+
+
+
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_5, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 116, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 116, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_5._Automaton = _BuildAutomaton_5()
+
+
+
+
+CTD_ANON_6._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_6, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
+
+def _BuildAutomaton_6 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_6
+ del _BuildAutomaton_6
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 127, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 127, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
transitions = []
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-ContigSetType._Automaton = _BuildAutomaton_109()
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_6._Automaton = _BuildAutomaton_6()
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts'), CTD_ANON_, scope=CTD_ANON_7, documentation='A set of Chip Layouts deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 29, 1)))
-IndexedDataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), CTD_ANON_6, scope=IndexedDataType, documentation='Pointers to data that do not reside inside the parent structure', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 202, 1)))
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits'), CTD_ANON_2, scope=CTD_ANON_7, documentation='A set of reagent kits deemed compatible with the current plate', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 40, 1)))
-IndexedDataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'FileIndices'), CTD_ANON_7, scope=IndexedDataType, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 221, 5)))
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_7, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
-def _BuildAutomaton_110 ():
+def _BuildAutomaton_7 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_110
- del _BuildAutomaton_110
+ global _BuildAutomaton_7
+ del _BuildAutomaton_7
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 141, 4))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 221, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 232, 5))
- counters.add(cc_4)
states = []
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleSequencingKits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 139, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleChipLayouts')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 140, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 141, 4))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'FileIndices')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 221, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 232, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
+ ]))
transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
+ ]))
st_0._set_transitionSet(transitions)
transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
+ ]))
st_1._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
+ fac.UpdateInstruction(cc_0, True) ]))
st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-IndexedDataType._Automaton = _BuildAutomaton_110()
-
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_7._Automaton = _BuildAutomaton_7()
-SupplyKitBinding._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Control'), SupplyKitControl, scope=SupplyKitBinding, documentation='Defines the binding kit internal control name. Present when used, otherwise not used if not defined. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 477, 5)))
-SupplyKitBinding._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IsControlUsed'), pyxb.binding.datatypes.boolean, scope=SupplyKitBinding, documentation='True if the control was used during run, otherwise false. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 482, 5)))
+CTD_ANON_8._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_8, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
-def _BuildAutomaton_111 ():
+def _BuildAutomaton_8 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_111
- del _BuildAutomaton_111
+ global _BuildAutomaton_8
+ del _BuildAutomaton_8
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 151, 4))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 477, 5))
- counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 482, 5))
- counters.add(cc_6)
states = []
final_update = set()
final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 151, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Control')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 477, 5))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_6, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IsControlUsed')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 482, 5))
- st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_5, True) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_5, False) ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_6, True) ]))
- st_6._set_transitionSet(transitions)
return fac.Automaton(states, counters, True, containing_state=None)
-SupplyKitBinding._Automaton = _BuildAutomaton_111()
+CTD_ANON_8._Automaton = _BuildAutomaton_8()
-SupplyKitCellPack._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), pyxb.binding.datatypes.string, scope=SupplyKitCellPack, documentation='Defines the internal chip layout name, if any. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 498, 5)))
+CTD_ANON_9._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Run'), RunType, scope=CTD_ANON_9, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 277, 8)))
-def _BuildAutomaton_112 ():
+def _BuildAutomaton_9 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_112
- del _BuildAutomaton_112
+ global _BuildAutomaton_9
+ del _BuildAutomaton_9
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 498, 5))
- counters.add(cc_5)
states = []
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Run')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 277, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 498, 5))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
transitions = []
transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
+ ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_5, True) ]))
- st_5._set_transitionSet(transitions)
- return fac.Automaton(states, counters, True, containing_state=None)
-SupplyKitCellPack._Automaton = _BuildAutomaton_112()
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_9._Automaton = _BuildAutomaton_9()
-SupplyKitControl._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InternalControlName'), pyxb.binding.datatypes.string, scope=SupplyKitControl, documentation='Defines the internal control name, if any. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 514, 5)))
+CTD_ANON_10._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbds, 'DataSet'), _ImportedBinding__pbds.DataSetType, scope=CTD_ANON_10, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 34, 1)))
-def _BuildAutomaton_113 ():
+def _BuildAutomaton_10 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_113
- del _BuildAutomaton_113
+ global _BuildAutomaton_10
+ del _BuildAutomaton_10
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 287, 8))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 514, 5))
- counters.add(cc_5)
states = []
final_update = set()
final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbds, 'DataSet')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 287, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InternalControlName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 514, 5))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_5, True) ]))
- st_5._set_transitionSet(transitions)
return fac.Automaton(states, counters, True, containing_state=None)
-SupplyKitControl._Automaton = _BuildAutomaton_113()
-
-
-
-
-SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'LeftAdaptorSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, documentation='Left adapter DNA sequence.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 530, 5)))
+CTD_ANON_10._Automaton = _BuildAutomaton_10()
-SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'LeftPrimerSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 535, 5)))
-SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RightAdaptorSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, documentation='Right adapter DNA sequence. If not specified, a symmetric adapter model is inferred, where the left adapter sequence is used wherever needed.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 536, 5)))
-SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RightPrimerSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, documentation='Right primaer sequence. If not specified, a symmetric model is inferred, where the left primer sequence is used wherever needed.', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 541, 5)))
-SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertSize'), pyxb.binding.datatypes.int, scope=SupplyKitTemplate, documentation='Approximate size of insert. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 546, 5)))
+CTD_ANON_11._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), _ImportedBinding__pbbase.RecordedEventType, scope=CTD_ANON_11, documentation="Journal of metrics, system events, or alarms that were generated during this container's lifetime", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 297, 8)))
-def _BuildAutomaton_114 ():
+def _BuildAutomaton_11 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_114
- del _BuildAutomaton_114
+ global _BuildAutomaton_11
+ del _BuildAutomaton_11
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 297, 8))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 530, 5))
- counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 535, 5))
- counters.add(cc_6)
- cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 536, 5))
- counters.add(cc_7)
- cc_8 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 541, 5))
- counters.add(cc_8)
- cc_9 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 546, 5))
- counters.add(cc_9)
states = []
final_update = set()
final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 297, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'LeftAdaptorSequence')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 530, 5))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_6, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'LeftPrimerSequence')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 535, 5))
- st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_7, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RightAdaptorSequence')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 536, 5))
- st_7 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_8, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RightPrimerSequence')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 541, 5))
- st_8 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_9, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertSize')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 546, 5))
- st_9 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_9)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_5, True) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_5, False) ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_6, True) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_6, False) ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_7, True) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_7, False) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_7, False) ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_8, True) ]))
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_8, False) ]))
- st_8._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_9, [
- fac.UpdateInstruction(cc_9, True) ]))
- st_9._set_transitionSet(transitions)
return fac.Automaton(states, counters, True, containing_state=None)
-SupplyKitTemplate._Automaton = _BuildAutomaton_114()
+CTD_ANON_11._Automaton = _BuildAutomaton_11()
-def _BuildAutomaton_115 ():
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), _ImportedBinding__pbsample.BioSampleType, scope=CTD_ANON_12, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 308, 8)))
+
+def _BuildAutomaton_12 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_115
- del _BuildAutomaton_115
+ global _BuildAutomaton_12
+ del _BuildAutomaton_12
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 308, 8))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- counters.add(cc_3)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSample')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 308, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-SubreadSetType._Automaton = _BuildAutomaton_115()
-
-
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_12._Automaton = _BuildAutomaton_12()
-SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName'), pyxb.binding.datatypes.string, scope=SupplyKitSequencing, documentation='The reagent-mixing protocol used. ', location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 28, 5)))
-SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), SupplyKitSequencing, scope=SupplyKitSequencing, documentation="Tubes associated with the reagent kit - can have up to two; don't forget to set the location, 0 or 1", location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 33, 5)))
-SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), SequencingChemistry, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 38, 5)))
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Output'), _ImportedBinding__pbbase.InputOutputDataType, scope=CTD_ANON_13, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 66, 1)))
-SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), ReagentKitType, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 39, 5)))
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets'), CTD_ANON_17, scope=CTD_ANON_13, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 407, 1)))
-def _BuildAutomaton_116 ():
+def _BuildAutomaton_13 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_116
- del _BuildAutomaton_116
+ global _BuildAutomaton_13
+ del _BuildAutomaton_13
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 328, 8))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 329, 8))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 28, 5))
- counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=2, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 33, 5))
- counters.add(cc_6)
- cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 38, 5))
- counters.add(cc_7)
- cc_8 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 39, 5))
- counters.add(cc_8)
states = []
final_update = set()
final_update.add(fac.UpdateInstruction(cc_0, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Output')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 328, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
final_update = set()
final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 144, 5))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 329, 8))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 149, 5))
- st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 267, 5))
- st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_4, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 281, 5))
- st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_5, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 28, 5))
- st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_5)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_6, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 33, 5))
- st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_6)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_7, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 38, 5))
- st_7 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_7)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_8, False))
- symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioReagentKit.xsd', 39, 5))
- st_8 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_8)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
transitions.append(fac.Transition(st_1, [
fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_0, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_1, [
fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_1, False) ]))
st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_2, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_3, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_3, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_3, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_4, True) ]))
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_4, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_4, False) ]))
- st_4._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_5, [
- fac.UpdateInstruction(cc_5, True) ]))
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_5, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_5, False) ]))
- st_5._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_6, [
- fac.UpdateInstruction(cc_6, True) ]))
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_6, False) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_6, False) ]))
- st_6._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_7, [
- fac.UpdateInstruction(cc_7, True) ]))
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_7, False) ]))
- st_7._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_8, [
- fac.UpdateInstruction(cc_8, True) ]))
- st_8._set_transitionSet(transitions)
return fac.Automaton(states, counters, True, containing_state=None)
-SupplyKitSequencing._Automaton = _BuildAutomaton_116()
+CTD_ANON_13._Automaton = _BuildAutomaton_13()
-def _BuildAutomaton_117 ():
+CTD_ANON_14._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Input'), _ImportedBinding__pbbase.InputOutputDataType, scope=CTD_ANON_14, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 65, 1)))
+
+def _BuildAutomaton_14 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_117
- del _BuildAutomaton_117
+ global _BuildAutomaton_14
+ del _BuildAutomaton_14
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5))
- counters.add(cc_3)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_77._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Input')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 342, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_77._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_77._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_77._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_77._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_4._set_transitionSet(transitions)
+ st_0._set_transitionSet(transitions)
return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_77._Automaton = _BuildAutomaton_117()
+CTD_ANON_14._Automaton = _BuildAutomaton_14()
-def _BuildAutomaton_118 ():
+CTD_ANON_15._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent'), _ImportedBinding__pbbase.RecordedEventType, scope=CTD_ANON_15, documentation="Journal of metrics, system events, or alarms that were generated during this run's lifetime.\nIn the case of Primary generating the DataSet containing the sts.xml, this RecordedEvent object should be a pointer to the DataSet object generated.", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacB [...]
+
+def _BuildAutomaton_15 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_118
- del _BuildAutomaton_118
+ global _BuildAutomaton_15
+ del _BuildAutomaton_15
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 358, 8))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_78._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvent')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 358, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_78._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_78._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_78._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_78._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 35, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_78._Automaton = _BuildAutomaton_118()
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_15._Automaton = _BuildAutomaton_15()
-def _BuildAutomaton_119 ():
+CTD_ANON_16._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadataRef'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_16, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 403, 4)))
+
+def _BuildAutomaton_16 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_119
- del _BuildAutomaton_119
+ global _BuildAutomaton_16
+ del _BuildAutomaton_16
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
- counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5))
- counters.add(cc_3)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_79._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_16._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadataRef')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 403, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_79._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_79._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_79._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_79._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 67, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
- fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
- st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_16._Automaton = _BuildAutomaton_16()
+
+
+
+
+CTD_ANON_17._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbds, 'SubreadSet'), _ImportedBinding__pbds.CTD_ANON_15, scope=CTD_ANON_17, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 137, 1)))
+
+def _BuildAutomaton_17 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_17
+ del _BuildAutomaton_17
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_17._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbds, 'SubreadSet')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 410, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_4._set_transitionSet(transitions)
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_79._Automaton = _BuildAutomaton_119()
+CTD_ANON_17._Automaton = _BuildAutomaton_17()
-def _BuildAutomaton_120 ():
+CTD_ANON_18._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Validation'), CTD_ANON_19, scope=CTD_ANON_18, documentation='\n A validation type which is an element/part of every other element in the schema. It is used to communicate validation issues as part of the output.\n ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 156, 1)))
+
+def _BuildAutomaton_18 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_120
- del _BuildAutomaton_120
+ global _BuildAutomaton_18
+ del _BuildAutomaton_18
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 73, 4))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- counters.add(cc_2)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_80._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_18._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Validation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 73, 4))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_80._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
- st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
- states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_80._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_80._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_3)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_80._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 99, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
- transitions.append(fac.Transition(st_1, [
- fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
- st_1._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
- st_2._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
- st_3._set_transitionSet(transitions)
- transitions = []
- st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_80._Automaton = _BuildAutomaton_120()
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_18._Automaton = _BuildAutomaton_18()
+
+ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InvestigatorName'), pyxb.binding.datatypes.string, scope=ExperimentContainerType, documentation='An optional PI name', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 261, 5)))
-def _BuildAutomaton_121 ():
+ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CreatedDate'), pyxb.binding.datatypes.date, scope=ExperimentContainerType, documentation='Automatically generated creation date', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 266, 5)))
+
+ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Runs'), CTD_ANON_9, scope=ExperimentContainerType, documentation='Multiple acquisitions from different instrument runs', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 271, 5)))
+
+ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), CTD_ANON_10, scope=ExperimentContainerType, documentation='Pointers to various data elements associated with the acquisitions', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 281, 5)))
+
+ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), CTD_ANON_11, scope=ExperimentContainerType, documentation="Journal of metrics, system events, or alarms that were generated during this container's lifetime", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 291, 5)))
+
+ExperimentContainerType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_12, scope=ExperimentContainerType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 305, 5)))
+
+def _BuildAutomaton_19 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_121
- del _BuildAutomaton_121
+ global _BuildAutomaton_19
+ del _BuildAutomaton_19
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 261, 5))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 271, 5))
counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 281, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 291, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 305, 5))
+ counters.add(cc_5)
states = []
final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_81._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_81._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InvestigatorName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 261, 5))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_81._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CreatedDate')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 266, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_2)
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_81._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Runs')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 271, 5))
st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_3)
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_81._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioSecondaryDataModel.xsd', 99, 5))
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 281, 5))
st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 291, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(ExperimentContainerType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 305, 5))
+ st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
transitions.append(fac.Transition(st_1, [
fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
transitions.append(fac.Transition(st_2, [
- ]))
- transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
+ fac.UpdateInstruction(cc_1, False) ]))
st_1._set_transitionSet(transitions)
transitions = []
- transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
+ ]))
transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
+ ]))
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ transitions.append(fac.Transition(st_6, [
+ ]))
st_2._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_3, [
fac.UpdateInstruction(cc_2, True) ]))
transitions.append(fac.Transition(st_4, [
fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_2, False) ]))
st_3._set_transitionSet(transitions)
transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_3, False) ]))
st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ st_6._set_transitionSet(transitions)
return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_81._Automaton = _BuildAutomaton_121()
+ExperimentContainerType._Automaton = _BuildAutomaton_19()
+
+AssayType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets'), CTD_ANON_17, scope=AssayType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 407, 1)))
-def _BuildAutomaton_122 ():
+def _BuildAutomaton_20 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_122
- del _BuildAutomaton_122
+ global _BuildAutomaton_20
+ del _BuildAutomaton_20
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- counters.add(cc_3)
states = []
final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_82._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
- final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_82._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_82._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_2)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_82._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ symbol = pyxb.binding.content.ElementUse(AssayType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SubreadSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 245, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_3)
- final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_82._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
- states.append(st_4)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
transitions.append(fac.Transition(st_1, [
fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
transitions.append(fac.Transition(st_2, [
- ]))
+ fac.UpdateInstruction(cc_1, False) ]))
transitions.append(fac.Transition(st_3, [
- ]))
- transitions.append(fac.Transition(st_4, [
- ]))
+ fac.UpdateInstruction(cc_1, False) ]))
st_1._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
+ fac.UpdateInstruction(cc_2, True) ]))
transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
+ fac.UpdateInstruction(cc_2, False) ]))
st_2._set_transitionSet(transitions)
transitions = []
- transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
st_3._set_transitionSet(transitions)
- transitions = []
- transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
- st_4._set_transitionSet(transitions)
return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_82._Automaton = _BuildAutomaton_122()
+AssayType._Automaton = _BuildAutomaton_20()
-def _BuildAutomaton_123 ():
+RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Assay'), AssayType, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 11, 1)))
+
+RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunResources'), CTD_ANON_7, scope=RunType, documentation='This is an output field specifying the requirements for the run, e.g. number of tips, estimated run time, etc.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 133, 1)))
+
+RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Outputs'), CTD_ANON_13, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 325, 5)))
+
+RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Inputs'), CTD_ANON_14, scope=RunType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 339, 5)))
+
+RunType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents'), CTD_ANON_15, scope=RunType, documentation="Journal of metrics, system events, or alarms that were generated during this run's lifetime", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 352, 5)))
+
+def _BuildAutomaton_21 ():
# Remove this helper function from the namespace after it is invoked
- global _BuildAutomaton_123
- del _BuildAutomaton_123
+ global _BuildAutomaton_21
+ del _BuildAutomaton_21
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 325, 5))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 339, 5))
counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 346, 5))
counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 351, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 352, 5))
+ counters.add(cc_5)
states = []
- final_update = None
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_83._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioBaseDataModel.xsd', 57, 3))
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_83._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 106, 5))
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Outputs')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 325, 5))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_83._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 107, 5))
- st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Inputs')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 339, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_2)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_83._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 114, 5))
- st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Assay')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 346, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_3)
final_update = set()
- final_update.add(fac.UpdateInstruction(cc_3, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_83._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpl4vgfXxsds/PacBioCollectionMetadata.xsd', 26, 5))
- st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RunResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 351, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(RunType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RecordedEvents')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDataModel.xsd', 352, 5))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
transitions = []
transitions.append(fac.Transition(st_0, [
fac.UpdateInstruction(cc_0, True) ]))
transitions.append(fac.Transition(st_1, [
fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
st_0._set_transitionSet(transitions)
transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
transitions.append(fac.Transition(st_2, [
- ]))
+ fac.UpdateInstruction(cc_1, False) ]))
transitions.append(fac.Transition(st_3, [
- ]))
+ fac.UpdateInstruction(cc_1, False) ]))
transitions.append(fac.Transition(st_4, [
- ]))
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
st_1._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_2, [
- fac.UpdateInstruction(cc_1, True) ]))
+ fac.UpdateInstruction(cc_2, True) ]))
transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_1, False) ]))
+ fac.UpdateInstruction(cc_2, False) ]))
transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_1, False) ]))
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
st_2._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_3, [
- fac.UpdateInstruction(cc_2, True) ]))
+ fac.UpdateInstruction(cc_3, True) ]))
transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_2, False) ]))
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
st_3._set_transitionSet(transitions)
transitions = []
transitions.append(fac.Transition(st_4, [
- fac.UpdateInstruction(cc_3, True) ]))
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
st_4._set_transitionSet(transitions)
- return fac.Automaton(states, counters, False, containing_state=None)
-CTD_ANON_83._Automaton = _BuildAutomaton_123()
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+RunType._Automaton = _BuildAutomaton_21()
diff --git a/pbcore/io/dataset/EntryPoints.py b/pbcore/io/dataset/EntryPoints.py
index fcc2e1f..47aede4 100755
--- a/pbcore/io/dataset/EntryPoints.py
+++ b/pbcore/io/dataset/EntryPoints.py
@@ -2,22 +2,40 @@
import os
import argparse
-from pbcore.io import DataSet, ContigSet
+from pbcore.io import DataSet, ContigSet, openDataSet
from pbcore.io.dataset.DataSetValidator import validateFile
import logging
log = logging.getLogger(__name__)
+def summarizeXml(args):
+ dset = openDataSet(args.infile, strict=args.strict)
+ for fname in dset.toExternalFiles():
+ print fname
+ print "Number of records: {r}".format(r=dset.numRecords)
+ print "Total number of bases: {r}".format(r=dset.totalLength)
+
+def summarize_options(parser):
+ parser.description = "Summarize a DataSet XML file"
+ parser.add_argument("infile", type=str,
+ help="The xml file to summarize")
+ parser.set_defaults(func=summarizeXml)
+
def createXml(args):
dsTypes = DataSet.castableTypes()
- dset = dsTypes[args.dsType](*args.infile)
+ dset = dsTypes[args.dsType](*args.infile, strict=args.strict,
+ skipCounts=args.skipCounts)
log.debug("Dataset created")
- dset.write(args.outfile, validate=args.novalidate, relPaths=args.relative)
+ dset.write(args.outfile, validate=args.novalidate, modPaths=True,
+ relPaths=args.relative)
log.debug("Dataset written")
def create_options(parser):
- parser.description = 'Create an XML file from a fofn or bam'
+ parser.description = ('Create an XML file from a fofn or bam. Possible '
+ 'types: SubreadSet, AlignmentSet, ReferenceSet, '
+ 'HdfSubreadSet, BarcodeSet, ConsensusAlignmentSet, '
+ 'ConsensusReadSet, ContigSet')
parser.add_argument("outfile", type=str, help="The XML to create")
#parser.add_argument("infile", type=validate_file, nargs='+',
parser.add_argument("infile", type=str, nargs='+',
@@ -36,7 +54,7 @@ def filterXml(args):
log.error("Adding filters via CLI is temporarily out of order")
exit(1)
if args.infile.endswith('xml'):
- dataSet = DataSet(args.infile, strict=args.strict)
+ dataSet = openDataSet(args.infile, strict=args.strict)
filters = []
separators = ['<=', '>=', '!=', '==', '>', '<', '=']
for filt in args.filters:
@@ -65,7 +83,7 @@ def filter_options(parser):
def splitXml(args):
log.debug("Starting split")
- dataSet = DataSet(args.infile, strict=args.strict)
+ dataSet = openDataSet(args.infile, strict=args.strict)
chunks = len(args.outfiles)
if args.chunks:
chunks = args.chunks
@@ -73,8 +91,13 @@ def splitXml(args):
ignoreSubDatasets=(not args.subdatasets),
contigs=args.contigs,
maxChunks=args.maxChunks,
- breakContigs=args.breakContigs)
- log.debug("Split into {i} chunks".format(i=len(dss)))
+ breakContigs=args.breakContigs,
+ targetSize=args.targetSize,
+ zmws=args.zmws,
+ barcodes=args.barcodes,
+ byRecords=(not args.byRefLength),
+ updateCounts=(not args.noCounts))
+ log.debug("Splitting into {i} chunks".format(i=len(dss)))
infix = 'chunk{i}'
if args.contigs:
infix += 'contigs'
@@ -109,10 +132,20 @@ def split_options(parser):
help="The xml file to split")
parser.add_argument("--contigs", default=False, action='store_true',
help="Split on contigs")
- parser.add_argument("--chunks", default=False, type=int,
+ parser.add_argument("--barcodes", default=False, action='store_true',
+ help="Split on barcodes")
+ parser.add_argument("--zmws", default=False, action='store_true',
+ help="Split on zmws")
+ parser.add_argument("--byRefLength", default=False, action='store_true',
+ help="Split contigs by contig length")
+ parser.add_argument("--noCounts", default=False, action='store_true',
+ help="Update dataset counts after split")
+ parser.add_argument("--chunks", default=0, type=int,
help="Split contigs into <chunks> total windows")
- parser.add_argument("--maxChunks", default=False, type=int,
+ parser.add_argument("--maxChunks", default=0, type=int,
help="Split contig list into at most <chunks> groups")
+ parser.add_argument("--targetSize", default=5000, type=int,
+ help="Target number of records per chunk")
parser.add_argument("--breakContigs", default=False, action='store_true',
help="Break contigs to get closer to maxCounts")
parser.add_argument("--subdatasets", default=False, action='store_true',
@@ -126,7 +159,7 @@ def split_options(parser):
def mergeXml(args):
dss = []
for infn in args.infiles:
- dss.append(DataSet(infn, strict=args.strict))
+ dss.append(openDataSet(infn, strict=args.strict))
reduce(lambda ds1, ds2: ds1 + ds2, dss).write(args.outfile)
def merge_options(parser):
@@ -139,7 +172,7 @@ def merge_options(parser):
parser.set_defaults(func=mergeXml)
def loadStatsXml(args):
- dset = DataSet(args.infile, strict=args.strict)
+ dset = openDataSet(args.infile, strict=args.strict)
dset.loadStats(args.statsfile)
if args.outfile:
dset.write(args.outfile, validate=False)
@@ -173,13 +206,15 @@ def validate_options(parser):
def consolidateXml(args):
"""Combine BAMs and apply the filters described in the XML file, producing
one consolidated XML"""
- dset = ContigSet(args.infile)
- dset.consolidate(args.datafile)
+ dset = openDataSet(args.infile)
+ dset.consolidate(args.datafile, numFiles=args.numFiles)
dset.write(args.xmlfile)
def consolidate_options(parser):
parser.description = 'Consolidate the XML files'
#parser.add_argument("infile", type=validate_file,
+ parser.add_argument("--numFiles", type=int, default=1,
+ help="The number of data files to produce (1)")
parser.add_argument("infile", type=str,
help="The XML file to consolidate")
parser.add_argument("datafile", type=str,
diff --git a/pbcore/io/dataset/_pbbase.py b/pbcore/io/dataset/_pbbase.py
new file mode 100755
index 0000000..19d9364
--- /dev/null
+++ b/pbcore/io/dataset/_pbbase.py
@@ -0,0 +1,4563 @@
+# ./_pbbase.py
+# -*- coding: utf-8 -*-
+# PyXB bindings for NM:304355e4be645ec0738f0143f32dd444bf98ad15
+# Generated 2015-08-04 20:41:05.062739 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Namespace http://pacificbiosciences.com/PacBioBaseDataModel.xsd [xmlns:pbbase]
+
+from __future__ import unicode_literals
+import pyxb
+import pyxb.binding
+import pyxb.binding.saxer
+import io
+import pyxb.utils.utility
+import pyxb.utils.domutils
+import sys
+import pyxb.utils.six as _six
+
+# Unique identifier for bindings created at the same time
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
+
+# Version of PyXB used to generate the bindings
+_PyXBVersion = '1.2.4'
+# Generated bindings are not compatible across PyXB versions
+if pyxb.__version__ != _PyXBVersion:
+ raise pyxb.PyXBVersionError(_PyXBVersion)
+
+# Import bindings for namespaces imported into schema
+import pyxb.binding.datatypes
+
+# NOTE: All namespace declarations are reserved within the binding
+Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioBaseDataModel.xsd', create_if_missing=True)
+Namespace.configureCategories(['typeBinding', 'elementBinding'])
+
+def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
+ """Parse the given XML and use the document element to create a
+ Python instance.
+
+ @param xml_text An XML document. This should be data (Python 2
+ str or Python 3 bytes), or a text (Python 2 unicode or Python 3
+ str) in the L{pyxb._InputEncoding} encoding.
+
+ @keyword default_namespace The L{pyxb.Namespace} instance to use as the
+ default namespace where there is no default namespace in scope.
+ If unspecified or C{None}, the namespace of the module containing
+ this function will be used.
+
+ @keyword location_base: An object to be recorded as the base of all
+ L{pyxb.utils.utility.Location} instances associated with events and
+ objects handled by the parser. You might pass the URI from which
+ the document was obtained.
+ """
+
+ if pyxb.XMLStyle_saxer != pyxb._XMLStyle:
+ dom = pyxb.utils.domutils.StringToDOM(xml_text)
+ return CreateFromDOM(dom.documentElement, default_namespace=default_namespace)
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ saxer = pyxb.binding.saxer.make_parser(fallback_namespace=default_namespace, location_base=location_base)
+ handler = saxer.getContentHandler()
+ xmld = xml_text
+ if isinstance(xmld, _six.text_type):
+ xmld = xmld.encode(pyxb._InputEncoding)
+ saxer.parse(io.BytesIO(xmld))
+ instance = handler.rootObject()
+ return instance
+
+def CreateFromDOM (node, default_namespace=None):
+ """Create a Python instance from the given DOM node.
+ The node tag must correspond to an element declaration in this module.
+
+ @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}."""
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ return pyxb.binding.basis.element.AnyCreateFromDOM(node, default_namespace)
+
+
+# Atomic simple type: [anonymous]
+class STD_ANON (pyxb.binding.datatypes.dateTime):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 128, 3)
+ _Documentation = None
+STD_ANON._InitializeFacetMap()
+
+# Atomic simple type: [anonymous]
+class STD_ANON_ (pyxb.binding.datatypes.dateTime):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 136, 3)
+ _Documentation = None
+STD_ANON_._InitializeFacetMap()
+
+# Atomic simple type: [anonymous]
+class STD_ANON_2 (pyxb.binding.datatypes.ID):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 151, 5)
+ _Documentation = None
+STD_ANON_2._CF_pattern = pyxb.binding.facets.CF_pattern()
+STD_ANON_2._CF_pattern.addPattern(pattern='[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}')
+STD_ANON_2._InitializeFacetMap(STD_ANON_2._CF_pattern)
+
+# Atomic simple type: [anonymous]
+class STD_ANON_3 (pyxb.binding.datatypes.ID):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 213, 5)
+ _Documentation = None
+STD_ANON_3._CF_pattern = pyxb.binding.facets.CF_pattern()
+STD_ANON_3._CF_pattern.addPattern(pattern='[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}')
+STD_ANON_3._InitializeFacetMap(STD_ANON_3._CF_pattern)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupportedAcquisitionStates
+class SupportedAcquisitionStates (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedAcquisitionStates')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 624, 1)
+ _Documentation = None
+SupportedAcquisitionStates._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedAcquisitionStates, enum_prefix=None)
+SupportedAcquisitionStates.Ready = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Ready', tag='Ready')
+SupportedAcquisitionStates.Initializing = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Initializing', tag='Initializing')
+SupportedAcquisitionStates.Acquiring = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Acquiring', tag='Acquiring')
+SupportedAcquisitionStates.Aligning = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aligning', tag='Aligning')
+SupportedAcquisitionStates.Aligned = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aligned', tag='Aligned')
+SupportedAcquisitionStates.Aborting = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aborting', tag='Aborting')
+SupportedAcquisitionStates.Aborted = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Aborted', tag='Aborted')
+SupportedAcquisitionStates.Failed = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Failed', tag='Failed')
+SupportedAcquisitionStates.Completing = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Completing', tag='Completing')
+SupportedAcquisitionStates.Complete = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Complete', tag='Complete')
+SupportedAcquisitionStates.Calibrating = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Calibrating', tag='Calibrating')
+SupportedAcquisitionStates.Unknown = SupportedAcquisitionStates._CF_enumeration.addEnumeration(unicode_value='Unknown', tag='Unknown')
+SupportedAcquisitionStates._InitializeFacetMap(SupportedAcquisitionStates._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'SupportedAcquisitionStates', SupportedAcquisitionStates)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupportedDataTypes
+class SupportedDataTypes (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedDataTypes')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 640, 1)
+ _Documentation = None
+SupportedDataTypes._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedDataTypes, enum_prefix=None)
+SupportedDataTypes.Int16 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int16', tag='Int16')
+SupportedDataTypes.Int32 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int32', tag='Int32')
+SupportedDataTypes.Int64 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int64', tag='Int64')
+SupportedDataTypes.UInt16 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt16', tag='UInt16')
+SupportedDataTypes.UInt32 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt32', tag='UInt32')
+SupportedDataTypes.UInt64 = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt64', tag='UInt64')
+SupportedDataTypes.Single = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Single', tag='Single')
+SupportedDataTypes.Double = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Double', tag='Double')
+SupportedDataTypes.String = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='String', tag='String')
+SupportedDataTypes.DateTime = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='DateTime', tag='DateTime')
+SupportedDataTypes.Int16_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int16_1D', tag='Int16_1D')
+SupportedDataTypes.Int32_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int32_1D', tag='Int32_1D')
+SupportedDataTypes.Int64_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int64_1D', tag='Int64_1D')
+SupportedDataTypes.UInt16_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt16_1D', tag='UInt16_1D')
+SupportedDataTypes.UInt32_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt32_1D', tag='UInt32_1D')
+SupportedDataTypes.UInt64_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt64_1D', tag='UInt64_1D')
+SupportedDataTypes.Single_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Single_1D', tag='Single_1D')
+SupportedDataTypes.Double_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Double_1D', tag='Double_1D')
+SupportedDataTypes.String_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='String_1D', tag='String_1D')
+SupportedDataTypes.DateTime_1D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='DateTime_1D', tag='DateTime_1D')
+SupportedDataTypes.Int16_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int16_2D', tag='Int16_2D')
+SupportedDataTypes.Int32_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int32_2D', tag='Int32_2D')
+SupportedDataTypes.Int64_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Int64_2D', tag='Int64_2D')
+SupportedDataTypes.UInt16_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt16_2D', tag='UInt16_2D')
+SupportedDataTypes.UInt32_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt32_2D', tag='UInt32_2D')
+SupportedDataTypes.UInt64_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='UInt64_2D', tag='UInt64_2D')
+SupportedDataTypes.Single_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Single_2D', tag='Single_2D')
+SupportedDataTypes.Double_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Double_2D', tag='Double_2D')
+SupportedDataTypes.String_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='String_2D', tag='String_2D')
+SupportedDataTypes.DateTime_2D = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='DateTime_2D', tag='DateTime_2D')
+SupportedDataTypes.XML = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='XML', tag='XML')
+SupportedDataTypes.JSON = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='JSON', tag='JSON')
+SupportedDataTypes.Object = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Object', tag='Object')
+SupportedDataTypes.Other = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Other', tag='Other')
+SupportedDataTypes.Unknown = SupportedDataTypes._CF_enumeration.addEnumeration(unicode_value='Unknown', tag='Unknown')
+SupportedDataTypes._InitializeFacetMap(SupportedDataTypes._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'SupportedDataTypes', SupportedDataTypes)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupportedNucleotides
+class SupportedNucleotides (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedNucleotides')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 679, 1)
+ _Documentation = None
+SupportedNucleotides._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedNucleotides, enum_prefix=None)
+SupportedNucleotides.A = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='A', tag='A')
+SupportedNucleotides.C = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='C', tag='C')
+SupportedNucleotides.T = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='T', tag='T')
+SupportedNucleotides.G = SupportedNucleotides._CF_enumeration.addEnumeration(unicode_value='G', tag='G')
+SupportedNucleotides._InitializeFacetMap(SupportedNucleotides._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'SupportedNucleotides', SupportedNucleotides)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupportedRunStates
+class SupportedRunStates (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupportedRunStates')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 687, 1)
+ _Documentation = None
+SupportedRunStates._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=SupportedRunStates, enum_prefix=None)
+SupportedRunStates.Ready = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Ready', tag='Ready')
+SupportedRunStates.Idle = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Idle', tag='Idle')
+SupportedRunStates.System_Test = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='System Test', tag='System_Test')
+SupportedRunStates.Starting = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Starting', tag='Starting')
+SupportedRunStates.Running = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Running', tag='Running')
+SupportedRunStates.Aborting = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Aborting', tag='Aborting')
+SupportedRunStates.Aborted = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Aborted', tag='Aborted')
+SupportedRunStates.Terminated = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Terminated', tag='Terminated')
+SupportedRunStates.Completing = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Completing', tag='Completing')
+SupportedRunStates.Complete = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Complete', tag='Complete')
+SupportedRunStates.Unknown = SupportedRunStates._CF_enumeration.addEnumeration(unicode_value='Unknown', tag='Unknown')
+SupportedRunStates._InitializeFacetMap(SupportedRunStates._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'SupportedRunStates', SupportedRunStates)
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
+ """A vector of probabilities, given in the order of increasing filter-bin wavelength, that light emitted by the analog will fall in the corresponding filter bin of the instrument detection system. By convention, the values are normalized to sum to 1."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 14, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Values uses Python identifier Values
+ __Values = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Values'), 'Values', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_httppacificbiosciences_comPacBioBaseDataModel_xsdValues', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 16, 8), )
+
+
+ Values = property(__Values.value, __Values.set, None, None)
+
+
+ # Attribute NumberFilterBins uses Python identifier NumberFilterBins
+ __NumberFilterBins = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'NumberFilterBins'), 'NumberFilterBins', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_NumberFilterBins', pyxb.binding.datatypes.int, required=True)
+ __NumberFilterBins._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 29, 7)
+ __NumberFilterBins._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 29, 7)
+
+ NumberFilterBins = property(__NumberFilterBins.value, __NumberFilterBins.set, None, 'number of bins describing the spectrum, green to red')
+
+ _ElementMap.update({
+ __Values.name() : __Values
+ })
+ _AttributeMap.update({
+ __NumberFilterBins.name() : __NumberFilterBins
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 17, 9)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Value uses Python identifier Value
+ __Value = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Value'), 'Value', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON__httppacificbiosciences_comPacBioBaseDataModel_xsdValue', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 19, 11), )
+
+
+ Value = property(__Value.value, __Value.set, None, 'There should be as many values as specified in the Number of Filter Bins attribute.\nEach value is a probability, in the range of [0, 1].')
+
+ _ElementMap.update({
+ __Value.name() : __Value
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 87, 4)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExtensionElement uses Python identifier ExtensionElement
+ __ExtensionElement = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement'), 'ExtensionElement', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioBaseDataModel_xsdExtensionElement', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 709, 1), )
+
+
+ ExtensionElement = property(__ExtensionElement.value, __ExtensionElement.set, None, 'A generic element whose contents are undefined at the schema level. This is used to extend the data model.')
+
+ _ElementMap.update({
+ __ExtensionElement.name() : __ExtensionElement
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
+ """Pointer list to UniqueIds in the system"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 236, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataPointer uses Python identifier DataPointer
+ __DataPointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataPointer'), 'DataPointer', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioBaseDataModel_xsdDataPointer', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 238, 4), )
+
+
+ DataPointer = property(__DataPointer.value, __DataPointer.set, None, None)
+
+ _ElementMap.update({
+ __DataPointer.name() : __DataPointer
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
+ """Pointers to data that do not reside inside the parent structure"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 270, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResource uses Python identifier ExternalResource
+ __ExternalResource = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource'), 'ExternalResource', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioBaseDataModel_xsdExternalResource', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 731, 1), )
+
+
+ ExternalResource = property(__ExternalResource.value, __ExternalResource.set, None, 'for example, an output file could be the BAM file, which could be associated with multiple indices into it.')
+
+ _ElementMap.update({
+ __ExternalResource.name() : __ExternalResource
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_5 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 286, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}FileIndex uses Python identifier FileIndex
+ __FileIndex = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'FileIndex'), 'FileIndex', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioBaseDataModel_xsdFileIndex', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 288, 8), )
+
+
+ FileIndex = property(__FileIndex.value, __FileIndex.set, None, 'e.g. index for output files, allowing one to find information in the output file')
+
+ _ElementMap.update({
+ __FileIndex.name() : __FileIndex
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_6 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 306, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AutomationParameter uses Python identifier AutomationParameter
+ __AutomationParameter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), 'AutomationParameter', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_6_httppacificbiosciences_comPacBioBaseDataModel_xsdAutomationParameter', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 317, 1), )
+
+
+ AutomationParameter = property(__AutomationParameter.value, __AutomationParameter.set, None, 'One or more collection parameters, such as MovieLength, InsertSize, UseStageStart, IsControl, etc..')
+
+ _ElementMap.update({
+ __AutomationParameter.name() : __AutomationParameter
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_7 (pyxb.binding.basis.complexTypeDefinition):
+ """By default, a PN is compatible for use with other PNs in the system. In order to exclude the usage of one or more PNs with this one, the incompatible PNs are listed here."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 335, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumber uses Python identifier IncompatiblePartNumber
+ __IncompatiblePartNumber = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumber'), 'IncompatiblePartNumber', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioBaseDataModel_xsdIncompatiblePartNumber', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 337, 8), )
+
+
+ IncompatiblePartNumber = property(__IncompatiblePartNumber.value, __IncompatiblePartNumber.set, None, 'A reference to the incompatible part number UID')
+
+ _ElementMap.update({
+ __IncompatiblePartNumber.name() : __IncompatiblePartNumber
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_8 (pyxb.binding.basis.complexTypeDefinition):
+ """By default, a PN is compatible for use with all automations in the system. In order to exclude the usage of automations with this PN, the incompatible automation names are listed here."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 349, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomation uses Python identifier IncompatibleAutomation
+ __IncompatibleAutomation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomation'), 'IncompatibleAutomation', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_8_httppacificbiosciences_comPacBioBaseDataModel_xsdIncompatibleAutomation', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 351, 8), )
+
+
+ IncompatibleAutomation = property(__IncompatibleAutomation.value, __IncompatibleAutomation.set, None, 'A reference to the incompatible automation type UID')
+
+ _ElementMap.update({
+ __IncompatibleAutomation.name() : __IncompatibleAutomation
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_9 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 411, 11)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Analog uses Python identifier Analog
+ __Analog = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analog'), 'Analog', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_9_httppacificbiosciences_comPacBioBaseDataModel_xsdAnalog', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 413, 13), )
+
+
+ Analog = property(__Analog.value, __Analog.set, None, None)
+
+ _ElementMap.update({
+ __Analog.name() : __Analog
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_10 (pyxb.binding.basis.complexTypeDefinition):
+ """Root element for document containing the container of analog set, SequencingChemistryConfig"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 430, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ChemistryConfig uses Python identifier ChemistryConfig
+ __ChemistryConfig = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfig'), 'ChemistryConfig', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_10_httppacificbiosciences_comPacBioBaseDataModel_xsdChemistryConfig', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 432, 4), )
+
+
+ ChemistryConfig = property(__ChemistryConfig.value, __ChemistryConfig.set, None, None)
+
+ _ElementMap.update({
+ __ChemistryConfig.name() : __ChemistryConfig
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_11 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 444, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Analog uses Python identifier Analog
+ __Analog = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analog'), 'Analog', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_11_httppacificbiosciences_comPacBioBaseDataModel_xsdAnalog', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 446, 8), )
+
+
+ Analog = property(__Analog.value, __Analog.set, None, None)
+
+ _ElementMap.update({
+ __Analog.name() : __Analog
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_12 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 468, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinCount uses Python identifier BinCount
+ __BinCount = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), 'BinCount', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioBaseDataModel_xsdBinCount', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 470, 8), )
+
+
+ BinCount = property(__BinCount.value, __BinCount.set, None, None)
+
+ _ElementMap.update({
+ __BinCount.name() : __BinCount
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_13 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 494, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinCount uses Python identifier BinCount
+ __BinCount = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), 'BinCount', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioBaseDataModel_xsdBinCount', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 496, 8), )
+
+
+ BinCount = property(__BinCount.value, __BinCount.set, None, None)
+
+ _ElementMap.update({
+ __BinCount.name() : __BinCount
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_14 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 502, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinLabel uses Python identifier BinLabel
+ __BinLabel = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinLabel'), 'BinLabel', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_14_httppacificbiosciences_comPacBioBaseDataModel_xsdBinLabel', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 504, 8), )
+
+
+ BinLabel = property(__BinLabel.value, __BinLabel.set, None, None)
+
+ _ElementMap.update({
+ __BinLabel.name() : __BinLabel
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_15 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 524, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Val uses Python identifier Val
+ __Val = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Val'), 'Val', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_15_httppacificbiosciences_comPacBioBaseDataModel_xsdVal', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 526, 8), )
+
+
+ Val = property(__Val.value, __Val.set, None, None)
+
+ _ElementMap.update({
+ __Val.name() : __Val
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}UserDefinedFieldsType with content type ELEMENT_ONLY
+class UserDefinedFieldsType (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}UserDefinedFieldsType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFieldsType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 702, 1)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntities uses Python identifier DataEntities
+ __DataEntities = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataEntities'), 'DataEntities', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_UserDefinedFieldsType_httppacificbiosciences_comPacBioBaseDataModel_xsdDataEntities', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 704, 3), )
+
+
+ DataEntities = property(__DataEntities.value, __DataEntities.set, None, None)
+
+ _ElementMap.update({
+ __DataEntities.name() : __DataEntities
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'UserDefinedFieldsType', UserDefinedFieldsType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}FilterType with content type ELEMENT_ONLY
+class FilterType (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}FilterType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'FilterType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 714, 1)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Properties uses Python identifier Properties
+ __Properties = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Properties'), 'Properties', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_FilterType_httppacificbiosciences_comPacBioBaseDataModel_xsdProperties', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 716, 3), )
+
+
+ Properties = property(__Properties.value, __Properties.set, None, None)
+
+ _ElementMap.update({
+ __Properties.name() : __Properties
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'FilterType', FilterType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_16 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 717, 4)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Property uses Python identifier Property
+ __Property = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Property'), 'Property', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_16_httppacificbiosciences_comPacBioBaseDataModel_xsdProperty', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 719, 6), )
+
+
+ Property = property(__Property.value, __Property.set, None, None)
+
+ _ElementMap.update({
+ __Property.name() : __Property
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type EMPTY
+class CTD_ANON_17 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type EMPTY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_EMPTY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 720, 7)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Attribute Name uses Python identifier Name
+ __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_17_Name', pyxb.binding.datatypes.string, required=True)
+ __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 721, 8)
+ __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 721, 8)
+
+ Name = property(__Name.value, __Name.set, None, None)
+
+
+ # Attribute Value uses Python identifier Value
+ __Value = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Value'), 'Value', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_17_Value', pyxb.binding.datatypes.string, required=True)
+ __Value._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 722, 8)
+ __Value._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 722, 8)
+
+ Value = property(__Value.value, __Value.set, None, None)
+
+
+ # Attribute Operator uses Python identifier Operator
+ __Operator = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Operator'), 'Operator', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_17_Operator', pyxb.binding.datatypes.string, required=True)
+ __Operator._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 723, 8)
+ __Operator._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 723, 8)
+
+ Operator = property(__Operator.value, __Operator.set, None, None)
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __Name.name() : __Name,
+ __Value.name() : __Value,
+ __Operator.name() : __Operator
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType with content type ELEMENT_ONLY
+class BaseEntityType (pyxb.binding.basis.complexTypeDefinition):
+ """This is the base element type for all types in this data model"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BaseEntityType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 81, 1)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions uses Python identifier Extensions
+ __Extensions = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Extensions'), 'Extensions', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_httppacificbiosciences_comPacBioBaseDataModel_xsdExtensions', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3), )
+
+
+ Extensions = property(__Extensions.value, __Extensions.set, None, None)
+
+
+ # Attribute Name uses Python identifier Name
+ __Name = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Name'), 'Name', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_Name', pyxb.binding.datatypes.string)
+ __Name._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 94, 2)
+ __Name._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 94, 2)
+
+ Name = property(__Name.value, __Name.set, None, 'A short text identifier; uniqueness not necessary')
+
+
+ # Attribute Description uses Python identifier Description
+ __Description = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Description'), 'Description', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_Description', pyxb.binding.datatypes.string)
+ __Description._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 99, 2)
+ __Description._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 99, 2)
+
+ Description = property(__Description.value, __Description.set, None, 'A long text description of the object')
+
+
+ # Attribute Tags uses Python identifier Tags
+ __Tags = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Tags'), 'Tags', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_Tags', pyxb.binding.datatypes.string)
+ __Tags._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 104, 2)
+ __Tags._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 104, 2)
+
+ Tags = property(__Tags.value, __Tags.set, None, 'A set of keywords assigned to the object to help describe it and allow it to be found via search')
+
+
+ # Attribute Format uses Python identifier Format
+ __Format = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Format'), 'Format', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_Format', pyxb.binding.datatypes.string)
+ __Format._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 109, 2)
+ __Format._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 109, 2)
+
+ Format = property(__Format.value, __Format.set, None, 'Optional, but recommended. The MIME-Type of the referenced file. See http://www.iana.org/assignments/media-types/media-types.xhtml for examples')
+
+
+ # Attribute ResourceId uses Python identifier ResourceId
+ __ResourceId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ResourceId'), 'ResourceId', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_ResourceId', pyxb.binding.datatypes.anyURI)
+ __ResourceId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 114, 2)
+ __ResourceId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 114, 2)
+
+ ResourceId = property(__ResourceId.value, __ResourceId.set, None, 'A uniform resource identifier used to identify a "web" resource. e.g. svc://run/acquisition/alignment/gridding')
+
+
+ # Attribute Version uses Python identifier Version
+ __Version = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Version'), 'Version', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_Version', pyxb.binding.datatypes.string)
+ __Version._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 119, 2)
+ __Version._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 119, 2)
+
+ Version = property(__Version.value, __Version.set, None, 'An optional identifier denoting the revision of this particular entity')
+
+
+ # Attribute CreatedAt uses Python identifier CreatedAt
+ __CreatedAt = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CreatedAt'), 'CreatedAt', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_CreatedAt', STD_ANON)
+ __CreatedAt._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 124, 2)
+ __CreatedAt._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 124, 2)
+
+ CreatedAt = property(__CreatedAt.value, __CreatedAt.set, None, 'Timestamp designating the creation of this object, relative to UTC; millisecond precision is expected.')
+
+
+ # Attribute ModifiedAt uses Python identifier ModifiedAt
+ __ModifiedAt = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ModifiedAt'), 'ModifiedAt', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_BaseEntityType_ModifiedAt', STD_ANON_)
+ __ModifiedAt._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 132, 2)
+ __ModifiedAt._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 132, 2)
+
+ ModifiedAt = property(__ModifiedAt.value, __ModifiedAt.set, None, 'Timestamp designating the modification of this object, relative to UTC; millisecond precision is expected.')
+
+ _ElementMap.update({
+ __Extensions.name() : __Extensions
+ })
+ _AttributeMap.update({
+ __Name.name() : __Name,
+ __Description.name() : __Description,
+ __Tags.name() : __Tags,
+ __Format.name() : __Format,
+ __ResourceId.name() : __ResourceId,
+ __Version.name() : __Version,
+ __CreatedAt.name() : __CreatedAt,
+ __ModifiedAt.name() : __ModifiedAt
+ })
+Namespace.addCategoryObject('typeBinding', 'BaseEntityType', BaseEntityType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType with content type ELEMENT_ONLY
+class AnalogType (BaseEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AnalogType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 6, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Spectrum uses Python identifier Spectrum
+ __Spectrum = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Spectrum'), 'Spectrum', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_httppacificbiosciences_comPacBioBaseDataModel_xsdSpectrum', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 10, 5), )
+
+
+ Spectrum = property(__Spectrum.value, __Spectrum.set, None, 'A vector of probabilities, given in the order of increasing filter-bin wavelength, that light emitted by the analog will fall in the corresponding filter bin of the instrument detection system. By convention, the values are normalized to sum to 1.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}RelativeAmplitude uses Python identifier RelativeAmplitude
+ __RelativeAmplitude = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RelativeAmplitude'), 'RelativeAmplitude', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_httppacificbiosciences_comPacBioBaseDataModel_xsdRelativeAmplitude', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 36, 5), )
+
+
+ RelativeAmplitude = property(__RelativeAmplitude.value, __RelativeAmplitude.set, None, 'Relative intensity of emission vs. a reference analog using standardized metrology \u2013 e.g., relative to the amplitude of the \u201c542\u201d analog as measured by the mean DWS pkMid on the Astro instrument.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IntraPulseXsnCV uses Python identifier IntraPulseXsnCV
+ __IntraPulseXsnCV = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IntraPulseXsnCV'), 'IntraPulseXsnCV', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_httppacificbiosciences_comPacBioBaseDataModel_xsdIntraPulseXsnCV', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 41, 5), )
+
+
+ IntraPulseXsnCV = property(__IntraPulseXsnCV.value, __IntraPulseXsnCV.set, None, 'The 1-sigma fractional variation of the intra-pulse signal, independent of any Shot noise associated with that signal')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InterPulseXsnCV uses Python identifier InterPulseXsnCV
+ __InterPulseXsnCV = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InterPulseXsnCV'), 'InterPulseXsnCV', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_httppacificbiosciences_comPacBioBaseDataModel_xsdInterPulseXsnCV', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 46, 5), )
+
+
+ InterPulseXsnCV = property(__InterPulseXsnCV.value, __InterPulseXsnCV.set, None, 'The 1-sigma fractional variation, pulse-to-pulse, of the mean signal level (i.e., the pkMid).')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DiffusionXsnCV uses Python identifier DiffusionXsnCV
+ __DiffusionXsnCV = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DiffusionXsnCV'), 'DiffusionXsnCV', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_httppacificbiosciences_comPacBioBaseDataModel_xsdDiffusionXsnCV', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 51, 5), )
+
+
+ DiffusionXsnCV = property(__DiffusionXsnCV.value, __DiffusionXsnCV.set, None, None)
+
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Base uses Python identifier Base
+ __Base = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Base'), 'Base', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_Base', SupportedNucleotides)
+ __Base._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 53, 4)
+ __Base._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 53, 4)
+
+ Base = property(__Base.value, __Base.set, None, 'The base label, A, C, T, or G')
+
+
+ # Attribute Nucleotide uses Python identifier Nucleotide
+ __Nucleotide = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Nucleotide'), 'Nucleotide', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_Nucleotide', pyxb.binding.datatypes.string)
+ __Nucleotide._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 58, 4)
+ __Nucleotide._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 58, 4)
+
+ Nucleotide = property(__Nucleotide.value, __Nucleotide.set, None, 'The type and number of nucleotides on a given analog. e.g. (dT6P)6')
+
+
+ # Attribute Wavelength uses Python identifier Wavelength
+ __Wavelength = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Wavelength'), 'Wavelength', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_Wavelength', pyxb.binding.datatypes.float)
+ __Wavelength._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 63, 4)
+ __Wavelength._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 63, 4)
+
+ Wavelength = property(__Wavelength.value, __Wavelength.set, None, 'The peak emission wavelength associated with the dye label in nm.')
+
+
+ # Attribute CompoundID uses Python identifier CompoundID
+ __CompoundID = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CompoundID'), 'CompoundID', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_CompoundID', pyxb.binding.datatypes.string)
+ __CompoundID._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 68, 4)
+ __CompoundID._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 68, 4)
+
+ CompoundID = property(__CompoundID.value, __CompoundID.set, None, 'Identification code of the final compound. The suffix \u2018N\u2019 should be used to distinguish these values from enzyme identifiers.\te.g. 5031N')
+
+
+ # Attribute LotID uses Python identifier LotID
+ __LotID = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'LotID'), 'LotID', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AnalogType_LotID', pyxb.binding.datatypes.string)
+ __LotID._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 73, 4)
+ __LotID._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 73, 4)
+
+ LotID = property(__LotID.value, __LotID.set, None, 'Identification code for the build of the final compound, written as initials/date, where date is written as YYYY-MM-DD.\te.g. js/2014-06-30')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __Spectrum.name() : __Spectrum,
+ __RelativeAmplitude.name() : __RelativeAmplitude,
+ __IntraPulseXsnCV.name() : __IntraPulseXsnCV,
+ __InterPulseXsnCV.name() : __InterPulseXsnCV,
+ __DiffusionXsnCV.name() : __DiffusionXsnCV
+ })
+ _AttributeMap.update({
+ __Base.name() : __Base,
+ __Nucleotide.name() : __Nucleotide,
+ __Wavelength.name() : __Wavelength,
+ __CompoundID.name() : __CompoundID,
+ __LotID.name() : __LotID
+ })
+Namespace.addCategoryObject('typeBinding', 'AnalogType', AnalogType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType with content type ELEMENT_ONLY
+class StrictEntityType (BaseEntityType):
+ """This is the base element type for all types in this data model"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StrictEntityType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 141, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId uses Python identifier UniqueId
+ __UniqueId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'UniqueId'), 'UniqueId', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StrictEntityType_UniqueId', STD_ANON_2, required=True)
+ __UniqueId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 147, 4)
+ __UniqueId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 147, 4)
+
+ UniqueId = property(__UniqueId.value, __UniqueId.set, None, 'A unique identifier, such as a GUID - likely autogenerated')
+
+
+ # Attribute MetaType uses Python identifier MetaType
+ __MetaType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MetaType'), 'MetaType', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StrictEntityType_MetaType', pyxb.binding.datatypes.string, required=True)
+ __MetaType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 157, 4)
+ __MetaType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 157, 4)
+
+ MetaType = property(__MetaType.value, __MetaType.set, None, 'Controlled Vocabulary, meant as a means to group similar entities; the type of the object, e.g. Instrument Run, Secondary Run, Assay, Sample, Barcode, Alignment File, Alarm, Exception, Metric, SystemEvent, etc.')
+
+
+ # Attribute TimeStampedName uses Python identifier TimeStampedName
+ __TimeStampedName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TimeStampedName'), 'TimeStampedName', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StrictEntityType_TimeStampedName', pyxb.binding.datatypes.string, required=True)
+ __TimeStampedName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 162, 4)
+ __TimeStampedName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 162, 4)
+
+ TimeStampedName = property(__TimeStampedName.value, __TimeStampedName.set, None, 'This is NOT intended to be used as a unique field. For uniqueness, use UniqueId. In order to not utilize customer provided names, this attribute may be used as an alternative means of Human Readable ID, e.g. instrumentId-Run-150304_231155')
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __UniqueId.name() : __UniqueId,
+ __MetaType.name() : __MetaType,
+ __TimeStampedName.name() : __TimeStampedName
+ })
+Namespace.addCategoryObject('typeBinding', 'StrictEntityType', StrictEntityType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType with content type ELEMENT_ONLY
+class DataEntityType (BaseEntityType):
+ """Extends BaseEntityType and adds a value element. The intent is to have only one of the value elements exist at any point in time; however, this is not enforced."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DataEntityType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 181, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue uses Python identifier EncodedValue
+ __EncodedValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue'), 'EncodedValue', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_httppacificbiosciences_comPacBioBaseDataModel_xsdEncodedValue', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5), )
+
+
+ EncodedValue = property(__EncodedValue.value, __EncodedValue.set, None, 'A complex data type element, such as an image, file, binary object, etc.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum uses Python identifier CheckSum
+ __CheckSum = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CheckSum'), 'CheckSum', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_httppacificbiosciences_comPacBioBaseDataModel_xsdCheckSum', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5), )
+
+
+ CheckSum = property(__CheckSum.value, __CheckSum.set, None, 'small-size datum of the attached value for the purpose of detecting errors or modification which may have been introduced during its transmission or storage')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType uses Python identifier ValueDataType
+ __ValueDataType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ValueDataType'), 'ValueDataType', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_ValueDataType', SupportedDataTypes, unicode_default='Object')
+ __ValueDataType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 199, 4)
+ __ValueDataType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 199, 4)
+
+ ValueDataType = property(__ValueDataType.value, __ValueDataType.set, None, 'The datatype of the simple or encoded value. If not specified, a string is assumed.')
+
+
+ # Attribute SimpleValue uses Python identifier SimpleValue
+ __SimpleValue = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SimpleValue'), 'SimpleValue', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_SimpleValue', pyxb.binding.datatypes.anySimpleType)
+ __SimpleValue._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 204, 4)
+ __SimpleValue._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 204, 4)
+
+ SimpleValue = property(__SimpleValue.value, __SimpleValue.set, None, 'A simple data type element, such as a string, int, float, etc.')
+
+
+ # Attribute UniqueId uses Python identifier UniqueId
+ __UniqueId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'UniqueId'), 'UniqueId', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_UniqueId', STD_ANON_3)
+ __UniqueId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 209, 4)
+ __UniqueId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 209, 4)
+
+ UniqueId = property(__UniqueId.value, __UniqueId.set, None, 'A unique identifier, such as a GUID - likely autogenerated')
+
+
+ # Attribute MetaType uses Python identifier MetaType
+ __MetaType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MetaType'), 'MetaType', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_MetaType', pyxb.binding.datatypes.string)
+ __MetaType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 219, 4)
+ __MetaType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 219, 4)
+
+ MetaType = property(__MetaType.value, __MetaType.set, None, 'Controlled Vocabulary, meant as a means to group similar entities; the type of the object, e.g. Instrument Run, Secondary Run, Assay, Sample, Barcode, Alignment File, Alarm, Exception, Metric, SystemEvent, etc.')
+
+
+ # Attribute TimeStampedName uses Python identifier TimeStampedName
+ __TimeStampedName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TimeStampedName'), 'TimeStampedName', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DataEntityType_TimeStampedName', pyxb.binding.datatypes.string)
+ __TimeStampedName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 224, 4)
+ __TimeStampedName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 224, 4)
+
+ TimeStampedName = property(__TimeStampedName.value, __TimeStampedName.set, None, 'This is NOT intended to be used as a unique field. For uniqueness, use UniqueId. In order to not utilize customer provided names, this attribute may be used as an alternative means of Human Readable ID, e.g. instrumentId-Run-150304_231155')
+
+ _ElementMap.update({
+ __EncodedValue.name() : __EncodedValue,
+ __CheckSum.name() : __CheckSum
+ })
+ _AttributeMap.update({
+ __ValueDataType.name() : __ValueDataType,
+ __SimpleValue.name() : __SimpleValue,
+ __UniqueId.name() : __UniqueId,
+ __MetaType.name() : __MetaType,
+ __TimeStampedName.name() : __TimeStampedName
+ })
+Namespace.addCategoryObject('typeBinding', 'DataEntityType', DataEntityType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DNABarcode with content type ELEMENT_ONLY
+class DNABarcode (BaseEntityType):
+ """Composite of uuid, sequence, and name"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DNABarcode')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 242, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute DNASequence uses Python identifier DNASequence
+ __DNASequence = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DNASequence'), 'DNASequence', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_DNABarcode_DNASequence', pyxb.binding.datatypes.anySimpleType)
+ __DNASequence._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 248, 4)
+ __DNASequence._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 248, 4)
+
+ DNASequence = property(__DNASequence.value, __DNASequence.set, None, "This is the sample's DNA barcode")
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __DNASequence.name() : __DNASequence
+ })
+Namespace.addCategoryObject('typeBinding', 'DNABarcode', DNABarcode)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AutomationType with content type ELEMENT_ONLY
+class AutomationType (BaseEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AutomationType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AutomationType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 301, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AutomationParameters uses Python identifier AutomationParameters
+ __AutomationParameters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), 'AutomationParameters', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AutomationType_httppacificbiosciences_comPacBioBaseDataModel_xsdAutomationParameters', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 305, 5), )
+
+
+ AutomationParameters = property(__AutomationParameters.value, __AutomationParameters.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute IsObsolete uses Python identifier IsObsolete
+ __IsObsolete = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'IsObsolete'), 'IsObsolete', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_AutomationType_IsObsolete', pyxb.binding.datatypes.boolean)
+ __IsObsolete._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 313, 4)
+ __IsObsolete._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 313, 4)
+
+ IsObsolete = property(__IsObsolete.value, __IsObsolete.set, None, None)
+
+ _ElementMap.update({
+ __AutomationParameters.name() : __AutomationParameters
+ })
+ _AttributeMap.update({
+ __IsObsolete.name() : __IsObsolete
+ })
+Namespace.addCategoryObject('typeBinding', 'AutomationType', AutomationType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_18 (BaseEntityType):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 406, 6)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Analogs uses Python identifier Analogs
+ __Analogs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), 'Analogs', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_CTD_ANON_18_httppacificbiosciences_comPacBioBaseDataModel_xsdAnalogs', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 410, 10), )
+
+
+ Analogs = property(__Analogs.value, __Analogs.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __Analogs.name() : __Analogs
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SequencingChemistryConfig with content type ELEMENT_ONLY
+class SequencingChemistryConfig (BaseEntityType):
+ """A container for a set of analogs"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistryConfig')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 436, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Analogs uses Python identifier Analogs
+ __Analogs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), 'Analogs', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SequencingChemistryConfig_httppacificbiosciences_comPacBioBaseDataModel_xsdAnalogs', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 443, 5), )
+
+
+ Analogs = property(__Analogs.value, __Analogs.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __Analogs.name() : __Analogs
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SequencingChemistryConfig', SequencingChemistryConfig)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StatsContinuousDistType with content type ELEMENT_ONLY
+class StatsContinuousDistType (BaseEntityType):
+ """Continuous distribution class"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StatsContinuousDistType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 454, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SampleSize uses Python identifier SampleSize
+ __SampleSize = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleSize'), 'SampleSize', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdSampleSize', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 461, 5), )
+
+
+ SampleSize = property(__SampleSize.value, __SampleSize.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SampleMean uses Python identifier SampleMean
+ __SampleMean = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleMean'), 'SampleMean', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdSampleMean', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 462, 5), )
+
+
+ SampleMean = property(__SampleMean.value, __SampleMean.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SampleMed uses Python identifier SampleMed
+ __SampleMed = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleMed'), 'SampleMed', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdSampleMed', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 463, 5), )
+
+
+ SampleMed = property(__SampleMed.value, __SampleMed.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SampleStd uses Python identifier SampleStd
+ __SampleStd = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleStd'), 'SampleStd', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdSampleStd', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 464, 5), )
+
+
+ SampleStd = property(__SampleStd.value, __SampleStd.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Sample95thPct uses Python identifier Sample95thPct
+ __Sample95thPct = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Sample95thPct'), 'Sample95thPct', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdSample95thPct', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 465, 5), )
+
+
+ Sample95thPct = property(__Sample95thPct.value, __Sample95thPct.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}NumBins uses Python identifier NumBins
+ __NumBins = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), 'NumBins', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdNumBins', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 466, 5), )
+
+
+ NumBins = property(__NumBins.value, __NumBins.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinCounts uses Python identifier BinCounts
+ __BinCounts = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), 'BinCounts', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdBinCounts', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 467, 5), )
+
+
+ BinCounts = property(__BinCounts.value, __BinCounts.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinWidth uses Python identifier BinWidth
+ __BinWidth = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinWidth'), 'BinWidth', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdBinWidth', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 474, 5), )
+
+
+ BinWidth = property(__BinWidth.value, __BinWidth.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MinOutlierValue uses Python identifier MinOutlierValue
+ __MinOutlierValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MinOutlierValue'), 'MinOutlierValue', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdMinOutlierValue', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 475, 5), )
+
+
+ MinOutlierValue = property(__MinOutlierValue.value, __MinOutlierValue.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MinBinValue uses Python identifier MinBinValue
+ __MinBinValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MinBinValue'), 'MinBinValue', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdMinBinValue', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 476, 5), )
+
+
+ MinBinValue = property(__MinBinValue.value, __MinBinValue.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MaxBinValue uses Python identifier MaxBinValue
+ __MaxBinValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MaxBinValue'), 'MaxBinValue', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdMaxBinValue', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 477, 5), )
+
+
+ MaxBinValue = property(__MaxBinValue.value, __MaxBinValue.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MaxOutlierValue uses Python identifier MaxOutlierValue
+ __MaxOutlierValue = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MaxOutlierValue'), 'MaxOutlierValue', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdMaxOutlierValue', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 478, 5), )
+
+
+ MaxOutlierValue = property(__MaxOutlierValue.value, __MaxOutlierValue.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MetricDescription uses Python identifier MetricDescription
+ __MetricDescription = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), 'MetricDescription', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdMetricDescription', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 479, 5), )
+
+
+ MetricDescription = property(__MetricDescription.value, __MetricDescription.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Channel uses Python identifier Channel
+ __Channel = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Channel'), 'Channel', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsContinuousDistType_Channel', pyxb.binding.datatypes.string)
+ __Channel._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 481, 4)
+ __Channel._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 481, 4)
+
+ Channel = property(__Channel.value, __Channel.set, None, None)
+
+ _ElementMap.update({
+ __SampleSize.name() : __SampleSize,
+ __SampleMean.name() : __SampleMean,
+ __SampleMed.name() : __SampleMed,
+ __SampleStd.name() : __SampleStd,
+ __Sample95thPct.name() : __Sample95thPct,
+ __NumBins.name() : __NumBins,
+ __BinCounts.name() : __BinCounts,
+ __BinWidth.name() : __BinWidth,
+ __MinOutlierValue.name() : __MinOutlierValue,
+ __MinBinValue.name() : __MinBinValue,
+ __MaxBinValue.name() : __MaxBinValue,
+ __MaxOutlierValue.name() : __MaxOutlierValue,
+ __MetricDescription.name() : __MetricDescription
+ })
+ _AttributeMap.update({
+ __Channel.name() : __Channel
+ })
+Namespace.addCategoryObject('typeBinding', 'StatsContinuousDistType', StatsContinuousDistType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StatsDiscreteDistType with content type ELEMENT_ONLY
+class StatsDiscreteDistType (BaseEntityType):
+ """Discrete distribution class"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StatsDiscreteDistType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 485, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}NumBins uses Python identifier NumBins
+ __NumBins = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), 'NumBins', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdNumBins', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 492, 5), )
+
+
+ NumBins = property(__NumBins.value, __NumBins.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinCounts uses Python identifier BinCounts
+ __BinCounts = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), 'BinCounts', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdBinCounts', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 493, 5), )
+
+
+ BinCounts = property(__BinCounts.value, __BinCounts.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MetricDescription uses Python identifier MetricDescription
+ __MetricDescription = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), 'MetricDescription', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdMetricDescription', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 500, 5), )
+
+
+ MetricDescription = property(__MetricDescription.value, __MetricDescription.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BinLabels uses Python identifier BinLabels
+ __BinLabels = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BinLabels'), 'BinLabels', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsDiscreteDistType_httppacificbiosciences_comPacBioBaseDataModel_xsdBinLabels', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 501, 5), )
+
+
+ BinLabels = property(__BinLabels.value, __BinLabels.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __NumBins.name() : __NumBins,
+ __BinCounts.name() : __BinCounts,
+ __MetricDescription.name() : __MetricDescription,
+ __BinLabels.name() : __BinLabels
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'StatsDiscreteDistType', StatsDiscreteDistType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StatsTimeSeriesType with content type ELEMENT_ONLY
+class StatsTimeSeriesType (BaseEntityType):
+ """Time series (for time-dependent metrics)"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'StatsTimeSeriesType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 512, 1)
+ _ElementMap = BaseEntityType._ElementMap.copy()
+ _AttributeMap = BaseEntityType._AttributeMap.copy()
+ # Base type is BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}TimeUnits uses Python identifier TimeUnits
+ __TimeUnits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TimeUnits'), 'TimeUnits', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioBaseDataModel_xsdTimeUnits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 519, 5), )
+
+
+ TimeUnits = property(__TimeUnits.value, __TimeUnits.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ValueUnits uses Python identifier ValueUnits
+ __ValueUnits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ValueUnits'), 'ValueUnits', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioBaseDataModel_xsdValueUnits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 520, 5), )
+
+
+ ValueUnits = property(__ValueUnits.value, __ValueUnits.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StartTime uses Python identifier StartTime
+ __StartTime = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'StartTime'), 'StartTime', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioBaseDataModel_xsdStartTime', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 521, 5), )
+
+
+ StartTime = property(__StartTime.value, __StartTime.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}MeasInterval uses Python identifier MeasInterval
+ __MeasInterval = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MeasInterval'), 'MeasInterval', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioBaseDataModel_xsdMeasInterval', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 522, 5), )
+
+
+ MeasInterval = property(__MeasInterval.value, __MeasInterval.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Values uses Python identifier Values
+ __Values = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Values'), 'Values', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_StatsTimeSeriesType_httppacificbiosciences_comPacBioBaseDataModel_xsdValues', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 523, 5), )
+
+
+ Values = property(__Values.value, __Values.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __TimeUnits.name() : __TimeUnits,
+ __ValueUnits.name() : __ValueUnits,
+ __StartTime.name() : __StartTime,
+ __MeasInterval.name() : __MeasInterval,
+ __Values.name() : __Values
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'StatsTimeSeriesType', StatsTimeSeriesType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_19 (AnalogType):
+ """An unlimited number of analogs listed for the purposes of hosting in a configuration file. e.g. a list of all possible analogs on the system"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 174, 2)
+ _ElementMap = AnalogType._ElementMap.copy()
+ _AttributeMap = AnalogType._AttributeMap.copy()
+ # Base type is AnalogType
+
+ # Element Spectrum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Spectrum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element RelativeAmplitude ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}RelativeAmplitude) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element IntraPulseXsnCV ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IntraPulseXsnCV) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element InterPulseXsnCV ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InterPulseXsnCV) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element DiffusionXsnCV ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DiffusionXsnCV) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Base inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute Nucleotide inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute Wavelength inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute CompoundID inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute LotID inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_20 (AnalogType):
+ """A set of four analogs, one for each of the nucleotides, grouped together for the purposes of a single experiment."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 260, 2)
+ _ElementMap = AnalogType._ElementMap.copy()
+ _AttributeMap = AnalogType._AttributeMap.copy()
+ # Base type is AnalogType
+
+ # Element Spectrum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Spectrum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element RelativeAmplitude ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}RelativeAmplitude) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element IntraPulseXsnCV ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IntraPulseXsnCV) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element InterPulseXsnCV ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InterPulseXsnCV) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element DiffusionXsnCV ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DiffusionXsnCV) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Base inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute Nucleotide inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute Wavelength inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute CompoundID inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute LotID inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}AnalogType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InputOutputDataType with content type ELEMENT_ONLY
+class InputOutputDataType (StrictEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InputOutputDataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'InputOutputDataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 276, 1)
+ _ElementMap = StrictEntityType._ElementMap.copy()
+ _AttributeMap = StrictEntityType._AttributeMap.copy()
+ # Base type is StrictEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'InputOutputDataType', InputOutputDataType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType with content type ELEMENT_ONLY
+class PartNumberType (DataEntityType):
+ """Generic representation of a supply kit.
+
+If the part number has an NFC associated with it, the contents of the NFC may be encoded here."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'PartNumberType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 322, 1)
+ _ElementMap = DataEntityType._ElementMap.copy()
+ _AttributeMap = DataEntityType._AttributeMap.copy()
+ # Base type is DataEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumbers uses Python identifier IncompatiblePartNumbers
+ __IncompatiblePartNumbers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers'), 'IncompatiblePartNumbers', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_httppacificbiosciences_comPacBioBaseDataModel_xsdIncompatiblePartNumbers', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5), )
+
+
+ IncompatiblePartNumbers = property(__IncompatiblePartNumbers.value, __IncompatiblePartNumbers.set, None, 'By default, a PN is compatible for use with other PNs in the system. In order to exclude the usage of one or more PNs with this one, the incompatible PNs are listed here.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomations uses Python identifier IncompatibleAutomations
+ __IncompatibleAutomations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations'), 'IncompatibleAutomations', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_httppacificbiosciences_comPacBioBaseDataModel_xsdIncompatibleAutomations', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5), )
+
+
+ IncompatibleAutomations = property(__IncompatibleAutomations.value, __IncompatibleAutomations.set, None, 'By default, a PN is compatible for use with all automations in the system. In order to exclude the usage of automations with this PN, the incompatible automation names are listed here.')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute PartNumber uses Python identifier PartNumber
+ __PartNumber = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PartNumber'), 'PartNumber', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_PartNumber', pyxb.binding.datatypes.string)
+ __PartNumber._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 360, 4)
+ __PartNumber._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 360, 4)
+
+ PartNumber = property(__PartNumber.value, __PartNumber.set, None, 'The kit part number')
+
+
+ # Attribute LotNumber uses Python identifier LotNumber
+ __LotNumber = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'LotNumber'), 'LotNumber', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_LotNumber', pyxb.binding.datatypes.string)
+ __LotNumber._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 365, 4)
+ __LotNumber._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 365, 4)
+
+ LotNumber = property(__LotNumber.value, __LotNumber.set, None, 'The kit lot number')
+
+
+ # Attribute Barcode uses Python identifier Barcode
+ __Barcode = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Barcode'), 'Barcode', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_Barcode', pyxb.binding.datatypes.string)
+ __Barcode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 370, 4)
+ __Barcode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 370, 4)
+
+ Barcode = property(__Barcode.value, __Barcode.set, None, 'The kit barcode; used for tracking purposes.')
+
+
+ # Attribute ExpirationDate uses Python identifier ExpirationDate
+ __ExpirationDate = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ExpirationDate'), 'ExpirationDate', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_ExpirationDate', pyxb.binding.datatypes.date)
+ __ExpirationDate._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 375, 4)
+ __ExpirationDate._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 375, 4)
+
+ ExpirationDate = property(__ExpirationDate.value, __ExpirationDate.set, None, "The kit's shelf life")
+
+
+ # Attribute IsObsolete uses Python identifier IsObsolete
+ __IsObsolete = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'IsObsolete'), 'IsObsolete', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_PartNumberType_IsObsolete', pyxb.binding.datatypes.boolean, unicode_default='false')
+ __IsObsolete._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 380, 4)
+ __IsObsolete._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 380, 4)
+
+ IsObsolete = property(__IsObsolete.value, __IsObsolete.set, None, None)
+
+ _ElementMap.update({
+ __IncompatiblePartNumbers.name() : __IncompatiblePartNumbers,
+ __IncompatibleAutomations.name() : __IncompatibleAutomations
+ })
+ _AttributeMap.update({
+ __PartNumber.name() : __PartNumber,
+ __LotNumber.name() : __LotNumber,
+ __Barcode.name() : __Barcode,
+ __ExpirationDate.name() : __ExpirationDate,
+ __IsObsolete.name() : __IsObsolete
+ })
+Namespace.addCategoryObject('typeBinding', 'PartNumberType', PartNumberType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}RecordedEventType with content type ELEMENT_ONLY
+class RecordedEventType (DataEntityType):
+ """Metrics, system events, alarms, and logs may utilize this type"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'RecordedEventType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 384, 1)
+ _ElementMap = DataEntityType._ElementMap.copy()
+ _AttributeMap = DataEntityType._AttributeMap.copy()
+ # Base type is DataEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute Context uses Python identifier Context
+ __Context = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Context'), 'Context', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_RecordedEventType_Context', pyxb.binding.datatypes.string)
+ __Context._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 390, 4)
+ __Context._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 390, 4)
+
+ Context = property(__Context.value, __Context.set, None, 'The part of the system in effect when the event was recorded')
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __Context.name() : __Context
+ })
+Namespace.addCategoryObject('typeBinding', 'RecordedEventType', RecordedEventType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SequencingChemistry with content type ELEMENT_ONLY
+class SequencingChemistry (DataEntityType):
+ """A container for a set of analogs"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 398, 1)
+ _ElementMap = DataEntityType._ElementMap.copy()
+ _AttributeMap = DataEntityType._AttributeMap.copy()
+ # Base type is DataEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DyeSet uses Python identifier DyeSet
+ __DyeSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DyeSet'), 'DyeSet', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SequencingChemistry_httppacificbiosciences_comPacBioBaseDataModel_xsdDyeSet', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 405, 5), )
+
+
+ DyeSet = property(__DyeSet.value, __DyeSet.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+ _ElementMap.update({
+ __DyeSet.name() : __DyeSet
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SequencingChemistry', SequencingChemistry)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IndexedDataType with content type ELEMENT_ONLY
+class IndexedDataType (InputOutputDataType):
+ """Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IndexedDataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'IndexedDataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 281, 1)
+ _ElementMap = InputOutputDataType._ElementMap.copy()
+ _AttributeMap = InputOutputDataType._AttributeMap.copy()
+ # Base type is InputOutputDataType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources uses Python identifier ExternalResources
+ __ExternalResources = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), 'ExternalResources', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_IndexedDataType_httppacificbiosciences_comPacBioBaseDataModel_xsdExternalResources', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 266, 1), )
+
+
+ ExternalResources = property(__ExternalResources.value, __ExternalResources.set, None, 'Pointers to data that do not reside inside the parent structure')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}FileIndices uses Python identifier FileIndices
+ __FileIndices = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'FileIndices'), 'FileIndices', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_IndexedDataType_httppacificbiosciences_comPacBioBaseDataModel_xsdFileIndices', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 285, 5), )
+
+
+ FileIndices = property(__FileIndices.value, __FileIndices.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __ExternalResources.name() : __ExternalResources,
+ __FileIndices.name() : __FileIndices
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'IndexedDataType', IndexedDataType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupplyKitBinding with content type ELEMENT_ONLY
+class SupplyKitBinding (PartNumberType):
+ """A more specific binding kit representation (includes SupplyKit fields). """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitBinding')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 534, 1)
+ _ElementMap = PartNumberType._ElementMap.copy()
+ _AttributeMap = PartNumberType._AttributeMap.copy()
+ # Base type is PartNumberType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Control uses Python identifier Control
+ __Control = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Control'), 'Control', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitBinding_httppacificbiosciences_comPacBioBaseDataModel_xsdControl', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 541, 5), )
+
+
+ Control = property(__Control.value, __Control.set, None, 'Defines the binding kit internal control name. Present when used, otherwise not used if not defined. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IsControlUsed uses Python identifier IsControlUsed
+ __IsControlUsed = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'IsControlUsed'), 'IsControlUsed', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitBinding_httppacificbiosciences_comPacBioBaseDataModel_xsdIsControlUsed', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 546, 5), )
+
+
+ IsControlUsed = property(__IsControlUsed.value, __IsControlUsed.set, None, 'True if the control was used during run, otherwise false. ')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+ _ElementMap.update({
+ __Control.name() : __Control,
+ __IsControlUsed.name() : __IsControlUsed
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SupplyKitBinding', SupplyKitBinding)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupplyKitCellPack with content type ELEMENT_ONLY
+class SupplyKitCellPack (PartNumberType):
+ """Represents the package of cells. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitCellPack')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 555, 1)
+ _ElementMap = PartNumberType._ElementMap.copy()
+ _AttributeMap = PartNumberType._AttributeMap.copy()
+ # Base type is PartNumberType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ChipLayout uses Python identifier ChipLayout
+ __ChipLayout = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), 'ChipLayout', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitCellPack_httppacificbiosciences_comPacBioBaseDataModel_xsdChipLayout', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 562, 5), )
+
+
+ ChipLayout = property(__ChipLayout.value, __ChipLayout.set, None, 'Defines the internal chip layout name, if any. ')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute SupportsCellReuse uses Python identifier SupportsCellReuse
+ __SupportsCellReuse = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SupportsCellReuse'), 'SupportsCellReuse', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitCellPack_SupportsCellReuse', pyxb.binding.datatypes.anySimpleType)
+ __SupportsCellReuse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 568, 4)
+ __SupportsCellReuse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 568, 4)
+
+ SupportsCellReuse = property(__SupportsCellReuse.value, __SupportsCellReuse.set, None, 'If SupportsCellReuse is true, it can be used for regular sequencing as well as in a reuse scenario.')
+
+ _ElementMap.update({
+ __ChipLayout.name() : __ChipLayout
+ })
+ _AttributeMap.update({
+ __SupportsCellReuse.name() : __SupportsCellReuse
+ })
+Namespace.addCategoryObject('typeBinding', 'SupplyKitCellPack', SupplyKitCellPack)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupplyKitControl with content type ELEMENT_ONLY
+class SupplyKitControl (PartNumberType):
+ """Represents the DNA control complex. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitControl')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 576, 1)
+ _ElementMap = PartNumberType._ElementMap.copy()
+ _AttributeMap = PartNumberType._AttributeMap.copy()
+ # Base type is PartNumberType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InternalControlName uses Python identifier InternalControlName
+ __InternalControlName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InternalControlName'), 'InternalControlName', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitControl_httppacificbiosciences_comPacBioBaseDataModel_xsdInternalControlName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 583, 5), )
+
+
+ InternalControlName = property(__InternalControlName.value, __InternalControlName.set, None, 'Defines the internal control name, if any. ')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+ _ElementMap.update({
+ __InternalControlName.name() : __InternalControlName
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SupplyKitControl', SupplyKitControl)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}SupplyKitTemplate with content type ELEMENT_ONLY
+class SupplyKitTemplate (PartNumberType):
+ """A more specific template kit representation (includes SupplyKit fields). """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitTemplate')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 592, 1)
+ _ElementMap = PartNumberType._ElementMap.copy()
+ _AttributeMap = PartNumberType._AttributeMap.copy()
+ # Base type is PartNumberType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}LeftAdaptorSequence uses Python identifier LeftAdaptorSequence
+ __LeftAdaptorSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'LeftAdaptorSequence'), 'LeftAdaptorSequence', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioBaseDataModel_xsdLeftAdaptorSequence', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 599, 5), )
+
+
+ LeftAdaptorSequence = property(__LeftAdaptorSequence.value, __LeftAdaptorSequence.set, None, 'Left adapter DNA sequence.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}LeftPrimerSequence uses Python identifier LeftPrimerSequence
+ __LeftPrimerSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'LeftPrimerSequence'), 'LeftPrimerSequence', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioBaseDataModel_xsdLeftPrimerSequence', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 604, 5), )
+
+
+ LeftPrimerSequence = property(__LeftPrimerSequence.value, __LeftPrimerSequence.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}RightAdaptorSequence uses Python identifier RightAdaptorSequence
+ __RightAdaptorSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RightAdaptorSequence'), 'RightAdaptorSequence', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioBaseDataModel_xsdRightAdaptorSequence', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 605, 5), )
+
+
+ RightAdaptorSequence = property(__RightAdaptorSequence.value, __RightAdaptorSequence.set, None, 'Right adapter DNA sequence. If not specified, a symmetric adapter model is inferred, where the left adapter sequence is used wherever needed.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}RightPrimerSequence uses Python identifier RightPrimerSequence
+ __RightPrimerSequence = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RightPrimerSequence'), 'RightPrimerSequence', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioBaseDataModel_xsdRightPrimerSequence', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 610, 5), )
+
+
+ RightPrimerSequence = property(__RightPrimerSequence.value, __RightPrimerSequence.set, None, 'Right primaer sequence. If not specified, a symmetric model is inferred, where the left primer sequence is used wherever needed.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}InsertSize uses Python identifier InsertSize
+ __InsertSize = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertSize'), 'InsertSize', '__httppacificbiosciences_comPacBioBaseDataModel_xsd_SupplyKitTemplate_httppacificbiosciences_comPacBioBaseDataModel_xsdInsertSize', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 615, 5), )
+
+
+ InsertSize = property(__InsertSize.value, __InsertSize.set, None, 'Approximate size of insert. ')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+ _ElementMap.update({
+ __LeftAdaptorSequence.name() : __LeftAdaptorSequence,
+ __LeftPrimerSequence.name() : __LeftPrimerSequence,
+ __RightAdaptorSequence.name() : __RightAdaptorSequence,
+ __RightPrimerSequence.name() : __RightPrimerSequence,
+ __InsertSize.name() : __InsertSize
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SupplyKitTemplate', SupplyKitTemplate)
+
+
+ExtensionElement = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement'), pyxb.binding.datatypes.anyType, documentation='A generic element whose contents are undefined at the schema level. This is used to extend the data model.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 709, 1))
+Namespace.addCategoryObject('elementBinding', ExtensionElement.name().localName(), ExtensionElement)
+
+DataPointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataPointers'), CTD_ANON_3, documentation='Pointer list to UniqueIds in the system', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 232, 1))
+Namespace.addCategoryObject('elementBinding', DataPointers.name().localName(), DataPointers)
+
+ExternalResources = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), CTD_ANON_4, documentation='Pointers to data that do not reside inside the parent structure', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 266, 1))
+Namespace.addCategoryObject('elementBinding', ExternalResources.name().localName(), ExternalResources)
+
+PacBioSequencingChemistry = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioSequencingChemistry'), CTD_ANON_10, documentation='Root element for document containing the container of analog set, SequencingChemistryConfig', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 426, 1))
+Namespace.addCategoryObject('elementBinding', PacBioSequencingChemistry.name().localName(), PacBioSequencingChemistry)
+
+ValueDataType = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ValueDataType'), SupportedDataTypes, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 707, 1))
+Namespace.addCategoryObject('elementBinding', ValueDataType.name().localName(), ValueDataType)
+
+DataEntity = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataEntity'), DataEntityType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 180, 1))
+Namespace.addCategoryObject('elementBinding', DataEntity.name().localName(), DataEntity)
+
+AutomationParameter = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), DataEntityType, documentation='One or more collection parameters, such as MovieLength, InsertSize, UseStageStart, IsControl, etc..', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 317, 1))
+Namespace.addCategoryObject('elementBinding', AutomationParameter.name().localName(), AutomationParameter)
+
+ConfigSetAnalog = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConfigSetAnalog'), CTD_ANON_19, documentation='An unlimited number of analogs listed for the purposes of hosting in a configuration file. e.g. a list of all possible analogs on the system', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 170, 1))
+Namespace.addCategoryObject('elementBinding', ConfigSetAnalog.name().localName(), ConfigSetAnalog)
+
+DyeSetAnalog = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DyeSetAnalog'), CTD_ANON_20, documentation='A set of four analogs, one for each of the nucleotides, grouped together for the purposes of a single experiment.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 256, 1))
+Namespace.addCategoryObject('elementBinding', DyeSetAnalog.name().localName(), DyeSetAnalog)
+
+ExternalResource = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource'), IndexedDataType, documentation='for example, an output file could be the BAM file, which could be associated with multiple indices into it.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 731, 1))
+Namespace.addCategoryObject('elementBinding', ExternalResource.name().localName(), ExternalResource)
+
+
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Values'), CTD_ANON_, scope=CTD_ANON, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 16, 8)))
+
+def _BuildAutomaton ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton
+ del _BuildAutomaton
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Values')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 16, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+
+
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Value'), pyxb.binding.datatypes.float, scope=CTD_ANON_, documentation='There should be as many values as specified in the Number of Filter Bins attribute.\nEach value is a probability, in the range of [0, 1].', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 19, 11)))
+
+def _BuildAutomaton_ ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_
+ del _BuildAutomaton_
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Value')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 19, 11))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_._Automaton = _BuildAutomaton_()
+
+
+
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement'), pyxb.binding.datatypes.anyType, scope=CTD_ANON_2, documentation='A generic element whose contents are undefined at the schema level. This is used to extend the data model.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 709, 1)))
+
+def _BuildAutomaton_2 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 89, 6))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExtensionElement')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 89, 6))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_2._Automaton = _BuildAutomaton_2()
+
+
+
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataPointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 238, 4)))
+
+def _BuildAutomaton_3 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 238, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataPointer')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 238, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_3()
+
+
+
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource'), IndexedDataType, scope=CTD_ANON_4, documentation='for example, an output file could be the BAM file, which could be associated with multiple indices into it.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 731, 1)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResource')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 272, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_4._Automaton = _BuildAutomaton_4()
+
+
+
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'FileIndex'), InputOutputDataType, scope=CTD_ANON_5, documentation='e.g. index for output files, allowing one to find information in the output file', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 288, 8)))
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'FileIndex')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 288, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_5._Automaton = _BuildAutomaton_5()
+
+
+
+
+CTD_ANON_6._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), DataEntityType, scope=CTD_ANON_6, documentation='One or more collection parameters, such as MovieLength, InsertSize, UseStageStart, IsControl, etc..', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 317, 1)))
+
+def _BuildAutomaton_6 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_6
+ del _BuildAutomaton_6
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 308, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_6._Automaton = _BuildAutomaton_6()
+
+
+
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumber'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_7, documentation='A reference to the incompatible part number UID', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 337, 8)))
+
+def _BuildAutomaton_7 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_7
+ del _BuildAutomaton_7
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumber')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 337, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_7._Automaton = _BuildAutomaton_7()
+
+
+
+
+CTD_ANON_8._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomation'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_8, documentation='A reference to the incompatible automation type UID', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 351, 8)))
+
+def _BuildAutomaton_8 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_8
+ del _BuildAutomaton_8
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 351, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_8._Automaton = _BuildAutomaton_8()
+
+
+
+
+CTD_ANON_9._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analog'), AnalogType, scope=CTD_ANON_9, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 413, 13)))
+
+def _BuildAutomaton_9 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_9
+ del _BuildAutomaton_9
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=1, max=4, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 413, 13))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analog')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 413, 13))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_9._Automaton = _BuildAutomaton_9()
+
+
+
+
+CTD_ANON_10._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfig'), SequencingChemistryConfig, scope=CTD_ANON_10, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 432, 4)))
+
+def _BuildAutomaton_10 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_10
+ del _BuildAutomaton_10
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfig')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 432, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_10._Automaton = _BuildAutomaton_10()
+
+
+
+
+CTD_ANON_11._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analog'), AnalogType, scope=CTD_ANON_11, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 446, 8)))
+
+def _BuildAutomaton_11 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_11
+ del _BuildAutomaton_11
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=1, max=4, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 446, 8))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analog')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 446, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_11._Automaton = _BuildAutomaton_11()
+
+
+
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), pyxb.binding.datatypes.int, scope=CTD_ANON_12, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 470, 8)))
+
+def _BuildAutomaton_12 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_12
+ del _BuildAutomaton_12
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCount')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 470, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_12._Automaton = _BuildAutomaton_12()
+
+
+
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCount'), pyxb.binding.datatypes.int, scope=CTD_ANON_13, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 496, 8)))
+
+def _BuildAutomaton_13 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_13
+ del _BuildAutomaton_13
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCount')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 496, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_13._Automaton = _BuildAutomaton_13()
+
+
+
+
+CTD_ANON_14._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinLabel'), pyxb.binding.datatypes.string, scope=CTD_ANON_14, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 504, 8)))
+
+def _BuildAutomaton_14 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_14
+ del _BuildAutomaton_14
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinLabel')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 504, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_14._Automaton = _BuildAutomaton_14()
+
+
+
+
+CTD_ANON_15._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Val'), pyxb.binding.datatypes.float, scope=CTD_ANON_15, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 526, 8)))
+
+def _BuildAutomaton_15 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_15
+ del _BuildAutomaton_15
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 526, 8))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Val')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 526, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_15._Automaton = _BuildAutomaton_15()
+
+
+
+
+UserDefinedFieldsType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataEntities'), DataEntityType, scope=UserDefinedFieldsType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 704, 3)))
+
+def _BuildAutomaton_16 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_16
+ del _BuildAutomaton_16
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(UserDefinedFieldsType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataEntities')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 704, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+UserDefinedFieldsType._Automaton = _BuildAutomaton_16()
+
+
+
+
+FilterType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Properties'), CTD_ANON_16, scope=FilterType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 716, 3)))
+
+def _BuildAutomaton_17 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_17
+ del _BuildAutomaton_17
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(FilterType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Properties')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 716, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+FilterType._Automaton = _BuildAutomaton_17()
+
+
+
+
+CTD_ANON_16._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Property'), CTD_ANON_17, scope=CTD_ANON_16, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 719, 6)))
+
+def _BuildAutomaton_18 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_18
+ del _BuildAutomaton_18
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_16._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Property')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 719, 6))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_16._Automaton = _BuildAutomaton_18()
+
+
+
+
+BaseEntityType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Extensions'), CTD_ANON_2, scope=BaseEntityType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3)))
+
+def _BuildAutomaton_19 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_19
+ del _BuildAutomaton_19
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(BaseEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+BaseEntityType._Automaton = _BuildAutomaton_19()
+
+
+
+
+AnalogType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Spectrum'), CTD_ANON, scope=AnalogType, documentation='A vector of probabilities, given in the order of increasing filter-bin wavelength, that light emitted by the analog will fall in the corresponding filter bin of the instrument detection system. By convention, the values are normalized to sum to 1.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 10, 5)))
+
+AnalogType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RelativeAmplitude'), pyxb.binding.datatypes.float, scope=AnalogType, documentation='Relative intensity of emission vs. a reference analog using standardized metrology \u2013 e.g., relative to the amplitude of the \u201c542\u201d analog as measured by the mean DWS pkMid on the Astro instrument.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 36, 5)))
+
+AnalogType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IntraPulseXsnCV'), pyxb.binding.datatypes.float, scope=AnalogType, documentation='The 1-sigma fractional variation of the intra-pulse signal, independent of any Shot noise associated with that signal', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 41, 5)))
+
+AnalogType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InterPulseXsnCV'), pyxb.binding.datatypes.float, scope=AnalogType, documentation='The 1-sigma fractional variation, pulse-to-pulse, of the mean signal level (i.e., the pkMid).', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 46, 5)))
+
+AnalogType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DiffusionXsnCV'), pyxb.binding.datatypes.float, scope=AnalogType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 51, 5)))
+
+def _BuildAutomaton_20 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_20
+ del _BuildAutomaton_20
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Spectrum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 10, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RelativeAmplitude')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 36, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IntraPulseXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 41, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InterPulseXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 46, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(AnalogType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DiffusionXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 51, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+AnalogType._Automaton = _BuildAutomaton_20()
+
+
+
+
+def _BuildAutomaton_21 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_21
+ del _BuildAutomaton_21
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(StrictEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+StrictEntityType._Automaton = _BuildAutomaton_21()
+
+
+
+
+DataEntityType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue'), pyxb.binding.datatypes.base64Binary, scope=DataEntityType, documentation='A complex data type element, such as an image, file, binary object, etc.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5)))
+
+DataEntityType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CheckSum'), pyxb.binding.datatypes.string, scope=DataEntityType, documentation='small-size datum of the attached value for the purpose of detecting errors or modification which may have been introduced during its transmission or storage', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5)))
+
+def _BuildAutomaton_22 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_22
+ del _BuildAutomaton_22
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(DataEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(DataEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(DataEntityType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+DataEntityType._Automaton = _BuildAutomaton_22()
+
+
+
+
+def _BuildAutomaton_23 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_23
+ del _BuildAutomaton_23
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(DNABarcode._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+DNABarcode._Automaton = _BuildAutomaton_23()
+
+
+
+
+AutomationType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), CTD_ANON_6, scope=AutomationType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 305, 5)))
+
+def _BuildAutomaton_24 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_24
+ del _BuildAutomaton_24
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 305, 5))
+ counters.add(cc_1)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(AutomationType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(AutomationType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 305, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+AutomationType._Automaton = _BuildAutomaton_24()
+
+
+
+
+CTD_ANON_18._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), CTD_ANON_9, scope=CTD_ANON_18, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 410, 10)))
+
+def _BuildAutomaton_25 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_25
+ del _BuildAutomaton_25
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_18._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_18._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analogs')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 410, 10))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_18._Automaton = _BuildAutomaton_25()
+
+
+
+
+SequencingChemistryConfig._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Analogs'), CTD_ANON_11, scope=SequencingChemistryConfig, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 443, 5)))
+
+def _BuildAutomaton_26 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_26
+ del _BuildAutomaton_26
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SequencingChemistryConfig._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(SequencingChemistryConfig._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Analogs')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 443, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+SequencingChemistryConfig._Automaton = _BuildAutomaton_26()
+
+
+
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleSize'), pyxb.binding.datatypes.int, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 461, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleMean'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 462, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleMed'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 463, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleStd'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 464, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Sample95thPct'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 465, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), pyxb.binding.datatypes.int, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 466, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), CTD_ANON_12, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 467, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinWidth'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 474, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MinOutlierValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 475, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MinBinValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 476, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MaxBinValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 477, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MaxOutlierValue'), pyxb.binding.datatypes.float, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 478, 5)))
+
+StatsContinuousDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), pyxb.binding.datatypes.string, scope=StatsContinuousDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 479, 5)))
+
+def _BuildAutomaton_27 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_27
+ del _BuildAutomaton_27
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleSize')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 461, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleMean')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 462, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleMed')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 463, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleStd')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 464, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Sample95thPct')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 465, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumBins')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 466, 5))
+ st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCounts')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 467, 5))
+ st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_7)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinWidth')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 474, 5))
+ st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_8)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MinOutlierValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 475, 5))
+ st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_9)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MinBinValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 476, 5))
+ st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_10)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MaxBinValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 477, 5))
+ st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_11)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MaxOutlierValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 478, 5))
+ st_12 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_12)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(StatsContinuousDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 479, 5))
+ st_13 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_13)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ ]))
+ st_6._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ ]))
+ st_7._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_9, [
+ ]))
+ st_8._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_10, [
+ ]))
+ st_9._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_11, [
+ ]))
+ st_10._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_12, [
+ ]))
+ st_11._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_13, [
+ ]))
+ st_12._set_transitionSet(transitions)
+ transitions = []
+ st_13._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+StatsContinuousDistType._Automaton = _BuildAutomaton_27()
+
+
+
+
+StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumBins'), pyxb.binding.datatypes.int, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 492, 5)))
+
+StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinCounts'), CTD_ANON_13, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 493, 5)))
+
+StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription'), pyxb.binding.datatypes.string, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 500, 5)))
+
+StatsDiscreteDistType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BinLabels'), CTD_ANON_14, scope=StatsDiscreteDistType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 501, 5)))
+
+def _BuildAutomaton_28 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_28
+ del _BuildAutomaton_28
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumBins')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 492, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinCounts')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 493, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MetricDescription')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 500, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(StatsDiscreteDistType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BinLabels')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 501, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+StatsDiscreteDistType._Automaton = _BuildAutomaton_28()
+
+
+
+
+StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TimeUnits'), pyxb.binding.datatypes.string, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 519, 5)))
+
+StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ValueUnits'), pyxb.binding.datatypes.string, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 520, 5)))
+
+StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'StartTime'), pyxb.binding.datatypes.float, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 521, 5)))
+
+StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MeasInterval'), pyxb.binding.datatypes.float, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 522, 5)))
+
+StatsTimeSeriesType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Values'), CTD_ANON_15, scope=StatsTimeSeriesType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 523, 5)))
+
+def _BuildAutomaton_29 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_29
+ del _BuildAutomaton_29
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 523, 5))
+ counters.add(cc_1)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TimeUnits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 519, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ValueUnits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 520, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'StartTime')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 521, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MeasInterval')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 522, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(StatsTimeSeriesType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Values')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 523, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+StatsTimeSeriesType._Automaton = _BuildAutomaton_29()
+
+
+
+
+def _BuildAutomaton_30 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_30
+ del _BuildAutomaton_30
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_19._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_19._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Spectrum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 10, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_19._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RelativeAmplitude')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 36, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_19._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IntraPulseXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 41, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_19._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InterPulseXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 46, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_19._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DiffusionXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 51, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_19._Automaton = _BuildAutomaton_30()
+
+
+
+
+def _BuildAutomaton_31 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_31
+ del _BuildAutomaton_31
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Spectrum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 10, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RelativeAmplitude')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 36, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IntraPulseXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 41, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InterPulseXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 46, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_20._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DiffusionXsnCV')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 51, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_20._Automaton = _BuildAutomaton_31()
+
+
+
+
+def _BuildAutomaton_32 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_32
+ del _BuildAutomaton_32
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(InputOutputDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+InputOutputDataType._Automaton = _BuildAutomaton_32()
+
+
+
+
+PartNumberType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers'), CTD_ANON_7, scope=PartNumberType, documentation='By default, a PN is compatible for use with other PNs in the system. In order to exclude the usage of one or more PNs with this one, the incompatible PNs are listed here.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5)))
+
+PartNumberType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations'), CTD_ANON_8, scope=PartNumberType, documentation='By default, a PN is compatible for use with all automations in the system. In order to exclude the usage of automations with this PN, the incompatible automation names are listed here.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5)))
+
+def _BuildAutomaton_33 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_33
+ del _BuildAutomaton_33
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ counters.add(cc_4)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(PartNumberType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+PartNumberType._Automaton = _BuildAutomaton_33()
+
+
+
+
+def _BuildAutomaton_34 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_34
+ del _BuildAutomaton_34
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(RecordedEventType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(RecordedEventType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(RecordedEventType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+RecordedEventType._Automaton = _BuildAutomaton_34()
+
+
+
+
+SequencingChemistry._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DyeSet'), CTD_ANON_18, scope=SequencingChemistry, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 405, 5)))
+
+def _BuildAutomaton_35 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_35
+ del _BuildAutomaton_35
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(SequencingChemistry._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DyeSet')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 405, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+SequencingChemistry._Automaton = _BuildAutomaton_35()
+
+
+
+
+IndexedDataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources'), CTD_ANON_4, scope=IndexedDataType, documentation='Pointers to data that do not reside inside the parent structure', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 266, 1)))
+
+IndexedDataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'FileIndices'), CTD_ANON_5, scope=IndexedDataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 285, 5)))
+
+def _BuildAutomaton_36 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_36
+ del _BuildAutomaton_36
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 285, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 296, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'FileIndices')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 285, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(IndexedDataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 296, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+IndexedDataType._Automaton = _BuildAutomaton_36()
+
+
+
+
+SupplyKitBinding._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Control'), SupplyKitControl, scope=SupplyKitBinding, documentation='Defines the binding kit internal control name. Present when used, otherwise not used if not defined. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 541, 5)))
+
+SupplyKitBinding._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'IsControlUsed'), pyxb.binding.datatypes.boolean, scope=SupplyKitBinding, documentation='True if the control was used during run, otherwise false. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 546, 5)))
+
+def _BuildAutomaton_37 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_37
+ del _BuildAutomaton_37
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 541, 5))
+ counters.add(cc_5)
+ cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 546, 5))
+ counters.add(cc_6)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Control')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 541, 5))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_6, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitBinding._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IsControlUsed')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 546, 5))
+ st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_6, True) ]))
+ st_6._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+SupplyKitBinding._Automaton = _BuildAutomaton_37()
+
+
+
+
+SupplyKitCellPack._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout'), pyxb.binding.datatypes.string, scope=SupplyKitCellPack, documentation='Defines the internal chip layout name, if any. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 562, 5)))
+
+def _BuildAutomaton_38 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_38
+ del _BuildAutomaton_38
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 562, 5))
+ counters.add(cc_5)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitCellPack._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChipLayout')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 562, 5))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+SupplyKitCellPack._Automaton = _BuildAutomaton_38()
+
+
+
+
+SupplyKitControl._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InternalControlName'), pyxb.binding.datatypes.string, scope=SupplyKitControl, documentation='Defines the internal control name, if any. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 583, 5)))
+
+def _BuildAutomaton_39 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_39
+ del _BuildAutomaton_39
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 583, 5))
+ counters.add(cc_5)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitControl._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InternalControlName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 583, 5))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+SupplyKitControl._Automaton = _BuildAutomaton_39()
+
+
+
+
+SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'LeftAdaptorSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, documentation='Left adapter DNA sequence.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 599, 5)))
+
+SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'LeftPrimerSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 604, 5)))
+
+SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RightAdaptorSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, documentation='Right adapter DNA sequence. If not specified, a symmetric adapter model is inferred, where the left adapter sequence is used wherever needed.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 605, 5)))
+
+SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RightPrimerSequence'), pyxb.binding.datatypes.string, scope=SupplyKitTemplate, documentation='Right primaer sequence. If not specified, a symmetric model is inferred, where the left primer sequence is used wherever needed.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 610, 5)))
+
+SupplyKitTemplate._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertSize'), pyxb.binding.datatypes.int, scope=SupplyKitTemplate, documentation='Approximate size of insert. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 615, 5)))
+
+def _BuildAutomaton_40 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_40
+ del _BuildAutomaton_40
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 599, 5))
+ counters.add(cc_5)
+ cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 604, 5))
+ counters.add(cc_6)
+ cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 605, 5))
+ counters.add(cc_7)
+ cc_8 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 610, 5))
+ counters.add(cc_8)
+ cc_9 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 615, 5))
+ counters.add(cc_9)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'LeftAdaptorSequence')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 599, 5))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_6, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'LeftPrimerSequence')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 604, 5))
+ st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_7, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RightAdaptorSequence')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 605, 5))
+ st_7 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_7)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_8, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RightPrimerSequence')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 610, 5))
+ st_8 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_8)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_9, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitTemplate._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertSize')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 615, 5))
+ st_9 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_9)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_6, True) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ st_6._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_7, True) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ st_7._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_8, True) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ st_8._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_9, True) ]))
+ st_9._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+SupplyKitTemplate._Automaton = _BuildAutomaton_40()
+
diff --git a/pbcore/io/dataset/_pbds.py b/pbcore/io/dataset/_pbds.py
new file mode 100755
index 0000000..a027058
--- /dev/null
+++ b/pbcore/io/dataset/_pbds.py
@@ -0,0 +1,3435 @@
+# ./_pbds.py
+# -*- coding: utf-8 -*-
+# PyXB bindings for NM:3dc5b3a98cc462befd746fd05a18986be8ba2691
+# Generated 2015-08-04 20:41:05.069985 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Namespace http://pacificbiosciences.com/PacBioDatasets.xsd [xmlns:pbds]
+
+from __future__ import unicode_literals
+import pyxb
+import pyxb.binding
+import pyxb.binding.saxer
+import io
+import pyxb.utils.utility
+import pyxb.utils.domutils
+import sys
+import pyxb.utils.six as _six
+
+# Unique identifier for bindings created at the same time
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
+
+# Version of PyXB used to generate the bindings
+_PyXBVersion = '1.2.4'
+# Generated bindings are not compatible across PyXB versions
+if pyxb.__version__ != _PyXBVersion:
+ raise pyxb.PyXBVersionError(_PyXBVersion)
+
+# Import bindings for namespaces imported into schema
+import _pbsample as _ImportedBinding__pbsample
+import _pbbase as _ImportedBinding__pbbase
+import pyxb.binding.datatypes
+import _pbmeta as _ImportedBinding__pbmeta
+
+# NOTE: All namespace declarations are reserved within the binding
+Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioDatasets.xsd', create_if_missing=True)
+Namespace.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbmeta = _ImportedBinding__pbmeta.Namespace
+_Namespace_pbmeta.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbsample = _ImportedBinding__pbsample.Namespace
+_Namespace_pbsample.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbbase = _ImportedBinding__pbbase.Namespace
+_Namespace_pbbase.configureCategories(['typeBinding', 'elementBinding'])
+
+def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
+ """Parse the given XML and use the document element to create a
+ Python instance.
+
+ @param xml_text An XML document. This should be data (Python 2
+ str or Python 3 bytes), or a text (Python 2 unicode or Python 3
+ str) in the L{pyxb._InputEncoding} encoding.
+
+ @keyword default_namespace The L{pyxb.Namespace} instance to use as the
+ default namespace where there is no default namespace in scope.
+ If unspecified or C{None}, the namespace of the module containing
+ this function will be used.
+
+ @keyword location_base: An object to be recorded as the base of all
+ L{pyxb.utils.utility.Location} instances associated with events and
+ objects handled by the parser. You might pass the URI from which
+ the document was obtained.
+ """
+
+ if pyxb.XMLStyle_saxer != pyxb._XMLStyle:
+ dom = pyxb.utils.domutils.StringToDOM(xml_text)
+ return CreateFromDOM(dom.documentElement, default_namespace=default_namespace)
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ saxer = pyxb.binding.saxer.make_parser(fallback_namespace=default_namespace, location_base=location_base)
+ handler = saxer.getContentHandler()
+ xmld = xml_text
+ if isinstance(xmld, _six.text_type):
+ xmld = xmld.encode(pyxb._InputEncoding)
+ saxer.parse(io.BytesIO(xmld))
+ instance = handler.rootObject()
+ return instance
+
+def CreateFromDOM (node, default_namespace=None):
+ """Create a Python instance from the given DOM node.
+ The node tag must correspond to an element declaration in this module.
+
+ @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}."""
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ return pyxb.binding.basis.element.AnyCreateFromDOM(node, default_namespace)
+
+
+# Atomic simple type: [anonymous]
+class STD_ANON (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 63, 6)
+ _Documentation = None
+STD_ANON._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON, enum_prefix=None)
+STD_ANON.Instrument = STD_ANON._CF_enumeration.addEnumeration(unicode_value='Instrument', tag='Instrument')
+STD_ANON.User = STD_ANON._CF_enumeration.addEnumeration(unicode_value='User', tag='User')
+STD_ANON.AnalysisJob = STD_ANON._CF_enumeration.addEnumeration(unicode_value='AnalysisJob', tag='AnalysisJob')
+STD_ANON._InitializeFacetMap(STD_ANON._CF_enumeration)
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
+ """The set of filters defined here apply to the resident data set. Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 17, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Filter uses Python identifier Filter
+ __Filter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Filter'), 'Filter', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_httppacificbiosciences_comPacBioDatasets_xsdFilter', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 19, 8), )
+
+
+ Filter = property(__Filter.value, __Filter.set, None, None)
+
+ _ElementMap.update({
+ __Filter.name() : __Filter
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 24, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSet uses Python identifier DataSet
+ __DataSet = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), 'DataSet', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON__httppacificbiosciences_comPacBioDatasets_xsdDataSet', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 34, 1), )
+
+
+ DataSet = property(__DataSet.value, __DataSet.set, None, None)
+
+ _ElementMap.update({
+ __DataSet.name() : __DataSet
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType with content type ELEMENT_ONLY
+class DataSetMetadataType (pyxb.binding.basis.complexTypeDefinition):
+ """Extend this type to provide DataSetMetadata element in each DataSet."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 47, 1)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}TotalLength uses Python identifier TotalLength
+ __TotalLength = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TotalLength'), 'TotalLength', '__httppacificbiosciences_comPacBioDatasets_xsd_DataSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdTotalLength', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3), )
+
+
+ TotalLength = property(__TotalLength.value, __TotalLength.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}NumRecords uses Python identifier NumRecords
+ __NumRecords = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumRecords'), 'NumRecords', '__httppacificbiosciences_comPacBioDatasets_xsd_DataSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdNumRecords', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3), )
+
+
+ NumRecords = property(__NumRecords.value, __NumRecords.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Provenance uses Python identifier Provenance
+ __Provenance = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Provenance'), 'Provenance', '__httppacificbiosciences_comPacBioDatasets_xsd_DataSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdProvenance', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3), )
+
+
+ Provenance = property(__Provenance.value, __Provenance.set, None, None)
+
+ _ElementMap.update({
+ __TotalLength.name() : __TotalLength,
+ __NumRecords.name() : __NumRecords,
+ __Provenance.name() : __Provenance
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'DataSetMetadataType', DataSetMetadataType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 82, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}AdapterDimerFraction uses Python identifier AdapterDimerFraction
+ __AdapterDimerFraction = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AdapterDimerFraction'), 'AdapterDimerFraction', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdAdapterDimerFraction', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 84, 8), )
+
+
+ AdapterDimerFraction = property(__AdapterDimerFraction.value, __AdapterDimerFraction.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ShortInsertFraction uses Python identifier ShortInsertFraction
+ __ShortInsertFraction = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ShortInsertFraction'), 'ShortInsertFraction', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdShortInsertFraction', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 85, 8), )
+
+
+ ShortInsertFraction = property(__ShortInsertFraction.value, __ShortInsertFraction.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}NumSequencingZmws uses Python identifier NumSequencingZmws
+ __NumSequencingZmws = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'NumSequencingZmws'), 'NumSequencingZmws', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdNumSequencingZmws', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 86, 8), )
+
+
+ NumSequencingZmws = property(__NumSequencingZmws.value, __NumSequencingZmws.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ProdDist uses Python identifier ProdDist
+ __ProdDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ProdDist'), 'ProdDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdProdDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 87, 8), )
+
+
+ ProdDist = property(__ProdDist.value, __ProdDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadTypeDist uses Python identifier ReadTypeDist
+ __ReadTypeDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReadTypeDist'), 'ReadTypeDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdReadTypeDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 88, 8), )
+
+
+ ReadTypeDist = property(__ReadTypeDist.value, __ReadTypeDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadLenDist uses Python identifier ReadLenDist
+ __ReadLenDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReadLenDist'), 'ReadLenDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdReadLenDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 89, 8), )
+
+
+ ReadLenDist = property(__ReadLenDist.value, __ReadLenDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadQualDist uses Python identifier ReadQualDist
+ __ReadQualDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReadQualDist'), 'ReadQualDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdReadQualDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 90, 8), )
+
+
+ ReadQualDist = property(__ReadQualDist.value, __ReadQualDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ControlReadLenDist uses Python identifier ControlReadLenDist
+ __ControlReadLenDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlReadLenDist'), 'ControlReadLenDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdControlReadLenDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 91, 8), )
+
+
+ ControlReadLenDist = property(__ControlReadLenDist.value, __ControlReadLenDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ControlReadQualDist uses Python identifier ControlReadQualDist
+ __ControlReadQualDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlReadQualDist'), 'ControlReadQualDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdControlReadQualDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 92, 8), )
+
+
+ ControlReadQualDist = property(__ControlReadQualDist.value, __ControlReadQualDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}MedianInsertDist uses Python identifier MedianInsertDist
+ __MedianInsertDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MedianInsertDist'), 'MedianInsertDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdMedianInsertDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 93, 8), )
+
+
+ MedianInsertDist = property(__MedianInsertDist.value, __MedianInsertDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}InsertReadLenDist uses Python identifier InsertReadLenDist
+ __InsertReadLenDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertReadLenDist'), 'InsertReadLenDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdInsertReadLenDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 94, 8), )
+
+
+ InsertReadLenDist = property(__InsertReadLenDist.value, __InsertReadLenDist.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}InsertReadQualDist uses Python identifier InsertReadQualDist
+ __InsertReadQualDist = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InsertReadQualDist'), 'InsertReadQualDist', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioDatasets_xsdInsertReadQualDist', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 95, 8), )
+
+
+ InsertReadQualDist = property(__InsertReadQualDist.value, __InsertReadQualDist.set, None, None)
+
+ _ElementMap.update({
+ __AdapterDimerFraction.name() : __AdapterDimerFraction,
+ __ShortInsertFraction.name() : __ShortInsertFraction,
+ __NumSequencingZmws.name() : __NumSequencingZmws,
+ __ProdDist.name() : __ProdDist,
+ __ReadTypeDist.name() : __ReadTypeDist,
+ __ReadLenDist.name() : __ReadLenDist,
+ __ReadQualDist.name() : __ReadQualDist,
+ __ControlReadLenDist.name() : __ControlReadLenDist,
+ __ControlReadQualDist.name() : __ControlReadQualDist,
+ __MedianInsertDist.name() : __MedianInsertDist,
+ __InsertReadLenDist.name() : __InsertReadLenDist,
+ __InsertReadQualDist.name() : __InsertReadQualDist
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
+ """The set of filters defined here apply to the resident data set. Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 126, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Filter uses Python identifier Filter
+ __Filter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Filter'), 'Filter', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioDatasets_xsdFilter', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 128, 8), )
+
+
+ Filter = property(__Filter.value, __Filter.set, None, None)
+
+ _ElementMap.update({
+ __Filter.name() : __Filter
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 303, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Subset uses Python identifier Subset
+ __Subset = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Subset'), 'Subset', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioDatasets_xsdSubset', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 305, 4), )
+
+
+ Subset = property(__Subset.value, __Subset.set, None, None)
+
+ _ElementMap.update({
+ __Subset.name() : __Subset
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_5 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 55, 4)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}CommonServicesInstanceId uses Python identifier CommonServicesInstanceId
+ __CommonServicesInstanceId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CommonServicesInstanceId'), 'CommonServicesInstanceId', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioDatasets_xsdCommonServicesInstanceId', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 57, 6), )
+
+
+ CommonServicesInstanceId = property(__CommonServicesInstanceId.value, __CommonServicesInstanceId.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}CreatorUserId uses Python identifier CreatorUserId
+ __CreatorUserId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CreatorUserId'), 'CreatorUserId', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioDatasets_xsdCreatorUserId', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 58, 6), )
+
+
+ CreatorUserId = property(__CreatorUserId.value, __CreatorUserId.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ParentJobId uses Python identifier ParentJobId
+ __ParentJobId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ParentJobId'), 'ParentJobId', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioDatasets_xsdParentJobId', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 59, 6), )
+
+
+ ParentJobId = property(__ParentJobId.value, __ParentJobId.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}ParentTool uses Python identifier ParentTool
+ __ParentTool = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ParentTool'), 'ParentTool', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioDatasets_xsdParentTool', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 60, 6), )
+
+
+ ParentTool = property(__ParentTool.value, __ParentTool.set, None, None)
+
+
+ # Attribute CreatedBy uses Python identifier CreatedBy
+ __CreatedBy = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'CreatedBy'), 'CreatedBy', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_5_CreatedBy', STD_ANON, required=True)
+ __CreatedBy._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 62, 5)
+ __CreatedBy._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 62, 5)
+
+ CreatedBy = property(__CreatedBy.value, __CreatedBy.set, None, None)
+
+ _ElementMap.update({
+ __CommonServicesInstanceId.name() : __CommonServicesInstanceId,
+ __CreatorUserId.name() : __CreatorUserId,
+ __ParentJobId.name() : __ParentJobId,
+ __ParentTool.name() : __ParentTool
+ })
+ _AttributeMap.update({
+ __CreatedBy.name() : __CreatedBy
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadSetMetadataType with content type ELEMENT_ONLY
+class ReadSetMetadataType (DataSetMetadataType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadSetMetadataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReadSetMetadataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 75, 1)
+ _ElementMap = DataSetMetadataType._ElementMap.copy()
+ _AttributeMap = DataSetMetadataType._AttributeMap.copy()
+ # Base type is DataSetMetadataType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Collections uses Python identifier Collections
+ __Collections = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbmeta, 'Collections'), 'Collections', '__httppacificbiosciences_comPacBioDatasets_xsd_ReadSetMetadataType_httppacificbiosciences_comPacBioCollectionMetadata_xsdCollections', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 20, 1), )
+
+
+ Collections = property(__Collections.value, __Collections.set, None, 'A set of acquisition definitions')
+
+
+ # Element TotalLength ({http://pacificbiosciences.com/PacBioDatasets.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element NumRecords ({http://pacificbiosciences.com/PacBioDatasets.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element Provenance ({http://pacificbiosciences.com/PacBioDatasets.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}SummaryStats uses Python identifier SummaryStats
+ __SummaryStats = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SummaryStats'), 'SummaryStats', '__httppacificbiosciences_comPacBioDatasets_xsd_ReadSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdSummaryStats', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 81, 5), )
+
+
+ SummaryStats = property(__SummaryStats.value, __SummaryStats.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSamples uses Python identifier BioSamples
+ __BioSamples = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbsample, 'BioSamples'), 'BioSamples', '__httppacificbiosciences_comPacBioDatasets_xsd_ReadSetMetadataType_httppacificbiosciences_comPacBioSampleInfo_xsdBioSamples', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 134, 1), )
+
+
+ BioSamples = property(__BioSamples.value, __BioSamples.set, None, None)
+
+ _ElementMap.update({
+ __Collections.name() : __Collections,
+ __SummaryStats.name() : __SummaryStats,
+ __BioSamples.name() : __BioSamples
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'ReadSetMetadataType', ReadSetMetadataType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}SubreadSetMetadataType with content type ELEMENT_ONLY
+class SubreadSetMetadataType (DataSetMetadataType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}SubreadSetMetadataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SubreadSetMetadataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 103, 1)
+ _ElementMap = DataSetMetadataType._ElementMap.copy()
+ _AttributeMap = DataSetMetadataType._AttributeMap.copy()
+ # Base type is DataSetMetadataType
+
+ # Element TotalLength ({http://pacificbiosciences.com/PacBioDatasets.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element NumRecords ({http://pacificbiosciences.com/PacBioDatasets.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element Provenance ({http://pacificbiosciences.com/PacBioDatasets.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}AverageSubreadLength uses Python identifier AverageSubreadLength
+ __AverageSubreadLength = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadLength'), 'AverageSubreadLength', '__httppacificbiosciences_comPacBioDatasets_xsd_SubreadSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdAverageSubreadLength', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 107, 5), )
+
+
+ AverageSubreadLength = property(__AverageSubreadLength.value, __AverageSubreadLength.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}AverageSubreadQuality uses Python identifier AverageSubreadQuality
+ __AverageSubreadQuality = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadQuality'), 'AverageSubreadQuality', '__httppacificbiosciences_comPacBioDatasets_xsd_SubreadSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdAverageSubreadQuality', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 108, 5), )
+
+
+ AverageSubreadQuality = property(__AverageSubreadQuality.value, __AverageSubreadQuality.set, None, None)
+
+ _ElementMap.update({
+ __AverageSubreadLength.name() : __AverageSubreadLength,
+ __AverageSubreadQuality.name() : __AverageSubreadQuality
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SubreadSetMetadataType', SubreadSetMetadataType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}AlignmentSetMetadataType with content type ELEMENT_ONLY
+class AlignmentSetMetadataType (DataSetMetadataType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}AlignmentSetMetadataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AlignmentSetMetadataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 273, 1)
+ _ElementMap = DataSetMetadataType._ElementMap.copy()
+ _AttributeMap = DataSetMetadataType._AttributeMap.copy()
+ # Base type is DataSetMetadataType
+
+ # Element TotalLength ({http://pacificbiosciences.com/PacBioDatasets.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element NumRecords ({http://pacificbiosciences.com/PacBioDatasets.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element Provenance ({http://pacificbiosciences.com/PacBioDatasets.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Aligner uses Python identifier Aligner
+ __Aligner = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Aligner'), 'Aligner', '__httppacificbiosciences_comPacBioDatasets_xsd_AlignmentSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdAligner', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 277, 5), )
+
+
+ Aligner = property(__Aligner.value, __Aligner.set, None, None)
+
+ _ElementMap.update({
+ __Aligner.name() : __Aligner
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'AlignmentSetMetadataType', AlignmentSetMetadataType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}ContigSetMetadataType with content type ELEMENT_ONLY
+class ContigSetMetadataType (DataSetMetadataType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}ContigSetMetadataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ContigSetMetadataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 282, 1)
+ _ElementMap = DataSetMetadataType._ElementMap.copy()
+ _AttributeMap = DataSetMetadataType._AttributeMap.copy()
+ # Base type is DataSetMetadataType
+
+ # Element TotalLength ({http://pacificbiosciences.com/PacBioDatasets.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element NumRecords ({http://pacificbiosciences.com/PacBioDatasets.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element Provenance ({http://pacificbiosciences.com/PacBioDatasets.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Contigs uses Python identifier Contigs
+ __Contigs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Contigs'), 'Contigs', '__httppacificbiosciences_comPacBioDatasets_xsd_ContigSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdContigs', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 250, 1), )
+
+
+ Contigs = property(__Contigs.value, __Contigs.set, None, 'List of contigs in a ContigSet')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Organism uses Python identifier Organism
+ __Organism = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Organism'), 'Organism', '__httppacificbiosciences_comPacBioDatasets_xsd_ContigSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdOrganism', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 286, 5), )
+
+
+ Organism = property(__Organism.value, __Organism.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Ploidy uses Python identifier Ploidy
+ __Ploidy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Ploidy'), 'Ploidy', '__httppacificbiosciences_comPacBioDatasets_xsd_ContigSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdPloidy', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 287, 5), )
+
+
+ Ploidy = property(__Ploidy.value, __Ploidy.set, None, None)
+
+ _ElementMap.update({
+ __Contigs.name() : __Contigs,
+ __Organism.name() : __Organism,
+ __Ploidy.name() : __Ploidy
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'ContigSetMetadataType', ContigSetMetadataType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}BarcodeSetMetadataType with content type ELEMENT_ONLY
+class BarcodeSetMetadataType (DataSetMetadataType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}BarcodeSetMetadataType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BarcodeSetMetadataType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 293, 1)
+ _ElementMap = DataSetMetadataType._ElementMap.copy()
+ _AttributeMap = DataSetMetadataType._AttributeMap.copy()
+ # Base type is DataSetMetadataType
+
+ # Element TotalLength ({http://pacificbiosciences.com/PacBioDatasets.xsd}TotalLength) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element NumRecords ({http://pacificbiosciences.com/PacBioDatasets.xsd}NumRecords) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element Provenance ({http://pacificbiosciences.com/PacBioDatasets.xsd}Provenance) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadataType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}BarcodeConstruction uses Python identifier BarcodeConstruction
+ __BarcodeConstruction = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodeConstruction'), 'BarcodeConstruction', '__httppacificbiosciences_comPacBioDatasets_xsd_BarcodeSetMetadataType_httppacificbiosciences_comPacBioDatasets_xsdBarcodeConstruction', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 297, 5), )
+
+
+ BarcodeConstruction = property(__BarcodeConstruction.value, __BarcodeConstruction.set, None, None)
+
+ _ElementMap.update({
+ __BarcodeConstruction.name() : __BarcodeConstruction
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'BarcodeSetMetadataType', BarcodeSetMetadataType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_6 (_ImportedBinding__pbbase.BaseEntityType):
+ """List of contigs in a ContigSet"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 254, 2)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Contig uses Python identifier Contig
+ __Contig = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Contig'), 'Contig', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_6_httppacificbiosciences_comPacBioDatasets_xsdContig', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 258, 6), )
+
+
+ Contig = property(__Contig.value, __Contig.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __Contig.name() : __Contig
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_7 (_ImportedBinding__pbbase.BaseEntityType):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 259, 7)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Length uses Python identifier Length
+ __Length = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Length'), 'Length', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_7_Length', pyxb.binding.datatypes.anySimpleType, required=True)
+ __Length._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 262, 10)
+ __Length._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 262, 10)
+
+ Length = property(__Length.value, __Length.set, None, None)
+
+
+ # Attribute Digest uses Python identifier Digest
+ __Digest = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Digest'), 'Digest', '__httppacificbiosciences_comPacBioDatasets_xsd_CTD_ANON_7_Digest', pyxb.binding.datatypes.anySimpleType, required=True)
+ __Digest._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 263, 10)
+ __Digest._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 263, 10)
+
+ Digest = property(__Digest.value, __Digest.set, None, None)
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __Length.name() : __Length,
+ __Digest.name() : __Digest
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType with content type ELEMENT_ONLY
+class DataSetType (_ImportedBinding__pbbase.StrictEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'DataSetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 8, 1)
+ _ElementMap = _ImportedBinding__pbbase.StrictEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.StrictEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.StrictEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources uses Python identifier ExternalResources
+ __ExternalResources = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources'), 'ExternalResources', '__httppacificbiosciences_comPacBioDatasets_xsd_DataSetType_httppacificbiosciences_comPacBioBaseDataModel_xsdExternalResources', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 266, 1), )
+
+
+ ExternalResources = property(__ExternalResources.value, __ExternalResources.set, None, 'Pointers to data that do not reside inside the parent structure')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Filters uses Python identifier Filters
+ __Filters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Filters'), 'Filters', '__httppacificbiosciences_comPacBioDatasets_xsd_DataSetType_httppacificbiosciences_comPacBioDatasets_xsdFilters', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5), )
+
+
+ Filters = property(__Filters.value, __Filters.set, None, 'The set of filters defined here apply to the resident data set. Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets uses Python identifier DataSets
+ __DataSets = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), 'DataSets', '__httppacificbiosciences_comPacBioDatasets_xsd_DataSetType_httppacificbiosciences_comPacBioDatasets_xsdDataSets', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5), )
+
+
+ DataSets = property(__DataSets.value, __DataSets.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __ExternalResources.name() : __ExternalResources,
+ __Filters.name() : __Filters,
+ __DataSets.name() : __DataSets
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'DataSetType', DataSetType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}SubsetType with content type ELEMENT_ONLY
+class SubsetType (_ImportedBinding__pbbase.StrictEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}SubsetType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SubsetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 118, 1)
+ _ElementMap = _ImportedBinding__pbbase.StrictEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.StrictEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.StrictEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataPointers uses Python identifier DataPointers
+ __DataPointers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'DataPointers'), 'DataPointers', '__httppacificbiosciences_comPacBioDatasets_xsd_SubsetType_httppacificbiosciences_comPacBioBaseDataModel_xsdDataPointers', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 232, 1), )
+
+
+ DataPointers = property(__DataPointers.value, __DataPointers.set, None, 'Pointer list to UniqueIds in the system')
+
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}Filters uses Python identifier Filters
+ __Filters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Filters'), 'Filters', '__httppacificbiosciences_comPacBioDatasets_xsd_SubsetType_httppacificbiosciences_comPacBioDatasets_xsdFilters', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 122, 5), )
+
+
+ Filters = property(__Filters.value, __Filters.set, None, 'The set of filters defined here apply to the resident data set. Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters.')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __DataPointers.name() : __DataPointers,
+ __Filters.name() : __Filters
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SubsetType', SubsetType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadSetType with content type ELEMENT_ONLY
+class ReadSetType (DataSetType):
+ """Type for DataSets consisting of unaligned subreads and CCS reads DataSets"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReadSetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 35, 1)
+ _ElementMap = DataSetType._ElementMap.copy()
+ _AttributeMap = DataSetType._AttributeMap.copy()
+ # Base type is DataSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata uses Python identifier DataSetMetadata
+ __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDatasets_xsd_ReadSetType_httppacificbiosciences_comPacBioDatasets_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5), )
+
+
+ DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __DataSetMetadata.name() : __DataSetMetadata
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'ReadSetType', ReadSetType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}BarcodeSetType with content type ELEMENT_ONLY
+class BarcodeSetType (DataSetType):
+ """Type for the Barcode DataSet."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BarcodeSetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 164, 1)
+ _ElementMap = DataSetType._ElementMap.copy()
+ _AttributeMap = DataSetType._AttributeMap.copy()
+ # Base type is DataSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata uses Python identifier DataSetMetadata
+ __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDatasets_xsd_BarcodeSetType_httppacificbiosciences_comPacBioDatasets_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 171, 5), )
+
+
+ DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __DataSetMetadata.name() : __DataSetMetadata
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'BarcodeSetType', BarcodeSetType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_8 (DataSetType):
+ """DataSets of CCS reads (typically in unaligned BAM format)."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 190, 2)
+ _ElementMap = DataSetType._ElementMap.copy()
+ _AttributeMap = DataSetType._AttributeMap.copy()
+ # Base type is DataSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}AlignmentSetType with content type ELEMENT_ONLY
+class AlignmentSetType (DataSetType):
+ """Type for DataSets consisting of aligned subreads and CCS reads."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'AlignmentSetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 196, 1)
+ _ElementMap = DataSetType._ElementMap.copy()
+ _AttributeMap = DataSetType._AttributeMap.copy()
+ # Base type is DataSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata uses Python identifier DataSetMetadata
+ __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDatasets_xsd_AlignmentSetType_httppacificbiosciences_comPacBioDatasets_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5), )
+
+
+ DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __DataSetMetadata.name() : __DataSetMetadata
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'AlignmentSetType', AlignmentSetType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}ContigSetType with content type ELEMENT_ONLY
+class ContigSetType (DataSetType):
+ """Type for a Contig DataSet."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ContigSetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 228, 1)
+ _ElementMap = DataSetType._ElementMap.copy()
+ _AttributeMap = DataSetType._AttributeMap.copy()
+ # Base type is DataSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata uses Python identifier DataSetMetadata
+ __DataSetMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), 'DataSetMetadata', '__httppacificbiosciences_comPacBioDatasets_xsd_ContigSetType_httppacificbiosciences_comPacBioDatasets_xsdDataSetMetadata', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 235, 5), )
+
+
+ DataSetMetadata = property(__DataSetMetadata.value, __DataSetMetadata.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+ __DataSetMetadata.name() : __DataSetMetadata
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'ContigSetType', ContigSetType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}SubreadSetType with content type ELEMENT_ONLY
+class SubreadSetType (ReadSetType):
+ """Complex type {http://pacificbiosciences.com/PacBioDatasets.xsd}SubreadSetType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SubreadSetType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 113, 1)
+ _ElementMap = ReadSetType._ElementMap.copy()
+ _AttributeMap = ReadSetType._AttributeMap.copy()
+ # Base type is ReadSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'SubreadSetType', SubreadSetType)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_9 (AlignmentSetType):
+ """DataSets for aligned subreads and CCS reads."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 148, 2)
+ _ElementMap = AlignmentSetType._ElementMap.copy()
+ _AttributeMap = AlignmentSetType._AttributeMap.copy()
+ # Base type is AlignmentSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}AlignmentSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_10 (BarcodeSetType):
+ """DataSets of Barcodes. Basically a thin metadata layer on top of the barcode FASTA."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 158, 2)
+ _ElementMap = BarcodeSetType._ElementMap.copy()
+ _AttributeMap = BarcodeSetType._AttributeMap.copy()
+ # Base type is BarcodeSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}BarcodeSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_11 (AlignmentSetType):
+ """DataSets of aligned CCS reads."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 180, 2)
+ _ElementMap = AlignmentSetType._ElementMap.copy()
+ _AttributeMap = AlignmentSetType._AttributeMap.copy()
+ # Base type is AlignmentSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}AlignmentSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_12 (ContigSetType):
+ """DataSets of reference sequences. Replaces the reference.info.xml."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 212, 2)
+ _ElementMap = ContigSetType._ElementMap.copy()
+ _AttributeMap = ContigSetType._AttributeMap.copy()
+ # Base type is ContigSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}ContigSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_13 (ContigSetType):
+ """DataSets of contigs sequences. Basically a thin metadata layer on top of a contigs FASTA (e.g. from HGAP)."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 222, 2)
+ _ElementMap = ContigSetType._ElementMap.copy()
+ _AttributeMap = ContigSetType._AttributeMap.copy()
+ # Base type is ContigSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}ContigSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_14 (ReadSetType):
+ """DataSets of subreads in bax.h5 or bas.h5 format."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 244, 2)
+ _ElementMap = ReadSetType._ElementMap.copy()
+ _AttributeMap = ReadSetType._AttributeMap.copy()
+ # Base type is ReadSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_15 (SubreadSetType):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 138, 2)
+ _ElementMap = SubreadSetType._ElementMap.copy()
+ _AttributeMap = SubreadSetType._AttributeMap.copy()
+ # Base type is SubreadSetType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element ExternalResources ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}ExternalResources) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element Filters ({http://pacificbiosciences.com/PacBioDatasets.xsd}Filters) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSets ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSets) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetType
+
+ # Element DataSetMetadata ({http://pacificbiosciences.com/PacBioDatasets.xsd}DataSetMetadata) inherited from {http://pacificbiosciences.com/PacBioDatasets.xsd}ReadSetType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+Subsets = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Subsets'), CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 302, 1))
+Namespace.addCategoryObject('elementBinding', Subsets.name().localName(), Subsets)
+
+Contigs = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Contigs'), CTD_ANON_6, documentation='List of contigs in a ContigSet', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 250, 1))
+Namespace.addCategoryObject('elementBinding', Contigs.name().localName(), Contigs)
+
+DataSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), DataSetType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 34, 1))
+Namespace.addCategoryObject('elementBinding', DataSet.name().localName(), DataSet)
+
+ConsensusReadSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConsensusReadSet'), CTD_ANON_8, documentation='DataSets of CCS reads (typically in unaligned BAM format).', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 186, 1))
+Namespace.addCategoryObject('elementBinding', ConsensusReadSet.name().localName(), ConsensusReadSet)
+
+AlignmentSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AlignmentSet'), CTD_ANON_9, documentation='DataSets for aligned subreads and CCS reads.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 144, 1))
+Namespace.addCategoryObject('elementBinding', AlignmentSet.name().localName(), AlignmentSet)
+
+BarcodeSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodeSet'), CTD_ANON_10, documentation='DataSets of Barcodes. Basically a thin metadata layer on top of the barcode FASTA.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 154, 1))
+Namespace.addCategoryObject('elementBinding', BarcodeSet.name().localName(), BarcodeSet)
+
+ConsensusAlignmentSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConsensusAlignmentSet'), CTD_ANON_11, documentation='DataSets of aligned CCS reads.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 176, 1))
+Namespace.addCategoryObject('elementBinding', ConsensusAlignmentSet.name().localName(), ConsensusAlignmentSet)
+
+ReferenceSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReferenceSet'), CTD_ANON_12, documentation='DataSets of reference sequences. Replaces the reference.info.xml.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 208, 1))
+Namespace.addCategoryObject('elementBinding', ReferenceSet.name().localName(), ReferenceSet)
+
+ContigSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ContigSet'), CTD_ANON_13, documentation='DataSets of contigs sequences. Basically a thin metadata layer on top of a contigs FASTA (e.g. from HGAP).', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 218, 1))
+Namespace.addCategoryObject('elementBinding', ContigSet.name().localName(), ContigSet)
+
+HdfSubreadSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'HdfSubreadSet'), CTD_ANON_14, documentation='DataSets of subreads in bax.h5 or bas.h5 format.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 240, 1))
+Namespace.addCategoryObject('elementBinding', HdfSubreadSet.name().localName(), HdfSubreadSet)
+
+SubreadSet = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SubreadSet'), CTD_ANON_15, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 137, 1))
+Namespace.addCategoryObject('elementBinding', SubreadSet.name().localName(), SubreadSet)
+
+
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Filter'), _ImportedBinding__pbbase.FilterType, scope=CTD_ANON, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 19, 8)))
+
+def _BuildAutomaton ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton
+ del _BuildAutomaton
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filter')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 19, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+
+
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSet'), DataSetType, scope=CTD_ANON_, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 34, 1)))
+
+def _BuildAutomaton_ ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_
+ del _BuildAutomaton_
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 26, 8))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSet')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 26, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_._Automaton = _BuildAutomaton_()
+
+
+
+
+DataSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TotalLength'), pyxb.binding.datatypes.int, scope=DataSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3)))
+
+DataSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumRecords'), pyxb.binding.datatypes.int, scope=DataSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3)))
+
+DataSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Provenance'), CTD_ANON_5, scope=DataSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3)))
+
+def _BuildAutomaton_2 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(DataSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(DataSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(DataSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+DataSetMetadataType._Automaton = _BuildAutomaton_2()
+
+
+
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AdapterDimerFraction'), pyxb.binding.datatypes.float, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 84, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ShortInsertFraction'), pyxb.binding.datatypes.float, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 85, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'NumSequencingZmws'), pyxb.binding.datatypes.int, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 86, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ProdDist'), _ImportedBinding__pbbase.StatsDiscreteDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 87, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReadTypeDist'), _ImportedBinding__pbbase.StatsDiscreteDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 88, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReadLenDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 89, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReadQualDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 90, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlReadLenDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 91, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlReadQualDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 92, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MedianInsertDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 93, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertReadLenDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 94, 8)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InsertReadQualDist'), _ImportedBinding__pbbase.StatsContinuousDistType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 95, 8)))
+
+def _BuildAutomaton_3 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AdapterDimerFraction')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 84, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ShortInsertFraction')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 85, 8))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumSequencingZmws')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 86, 8))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ProdDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 87, 8))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReadTypeDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 88, 8))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReadLenDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 89, 8))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReadQualDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 90, 8))
+ st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlReadLenDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 91, 8))
+ st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_7)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlReadQualDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 92, 8))
+ st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_8)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MedianInsertDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 93, 8))
+ st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_9)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertReadLenDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 94, 8))
+ st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_10)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InsertReadQualDist')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 95, 8))
+ st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_11)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ ]))
+ st_6._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ ]))
+ st_7._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_9, [
+ ]))
+ st_8._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_10, [
+ ]))
+ st_9._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_11, [
+ ]))
+ st_10._set_transitionSet(transitions)
+ transitions = []
+ st_11._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_2._Automaton = _BuildAutomaton_3()
+
+
+
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Filter'), _ImportedBinding__pbbase.FilterType, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 128, 8)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filter')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 128, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_4()
+
+
+
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Subset'), SubsetType, scope=CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 305, 4)))
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Subset')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 305, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_4._Automaton = _BuildAutomaton_5()
+
+
+
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CommonServicesInstanceId'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 57, 6)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CreatorUserId'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 58, 6)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ParentJobId'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 59, 6)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ParentTool'), _ImportedBinding__pbbase.BaseEntityType, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 60, 6)))
+
+def _BuildAutomaton_6 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_6
+ del _BuildAutomaton_6
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 57, 6))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 58, 6))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 59, 6))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 60, 6))
+ counters.add(cc_3)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CommonServicesInstanceId')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 57, 6))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CreatorUserId')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 58, 6))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ParentJobId')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 59, 6))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ParentTool')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 60, 6))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_5._Automaton = _BuildAutomaton_6()
+
+
+
+
+ReadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbmeta, 'Collections'), _ImportedBinding__pbmeta.CTD_ANON_, scope=ReadSetMetadataType, documentation='A set of acquisition definitions', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 20, 1)))
+
+ReadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SummaryStats'), CTD_ANON_2, scope=ReadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 81, 5)))
+
+ReadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbsample, 'BioSamples'), _ImportedBinding__pbsample.CTD_ANON_3, scope=ReadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 134, 1)))
+
+def _BuildAutomaton_7 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_7
+ del _BuildAutomaton_7
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 79, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 80, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 81, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbmeta, 'Collections')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 79, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbsample, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 80, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SummaryStats')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 81, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+ReadSetMetadataType._Automaton = _BuildAutomaton_7()
+
+
+
+
+SubreadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadLength'), pyxb.binding.datatypes.int, scope=SubreadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 107, 5)))
+
+SubreadSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadQuality'), pyxb.binding.datatypes.float, scope=SubreadSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 108, 5)))
+
+def _BuildAutomaton_8 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_8
+ del _BuildAutomaton_8
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 107, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(SubreadSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AverageSubreadQuality')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 108, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+SubreadSetMetadataType._Automaton = _BuildAutomaton_8()
+
+
+
+
+AlignmentSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Aligner'), pyxb.binding.datatypes.anyType, scope=AlignmentSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 277, 5)))
+
+def _BuildAutomaton_9 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_9
+ del _BuildAutomaton_9
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 277, 5))
+ counters.add(cc_1)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Aligner')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 277, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+AlignmentSetMetadataType._Automaton = _BuildAutomaton_9()
+
+
+
+
+ContigSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Contigs'), CTD_ANON_6, scope=ContigSetMetadataType, documentation='List of contigs in a ContigSet', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 250, 1)))
+
+ContigSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Organism'), pyxb.binding.datatypes.string, scope=ContigSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 286, 5)))
+
+ContigSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Ploidy'), pyxb.binding.datatypes.string, scope=ContigSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 287, 5)))
+
+def _BuildAutomaton_10 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_10
+ del _BuildAutomaton_10
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 286, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 287, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Organism')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 286, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Ploidy')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 287, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(ContigSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Contigs')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 288, 5))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+ContigSetMetadataType._Automaton = _BuildAutomaton_10()
+
+
+
+
+BarcodeSetMetadataType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodeConstruction'), pyxb.binding.datatypes.string, scope=BarcodeSetMetadataType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 297, 5)))
+
+def _BuildAutomaton_11 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_11
+ del _BuildAutomaton_11
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TotalLength')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 52, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'NumRecords')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 53, 3))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Provenance')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 54, 3))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetMetadataType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodeConstruction')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 297, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+BarcodeSetMetadataType._Automaton = _BuildAutomaton_11()
+
+
+
+
+CTD_ANON_6._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Contig'), CTD_ANON_7, scope=CTD_ANON_6, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 258, 6)))
+
+def _BuildAutomaton_12 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_12
+ del _BuildAutomaton_12
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Contig')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 258, 6))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_6._Automaton = _BuildAutomaton_12()
+
+
+
+
+def _BuildAutomaton_13 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_13
+ del _BuildAutomaton_13
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_7._Automaton = _BuildAutomaton_13()
+
+
+
+
+DataSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources'), _ImportedBinding__pbbase.CTD_ANON_4, scope=DataSetType, documentation='Pointers to data that do not reside inside the parent structure', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 266, 1)))
+
+DataSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Filters'), CTD_ANON, scope=DataSetType, documentation='The set of filters defined here apply to the resident data set. Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5)))
+
+DataSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSets'), CTD_ANON_, scope=DataSetType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5)))
+
+def _BuildAutomaton_14 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_14
+ del _BuildAutomaton_14
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(DataSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+DataSetType._Automaton = _BuildAutomaton_14()
+
+
+
+
+SubsetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'DataPointers'), _ImportedBinding__pbbase.CTD_ANON_3, scope=SubsetType, documentation='Pointer list to UniqueIds in the system', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 232, 1)))
+
+SubsetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Filters'), CTD_ANON_3, scope=SubsetType, documentation='The set of filters defined here apply to the resident data set. Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 122, 5)))
+
+def _BuildAutomaton_15 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_15
+ del _BuildAutomaton_15
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 122, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 132, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(SubsetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SubsetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 122, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SubsetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'DataPointers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 132, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+SubsetType._Automaton = _BuildAutomaton_15()
+
+
+
+
+ReadSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), ReadSetMetadataType, scope=ReadSetType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5)))
+
+def _BuildAutomaton_16 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_16
+ del _BuildAutomaton_16
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(ReadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+ReadSetType._Automaton = _BuildAutomaton_16()
+
+
+
+
+BarcodeSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), BarcodeSetMetadataType, scope=BarcodeSetType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 171, 5)))
+
+def _BuildAutomaton_17 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_17
+ del _BuildAutomaton_17
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(BarcodeSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 171, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+BarcodeSetType._Automaton = _BuildAutomaton_17()
+
+
+
+
+def _BuildAutomaton_18 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_18
+ del _BuildAutomaton_18
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_8._Automaton = _BuildAutomaton_18()
+
+
+
+
+AlignmentSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), AlignmentSetMetadataType, scope=AlignmentSetType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5)))
+
+def _BuildAutomaton_19 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_19
+ del _BuildAutomaton_19
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(AlignmentSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+AlignmentSetType._Automaton = _BuildAutomaton_19()
+
+
+
+
+ContigSetType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata'), ContigSetMetadataType, scope=ContigSetType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 235, 5)))
+
+def _BuildAutomaton_20 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_20
+ del _BuildAutomaton_20
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(ContigSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 235, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+ContigSetType._Automaton = _BuildAutomaton_20()
+
+
+
+
+def _BuildAutomaton_21 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_21
+ del _BuildAutomaton_21
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(SubreadSetType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+SubreadSetType._Automaton = _BuildAutomaton_21()
+
+
+
+
+def _BuildAutomaton_22 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_22
+ del _BuildAutomaton_22
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_9._Automaton = _BuildAutomaton_22()
+
+
+
+
+def _BuildAutomaton_23 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_23
+ del _BuildAutomaton_23
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 171, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_10._Automaton = _BuildAutomaton_23()
+
+
+
+
+def _BuildAutomaton_24 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_24
+ del _BuildAutomaton_24
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_11._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 203, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_11._Automaton = _BuildAutomaton_24()
+
+
+
+
+def _BuildAutomaton_25 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_25
+ del _BuildAutomaton_25
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 235, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_12._Automaton = _BuildAutomaton_25()
+
+
+
+
+def _BuildAutomaton_26 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_26
+ del _BuildAutomaton_26
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 235, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_13._Automaton = _BuildAutomaton_26()
+
+
+
+
+def _BuildAutomaton_27 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_27
+ del _BuildAutomaton_27
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_14._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_14._Automaton = _BuildAutomaton_27()
+
+
+
+
+def _BuildAutomaton_28 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_28
+ del _BuildAutomaton_28
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ counters.add(cc_3)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ExternalResources')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 12, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Filters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 13, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSets')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 23, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_15._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DataSetMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioDatasets.xsd', 42, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_15._Automaton = _BuildAutomaton_28()
+
diff --git a/pbcore/io/dataset/_pbmeta.py b/pbcore/io/dataset/_pbmeta.py
new file mode 100755
index 0000000..26d097a
--- /dev/null
+++ b/pbcore/io/dataset/_pbmeta.py
@@ -0,0 +1,2056 @@
+# ./_pbmeta.py
+# -*- coding: utf-8 -*-
+# PyXB bindings for NM:9efc6641c22b876b2d5ab7b8523f84c3396b188b
+# Generated 2015-08-04 20:41:05.068110 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Namespace http://pacificbiosciences.com/PacBioCollectionMetadata.xsd [xmlns:pbmeta]
+
+from __future__ import unicode_literals
+import pyxb
+import pyxb.binding
+import pyxb.binding.saxer
+import io
+import pyxb.utils.utility
+import pyxb.utils.domutils
+import sys
+import pyxb.utils.six as _six
+
+# Unique identifier for bindings created at the same time
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
+
+# Version of PyXB used to generate the bindings
+_PyXBVersion = '1.2.4'
+# Generated bindings are not compatible across PyXB versions
+if pyxb.__version__ != _PyXBVersion:
+ raise pyxb.PyXBVersionError(_PyXBVersion)
+
+# Import bindings for namespaces imported into schema
+import _pbbase as _ImportedBinding__pbbase
+import pyxb.binding.datatypes
+import _pbrk as _ImportedBinding__pbrk
+import _pbsample as _ImportedBinding__pbsample
+
+# NOTE: All namespace declarations are reserved within the binding
+Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioCollectionMetadata.xsd', create_if_missing=True)
+Namespace.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbsample = _ImportedBinding__pbsample.Namespace
+_Namespace_pbsample.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbbase = _ImportedBinding__pbbase.Namespace
+_Namespace_pbbase.configureCategories(['typeBinding', 'elementBinding'])
+
+def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
+ """Parse the given XML and use the document element to create a
+ Python instance.
+
+ @param xml_text An XML document. This should be data (Python 2
+ str or Python 3 bytes), or a text (Python 2 unicode or Python 3
+ str) in the L{pyxb._InputEncoding} encoding.
+
+ @keyword default_namespace The L{pyxb.Namespace} instance to use as the
+ default namespace where there is no default namespace in scope.
+ If unspecified or C{None}, the namespace of the module containing
+ this function will be used.
+
+ @keyword location_base: An object to be recorded as the base of all
+ L{pyxb.utils.utility.Location} instances associated with events and
+ objects handled by the parser. You might pass the URI from which
+ the document was obtained.
+ """
+
+ if pyxb.XMLStyle_saxer != pyxb._XMLStyle:
+ dom = pyxb.utils.domutils.StringToDOM(xml_text)
+ return CreateFromDOM(dom.documentElement, default_namespace=default_namespace)
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ saxer = pyxb.binding.saxer.make_parser(fallback_namespace=default_namespace, location_base=location_base)
+ handler = saxer.getContentHandler()
+ xmld = xml_text
+ if isinstance(xmld, _six.text_type):
+ xmld = xmld.encode(pyxb._InputEncoding)
+ saxer.parse(io.BytesIO(xmld))
+ instance = handler.rootObject()
+ return instance
+
+def CreateFromDOM (node, default_namespace=None):
+ """Create a Python instance from the given DOM node.
+ The node tag must correspond to an element declaration in this module.
+
+ @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}."""
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ return pyxb.binding.basis.element.AnyCreateFromDOM(node, default_namespace)
+
+
+# Atomic simple type: [anonymous]
+class STD_ANON (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 372, 8)
+ _Documentation = None
+STD_ANON._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON, enum_prefix=None)
+STD_ANON.Pulses = STD_ANON._CF_enumeration.addEnumeration(unicode_value='Pulses', tag='Pulses')
+STD_ANON.Bases = STD_ANON._CF_enumeration.addEnumeration(unicode_value='Bases', tag='Bases')
+STD_ANON._InitializeFacetMap(STD_ANON._CF_enumeration)
+
+# Atomic simple type: [anonymous]
+class STD_ANON_ (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 383, 8)
+ _Documentation = None
+STD_ANON_._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=STD_ANON_, enum_prefix=None)
+STD_ANON_.Minimal = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='Minimal', tag='Minimal')
+STD_ANON_.High = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='High', tag='High')
+STD_ANON_.None_ = STD_ANON_._CF_enumeration.addEnumeration(unicode_value='None', tag='None_')
+STD_ANON_._InitializeFacetMap(STD_ANON_._CF_enumeration)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}PapOutputFile
+class PapOutputFile (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """Defines a list of available file output types from primary output that can be copied out to the CollectionPathUri. The types Pulse, Base, Fasta, and Fastq are for legacy use only."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'PapOutputFile')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 454, 1)
+ _Documentation = 'Defines a list of available file output types from primary output that can be copied out to the CollectionPathUri. The types Pulse, Base, Fasta, and Fastq are for legacy use only.'
+PapOutputFile._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=PapOutputFile, enum_prefix=None)
+PapOutputFile.Movie = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Movie', tag='Movie')
+PapOutputFile.Trace = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Trace', tag='Trace')
+PapOutputFile.Pulse = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Pulse', tag='Pulse')
+PapOutputFile.Base = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Base', tag='Base')
+PapOutputFile.Baz = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Baz', tag='Baz')
+PapOutputFile.Bam = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Bam', tag='Bam')
+PapOutputFile.Fasta = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Fasta', tag='Fasta')
+PapOutputFile.Bam_ = PapOutputFile._CF_enumeration.addEnumeration(unicode_value='Bam', tag='Bam_')
+PapOutputFile._InitializeFacetMap(PapOutputFile._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'PapOutputFile', PapOutputFile)
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
+ """Root element of a standalone CollectionMetadata file."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 14, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CollectionMetadata uses Python identifier CollectionMetadata
+ __CollectionMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), 'CollectionMetadata', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_httppacificbiosciences_comPacBioCollectionMetadata_xsdCollectionMetadata', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 30, 1), )
+
+
+ CollectionMetadata = property(__CollectionMetadata.value, __CollectionMetadata.set, None, 'Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ')
+
+ _ElementMap.update({
+ __CollectionMetadata.name() : __CollectionMetadata
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
+ """A set of acquisition definitions"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 24, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CollectionMetadata uses Python identifier CollectionMetadata
+ __CollectionMetadata = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), 'CollectionMetadata', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON__httppacificbiosciences_comPacBioCollectionMetadata_xsdCollectionMetadata', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 30, 1), )
+
+
+ CollectionMetadata = property(__CollectionMetadata.value, __CollectionMetadata.set, None, 'Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ')
+
+ _ElementMap.update({
+ __CollectionMetadata.name() : __CollectionMetadata
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
+ """Information related to an instrument run. A run can contain multiple chips, wells, and movies. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 150, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}RunId uses Python identifier RunId
+ __RunId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RunId'), 'RunId', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioCollectionMetadata_xsdRunId', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 152, 4), )
+
+
+ RunId = property(__RunId.value, __RunId.set, None, 'A unique identifier for this run. Format is r[sid]_[iname]_[ts]. Where [id] is a system generated id and [iname] is the instrument name and [ts] is a timestamp YYMMDD Example: r000123_00117_100713 ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Name uses Python identifier Name
+ __Name = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Name'), 'Name', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioCollectionMetadata_xsdName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 157, 4), )
+
+
+ Name = property(__Name.value, __Name.set, None, 'Assigned name for a run, which consists of multiple wells. There is no constraint on the uniqueness of this data. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CreatedBy uses Python identifier CreatedBy
+ __CreatedBy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CreatedBy'), 'CreatedBy', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioCollectionMetadata_xsdCreatedBy', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 162, 4), )
+
+
+ CreatedBy = property(__CreatedBy.value, __CreatedBy.set, None, 'Who created the run. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}WhenCreated uses Python identifier WhenCreated
+ __WhenCreated = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WhenCreated'), 'WhenCreated', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioCollectionMetadata_xsdWhenCreated', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 167, 4), )
+
+
+ WhenCreated = property(__WhenCreated.value, __WhenCreated.set, None, 'Date and time of when the overall run was created in the system. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}StartedBy uses Python identifier StartedBy
+ __StartedBy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'StartedBy'), 'StartedBy', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioCollectionMetadata_xsdStartedBy', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 172, 4), )
+
+
+ StartedBy = property(__StartedBy.value, __StartedBy.set, None, 'Who started the run. Could be different from who created it. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}WhenStarted uses Python identifier WhenStarted
+ __WhenStarted = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), 'WhenStarted', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioCollectionMetadata_xsdWhenStarted', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 177, 4), )
+
+
+ WhenStarted = property(__WhenStarted.value, __WhenStarted.set, None, 'Date and time of when the overall run was started. ')
+
+ _ElementMap.update({
+ __RunId.name() : __RunId,
+ __Name.name() : __Name,
+ __CreatedBy.name() : __CreatedBy,
+ __WhenCreated.name() : __WhenCreated,
+ __StartedBy.name() : __StartedBy,
+ __WhenStarted.name() : __WhenStarted
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
+ """A movie corresponds to one acquisition for a chip, one set (look) and one strobe. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 189, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}WhenStarted uses Python identifier WhenStarted
+ __WhenStarted = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), 'WhenStarted', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioCollectionMetadata_xsdWhenStarted', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 191, 4), )
+
+
+ WhenStarted = property(__WhenStarted.value, __WhenStarted.set, None, 'Date and time of when this movie acquisition started. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}DurationInSec uses Python identifier DurationInSec
+ __DurationInSec = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DurationInSec'), 'DurationInSec', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioCollectionMetadata_xsdDurationInSec', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 196, 4), )
+
+
+ DurationInSec = property(__DurationInSec.value, __DurationInSec.set, None, 'The actual length of the movie acquisition (in seconds), irrespective of the movie duration specified by an automation parameter. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Number uses Python identifier Number
+ __Number = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Number'), 'Number', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioCollectionMetadata_xsdNumber', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 201, 4), )
+
+
+ Number = property(__Number.value, __Number.set, None, "The number of this movie within the set (i.e., look). This is unique when combined with the 'SetNumber'. ")
+
+ _ElementMap.update({
+ __WhenStarted.name() : __WhenStarted,
+ __DurationInSec.name() : __DurationInSec,
+ __Number.name() : __Number
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
+ """Container for the expired consumable data. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 213, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}EightPacPastExpiration uses Python identifier EightPacPastExpiration
+ __EightPacPastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'EightPacPastExpiration'), 'EightPacPastExpiration', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioCollectionMetadata_xsdEightPacPastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 215, 4), )
+
+
+ EightPacPastExpiration = property(__EightPacPastExpiration.value, __EightPacPastExpiration.set, None, 'Number of days past expiration the eight pac was (if at all). ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}ReagentKitPastExpiration uses Python identifier ReagentKitPastExpiration
+ __ReagentKitPastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentKitPastExpiration'), 'ReagentKitPastExpiration', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioCollectionMetadata_xsdReagentKitPastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 220, 4), )
+
+
+ ReagentKitPastExpiration = property(__ReagentKitPastExpiration.value, __ReagentKitPastExpiration.set, None, 'Number of days past expiration the reagent kit was (if at all). ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}ReagentTube0PastExpiration uses Python identifier ReagentTube0PastExpiration
+ __ReagentTube0PastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube0PastExpiration'), 'ReagentTube0PastExpiration', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioCollectionMetadata_xsdReagentTube0PastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 225, 4), )
+
+
+ ReagentTube0PastExpiration = property(__ReagentTube0PastExpiration.value, __ReagentTube0PastExpiration.set, None, 'Number of days past expiration the reagent tube 0 was (if at all). ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}ReagentTube1PastExpiration uses Python identifier ReagentTube1PastExpiration
+ __ReagentTube1PastExpiration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube1PastExpiration'), 'ReagentTube1PastExpiration', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioCollectionMetadata_xsdReagentTube1PastExpiration', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 230, 4), )
+
+
+ ReagentTube1PastExpiration = property(__ReagentTube1PastExpiration.value, __ReagentTube1PastExpiration.set, None, 'Number of days past expiration the reagent tube 1 was (if at all). ')
+
+ _ElementMap.update({
+ __EightPacPastExpiration.name() : __EightPacPastExpiration,
+ __ReagentKitPastExpiration.name() : __ReagentKitPastExpiration,
+ __ReagentTube0PastExpiration.name() : __ReagentTube0PastExpiration,
+ __ReagentTube1PastExpiration.name() : __ReagentTube1PastExpiration
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_5 (pyxb.binding.basis.complexTypeDefinition):
+ """Container for the primary analysis related data. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 308, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SampleTrace uses Python identifier SampleTrace
+ __SampleTrace = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleTrace'), 'SampleTrace', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioCollectionMetadata_xsdSampleTrace', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 310, 4), )
+
+
+ SampleTrace = property(__SampleTrace.value, __SampleTrace.set, None, 'Tag to indicate that the trace file will be sampled. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}AutomationName uses Python identifier AutomationName
+ __AutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), 'AutomationName', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioCollectionMetadata_xsdAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 329, 4), )
+
+
+ AutomationName = property(__AutomationName.value, __AutomationName.set, None, 'Name of primary analysis protocol. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}ConfigFileName uses Python identifier ConfigFileName
+ __ConfigFileName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ConfigFileName'), 'ConfigFileName', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioCollectionMetadata_xsdConfigFileName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 334, 4), )
+
+
+ ConfigFileName = property(__ConfigFileName.value, __ConfigFileName.set, None, 'Name of primary analysis config file. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SequencingCondition uses Python identifier SequencingCondition
+ __SequencingCondition = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingCondition'), 'SequencingCondition', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioCollectionMetadata_xsdSequencingCondition', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 339, 4), )
+
+
+ SequencingCondition = property(__SequencingCondition.value, __SequencingCondition.set, None, 'A sequencing condition tag to be used by primary analysis, e.g., to select basecaller calibration or training parameters. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}OutputOptions uses Python identifier OutputOptions
+ __OutputOptions = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'OutputOptions'), 'OutputOptions', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioCollectionMetadata_xsdOutputOptions', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 344, 4), )
+
+
+ OutputOptions = property(__OutputOptions.value, __OutputOptions.set, None, None)
+
+ _ElementMap.update({
+ __SampleTrace.name() : __SampleTrace,
+ __AutomationName.name() : __AutomationName,
+ __ConfigFileName.name() : __ConfigFileName,
+ __SequencingCondition.name() : __SequencingCondition,
+ __OutputOptions.name() : __OutputOptions
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_6 (pyxb.binding.basis.complexTypeDefinition):
+ """Tag to indicate that the trace file will be sampled. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 314, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}TraceSamplingFactor uses Python identifier TraceSamplingFactor
+ __TraceSamplingFactor = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TraceSamplingFactor'), 'TraceSamplingFactor', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_6_httppacificbiosciences_comPacBioCollectionMetadata_xsdTraceSamplingFactor', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 316, 7), )
+
+
+ TraceSamplingFactor = property(__TraceSamplingFactor.value, __TraceSamplingFactor.set, None, 'Percentage of traces to sample. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}FullPulseFile uses Python identifier FullPulseFile
+ __FullPulseFile = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'FullPulseFile'), 'FullPulseFile', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_6_httppacificbiosciences_comPacBioCollectionMetadata_xsdFullPulseFile', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 321, 7), )
+
+
+ FullPulseFile = property(__FullPulseFile.value, __FullPulseFile.set, None, 'Whether full or sampled pulse file is transferred if requested. ')
+
+ _ElementMap.update({
+ __TraceSamplingFactor.name() : __TraceSamplingFactor,
+ __FullPulseFile.name() : __FullPulseFile
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_7 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 345, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}ResultsFolder uses Python identifier ResultsFolder
+ __ResultsFolder = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ResultsFolder'), 'ResultsFolder', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioCollectionMetadata_xsdResultsFolder', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 347, 7), )
+
+
+ ResultsFolder = property(__ResultsFolder.value, __ResultsFolder.set, None, "NOTE: not for customers. A sub-folder under the CollectionPath created by Primary Analysis. This is a field that will be updated by the primary analysis pipeline. The default (as created by homer) should be set to 'Reports_Sms' for now. Consumers of the data should be aware that they will find collection metadata (and trace files if acquisition is so-configured) at the CollectionPathUri, and all primary ana [...]
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CollectionPathUri uses Python identifier CollectionPathUri
+ __CollectionPathUri = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionPathUri'), 'CollectionPathUri', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioCollectionMetadata_xsdCollectionPathUri', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 352, 7), )
+
+
+ CollectionPathUri = property(__CollectionPathUri.value, __CollectionPathUri.set, None, 'User-specified location of where the results should be copied after an analysis has been completed. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CopyFiles uses Python identifier CopyFiles
+ __CopyFiles = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CopyFiles'), 'CopyFiles', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioCollectionMetadata_xsdCopyFiles', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 357, 7), )
+
+
+ CopyFiles = property(__CopyFiles.value, __CopyFiles.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Readout uses Python identifier Readout
+ __Readout = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Readout'), 'Readout', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioCollectionMetadata_xsdReadout', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 368, 7), )
+
+
+ Readout = property(__Readout.value, __Readout.set, None, 'BazIO Readout option; valid values are Bases (default) and Pulses')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}MetricsVerbosity uses Python identifier MetricsVerbosity
+ __MetricsVerbosity = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'MetricsVerbosity'), 'MetricsVerbosity', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_7_httppacificbiosciences_comPacBioCollectionMetadata_xsdMetricsVerbosity', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 379, 7), )
+
+
+ MetricsVerbosity = property(__MetricsVerbosity.value, __MetricsVerbosity.set, None, 'BazIO MetricsVerbosity option; valid values are Minimal (default), High, and None')
+
+ _ElementMap.update({
+ __ResultsFolder.name() : __ResultsFolder,
+ __CollectionPathUri.name() : __CollectionPathUri,
+ __CopyFiles.name() : __CopyFiles,
+ __Readout.name() : __Readout,
+ __MetricsVerbosity.name() : __MetricsVerbosity
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_8 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 358, 8)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CollectionFileCopy uses Python identifier CollectionFileCopy
+ __CollectionFileCopy = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionFileCopy'), 'CollectionFileCopy', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_8_httppacificbiosciences_comPacBioCollectionMetadata_xsdCollectionFileCopy', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 360, 10), )
+
+
+ CollectionFileCopy = property(__CollectionFileCopy.value, __CollectionFileCopy.set, None, 'Defines the set of files to be copied to the CollectionPathUri. 1 or more. ')
+
+ _ElementMap.update({
+ __CollectionFileCopy.name() : __CollectionFileCopy
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_9 (pyxb.binding.basis.complexTypeDefinition):
+ """Container for the primary analysis related data. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 402, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}AutomationName uses Python identifier AutomationName
+ __AutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), 'AutomationName', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_9_httppacificbiosciences_comPacBioCollectionMetadata_xsdAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 404, 4), )
+
+
+ AutomationName = property(__AutomationName.value, __AutomationName.set, None, 'The secondary analysis protocol name specified in the sample sheet. Ignored by secondary. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}AutomationParameters uses Python identifier AutomationParameters
+ __AutomationParameters = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), 'AutomationParameters', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_9_httppacificbiosciences_comPacBioCollectionMetadata_xsdAutomationParameters', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 409, 4), )
+
+
+ AutomationParameters = property(__AutomationParameters.value, __AutomationParameters.set, None, 'The parameters for secondary analysis specified in the sample sheet. Ignored by secondary. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CellCountInJob uses Python identifier CellCountInJob
+ __CellCountInJob = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellCountInJob'), 'CellCountInJob', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_9_httppacificbiosciences_comPacBioCollectionMetadata_xsdCellCountInJob', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 423, 4), )
+
+
+ CellCountInJob = property(__CellCountInJob.value, __CellCountInJob.set, None, "The number of cells in this secondary analysis job, identified by the secondary analysis parameter 'JobName'. Supports automated secondary analysis. ")
+
+ _ElementMap.update({
+ __AutomationName.name() : __AutomationName,
+ __AutomationParameters.name() : __AutomationParameters,
+ __CellCountInJob.name() : __CellCountInJob
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_10 (pyxb.binding.basis.complexTypeDefinition):
+ """The parameters for secondary analysis specified in the sample sheet. Ignored by secondary. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 413, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}AutomationParameter uses Python identifier AutomationParameter
+ __AutomationParameter = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), 'AutomationParameter', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_10_httppacificbiosciences_comPacBioCollectionMetadata_xsdAutomationParameter', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 415, 7), )
+
+
+ AutomationParameter = property(__AutomationParameter.value, __AutomationParameter.set, None, 'One or more secondary analysis parameters, such as JobName, Workflow, etc..')
+
+ _ElementMap.update({
+ __AutomationParameter.name() : __AutomationParameter
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type SIMPLE
+class CTD_ANON_11 (pyxb.binding.basis.complexTypeDefinition):
+ """One custom, possibly non-unique, key-value pair. """
+ _TypeDefinition = pyxb.binding.datatypes.string
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_SIMPLE
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 441, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.string
+
+ # Attribute key uses Python identifier key
+ __key = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'key'), 'key', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_11_key', pyxb.binding.datatypes.string, required=True)
+ __key._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 444, 5)
+ __key._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 444, 5)
+
+ key = property(__key.value, __key.set, None, 'Key (attribute) and Value (element content). ')
+
+
+ # Attribute label uses Python identifier label
+ __label = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'label'), 'label', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_11_label', pyxb.binding.datatypes.string)
+ __label._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 449, 5)
+ __label._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 449, 5)
+
+ label = property(__label.value, __label.set, None, None)
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __key.name() : __key,
+ __label.name() : __label
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_12 (_ImportedBinding__pbbase.BaseEntityType):
+ """Container for the sample related data. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 242, 2)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}PlateId uses Python identifier PlateId
+ __PlateId = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'PlateId'), 'PlateId', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdPlateId', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 246, 6), )
+
+
+ PlateId = property(__PlateId.value, __PlateId.set, None, 'The ID or barcode of the sample plate. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}WellName uses Python identifier WellName
+ __WellName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WellName'), 'WellName', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdWellName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 251, 6), )
+
+
+ WellName = property(__WellName.value, __WellName.set, None, 'Identifies which well this sample came from (e.g., coordinate on a plate). ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Concentration uses Python identifier Concentration
+ __Concentration = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Concentration'), 'Concentration', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdConcentration', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 256, 6), )
+
+
+ Concentration = property(__Concentration.value, __Concentration.set, None, 'Sample input concentration. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SampleReuseEnabled uses Python identifier SampleReuseEnabled
+ __SampleReuseEnabled = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleReuseEnabled'), 'SampleReuseEnabled', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdSampleReuseEnabled', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 261, 6), )
+
+
+ SampleReuseEnabled = property(__SampleReuseEnabled.value, __SampleReuseEnabled.set, None, 'Whether or not complex reuse is enabled for this well. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}StageHotstartEnabled uses Python identifier StageHotstartEnabled
+ __StageHotstartEnabled = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'StageHotstartEnabled'), 'StageHotstartEnabled', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdStageHotstartEnabled', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 266, 6), )
+
+
+ StageHotstartEnabled = property(__StageHotstartEnabled.value, __StageHotstartEnabled.set, None, 'Whether or not hotstart at the stage is enabled for this well. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SizeSelectionEnabled uses Python identifier SizeSelectionEnabled
+ __SizeSelectionEnabled = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SizeSelectionEnabled'), 'SizeSelectionEnabled', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdSizeSelectionEnabled', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 271, 6), )
+
+
+ SizeSelectionEnabled = property(__SizeSelectionEnabled.value, __SizeSelectionEnabled.set, None, 'Whether or not size selection is enabled for this well. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}UseCount uses Python identifier UseCount
+ __UseCount = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'UseCount'), 'UseCount', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdUseCount', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 276, 6), )
+
+
+ UseCount = property(__UseCount.value, __UseCount.set, None, 'Count of usages for this batch of complex. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}DNAControlComplex uses Python identifier DNAControlComplex
+ __DNAControlComplex = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DNAControlComplex'), 'DNAControlComplex', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdDNAControlComplex', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 281, 6), )
+
+
+ DNAControlComplex = property(__DNAControlComplex.value, __DNAControlComplex.set, None, 'Indicating what kind (if any) control was used. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SampleBarcodeInfo uses Python identifier SampleBarcodeInfo
+ __SampleBarcodeInfo = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SampleBarcodeInfo'), 'SampleBarcodeInfo', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioCollectionMetadata_xsdSampleBarcodeInfo', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 286, 6), )
+
+
+ SampleBarcodeInfo = property(__SampleBarcodeInfo.value, __SampleBarcodeInfo.set, None, 'When utilizing DNA barcoding, store the list of smaple barcodes in this element.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSamplePointers uses Python identifier BioSamplePointers
+ __BioSamplePointers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbsample, 'BioSamplePointers'), 'BioSamplePointers', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_12_httppacificbiosciences_comPacBioSampleInfo_xsdBioSamplePointers', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 100, 1), )
+
+
+ BioSamplePointers = property(__BioSamplePointers.value, __BioSamplePointers.set, None, 'Back references to other BarcodedSampleType object UniqueIds which utilize this sample')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+ _ElementMap.update({
+ __PlateId.name() : __PlateId,
+ __WellName.name() : __WellName,
+ __Concentration.name() : __Concentration,
+ __SampleReuseEnabled.name() : __SampleReuseEnabled,
+ __StageHotstartEnabled.name() : __StageHotstartEnabled,
+ __SizeSelectionEnabled.name() : __SizeSelectionEnabled,
+ __UseCount.name() : __UseCount,
+ __DNAControlComplex.name() : __DNAControlComplex,
+ __SampleBarcodeInfo.name() : __SampleBarcodeInfo,
+ __BioSamplePointers.name() : __BioSamplePointers
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_13 (_ImportedBinding__pbbase.StrictEntityType):
+ """Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 34, 2)
+ _ElementMap = _ImportedBinding__pbbase.StrictEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.StrictEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.StrictEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}InstCtrlVer uses Python identifier InstCtrlVer
+ __InstCtrlVer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'InstCtrlVer'), 'InstCtrlVer', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdInstCtrlVer', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 38, 6), )
+
+
+ InstCtrlVer = property(__InstCtrlVer.value, __InstCtrlVer.set, None, 'Instrument control software version. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SigProcVer uses Python identifier SigProcVer
+ __SigProcVer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SigProcVer'), 'SigProcVer', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdSigProcVer', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 43, 6), )
+
+
+ SigProcVer = property(__SigProcVer.value, __SigProcVer.set, None, 'Signal processing software version. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Automation uses Python identifier Automation
+ __Automation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automation'), 'Automation', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdAutomation', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 65, 6), )
+
+
+ Automation = property(__Automation.value, __Automation.set, None, 'Defines the collection workflow (e.g., robotic movement, movie acquisition) for a particular cell. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CollectionNumber uses Python identifier CollectionNumber
+ __CollectionNumber = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CollectionNumber'), 'CollectionNumber', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdCollectionNumber', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 70, 6), )
+
+
+ CollectionNumber = property(__CollectionNumber.value, __CollectionNumber.set, None, 'Collection number for this plate well. Sample from one plate well or tube can be distributed to more than one cell. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CellIndex uses Python identifier CellIndex
+ __CellIndex = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellIndex'), 'CellIndex', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdCellIndex', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 75, 6), )
+
+
+ CellIndex = property(__CellIndex.value, __CellIndex.set, None, 'The zero-based index of this particular cell within the cell tray. Likely to be in the range of [0-3]')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SetNumber uses Python identifier SetNumber
+ __SetNumber = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SetNumber'), 'SetNumber', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdSetNumber', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 80, 6), )
+
+
+ SetNumber = property(__SetNumber.value, __SetNumber.set, None, 'Formerly known as the look number. 1 - N. Defaults to 1. 0 if the look is unknown. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}CellPac uses Python identifier CellPac
+ __CellPac = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellPac'), 'CellPac', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdCellPac', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 85, 6), )
+
+
+ CellPac = property(__CellPac.value, __CellPac.set, None, 'The SMRT cell packaging supply information. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}TemplatePrepKit uses Python identifier TemplatePrepKit
+ __TemplatePrepKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), 'TemplatePrepKit', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdTemplatePrepKit', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 90, 6), )
+
+
+ TemplatePrepKit = property(__TemplatePrepKit.value, __TemplatePrepKit.set, None, 'Defines the template (sample) prep kit used for this experiment. Can be used to get back to the primary and adapter used. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}BindingKit uses Python identifier BindingKit
+ __BindingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), 'BindingKit', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdBindingKit', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 95, 6), )
+
+
+ BindingKit = property(__BindingKit.value, __BindingKit.set, None, 'The binding kit supply information. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}SequencingKitPlate uses Python identifier SequencingKitPlate
+ __SequencingKitPlate = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitPlate'), 'SequencingKitPlate', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdSequencingKitPlate', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 100, 6), )
+
+
+ SequencingKitPlate = property(__SequencingKitPlate.value, __SequencingKitPlate.set, None, 'The sequencing kit supply information. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}RunDetails uses Python identifier RunDetails
+ __RunDetails = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'RunDetails'), 'RunDetails', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdRunDetails', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 146, 1), )
+
+
+ RunDetails = property(__RunDetails.value, __RunDetails.set, None, 'Information related to an instrument run. A run can contain multiple chips, wells, and movies. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Movie uses Python identifier Movie
+ __Movie = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Movie'), 'Movie', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdMovie', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 185, 1), )
+
+
+ Movie = property(__Movie.value, __Movie.set, None, 'A movie corresponds to one acquisition for a chip, one set (look) and one strobe. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}ExpirationData uses Python identifier ExpirationData
+ __ExpirationData = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData'), 'ExpirationData', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdExpirationData', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 209, 1), )
+
+
+ ExpirationData = property(__ExpirationData.value, __ExpirationData.set, None, 'Container for the expired consumable data. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}WellSample uses Python identifier WellSample
+ __WellSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'WellSample'), 'WellSample', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdWellSample', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 238, 1), )
+
+
+ WellSample = property(__WellSample.value, __WellSample.set, None, 'Container for the sample related data. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Primary uses Python identifier Primary
+ __Primary = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Primary'), 'Primary', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdPrimary', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 304, 1), )
+
+
+ Primary = property(__Primary.value, __Primary.set, None, 'Container for the primary analysis related data. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}Secondary uses Python identifier Secondary
+ __Secondary = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Secondary'), 'Secondary', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdSecondary', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 398, 1), )
+
+
+ Secondary = property(__Secondary.value, __Secondary.set, None, 'Container for the primary analysis related data. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioCollectionMetadata.xsd}UserDefinedFields uses Python identifier UserDefinedFields
+ __UserDefinedFields = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields'), 'UserDefinedFields', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_httppacificbiosciences_comPacBioCollectionMetadata_xsdUserDefinedFields', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 432, 1), )
+
+
+ UserDefinedFields = property(__UserDefinedFields.value, __UserDefinedFields.set, None, 'A set of key-value pairs specified by a user via the run input mechanism. Note that uniqueness of keys is not enforced here and so may contain duplicate keys. ')
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute Context uses Python identifier Context
+ __Context = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Context'), 'Context', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_Context', pyxb.binding.datatypes.string)
+ __Context._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 126, 5)
+ __Context._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 126, 5)
+
+ Context = property(__Context.value, __Context.set, None, 'Replace with TimeStampedName')
+
+
+ # Attribute Status uses Python identifier Status
+ __Status = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Status'), 'Status', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_Status', _ImportedBinding__pbbase.SupportedAcquisitionStates)
+ __Status._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 131, 5)
+ __Status._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 131, 5)
+
+ Status = property(__Status.value, __Status.set, None, None)
+
+
+ # Attribute InstrumentId uses Python identifier InstrumentId
+ __InstrumentId = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentId'), 'InstrumentId', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_InstrumentId', pyxb.binding.datatypes.string)
+ __InstrumentId._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 132, 5)
+ __InstrumentId._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 132, 5)
+
+ InstrumentId = property(__InstrumentId.value, __InstrumentId.set, None, 'World unique id assigned by PacBio. ')
+
+
+ # Attribute InstrumentName uses Python identifier InstrumentName
+ __InstrumentName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InstrumentName'), 'InstrumentName', '__httppacificbiosciences_comPacBioCollectionMetadata_xsd_CTD_ANON_13_InstrumentName', pyxb.binding.datatypes.string)
+ __InstrumentName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 137, 5)
+ __InstrumentName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 137, 5)
+
+ InstrumentName = property(__InstrumentName.value, __InstrumentName.set, None, 'Friendly name assigned by customer')
+
+ _ElementMap.update({
+ __InstCtrlVer.name() : __InstCtrlVer,
+ __SigProcVer.name() : __SigProcVer,
+ __Automation.name() : __Automation,
+ __CollectionNumber.name() : __CollectionNumber,
+ __CellIndex.name() : __CellIndex,
+ __SetNumber.name() : __SetNumber,
+ __CellPac.name() : __CellPac,
+ __TemplatePrepKit.name() : __TemplatePrepKit,
+ __BindingKit.name() : __BindingKit,
+ __SequencingKitPlate.name() : __SequencingKitPlate,
+ __RunDetails.name() : __RunDetails,
+ __Movie.name() : __Movie,
+ __ExpirationData.name() : __ExpirationData,
+ __WellSample.name() : __WellSample,
+ __Primary.name() : __Primary,
+ __Secondary.name() : __Secondary,
+ __UserDefinedFields.name() : __UserDefinedFields
+ })
+ _AttributeMap.update({
+ __Context.name() : __Context,
+ __Status.name() : __Status,
+ __InstrumentId.name() : __InstrumentId,
+ __InstrumentName.name() : __InstrumentName
+ })
+
+
+
+PacBioCollectionMetadata = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioCollectionMetadata'), CTD_ANON, documentation='Root element of a standalone CollectionMetadata file.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 10, 1))
+Namespace.addCategoryObject('elementBinding', PacBioCollectionMetadata.name().localName(), PacBioCollectionMetadata)
+
+Collections = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Collections'), CTD_ANON_, documentation='A set of acquisition definitions', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 20, 1))
+Namespace.addCategoryObject('elementBinding', Collections.name().localName(), Collections)
+
+RunDetails = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunDetails'), CTD_ANON_2, documentation='Information related to an instrument run. A run can contain multiple chips, wells, and movies. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 146, 1))
+Namespace.addCategoryObject('elementBinding', RunDetails.name().localName(), RunDetails)
+
+Movie = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Movie'), CTD_ANON_3, documentation='A movie corresponds to one acquisition for a chip, one set (look) and one strobe. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 185, 1))
+Namespace.addCategoryObject('elementBinding', Movie.name().localName(), Movie)
+
+ExpirationData = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData'), CTD_ANON_4, documentation='Container for the expired consumable data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 209, 1))
+Namespace.addCategoryObject('elementBinding', ExpirationData.name().localName(), ExpirationData)
+
+Primary = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Primary'), CTD_ANON_5, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 304, 1))
+Namespace.addCategoryObject('elementBinding', Primary.name().localName(), Primary)
+
+Secondary = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Secondary'), CTD_ANON_9, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 398, 1))
+Namespace.addCategoryObject('elementBinding', Secondary.name().localName(), Secondary)
+
+UserDefinedFields = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields'), _ImportedBinding__pbbase.UserDefinedFieldsType, documentation='A set of key-value pairs specified by a user via the run input mechanism. Note that uniqueness of keys is not enforced here and so may contain duplicate keys. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 432, 1))
+Namespace.addCategoryObject('elementBinding', UserDefinedFields.name().localName(), UserDefinedFields)
+
+KeyValue = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'KeyValue'), CTD_ANON_11, documentation='One custom, possibly non-unique, key-value pair. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 437, 1))
+Namespace.addCategoryObject('elementBinding', KeyValue.name().localName(), KeyValue)
+
+WellSample = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WellSample'), CTD_ANON_12, documentation='Container for the sample related data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 238, 1))
+Namespace.addCategoryObject('elementBinding', WellSample.name().localName(), WellSample)
+
+CollectionMetadata = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), CTD_ANON_13, documentation='Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ', location=pyxb.utils.utility.Location(' [...]
+Namespace.addCategoryObject('elementBinding', CollectionMetadata.name().localName(), CollectionMetadata)
+
+
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), CTD_ANON_13, scope=CTD_ANON, documentation='Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ', location=pyxb.utils.ut [...]
+
+def _BuildAutomaton ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton
+ del _BuildAutomaton
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 16, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+
+
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata'), CTD_ANON_13, scope=CTD_ANON_, documentation='Root-level element for the metadata. The purpose of which is to contain pertinent instrument information related to the conditions present during a movie acquisition. It also serves to provide key pieces of information for integration with primary and secondary analysis. This file is associated with 1 movie. ', location=pyxb.utils. [...]
+
+def _BuildAutomaton_ ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_
+ del _BuildAutomaton_
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionMetadata')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 26, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_._Automaton = _BuildAutomaton_()
+
+
+
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunId'), pyxb.binding.datatypes.string, scope=CTD_ANON_2, documentation='A unique identifier for this run. Format is r[sid]_[iname]_[ts]. Where [id] is a system generated id and [iname] is the instrument name and [ts] is a timestamp YYMMDD Example: r000123_00117_100713 ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 152, 4)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Name'), pyxb.binding.datatypes.string, scope=CTD_ANON_2, documentation='Assigned name for a run, which consists of multiple wells. There is no constraint on the uniqueness of this data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 157, 4)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CreatedBy'), pyxb.binding.datatypes.string, scope=CTD_ANON_2, documentation='Who created the run. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 162, 4)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WhenCreated'), pyxb.binding.datatypes.dateTime, scope=CTD_ANON_2, documentation='Date and time of when the overall run was created in the system. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 167, 4)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'StartedBy'), pyxb.binding.datatypes.string, scope=CTD_ANON_2, documentation='Who started the run. Could be different from who created it. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 172, 4)))
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), pyxb.binding.datatypes.dateTime, scope=CTD_ANON_2, documentation='Date and time of when the overall run was started. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 177, 4)))
+
+def _BuildAutomaton_2 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 157, 4))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 162, 4))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 167, 4))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 172, 4))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 177, 4))
+ counters.add(cc_4)
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RunId')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 152, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Name')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 157, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CreatedBy')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 162, 4))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WhenCreated')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 167, 4))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'StartedBy')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 172, 4))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 177, 4))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ st_5._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_2._Automaton = _BuildAutomaton_2()
+
+
+
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted'), pyxb.binding.datatypes.dateTime, scope=CTD_ANON_3, documentation='Date and time of when this movie acquisition started. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 191, 4)))
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DurationInSec'), pyxb.binding.datatypes.int, scope=CTD_ANON_3, documentation='The actual length of the movie acquisition (in seconds), irrespective of the movie duration specified by an automation parameter. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 196, 4), unicode_default='0'))
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Number'), pyxb.binding.datatypes.int, scope=CTD_ANON_3, documentation="The number of this movie within the set (i.e., look). This is unique when combined with the 'SetNumber'. ", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 201, 4), unicode_default='0'))
+
+def _BuildAutomaton_3 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WhenStarted')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 191, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DurationInSec')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 196, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Number')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 201, 4))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_3()
+
+
+
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'EightPacPastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_4, documentation='Number of days past expiration the eight pac was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 215, 4)))
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKitPastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_4, documentation='Number of days past expiration the reagent kit was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 220, 4)))
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube0PastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_4, documentation='Number of days past expiration the reagent tube 0 was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 225, 4)))
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube1PastExpiration'), pyxb.binding.datatypes.int, scope=CTD_ANON_4, documentation='Number of days past expiration the reagent tube 1 was (if at all). ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 230, 4)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'EightPacPastExpiration')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 215, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentKitPastExpiration')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 220, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube0PastExpiration')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 225, 4))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube1PastExpiration')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 230, 4))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ st_3._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_4._Automaton = _BuildAutomaton_4()
+
+
+
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleTrace'), CTD_ANON_6, scope=CTD_ANON_5, documentation='Tag to indicate that the trace file will be sampled. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 310, 4)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), pyxb.binding.datatypes.string, scope=CTD_ANON_5, documentation='Name of primary analysis protocol. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 329, 4)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ConfigFileName'), pyxb.binding.datatypes.string, scope=CTD_ANON_5, documentation='Name of primary analysis config file. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 334, 4)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingCondition'), pyxb.binding.datatypes.string, scope=CTD_ANON_5, documentation='A sequencing condition tag to be used by primary analysis, e.g., to select basecaller calibration or training parameters. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 339, 4)))
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'OutputOptions'), CTD_ANON_7, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 344, 4)))
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 310, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleTrace')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 310, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 329, 4))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ConfigFileName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 334, 4))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingCondition')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 339, 4))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'OutputOptions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 344, 4))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_5._Automaton = _BuildAutomaton_5()
+
+
+
+
+CTD_ANON_6._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TraceSamplingFactor'), pyxb.binding.datatypes.float, scope=CTD_ANON_6, documentation='Percentage of traces to sample. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 316, 7)))
+
+CTD_ANON_6._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'FullPulseFile'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_6, documentation='Whether full or sampled pulse file is transferred if requested. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 321, 7)))
+
+def _BuildAutomaton_6 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_6
+ del _BuildAutomaton_6
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TraceSamplingFactor')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 316, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_6._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'FullPulseFile')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 321, 7))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_6._Automaton = _BuildAutomaton_6()
+
+
+
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ResultsFolder'), pyxb.binding.datatypes.string, scope=CTD_ANON_7, documentation="NOTE: not for customers. A sub-folder under the CollectionPath created by Primary Analysis. This is a field that will be updated by the primary analysis pipeline. The default (as created by homer) should be set to 'Reports_Sms' for now. Consumers of the data should be aware that they will find collection metadata (and [...]
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionPathUri'), pyxb.binding.datatypes.anyURI, scope=CTD_ANON_7, documentation='User-specified location of where the results should be copied after an analysis has been completed. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 352, 7)))
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CopyFiles'), CTD_ANON_8, scope=CTD_ANON_7, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 357, 7)))
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Readout'), STD_ANON, scope=CTD_ANON_7, documentation='BazIO Readout option; valid values are Bases (default) and Pulses', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 368, 7), unicode_default='Bases'))
+
+CTD_ANON_7._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'MetricsVerbosity'), STD_ANON_, scope=CTD_ANON_7, documentation='BazIO MetricsVerbosity option; valid values are Minimal (default), High, and None', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 379, 7), unicode_default='Minimal'))
+
+def _BuildAutomaton_7 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_7
+ del _BuildAutomaton_7
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ResultsFolder')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 347, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionPathUri')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 352, 7))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CopyFiles')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 357, 7))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Readout')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 368, 7))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_7._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'MetricsVerbosity')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 379, 7))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_7._Automaton = _BuildAutomaton_7()
+
+
+
+
+CTD_ANON_8._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionFileCopy'), PapOutputFile, scope=CTD_ANON_8, documentation='Defines the set of files to be copied to the CollectionPathUri. 1 or more. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 360, 10)))
+
+def _BuildAutomaton_8 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_8
+ del _BuildAutomaton_8
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_8._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionFileCopy')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 360, 10))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_8._Automaton = _BuildAutomaton_8()
+
+
+
+
+CTD_ANON_9._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationName'), pyxb.binding.datatypes.string, scope=CTD_ANON_9, documentation='The secondary analysis protocol name specified in the sample sheet. Ignored by secondary. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 404, 4)))
+
+CTD_ANON_9._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters'), CTD_ANON_10, scope=CTD_ANON_9, documentation='The parameters for secondary analysis specified in the sample sheet. Ignored by secondary. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 409, 4)))
+
+CTD_ANON_9._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellCountInJob'), pyxb.binding.datatypes.int, scope=CTD_ANON_9, documentation="The number of cells in this secondary analysis job, identified by the secondary analysis parameter 'JobName'. Supports automated secondary analysis. ", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 423, 4)))
+
+def _BuildAutomaton_9 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_9
+ del _BuildAutomaton_9
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 409, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 404, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameters')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 409, 4))
+ st_1 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_9._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellCountInJob')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 423, 4))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ ]))
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_9._Automaton = _BuildAutomaton_9()
+
+
+
+
+CTD_ANON_10._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter'), _ImportedBinding__pbbase.DataEntityType, scope=CTD_ANON_10, documentation='One or more secondary analysis parameters, such as JobName, Workflow, etc..', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 415, 7)))
+
+def _BuildAutomaton_10 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_10
+ del _BuildAutomaton_10
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 415, 7))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_10._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'AutomationParameter')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 415, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_10._Automaton = _BuildAutomaton_10()
+
+
+
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PlateId'), pyxb.binding.datatypes.string, scope=CTD_ANON_12, documentation='The ID or barcode of the sample plate. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 246, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WellName'), pyxb.binding.datatypes.string, scope=CTD_ANON_12, documentation='Identifies which well this sample came from (e.g., coordinate on a plate). ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 251, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Concentration'), pyxb.binding.datatypes.double, scope=CTD_ANON_12, documentation='Sample input concentration. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 256, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleReuseEnabled'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_12, documentation='Whether or not complex reuse is enabled for this well. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 261, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'StageHotstartEnabled'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_12, documentation='Whether or not hotstart at the stage is enabled for this well. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 266, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SizeSelectionEnabled'), pyxb.binding.datatypes.boolean, scope=CTD_ANON_12, documentation='Whether or not size selection is enabled for this well. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 271, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'UseCount'), pyxb.binding.datatypes.int, scope=CTD_ANON_12, documentation='Count of usages for this batch of complex. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 276, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DNAControlComplex'), pyxb.binding.datatypes.string, scope=CTD_ANON_12, documentation='Indicating what kind (if any) control was used. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 281, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SampleBarcodeInfo'), _ImportedBinding__pbbase.DataEntityType, scope=CTD_ANON_12, documentation='When utilizing DNA barcoding, store the list of smaple barcodes in this element.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 286, 6)))
+
+CTD_ANON_12._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbsample, 'BioSamplePointers'), _ImportedBinding__pbsample.CTD_ANON_, scope=CTD_ANON_12, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 100, 1)))
+
+def _BuildAutomaton_11 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_11
+ del _BuildAutomaton_11
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 246, 6))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 281, 6))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 286, 6))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 291, 6))
+ counters.add(cc_4)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'PlateId')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 246, 6))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WellName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 251, 6))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Concentration')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 256, 6))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleReuseEnabled')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 261, 6))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'StageHotstartEnabled')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 266, 6))
+ st_5 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SizeSelectionEnabled')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 271, 6))
+ st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'UseCount')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 276, 6))
+ st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_7)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DNAControlComplex')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 281, 6))
+ st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_8)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SampleBarcodeInfo')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 286, 6))
+ st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_9)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_12._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbsample, 'BioSamplePointers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 291, 6))
+ st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_10)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ ]))
+ st_6._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ ]))
+ transitions.append(fac.Transition(st_9, [
+ ]))
+ transitions.append(fac.Transition(st_10, [
+ ]))
+ st_7._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_8._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_9._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ st_10._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_12._Automaton = _BuildAutomaton_11()
+
+
+
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'InstCtrlVer'), pyxb.binding.datatypes.string, scope=CTD_ANON_13, documentation='Instrument control software version. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 38, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SigProcVer'), pyxb.binding.datatypes.string, scope=CTD_ANON_13, documentation='Signal processing software version. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 43, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automation'), _ImportedBinding__pbbase.AutomationType, scope=CTD_ANON_13, documentation='Defines the collection workflow (e.g., robotic movement, movie acquisition) for a particular cell. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 65, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CollectionNumber'), pyxb.binding.datatypes.int, scope=CTD_ANON_13, documentation='Collection number for this plate well. Sample from one plate well or tube can be distributed to more than one cell. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 70, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellIndex'), pyxb.binding.datatypes.int, scope=CTD_ANON_13, documentation='The zero-based index of this particular cell within the cell tray. Likely to be in the range of [0-3]', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 75, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SetNumber'), pyxb.binding.datatypes.unsignedShort, scope=CTD_ANON_13, documentation='Formerly known as the look number. 1 - N. Defaults to 1. 0 if the look is unknown. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 80, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPac'), _ImportedBinding__pbbase.SupplyKitCellPack, scope=CTD_ANON_13, documentation='The SMRT cell packaging supply information. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 85, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), _ImportedBinding__pbbase.SupplyKitTemplate, scope=CTD_ANON_13, documentation='Defines the template (sample) prep kit used for this experiment. Can be used to get back to the primary and adapter used. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 90, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), _ImportedBinding__pbbase.SupplyKitBinding, scope=CTD_ANON_13, documentation='The binding kit supply information. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 95, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitPlate'), _ImportedBinding__pbrk.SupplyKitSequencing, scope=CTD_ANON_13, documentation='The sequencing kit supply information. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 100, 6)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'RunDetails'), CTD_ANON_2, scope=CTD_ANON_13, documentation='Information related to an instrument run. A run can contain multiple chips, wells, and movies. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 146, 1)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Movie'), CTD_ANON_3, scope=CTD_ANON_13, documentation='A movie corresponds to one acquisition for a chip, one set (look) and one strobe. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 185, 1)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData'), CTD_ANON_4, scope=CTD_ANON_13, documentation='Container for the expired consumable data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 209, 1)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'WellSample'), CTD_ANON_12, scope=CTD_ANON_13, documentation='Container for the sample related data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 238, 1)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Primary'), CTD_ANON_5, scope=CTD_ANON_13, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 304, 1)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Secondary'), CTD_ANON_9, scope=CTD_ANON_13, documentation='Container for the primary analysis related data. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 398, 1)))
+
+CTD_ANON_13._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields'), _ImportedBinding__pbbase.UserDefinedFieldsType, scope=CTD_ANON_13, documentation='A set of key-value pairs specified by a user via the run input mechanism. Note that uniqueness of keys is not enforced here and so may contain duplicate keys. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 432, 1)))
+
+def _BuildAutomaton_12 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_12
+ del _BuildAutomaton_12
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 38, 6))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 43, 6))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 48, 6))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 53, 6))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 70, 6))
+ counters.add(cc_5)
+ cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 75, 6))
+ counters.add(cc_6)
+ cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 80, 6))
+ counters.add(cc_7)
+ cc_8 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 85, 6))
+ counters.add(cc_8)
+ cc_9 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 90, 6))
+ counters.add(cc_9)
+ cc_10 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 95, 6))
+ counters.add(cc_10)
+ cc_11 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 100, 6))
+ counters.add(cc_11)
+ cc_12 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 105, 6))
+ counters.add(cc_12)
+ cc_13 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 110, 6))
+ counters.add(cc_13)
+ cc_14 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 115, 6))
+ counters.add(cc_14)
+ cc_15 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 120, 6))
+ counters.add(cc_15)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'InstCtrlVer')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 38, 6))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SigProcVer')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 43, 6))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'RunDetails')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 48, 6))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Movie')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 53, 6))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'WellSample')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 58, 6))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 65, 6))
+ st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CollectionNumber')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 70, 6))
+ st_7 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_7)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_6, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellIndex')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 75, 6))
+ st_8 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_8)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_7, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SetNumber')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 80, 6))
+ st_9 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_9)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_8, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellPac')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 85, 6))
+ st_10 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_10)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_9, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 90, 6))
+ st_11 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_11)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_10, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BindingKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 95, 6))
+ st_12 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_12)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_11, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitPlate')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 100, 6))
+ st_13 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_13)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_12, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Primary')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 105, 6))
+ st_14 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_14)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_13, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Secondary')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 110, 6))
+ st_15 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_15)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_14, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'UserDefinedFields')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 115, 6))
+ st_16 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_16)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_15, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_13._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ExpirationData')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioCollectionMetadata.xsd', 120, 6))
+ st_17 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_17)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ ]))
+ transitions.append(fac.Transition(st_8, [
+ ]))
+ transitions.append(fac.Transition(st_9, [
+ ]))
+ transitions.append(fac.Transition(st_10, [
+ ]))
+ transitions.append(fac.Transition(st_11, [
+ ]))
+ transitions.append(fac.Transition(st_12, [
+ ]))
+ transitions.append(fac.Transition(st_13, [
+ ]))
+ transitions.append(fac.Transition(st_14, [
+ ]))
+ transitions.append(fac.Transition(st_15, [
+ ]))
+ transitions.append(fac.Transition(st_16, [
+ ]))
+ transitions.append(fac.Transition(st_17, [
+ ]))
+ st_6._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_11, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_12, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ st_7._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_6, True) ]))
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_11, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_12, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ st_8._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_9, [
+ fac.UpdateInstruction(cc_7, True) ]))
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_11, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_12, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ st_9._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_10, [
+ fac.UpdateInstruction(cc_8, True) ]))
+ transitions.append(fac.Transition(st_11, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ transitions.append(fac.Transition(st_12, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_8, False) ]))
+ st_10._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_11, [
+ fac.UpdateInstruction(cc_9, True) ]))
+ transitions.append(fac.Transition(st_12, [
+ fac.UpdateInstruction(cc_9, False) ]))
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_9, False) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_9, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_9, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_9, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_9, False) ]))
+ st_11._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_12, [
+ fac.UpdateInstruction(cc_10, True) ]))
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_10, False) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_10, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_10, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_10, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_10, False) ]))
+ st_12._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_13, [
+ fac.UpdateInstruction(cc_11, True) ]))
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_11, False) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_11, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_11, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_11, False) ]))
+ st_13._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_14, [
+ fac.UpdateInstruction(cc_12, True) ]))
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_12, False) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_12, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_12, False) ]))
+ st_14._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_15, [
+ fac.UpdateInstruction(cc_13, True) ]))
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_13, False) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_13, False) ]))
+ st_15._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_16, [
+ fac.UpdateInstruction(cc_14, True) ]))
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_14, False) ]))
+ st_16._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_17, [
+ fac.UpdateInstruction(cc_15, True) ]))
+ st_17._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_13._Automaton = _BuildAutomaton_12()
+
diff --git a/pbcore/io/dataset/_pbpn.py b/pbcore/io/dataset/_pbpn.py
new file mode 100755
index 0000000..00d0fbb
--- /dev/null
+++ b/pbcore/io/dataset/_pbpn.py
@@ -0,0 +1,507 @@
+# ./_pbpn.py
+# -*- coding: utf-8 -*-
+# PyXB bindings for NM:20ebb32585e5dee1a245d71277cd3ba8c5a400aa
+# Generated 2015-08-04 20:41:05.071486 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Namespace http://pacificbiosciences.com/PacBioPartNumbers.xsd [xmlns:pbpn]
+
+from __future__ import unicode_literals
+import pyxb
+import pyxb.binding
+import pyxb.binding.saxer
+import io
+import pyxb.utils.utility
+import pyxb.utils.domutils
+import sys
+import pyxb.utils.six as _six
+
+# Unique identifier for bindings created at the same time
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
+
+# Version of PyXB used to generate the bindings
+_PyXBVersion = '1.2.4'
+# Generated bindings are not compatible across PyXB versions
+if pyxb.__version__ != _PyXBVersion:
+ raise pyxb.PyXBVersionError(_PyXBVersion)
+
+# Import bindings for namespaces imported into schema
+import _pbbase as _ImportedBinding__pbbase
+import pyxb.binding.datatypes
+import _pbrk as _ImportedBinding__pbrk
+
+# NOTE: All namespace declarations are reserved within the binding
+Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioPartNumbers.xsd', create_if_missing=True)
+Namespace.configureCategories(['typeBinding', 'elementBinding'])
+
+def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
+ """Parse the given XML and use the document element to create a
+ Python instance.
+
+ @param xml_text An XML document. This should be data (Python 2
+ str or Python 3 bytes), or a text (Python 2 unicode or Python 3
+ str) in the L{pyxb._InputEncoding} encoding.
+
+ @keyword default_namespace The L{pyxb.Namespace} instance to use as the
+ default namespace where there is no default namespace in scope.
+ If unspecified or C{None}, the namespace of the module containing
+ this function will be used.
+
+ @keyword location_base: An object to be recorded as the base of all
+ L{pyxb.utils.utility.Location} instances associated with events and
+ objects handled by the parser. You might pass the URI from which
+ the document was obtained.
+ """
+
+ if pyxb.XMLStyle_saxer != pyxb._XMLStyle:
+ dom = pyxb.utils.domutils.StringToDOM(xml_text)
+ return CreateFromDOM(dom.documentElement, default_namespace=default_namespace)
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ saxer = pyxb.binding.saxer.make_parser(fallback_namespace=default_namespace, location_base=location_base)
+ handler = saxer.getContentHandler()
+ xmld = xml_text
+ if isinstance(xmld, _six.text_type):
+ xmld = xmld.encode(pyxb._InputEncoding)
+ saxer.parse(io.BytesIO(xmld))
+ instance = handler.rootObject()
+ return instance
+
+def CreateFromDOM (node, default_namespace=None):
+ """Create a Python instance from the given DOM node.
+ The node tag must correspond to an element declaration in this module.
+
+ @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}."""
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ return pyxb.binding.basis.element.AnyCreateFromDOM(node, default_namespace)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
+ """The root element of the Part Numbers """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 12, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}SequencingKits uses Python identifier SequencingKits
+ __SequencingKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKits'), 'SequencingKits', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_httppacificbiosciences_comPacBioPartNumbers_xsdSequencingKits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 14, 4), )
+
+
+ SequencingKits = property(__SequencingKits.value, __SequencingKits.set, None, 'List the sequencing kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}BindingKits uses Python identifier BindingKits
+ __BindingKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BindingKits'), 'BindingKits', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_httppacificbiosciences_comPacBioPartNumbers_xsdBindingKits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 24, 4), )
+
+
+ BindingKits = property(__BindingKits.value, __BindingKits.set, None, 'List the binding kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}TemplatePrepKits uses Python identifier TemplatePrepKits
+ __TemplatePrepKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKits'), 'TemplatePrepKits', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_httppacificbiosciences_comPacBioPartNumbers_xsdTemplatePrepKits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 34, 4), )
+
+
+ TemplatePrepKits = property(__TemplatePrepKits.value, __TemplatePrepKits.set, None, 'List the sample prep kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}ControlKits uses Python identifier ControlKits
+ __ControlKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlKits'), 'ControlKits', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_httppacificbiosciences_comPacBioPartNumbers_xsdControlKits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 44, 4), )
+
+
+ ControlKits = property(__ControlKits.value, __ControlKits.set, None, 'List the DNA control complex part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
+
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}CellPackKits uses Python identifier CellPackKits
+ __CellPackKits = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellPackKits'), 'CellPackKits', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_httppacificbiosciences_comPacBioPartNumbers_xsdCellPackKits', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 54, 4), )
+
+
+ CellPackKits = property(__CellPackKits.value, __CellPackKits.set, None, 'List the cell tray part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.')
+
+ _ElementMap.update({
+ __SequencingKits.name() : __SequencingKits,
+ __BindingKits.name() : __BindingKits,
+ __TemplatePrepKits.name() : __TemplatePrepKits,
+ __ControlKits.name() : __ControlKits,
+ __CellPackKits.name() : __CellPackKits
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
+ """List the sequencing kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 18, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}SequencingKit uses Python identifier SequencingKit
+ __SequencingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), 'SequencingKit', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON__httppacificbiosciences_comPacBioPartNumbers_xsdSequencingKit', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 67, 1), )
+
+
+ SequencingKit = property(__SequencingKit.value, __SequencingKit.set, None, None)
+
+ _ElementMap.update({
+ __SequencingKit.name() : __SequencingKit
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
+ """List the binding kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 28, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}BindingKit uses Python identifier BindingKit
+ __BindingKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), 'BindingKit', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioPartNumbers_xsdBindingKit', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 68, 1), )
+
+
+ BindingKit = property(__BindingKit.value, __BindingKit.set, None, None)
+
+ _ElementMap.update({
+ __BindingKit.name() : __BindingKit
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
+ """List the sample prep kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 38, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}TemplatePrepKit uses Python identifier TemplatePrepKit
+ __TemplatePrepKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), 'TemplatePrepKit', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioPartNumbers_xsdTemplatePrepKit', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 69, 1), )
+
+
+ TemplatePrepKit = property(__TemplatePrepKit.value, __TemplatePrepKit.set, None, None)
+
+ _ElementMap.update({
+ __TemplatePrepKit.name() : __TemplatePrepKit
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
+ """List the DNA control complex part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 48, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}ControlKit uses Python identifier ControlKit
+ __ControlKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ControlKit'), 'ControlKit', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioPartNumbers_xsdControlKit', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 70, 1), )
+
+
+ ControlKit = property(__ControlKit.value, __ControlKit.set, None, None)
+
+ _ElementMap.update({
+ __ControlKit.name() : __ControlKit
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_5 (pyxb.binding.basis.complexTypeDefinition):
+ """List the cell tray part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 58, 5)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioPartNumbers.xsd}CellPackKit uses Python identifier CellPackKit
+ __CellPackKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit'), 'CellPackKit', '__httppacificbiosciences_comPacBioPartNumbers_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioPartNumbers_xsdCellPackKit', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 71, 1), )
+
+
+ CellPackKit = property(__CellPackKit.value, __CellPackKit.set, None, None)
+
+ _ElementMap.update({
+ __CellPackKit.name() : __CellPackKit
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+PacBioPartNumbers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioPartNumbers'), CTD_ANON, documentation='The root element of the Part Numbers ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 8, 1))
+Namespace.addCategoryObject('elementBinding', PacBioPartNumbers.name().localName(), PacBioPartNumbers)
+
+SequencingKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), _ImportedBinding__pbrk.SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 67, 1))
+Namespace.addCategoryObject('elementBinding', SequencingKit.name().localName(), SequencingKit)
+
+BindingKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), _ImportedBinding__pbbase.SupplyKitBinding, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 68, 1))
+Namespace.addCategoryObject('elementBinding', BindingKit.name().localName(), BindingKit)
+
+TemplatePrepKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), _ImportedBinding__pbbase.SupplyKitTemplate, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 69, 1))
+Namespace.addCategoryObject('elementBinding', TemplatePrepKit.name().localName(), TemplatePrepKit)
+
+ControlKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlKit'), _ImportedBinding__pbbase.SupplyKitControl, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 70, 1))
+Namespace.addCategoryObject('elementBinding', ControlKit.name().localName(), ControlKit)
+
+CellPackKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit'), _ImportedBinding__pbbase.SupplyKitCellPack, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 71, 1))
+Namespace.addCategoryObject('elementBinding', CellPackKit.name().localName(), CellPackKit)
+
+
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKits'), CTD_ANON_, scope=CTD_ANON, documentation='List the sequencing kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 14, 4)))
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKits'), CTD_ANON_2, scope=CTD_ANON, documentation='List the binding kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 24, 4)))
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKits'), CTD_ANON_3, scope=CTD_ANON, documentation='List the sample prep kit part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 34, 4)))
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlKits'), CTD_ANON_4, scope=CTD_ANON, documentation='List the DNA control complex part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 44, 4)))
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPackKits'), CTD_ANON_5, scope=CTD_ANON, documentation='List the cell tray part numbers. A list of incompatible part numbers and automations is available to specify in the PartNumber subtype.', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 54, 4)))
+
+def _BuildAutomaton ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton
+ del _BuildAutomaton
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 14, 4))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 24, 4))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 34, 4))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 44, 4))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 54, 4))
+ counters.add(cc_4)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 14, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BindingKits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 24, 4))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 34, 4))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlKits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 44, 4))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellPackKits')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 54, 4))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+
+
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit'), _ImportedBinding__pbrk.SupplyKitSequencing, scope=CTD_ANON_, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 67, 1)))
+
+def _BuildAutomaton_ ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_
+ del _BuildAutomaton_
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 20, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_._Automaton = _BuildAutomaton_()
+
+
+
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BindingKit'), _ImportedBinding__pbbase.SupplyKitBinding, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 68, 1)))
+
+def _BuildAutomaton_2 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BindingKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 30, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_2._Automaton = _BuildAutomaton_2()
+
+
+
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit'), _ImportedBinding__pbbase.SupplyKitTemplate, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 69, 1)))
+
+def _BuildAutomaton_3 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'TemplatePrepKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 40, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_3()
+
+
+
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ControlKit'), _ImportedBinding__pbbase.SupplyKitControl, scope=CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 70, 1)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ControlKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 50, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_4._Automaton = _BuildAutomaton_4()
+
+
+
+
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit'), _ImportedBinding__pbbase.SupplyKitCellPack, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 71, 1)))
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CellPackKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioPartNumbers.xsd', 60, 7))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_5._Automaton = _BuildAutomaton_5()
+
diff --git a/pbcore/io/dataset/_pbrk.py b/pbcore/io/dataset/_pbrk.py
new file mode 100755
index 0000000..763e3f9
--- /dev/null
+++ b/pbcore/io/dataset/_pbrk.py
@@ -0,0 +1,1218 @@
+# ./_pbrk.py
+# -*- coding: utf-8 -*-
+# PyXB bindings for NM:82fd17ff8c81a0cc423cbd13a9167bcda5f96419
+# Generated 2015-08-04 20:41:05.066443 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Namespace http://pacificbiosciences.com/PacBioReagentKit.xsd [xmlns:pbrk]
+
+from __future__ import unicode_literals
+import pyxb
+import pyxb.binding
+import pyxb.binding.saxer
+import io
+import pyxb.utils.utility
+import pyxb.utils.domutils
+import sys
+import pyxb.utils.six as _six
+
+# Unique identifier for bindings created at the same time
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
+
+# Version of PyXB used to generate the bindings
+_PyXBVersion = '1.2.4'
+# Generated bindings are not compatible across PyXB versions
+if pyxb.__version__ != _PyXBVersion:
+ raise pyxb.PyXBVersionError(_PyXBVersion)
+
+# Import bindings for namespaces imported into schema
+import _pbbase as _ImportedBinding__pbbase
+import pyxb.binding.datatypes
+
+# NOTE: All namespace declarations are reserved within the binding
+Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioReagentKit.xsd', create_if_missing=True)
+Namespace.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbbase = _ImportedBinding__pbbase.Namespace
+_Namespace_pbbase.configureCategories(['typeBinding', 'elementBinding'])
+
+def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
+ """Parse the given XML and use the document element to create a
+ Python instance.
+
+ @param xml_text An XML document. This should be data (Python 2
+ str or Python 3 bytes), or a text (Python 2 unicode or Python 3
+ str) in the L{pyxb._InputEncoding} encoding.
+
+ @keyword default_namespace The L{pyxb.Namespace} instance to use as the
+ default namespace where there is no default namespace in scope.
+ If unspecified or C{None}, the namespace of the module containing
+ this function will be used.
+
+ @keyword location_base: An object to be recorded as the base of all
+ L{pyxb.utils.utility.Location} instances associated with events and
+ objects handled by the parser. You might pass the URI from which
+ the document was obtained.
+ """
+
+ if pyxb.XMLStyle_saxer != pyxb._XMLStyle:
+ dom = pyxb.utils.domutils.StringToDOM(xml_text)
+ return CreateFromDOM(dom.documentElement, default_namespace=default_namespace)
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ saxer = pyxb.binding.saxer.make_parser(fallback_namespace=default_namespace, location_base=location_base)
+ handler = saxer.getContentHandler()
+ xmld = xml_text
+ if isinstance(xmld, _six.text_type):
+ xmld = xmld.encode(pyxb._InputEncoding)
+ saxer.parse(io.BytesIO(xmld))
+ instance = handler.rootObject()
+ return instance
+
+def CreateFromDOM (node, default_namespace=None):
+ """Create a Python instance from the given DOM node.
+ The node tag must correspond to an element declaration in this module.
+
+ @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}."""
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ return pyxb.binding.basis.element.AnyCreateFromDOM(node, default_namespace)
+
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioReagentKit.xsd}TubeLocation
+class TubeLocation (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'TubeLocation')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 128, 1)
+ _Documentation = None
+TubeLocation._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=TubeLocation, enum_prefix=None)
+TubeLocation.ReagentTube0 = TubeLocation._CF_enumeration.addEnumeration(unicode_value='ReagentTube0', tag='ReagentTube0')
+TubeLocation.ReagentTube1 = TubeLocation._CF_enumeration.addEnumeration(unicode_value='ReagentTube1', tag='ReagentTube1')
+TubeLocation._InitializeFacetMap(TubeLocation._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'TubeLocation', TubeLocation)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioReagentKit.xsd}TubeSize
+class TubeSize (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'TubeSize')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 134, 1)
+ _Documentation = None
+TubeSize._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=TubeSize, enum_prefix=None)
+TubeSize.DeepTube = TubeSize._CF_enumeration.addEnumeration(unicode_value='DeepTube', tag='DeepTube')
+TubeSize.ShallowTube = TubeSize._CF_enumeration.addEnumeration(unicode_value='ShallowTube', tag='ShallowTube')
+TubeSize._InitializeFacetMap(TubeSize._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'TubeSize', TubeSize)
+
+# Atomic simple type: {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentKey
+class ReagentKey (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mixin):
+
+ """An atomic simple type."""
+
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentKey')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 140, 1)
+ _Documentation = None
+ReagentKey._CF_enumeration = pyxb.binding.facets.CF_enumeration(value_datatype=ReagentKey, enum_prefix=None)
+ReagentKey.Base = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Base', tag='Base')
+ReagentKey.DTT = ReagentKey._CF_enumeration.addEnumeration(unicode_value='DTT', tag='DTT')
+ReagentKey.DilBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='DilBuffer', tag='DilBuffer')
+ReagentKey.MineralOil = ReagentKey._CF_enumeration.addEnumeration(unicode_value='MineralOil', tag='MineralOil')
+ReagentKey.MIXED_DilBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='MIXED_DilBuffer', tag='MIXED_DilBuffer')
+ReagentKey.MIXED_OS = ReagentKey._CF_enumeration.addEnumeration(unicode_value='MIXED_OS', tag='MIXED_OS')
+ReagentKey.OSbuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='OSbuffer', tag='OSbuffer')
+ReagentKey.OSenzyme = ReagentKey._CF_enumeration.addEnumeration(unicode_value='OSenzyme', tag='OSenzyme')
+ReagentKey.PhospholinkedNT = ReagentKey._CF_enumeration.addEnumeration(unicode_value='PhospholinkedNT', tag='PhospholinkedNT')
+ReagentKey.SABuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='SABuffer', tag='SABuffer')
+ReagentKey.Spike = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Spike', tag='Spike')
+ReagentKey.Streptavidin = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Streptavidin', tag='Streptavidin')
+ReagentKey.SubstrateOS = ReagentKey._CF_enumeration.addEnumeration(unicode_value='SubstrateOS', tag='SubstrateOS')
+ReagentKey.TSQ = ReagentKey._CF_enumeration.addEnumeration(unicode_value='TSQ', tag='TSQ')
+ReagentKey.WashBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='WashBuffer', tag='WashBuffer')
+ReagentKey.WettingBuffer = ReagentKey._CF_enumeration.addEnumeration(unicode_value='WettingBuffer', tag='WettingBuffer')
+ReagentKey.PCA = ReagentKey._CF_enumeration.addEnumeration(unicode_value='PCA', tag='PCA')
+ReagentKey.PCD = ReagentKey._CF_enumeration.addEnumeration(unicode_value='PCD', tag='PCD')
+ReagentKey.Analog = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Analog', tag='Analog')
+ReagentKey.Sample = ReagentKey._CF_enumeration.addEnumeration(unicode_value='Sample', tag='Sample')
+ReagentKey._InitializeFacetMap(ReagentKey._CF_enumeration)
+Namespace.addCategoryObject('typeBinding', 'ReagentKey', ReagentKey)
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
+ """The root element of the reagent kit standalone file"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 11, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentKit uses Python identifier ReagentKit
+ __ReagentKit = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), 'ReagentKit', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_httppacificbiosciences_comPacBioReagentKit_xsdReagentKit', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 18, 1), )
+
+
+ ReagentKit = property(__ReagentKit.value, __ReagentKit.set, None, None)
+
+ _ElementMap.update({
+ __ReagentKit.name() : __ReagentKit
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 70, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}Reagent uses Python identifier Reagent
+ __Reagent = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), 'Reagent', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON__httppacificbiosciences_comPacBioReagentKit_xsdReagent', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 17, 1), )
+
+
+ Reagent = property(__Reagent.value, __Reagent.set, None, None)
+
+ _ElementMap.update({
+ __Reagent.name() : __Reagent
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 77, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentTube uses Python identifier ReagentTube
+ __ReagentTube = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), 'ReagentTube', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioReagentKit_xsdReagentTube', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 19, 1), )
+
+
+ ReagentTube = property(__ReagentTube.value, __ReagentTube.set, None, None)
+
+ _ElementMap.update({
+ __ReagentTube.name() : __ReagentTube
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 84, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentPlateRow uses Python identifier ReagentPlateRow
+ __ReagentPlateRow = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), 'ReagentPlateRow', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioReagentKit_xsdReagentPlateRow', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 20, 1), )
+
+
+ ReagentPlateRow = property(__ReagentPlateRow.value, __ReagentPlateRow.set, None, None)
+
+ _ElementMap.update({
+ __ReagentPlateRow.name() : __ReagentPlateRow
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 91, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}CompatibleAutomation uses Python identifier CompatibleAutomation
+ __CompatibleAutomation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomation'), 'CompatibleAutomation', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioReagentKit_xsdCompatibleAutomation', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 93, 8), )
+
+
+ CompatibleAutomation = property(__CompatibleAutomation.value, __CompatibleAutomation.set, None, None)
+
+ _ElementMap.update({
+ __CompatibleAutomation.name() : __CompatibleAutomation
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentType with content type ELEMENT_ONLY
+class ReagentType (_ImportedBinding__pbbase.BaseEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 54, 1)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ReagentKey uses Python identifier ReagentKey
+ __ReagentKey = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentKey'), 'ReagentKey', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_ReagentKey', ReagentKey, required=True)
+ __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 57, 4)
+ __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 57, 4)
+
+ ReagentKey = property(__ReagentKey.value, __ReagentKey.set, None, None)
+
+
+ # Attribute PlateColumn uses Python identifier PlateColumn
+ __PlateColumn = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PlateColumn'), 'PlateColumn', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_PlateColumn', pyxb.binding.datatypes.string, required=True)
+ __PlateColumn._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 58, 4)
+ __PlateColumn._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 58, 4)
+
+ PlateColumn = property(__PlateColumn.value, __PlateColumn.set, None, None)
+
+
+ # Attribute Volume uses Python identifier Volume
+ __Volume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Volume'), 'Volume', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_Volume', pyxb.binding.datatypes.int, required=True)
+ __Volume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 59, 4)
+ __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 59, 4)
+
+ Volume = property(__Volume.value, __Volume.set, None, None)
+
+
+ # Attribute DeadVolume uses Python identifier DeadVolume
+ __DeadVolume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DeadVolume'), 'DeadVolume', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_DeadVolume', pyxb.binding.datatypes.int, required=True)
+ __DeadVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 60, 4)
+ __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 60, 4)
+
+ DeadVolume = property(__DeadVolume.value, __DeadVolume.set, None, None)
+
+
+ # Attribute ActiveInHour uses Python identifier ActiveInHour
+ __ActiveInHour = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveInHour'), 'ActiveInHour', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_ActiveInHour', pyxb.binding.datatypes.int, required=True)
+ __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 61, 4)
+ __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 61, 4)
+
+ ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __ReagentKey.name() : __ReagentKey,
+ __PlateColumn.name() : __PlateColumn,
+ __Volume.name() : __Volume,
+ __DeadVolume.name() : __DeadVolume,
+ __ActiveInHour.name() : __ActiveInHour
+ })
+Namespace.addCategoryObject('typeBinding', 'ReagentType', ReagentType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentKitType with content type ELEMENT_ONLY
+class ReagentKitType (_ImportedBinding__pbbase.BaseEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentKitType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentKitType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 65, 1)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}Reagents uses Python identifier Reagents
+ __Reagents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), 'Reagents', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdReagents', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 69, 5), )
+
+
+ Reagents = property(__Reagents.value, __Reagents.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentTubes uses Python identifier ReagentTubes
+ __ReagentTubes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), 'ReagentTubes', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdReagentTubes', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 76, 5), )
+
+
+ ReagentTubes = property(__ReagentTubes.value, __ReagentTubes.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentPlateRows uses Python identifier ReagentPlateRows
+ __ReagentPlateRows = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), 'ReagentPlateRows', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdReagentPlateRows', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 83, 5), )
+
+
+ ReagentPlateRows = property(__ReagentPlateRows.value, __ReagentPlateRows.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}CompatibleAutomations uses Python identifier CompatibleAutomations
+ __CompatibleAutomations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomations'), 'CompatibleAutomations', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdCompatibleAutomations', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 90, 5), )
+
+
+ CompatibleAutomations = property(__CompatibleAutomations.value, __CompatibleAutomations.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ProductCode uses Python identifier ProductCode
+ __ProductCode = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ProductCode'), 'ProductCode', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_ProductCode', pyxb.binding.datatypes.string)
+ __ProductCode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 98, 4)
+ __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 98, 4)
+
+ ProductCode = property(__ProductCode.value, __ProductCode.set, None, None)
+
+
+ # Attribute PlateType uses Python identifier PlateType
+ __PlateType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PlateType'), 'PlateType', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_PlateType', pyxb.binding.datatypes.string)
+ __PlateType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 99, 4)
+ __PlateType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 99, 4)
+
+ PlateType = property(__PlateType.value, __PlateType.set, None, None)
+
+
+ # Attribute ActiveInHour uses Python identifier ActiveInHour
+ __ActiveInHour = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveInHour'), 'ActiveInHour', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_ActiveInHour', pyxb.binding.datatypes.int)
+ __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 100, 4)
+ __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 100, 4)
+
+ ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
+
+
+ # Attribute BasesPerSecond uses Python identifier BasesPerSecond
+ __BasesPerSecond = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'BasesPerSecond'), 'BasesPerSecond', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_BasesPerSecond', pyxb.binding.datatypes.decimal)
+ __BasesPerSecond._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 101, 4)
+ __BasesPerSecond._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 101, 4)
+
+ BasesPerSecond = property(__BasesPerSecond.value, __BasesPerSecond.set, None, None)
+
+
+ # Attribute AcquisitionCount uses Python identifier AcquisitionCount
+ __AcquisitionCount = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'AcquisitionCount'), 'AcquisitionCount', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_AcquisitionCount', pyxb.binding.datatypes.int)
+ __AcquisitionCount._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 102, 4)
+ __AcquisitionCount._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 102, 4)
+
+ AcquisitionCount = property(__AcquisitionCount.value, __AcquisitionCount.set, None, None)
+
+ _ElementMap.update({
+ __Reagents.name() : __Reagents,
+ __ReagentTubes.name() : __ReagentTubes,
+ __ReagentPlateRows.name() : __ReagentPlateRows,
+ __CompatibleAutomations.name() : __CompatibleAutomations
+ })
+ _AttributeMap.update({
+ __ProductCode.name() : __ProductCode,
+ __PlateType.name() : __PlateType,
+ __ActiveInHour.name() : __ActiveInHour,
+ __BasesPerSecond.name() : __BasesPerSecond,
+ __AcquisitionCount.name() : __AcquisitionCount
+ })
+Namespace.addCategoryObject('typeBinding', 'ReagentKitType', ReagentKitType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentTubeType with content type ELEMENT_ONLY
+class ReagentTubeType (_ImportedBinding__pbbase.BaseEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentTubeType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentTubeType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 106, 1)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ProductCode uses Python identifier ProductCode
+ __ProductCode = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ProductCode'), 'ProductCode', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_ProductCode', pyxb.binding.datatypes.string, required=True)
+ __ProductCode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 109, 4)
+ __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 109, 4)
+
+ ProductCode = property(__ProductCode.value, __ProductCode.set, None, None)
+
+
+ # Attribute ReagentKey uses Python identifier ReagentKey
+ __ReagentKey = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentKey'), 'ReagentKey', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_ReagentKey', ReagentKey, required=True)
+ __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 110, 4)
+ __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 110, 4)
+
+ ReagentKey = property(__ReagentKey.value, __ReagentKey.set, None, None)
+
+
+ # Attribute Volume uses Python identifier Volume
+ __Volume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Volume'), 'Volume', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_Volume', pyxb.binding.datatypes.short, required=True)
+ __Volume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 111, 4)
+ __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 111, 4)
+
+ Volume = property(__Volume.value, __Volume.set, None, None)
+
+
+ # Attribute DeadVolume uses Python identifier DeadVolume
+ __DeadVolume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DeadVolume'), 'DeadVolume', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_DeadVolume', pyxb.binding.datatypes.short, required=True)
+ __DeadVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 112, 4)
+ __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 112, 4)
+
+ DeadVolume = property(__DeadVolume.value, __DeadVolume.set, None, None)
+
+
+ # Attribute ActiveInHour uses Python identifier ActiveInHour
+ __ActiveInHour = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveInHour'), 'ActiveInHour', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_ActiveInHour', pyxb.binding.datatypes.int, required=True)
+ __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 113, 4)
+ __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 113, 4)
+
+ ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
+
+
+ # Attribute TubeWellType uses Python identifier TubeWellType
+ __TubeWellType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TubeWellType'), 'TubeWellType', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_TubeWellType', TubeSize, required=True)
+ __TubeWellType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 114, 4)
+ __TubeWellType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 114, 4)
+
+ TubeWellType = property(__TubeWellType.value, __TubeWellType.set, None, None)
+
+
+ # Attribute ReagentTubeType uses Python identifier ReagentTubeType
+ __ReagentTubeType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentTubeType'), 'ReagentTubeType', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_ReagentTubeType', TubeLocation, required=True)
+ __ReagentTubeType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 115, 4)
+ __ReagentTubeType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 115, 4)
+
+ ReagentTubeType = property(__ReagentTubeType.value, __ReagentTubeType.set, None, None)
+
+
+ # Attribute InitialUse uses Python identifier InitialUse
+ __InitialUse = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InitialUse'), 'InitialUse', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_InitialUse', pyxb.binding.datatypes.dateTime)
+ __InitialUse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 116, 4)
+ __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 116, 4)
+
+ InitialUse = property(__InitialUse.value, __InitialUse.set, None, None)
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __ProductCode.name() : __ProductCode,
+ __ReagentKey.name() : __ReagentKey,
+ __Volume.name() : __Volume,
+ __DeadVolume.name() : __DeadVolume,
+ __ActiveInHour.name() : __ActiveInHour,
+ __TubeWellType.name() : __TubeWellType,
+ __ReagentTubeType.name() : __ReagentTubeType,
+ __InitialUse.name() : __InitialUse
+ })
+Namespace.addCategoryObject('typeBinding', 'ReagentTubeType', ReagentTubeType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentPlateRowType with content type ELEMENT_ONLY
+class ReagentPlateRowType (_ImportedBinding__pbbase.BaseEntityType):
+ """Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentPlateRowType with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRowType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 120, 1)
+ _ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.BaseEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute PlateRow uses Python identifier PlateRow
+ __PlateRow = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'PlateRow'), 'PlateRow', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentPlateRowType_PlateRow', pyxb.binding.datatypes.string, required=True)
+ __PlateRow._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 123, 4)
+ __PlateRow._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 123, 4)
+
+ PlateRow = property(__PlateRow.value, __PlateRow.set, None, None)
+
+
+ # Attribute InitialUse uses Python identifier InitialUse
+ __InitialUse = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'InitialUse'), 'InitialUse', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentPlateRowType_InitialUse', pyxb.binding.datatypes.dateTime)
+ __InitialUse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 124, 4)
+ __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 124, 4)
+
+ InitialUse = property(__InitialUse.value, __InitialUse.set, None, None)
+
+ _ElementMap.update({
+
+ })
+ _AttributeMap.update({
+ __PlateRow.name() : __PlateRow,
+ __InitialUse.name() : __InitialUse
+ })
+Namespace.addCategoryObject('typeBinding', 'ReagentPlateRowType', ReagentPlateRowType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioReagentKit.xsd}SupplyKitSequencing with content type ELEMENT_ONLY
+class SupplyKitSequencing (_ImportedBinding__pbbase.PartNumberType):
+ """A more specific template kit representation (includes SupplyKit fields). """
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitSequencing')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 21, 1)
+ _ElementMap = _ImportedBinding__pbbase.PartNumberType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.PartNumberType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.PartNumberType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element EncodedValue ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}EncodedValue) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element CheckSum ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}CheckSum) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Element IncompatiblePartNumbers ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatiblePartNumbers) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element IncompatibleAutomations ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}IncompatibleAutomations) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentAutomationName uses Python identifier ReagentAutomationName
+ __ReagentAutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName'), 'ReagentAutomationName', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdReagentAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 28, 5), )
+
+
+ ReagentAutomationName = property(__ReagentAutomationName.value, __ReagentAutomationName.set, None, 'The reagent-mixing protocol used. ')
+
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ReagentTubes uses Python identifier ReagentTubes
+ __ReagentTubes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), 'ReagentTubes', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdReagentTubes', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 33, 5), )
+
+
+ ReagentTubes = property(__ReagentTubes.value, __ReagentTubes.set, None, "Tubes associated with the reagent kit - can have up to two; don't forget to set the location, 0 or 1")
+
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}SequencingChemistry uses Python identifier SequencingChemistry
+ __SequencingChemistry = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), 'SequencingChemistry', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdSequencingChemistry', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 38, 5), )
+
+
+ SequencingChemistry = property(__SequencingChemistry.value, __SequencingChemistry.set, None, None)
+
+
+ # Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}SequencingKitDefinition uses Python identifier SequencingKitDefinition
+ __SequencingKitDefinition = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), 'SequencingKitDefinition', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdSequencingKitDefinition', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 39, 5), )
+
+
+ SequencingKitDefinition = property(__SequencingKitDefinition.value, __SequencingKitDefinition.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ValueDataType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute SimpleValue inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}DataEntityType
+
+ # Attribute PartNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute LotNumber inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute Barcode inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute ExpirationDate inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute IsObsolete inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}PartNumberType
+
+ # Attribute Location uses Python identifier Location
+ __Location = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Location'), 'Location', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_Location', pyxb.binding.datatypes.int, unicode_default='0')
+ __Location._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 41, 4)
+ __Location._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 41, 4)
+
+ Location = property(__Location.value, __Location.set, None, 'The location of the supply kit - for a reagent plate, it could be 0 or 1, and for a tube it could be 0 or 1')
+
+
+ # Attribute MaxCollections uses Python identifier MaxCollections
+ __MaxCollections = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MaxCollections'), 'MaxCollections', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_MaxCollections', pyxb.binding.datatypes.int, unicode_default='8')
+ __MaxCollections._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 46, 4)
+ __MaxCollections._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 46, 4)
+
+ MaxCollections = property(__MaxCollections.value, __MaxCollections.set, None, 'The number of collections this supply kit is capable of')
+
+ _ElementMap.update({
+ __ReagentAutomationName.name() : __ReagentAutomationName,
+ __ReagentTubes.name() : __ReagentTubes,
+ __SequencingChemistry.name() : __SequencingChemistry,
+ __SequencingKitDefinition.name() : __SequencingKitDefinition
+ })
+ _AttributeMap.update({
+ __Location.name() : __Location,
+ __MaxCollections.name() : __MaxCollections
+ })
+Namespace.addCategoryObject('typeBinding', 'SupplyKitSequencing', SupplyKitSequencing)
+
+
+PacBioReagentKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'PacBioReagentKit'), CTD_ANON, documentation='The root element of the reagent kit standalone file', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 7, 1))
+Namespace.addCategoryObject('elementBinding', PacBioReagentKit.name().localName(), PacBioReagentKit)
+
+Reagent = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 17, 1))
+Namespace.addCategoryObject('elementBinding', Reagent.name().localName(), Reagent)
+
+ReagentKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 18, 1))
+Namespace.addCategoryObject('elementBinding', ReagentKit.name().localName(), ReagentKit)
+
+ReagentTube = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 19, 1))
+Namespace.addCategoryObject('elementBinding', ReagentTube.name().localName(), ReagentTube)
+
+ReagentPlateRow = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 20, 1))
+Namespace.addCategoryObject('elementBinding', ReagentPlateRow.name().localName(), ReagentPlateRow)
+
+
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, scope=CTD_ANON, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 18, 1)))
+
+def _BuildAutomaton ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton
+ del _BuildAutomaton
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 13, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+
+
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, scope=CTD_ANON_, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 17, 1)))
+
+def _BuildAutomaton_ ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_
+ del _BuildAutomaton_
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagent')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 72, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_._Automaton = _BuildAutomaton_()
+
+
+
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 19, 1)))
+
+def _BuildAutomaton_2 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 79, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_2._Automaton = _BuildAutomaton_2()
+
+
+
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 20, 1)))
+
+def _BuildAutomaton_3 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 86, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_3()
+
+
+
+
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomation'), pyxb.binding.datatypes.string, scope=CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 93, 8)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 93, 8))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomation')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 93, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_4._Automaton = _BuildAutomaton_4()
+
+
+
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(ReagentType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+ReagentType._Automaton = _BuildAutomaton_5()
+
+
+
+
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), CTD_ANON_, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 69, 5)))
+
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), CTD_ANON_2, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 76, 5)))
+
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), CTD_ANON_3, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 83, 5)))
+
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomations'), CTD_ANON_4, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 90, 5)))
+
+def _BuildAutomaton_6 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_6
+ del _BuildAutomaton_6
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 90, 5))
+ counters.add(cc_1)
+ states = []
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagents')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 69, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = None
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 76, 5))
+ st_2 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 83, 5))
+ st_3 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'CompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 90, 5))
+ st_4 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ st_4._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+ReagentKitType._Automaton = _BuildAutomaton_6()
+
+
+
+
+def _BuildAutomaton_7 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_7
+ del _BuildAutomaton_7
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(ReagentTubeType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+ReagentTubeType._Automaton = _BuildAutomaton_7()
+
+
+
+
+def _BuildAutomaton_8 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_8
+ del _BuildAutomaton_8
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(ReagentPlateRowType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+ReagentPlateRowType._Automaton = _BuildAutomaton_8()
+
+
+
+
+SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName'), pyxb.binding.datatypes.string, scope=SupplyKitSequencing, documentation='The reagent-mixing protocol used. ', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 28, 5)))
+
+SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), SupplyKitSequencing, scope=SupplyKitSequencing, documentation="Tubes associated with the reagent kit - can have up to two; don't forget to set the location, 0 or 1", location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 33, 5)))
+
+SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), _ImportedBinding__pbbase.SequencingChemistry, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 38, 5)))
+
+SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), ReagentKitType, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 39, 5)))
+
+def _BuildAutomaton_9 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_9
+ del _BuildAutomaton_9
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ counters.add(cc_2)
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ counters.add(cc_3)
+ cc_4 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ counters.add(cc_4)
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 28, 5))
+ counters.add(cc_5)
+ cc_6 = fac.CounterCondition(min=0, max=2, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 33, 5))
+ counters.add(cc_6)
+ cc_7 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 38, 5))
+ counters.add(cc_7)
+ cc_8 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 39, 5))
+ counters.add(cc_8)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'EncodedValue')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 188, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 193, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_3, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'IncompatiblePartNumbers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 331, 5))
+ st_3 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_3)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_4, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'IncompatibleAutomations')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 345, 5))
+ st_4 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_4)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_5, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 28, 5))
+ st_5 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_5)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_6, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 33, 5))
+ st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_6)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_7, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 38, 5))
+ st_7 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_7)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_8, False))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioReagentKit.xsd', 39, 5))
+ st_8 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_8)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_2, False) ]))
+ st_2._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_3, [
+ fac.UpdateInstruction(cc_3, True) ]))
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_3, False) ]))
+ st_3._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_4, [
+ fac.UpdateInstruction(cc_4, True) ]))
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_4, False) ]))
+ st_4._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_5, [
+ fac.UpdateInstruction(cc_5, True) ]))
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_5, False) ]))
+ st_5._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_6, [
+ fac.UpdateInstruction(cc_6, True) ]))
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_6, False) ]))
+ st_6._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_7, [
+ fac.UpdateInstruction(cc_7, True) ]))
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_7, False) ]))
+ st_7._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_8, [
+ fac.UpdateInstruction(cc_8, True) ]))
+ st_8._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+SupplyKitSequencing._Automaton = _BuildAutomaton_9()
+
diff --git a/pbcore/io/dataset/_pbsample.py b/pbcore/io/dataset/_pbsample.py
new file mode 100755
index 0000000..e127355
--- /dev/null
+++ b/pbcore/io/dataset/_pbsample.py
@@ -0,0 +1,632 @@
+# ./_pbsample.py
+# -*- coding: utf-8 -*-
+# PyXB bindings for NM:a7c0866985dba806fe3112e9fbc4707c9f978443
+# Generated 2015-08-04 20:41:05.064669 by PyXB version 1.2.4 using Python 2.7.6.final.0
+# Namespace http://pacificbiosciences.com/PacBioSampleInfo.xsd [xmlns:pbsample]
+
+from __future__ import unicode_literals
+import pyxb
+import pyxb.binding
+import pyxb.binding.saxer
+import io
+import pyxb.utils.utility
+import pyxb.utils.domutils
+import sys
+import pyxb.utils.six as _six
+
+# Unique identifier for bindings created at the same time
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:cc7f6338-3b23-11e5-875e-001a4acb6b14')
+
+# Version of PyXB used to generate the bindings
+_PyXBVersion = '1.2.4'
+# Generated bindings are not compatible across PyXB versions
+if pyxb.__version__ != _PyXBVersion:
+ raise pyxb.PyXBVersionError(_PyXBVersion)
+
+# Import bindings for namespaces imported into schema
+import _pbbase as _ImportedBinding__pbbase
+import pyxb.binding.datatypes
+
+# NOTE: All namespace declarations are reserved within the binding
+Namespace = pyxb.namespace.NamespaceForURI('http://pacificbiosciences.com/PacBioSampleInfo.xsd', create_if_missing=True)
+Namespace.configureCategories(['typeBinding', 'elementBinding'])
+_Namespace_pbbase = _ImportedBinding__pbbase.Namespace
+_Namespace_pbbase.configureCategories(['typeBinding', 'elementBinding'])
+
+def CreateFromDocument (xml_text, default_namespace=None, location_base=None):
+ """Parse the given XML and use the document element to create a
+ Python instance.
+
+ @param xml_text An XML document. This should be data (Python 2
+ str or Python 3 bytes), or a text (Python 2 unicode or Python 3
+ str) in the L{pyxb._InputEncoding} encoding.
+
+ @keyword default_namespace The L{pyxb.Namespace} instance to use as the
+ default namespace where there is no default namespace in scope.
+ If unspecified or C{None}, the namespace of the module containing
+ this function will be used.
+
+ @keyword location_base: An object to be recorded as the base of all
+ L{pyxb.utils.utility.Location} instances associated with events and
+ objects handled by the parser. You might pass the URI from which
+ the document was obtained.
+ """
+
+ if pyxb.XMLStyle_saxer != pyxb._XMLStyle:
+ dom = pyxb.utils.domutils.StringToDOM(xml_text)
+ return CreateFromDOM(dom.documentElement, default_namespace=default_namespace)
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ saxer = pyxb.binding.saxer.make_parser(fallback_namespace=default_namespace, location_base=location_base)
+ handler = saxer.getContentHandler()
+ xmld = xml_text
+ if isinstance(xmld, _six.text_type):
+ xmld = xmld.encode(pyxb._InputEncoding)
+ saxer.parse(io.BytesIO(xmld))
+ instance = handler.rootObject()
+ return instance
+
+def CreateFromDOM (node, default_namespace=None):
+ """Create a Python instance from the given DOM node.
+ The node tag must correspond to an element declaration in this module.
+
+ @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}."""
+ if default_namespace is None:
+ default_namespace = Namespace.fallbackNamespace()
+ return pyxb.binding.basis.element.AnyCreateFromDOM(node, default_namespace)
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
+ """A list of barcodes associated with the biological sample"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 19, 6)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}Barcode uses Python identifier Barcode
+ __Barcode = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Barcode'), 'Barcode', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON_httppacificbiosciences_comPacBioSampleInfo_xsdBarcode', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 21, 8), )
+
+
+ Barcode = property(__Barcode.value, __Barcode.set, None, 'A sequence of barcodes associated with the biological sample')
+
+ _ElementMap.update({
+ __Barcode.name() : __Barcode
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
+ """Back references to other BarcodedSampleType object UniqueIds which utilize this sample"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 104, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSamplePointer uses Python identifier BioSamplePointer
+ __BioSamplePointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer'), 'BioSamplePointer', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON__httppacificbiosciences_comPacBioSampleInfo_xsdBioSamplePointer', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 111, 5), )
+
+
+ BioSamplePointer = property(__BioSamplePointer.value, __BioSamplePointer.set, None, 'Pointer to a single biological sample')
+
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BarcodedSamplePointers uses Python identifier BarcodedSamplePointers
+ __BarcodedSamplePointers = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), 'BarcodedSamplePointers', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON__httppacificbiosciences_comPacBioSampleInfo_xsdBarcodedSamplePointers', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 120, 1), )
+
+
+ BarcodedSamplePointers = property(__BarcodedSamplePointers.value, __BarcodedSamplePointers.set, None, 'Back references to other BarcodedSampleType object UniqueIds which utilize this sample')
+
+ _ElementMap.update({
+ __BioSamplePointer.name() : __BioSamplePointer,
+ __BarcodedSamplePointers.name() : __BarcodedSamplePointers
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
+ """Back references to other BarcodedSampleType object UniqueIds which utilize this sample"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 124, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BarcodedSamplePointer uses Python identifier BarcodedSamplePointer
+ __BarcodedSamplePointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), 'BarcodedSamplePointer', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioSampleInfo_xsdBarcodedSamplePointer', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 126, 4), )
+
+
+ BarcodedSamplePointer = property(__BarcodedSamplePointer.value, __BarcodedSamplePointer.set, None, 'Pointer to a group of barcoded samples')
+
+ _ElementMap.update({
+ __BarcodedSamplePointer.name() : __BarcodedSamplePointer
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type [anonymous] with content type ELEMENT_ONLY
+class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
+ """Complex type [anonymous] with content type ELEMENT_ONLY"""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = None
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 135, 2)
+ _ElementMap = {}
+ _AttributeMap = {}
+ # Base type is pyxb.binding.datatypes.anyType
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSample uses Python identifier BioSample
+ __BioSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), 'BioSample', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioSampleInfo_xsdBioSample', True, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 141, 1), )
+
+
+ BioSample = property(__BioSample.value, __BioSample.set, None, None)
+
+ _ElementMap.update({
+ __BioSample.name() : __BioSample
+ })
+ _AttributeMap.update({
+
+ })
+
+
+
+# Complex type {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType with content type ELEMENT_ONLY
+class BioSampleType (_ImportedBinding__pbbase.StrictEntityType):
+ """The actual biological sample; this could be prep'd, or in original form; could be bound, or annealed..."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BioSampleType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 33, 1)
+ _ElementMap = _ImportedBinding__pbbase.StrictEntityType._ElementMap.copy()
+ _AttributeMap = _ImportedBinding__pbbase.StrictEntityType._AttributeMap.copy()
+ # Base type is _ImportedBinding__pbbase.StrictEntityType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSamples uses Python identifier BioSamples
+ __BioSamples = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), 'BioSamples', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_httppacificbiosciences_comPacBioSampleInfo_xsdBioSamples', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 134, 1), )
+
+
+ BioSamples = property(__BioSamples.value, __BioSamples.set, None, None)
+
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute DateReceived uses Python identifier DateReceived
+ __DateReceived = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DateReceived'), 'DateReceived', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_DateReceived', pyxb.binding.datatypes.dateTime)
+ __DateReceived._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 42, 4)
+ __DateReceived._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 42, 4)
+
+ DateReceived = property(__DateReceived.value, __DateReceived.set, None, 'Date the sample was received by the lab')
+
+
+ # Attribute Organism uses Python identifier Organism
+ __Organism = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Organism'), 'Organism', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_Organism', pyxb.binding.datatypes.string)
+ __Organism._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 47, 4)
+ __Organism._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 47, 4)
+
+ Organism = property(__Organism.value, __Organism.set, None, 'e.g. HIV, E.coli')
+
+
+ # Attribute Reference uses Python identifier Reference
+ __Reference = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Reference'), 'Reference', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_Reference', pyxb.binding.datatypes.string)
+ __Reference._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 52, 4)
+ __Reference._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 52, 4)
+
+ Reference = property(__Reference.value, __Reference.set, None, 'Name of reference, or pointer to one at e.g. NCBI RefSeq')
+
+
+ # Attribute DNAType uses Python identifier DNAType
+ __DNAType = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'DNAType'), 'DNAType', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_DNAType', pyxb.binding.datatypes.string)
+ __DNAType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 57, 4)
+ __DNAType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 57, 4)
+
+ DNAType = property(__DNAType.value, __DNAType.set, None, 'shotgun library, amplicon, etc.')
+
+
+ # Attribute Concentration uses Python identifier Concentration
+ __Concentration = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Concentration'), 'Concentration', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_Concentration', pyxb.binding.datatypes.float)
+ __Concentration._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 62, 4)
+ __Concentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 62, 4)
+
+ Concentration = property(__Concentration.value, __Concentration.set, None, 'in ng/uL, e.g. 250')
+
+
+ # Attribute QuantificationMethod uses Python identifier QuantificationMethod
+ __QuantificationMethod = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'QuantificationMethod'), 'QuantificationMethod', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_QuantificationMethod', pyxb.binding.datatypes.string)
+ __QuantificationMethod._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 67, 4)
+ __QuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 67, 4)
+
+ QuantificationMethod = property(__QuantificationMethod.value, __QuantificationMethod.set, None, 'e.g. Qubit')
+
+
+ # Attribute SMRTBellConcentration uses Python identifier SMRTBellConcentration
+ __SMRTBellConcentration = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SMRTBellConcentration'), 'SMRTBellConcentration', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_SMRTBellConcentration', pyxb.binding.datatypes.float)
+ __SMRTBellConcentration._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 72, 4)
+ __SMRTBellConcentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 72, 4)
+
+ SMRTBellConcentration = property(__SMRTBellConcentration.value, __SMRTBellConcentration.set, None, 'in ng/uL, e.g. 4.5')
+
+
+ # Attribute SMRTBellQuantificationMethod uses Python identifier SMRTBellQuantificationMethod
+ __SMRTBellQuantificationMethod = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SMRTBellQuantificationMethod'), 'SMRTBellQuantificationMethod', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_SMRTBellQuantificationMethod', pyxb.binding.datatypes.string)
+ __SMRTBellQuantificationMethod._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 77, 4)
+ __SMRTBellQuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 77, 4)
+
+ SMRTBellQuantificationMethod = property(__SMRTBellQuantificationMethod.value, __SMRTBellQuantificationMethod.set, None, 'e.g. Qubit')
+
+
+ # Attribute BufferName uses Python identifier BufferName
+ __BufferName = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'BufferName'), 'BufferName', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_BufferName', pyxb.binding.datatypes.string)
+ __BufferName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 82, 4)
+ __BufferName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 82, 4)
+
+ BufferName = property(__BufferName.value, __BufferName.set, None, 'e.g. Tris HCl')
+
+
+ # Attribute SamplePrepKit uses Python identifier SamplePrepKit
+ __SamplePrepKit = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SamplePrepKit'), 'SamplePrepKit', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_SamplePrepKit', pyxb.binding.datatypes.string)
+ __SamplePrepKit._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 87, 4)
+ __SamplePrepKit._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 87, 4)
+
+ SamplePrepKit = property(__SamplePrepKit.value, __SamplePrepKit.set, None, 'e.g. SMRTbell Template Prep Kit')
+
+
+ # Attribute TargetLibrarySize uses Python identifier TargetLibrarySize
+ __TargetLibrarySize = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'TargetLibrarySize'), 'TargetLibrarySize', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_TargetLibrarySize', pyxb.binding.datatypes.string)
+ __TargetLibrarySize._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 92, 4)
+ __TargetLibrarySize._UseLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 92, 4)
+
+ TargetLibrarySize = property(__TargetLibrarySize.value, __TargetLibrarySize.set, None, '2000, 10000, 20000')
+
+ _ElementMap.update({
+ __BioSamples.name() : __BioSamples
+ })
+ _AttributeMap.update({
+ __DateReceived.name() : __DateReceived,
+ __Organism.name() : __Organism,
+ __Reference.name() : __Reference,
+ __DNAType.name() : __DNAType,
+ __Concentration.name() : __Concentration,
+ __QuantificationMethod.name() : __QuantificationMethod,
+ __SMRTBellConcentration.name() : __SMRTBellConcentration,
+ __SMRTBellQuantificationMethod.name() : __SMRTBellQuantificationMethod,
+ __BufferName.name() : __BufferName,
+ __SamplePrepKit.name() : __SamplePrepKit,
+ __TargetLibrarySize.name() : __TargetLibrarySize
+ })
+Namespace.addCategoryObject('typeBinding', 'BioSampleType', BioSampleType)
+
+
+# Complex type {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BarcodedSampleType with content type ELEMENT_ONLY
+class BarcodedSampleType (BioSampleType):
+ """This is a data type to hold a barcoded biological sample, or a raw biological sample - so, barcode is optional."""
+ _TypeDefinition = None
+ _ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
+ _Abstract = False
+ _ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BarcodedSampleType')
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 8, 1)
+ _ElementMap = BioSampleType._ElementMap.copy()
+ _AttributeMap = BioSampleType._AttributeMap.copy()
+ # Base type is BioSampleType
+
+ # Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}Barcodes uses Python identifier Barcodes
+ __Barcodes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Barcodes'), 'Barcodes', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BarcodedSampleType_httppacificbiosciences_comPacBioSampleInfo_xsdBarcodes', False, pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 15, 5), )
+
+
+ Barcodes = property(__Barcodes.value, __Barcodes.set, None, 'A list of barcodes associated with the biological sample')
+
+
+ # Element BioSamples ({http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSamples) inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute Name inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Description inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Tags inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Format inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ResourceId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute Version inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute CreatedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute ModifiedAt inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
+
+ # Attribute UniqueId inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute MetaType inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute TimeStampedName inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}StrictEntityType
+
+ # Attribute DateReceived inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute Organism inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute Reference inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute DNAType inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute Concentration inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute QuantificationMethod inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute SMRTBellConcentration inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute SMRTBellQuantificationMethod inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute BufferName inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute SamplePrepKit inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+
+ # Attribute TargetLibrarySize inherited from {http://pacificbiosciences.com/PacBioSampleInfo.xsd}BioSampleType
+ _ElementMap.update({
+ __Barcodes.name() : __Barcodes
+ })
+ _AttributeMap.update({
+
+ })
+Namespace.addCategoryObject('typeBinding', 'BarcodedSampleType', BarcodedSampleType)
+
+
+BioSamplePointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointers'), CTD_ANON_, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 100, 1))
+Namespace.addCategoryObject('elementBinding', BioSamplePointers.name().localName(), BioSamplePointers)
+
+BarcodedSamplePointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_2, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 120, 1))
+Namespace.addCategoryObject('elementBinding', BarcodedSamplePointers.name().localName(), BarcodedSamplePointers)
+
+BioSamples = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 134, 1))
+Namespace.addCategoryObject('elementBinding', BioSamples.name().localName(), BioSamples)
+
+BioSample = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 141, 1))
+Namespace.addCategoryObject('elementBinding', BioSample.name().localName(), BioSample)
+
+
+
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Barcode'), _ImportedBinding__pbbase.DNABarcode, scope=CTD_ANON, documentation='A sequence of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 21, 8)))
+
+def _BuildAutomaton ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton
+ del _BuildAutomaton
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 21, 8))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Barcode')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 21, 8))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON._Automaton = _BuildAutomaton()
+
+
+
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_, documentation='Pointer to a single biological sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 111, 5)))
+
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_2, scope=CTD_ANON_, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 120, 1)))
+
+def _BuildAutomaton_ ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_
+ del _BuildAutomaton_
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 110, 5))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 111, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_._Automaton = _BuildAutomaton_()
+
+
+
+
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_2, documentation='Pointer to a group of barcoded samples', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 126, 4)))
+
+def _BuildAutomaton_2 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_2
+ del _BuildAutomaton_2
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ states = []
+ final_update = set()
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 126, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, False, containing_state=None)
+CTD_ANON_2._Automaton = _BuildAutomaton_2()
+
+
+
+
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 141, 1)))
+
+def _BuildAutomaton_3 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_3
+ del _BuildAutomaton_3
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 137, 4))
+ counters.add(cc_0)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSample')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 137, 4))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ st_0._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+CTD_ANON_3._Automaton = _BuildAutomaton_3()
+
+
+
+
+BioSampleType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_3, scope=BioSampleType, location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 134, 1)))
+
+def _BuildAutomaton_4 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_4
+ del _BuildAutomaton_4
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 40, 5))
+ counters.add(cc_1)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 40, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ st_1._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+BioSampleType._Automaton = _BuildAutomaton_4()
+
+
+
+
+BarcodedSampleType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Barcodes'), CTD_ANON, scope=BarcodedSampleType, documentation='A list of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 15, 5)))
+
+def _BuildAutomaton_5 ():
+ # Remove this helper function from the namespace after it is invoked
+ global _BuildAutomaton_5
+ del _BuildAutomaton_5
+ import pyxb.utils.fac as fac
+
+ counters = set()
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ counters.add(cc_0)
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 40, 5))
+ counters.add(cc_1)
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 15, 5))
+ counters.add(cc_2)
+ states = []
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_0, False))
+ symbol = pyxb.binding.content.ElementUse(BarcodedSampleType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioBaseDataModel.xsd', 86, 3))
+ st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_0)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_1, False))
+ symbol = pyxb.binding.content.ElementUse(BarcodedSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamples')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 40, 5))
+ st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_1)
+ final_update = set()
+ final_update.add(fac.UpdateInstruction(cc_2, False))
+ symbol = pyxb.binding.content.ElementUse(BarcodedSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Barcodes')), pyxb.utils.utility.Location('/tmp/tmpoNuZaMxsds/PacBioSampleInfo.xsd', 15, 5))
+ st_2 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
+ states.append(st_2)
+ transitions = []
+ transitions.append(fac.Transition(st_0, [
+ fac.UpdateInstruction(cc_0, True) ]))
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_0, False) ]))
+ st_0._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_1, [
+ fac.UpdateInstruction(cc_1, True) ]))
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_1, False) ]))
+ st_1._set_transitionSet(transitions)
+ transitions = []
+ transitions.append(fac.Transition(st_2, [
+ fac.UpdateInstruction(cc_2, True) ]))
+ st_2._set_transitionSet(transitions)
+ return fac.Automaton(states, counters, True, containing_state=None)
+BarcodedSampleType._Automaton = _BuildAutomaton_5()
+
diff --git a/pbcore/io/dataset/utils.py b/pbcore/io/dataset/utils.py
new file mode 100755
index 0000000..05fccb4
--- /dev/null
+++ b/pbcore/io/dataset/utils.py
@@ -0,0 +1,125 @@
+"""
+Utils that support fringe DataSet features.
+"""
+import os
+import tempfile
+import logging
+import json
+from pbcore.util.Process import backticks
+
+log = logging.getLogger(__name__)
+
+def consolidateBams(inFiles, outFile, filterDset=None):
+ """Take a list of infiles, an outFile to produce, and optionally a dataset
+ (filters) to provide the definition and content of filtrations."""
+ if filterDset and filterDset.filters:
+ finalOutfile = outFile
+ outFile = _infixFname(outFile, "_unfiltered")
+ _mergeBams(inFiles, outFile)
+ if filterDset and filterDset.filters:
+ _filterBam(outFile, finalOutfile, filterDset)
+ outFile = finalOutfile
+ _indexBam(outFile)
+ _pbindexBam(outFile)
+
+def _pbindexBam(fname):
+ cmd = "pbindex {i}".format(i=fname)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+
+def _sortBam(fname):
+ tmpname = _infixFname(fname, "_sorted")
+ cmd = "bamtools sort -in {i} -out {o}".format(i=fname, o=tmpname)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+ _mvFile(tmpname, fname)
+
+def _mvFile(inFname, outFname):
+ cmd = "mv {i} {o}".format(i=inFname,
+ o=outFname)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+
+def _cpFile(inFname, outFname):
+ cmd = "cp {i} {o}".format(i=inFname,
+ o=outFname)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+
+def _indexBam(fname):
+ cmd = "samtools index {i}".format(i=fname)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+
+def _mergeBams(inFiles, outFile):
+ if len(inFiles) > 1:
+ cmd = "bamtools merge -in {i} -out {o}".format(i=' -in '.join(inFiles),
+ o=outFile)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+ else:
+ _cpFile(inFiles[0], outFile)
+
+def _maxDigits(numItems):
+ return len(str(numItems))
+
+def _filterBam(inFile, outFile, filterDset):
+ tmpout = tempfile.mkdtemp(suffix="consolidation-filtration")
+ filtScriptName = os.path.join(tmpout, "filtScript.json")
+ _emitFilterScript(filterDset, filtScriptName)
+ cmd = "bamtools filter -in {i} -out {o} -script {s}".format(
+ i=inFile, o=outFile, s=filtScriptName)
+ log.info(cmd)
+ o, r, m = backticks(cmd)
+ if r != 0:
+ raise RuntimeError(m)
+
+def _infixFname(fname, infix):
+ prefix, extension = os.path.splitext(fname)
+ return prefix + infix + extension
+
+def _emitFilterScript(filterDset, filtScriptName):
+ bamtoolsFilters = ['reference', 'insertSize', 'mapQuality', 'name',
+ 'position', 'queryBases']
+ filterMap = {'rname': 'reference',
+ 'pos': 'position',
+ 'length': 'queryBases',
+ 'qname': 'name',
+ 'rq': 'mapQuality'}
+ cheapFilters = True
+ for filt in filterDset.filters:
+ for req in filt:
+ if not filterMap.get(req.name):
+ cheapFilters = False
+ if cheapFilters:
+ script = {"filters":[]}
+ for filt in filterDset.filters:
+ filtDict = {}
+ for req in filt:
+ name = filterMap[req.name]
+ if name == 'reference':
+ if req.operator == '=' or req.operator == '==':
+ filtDict[name] = req.value
+ else:
+ raise NotImplementedError()
+ else:
+ filtDict[name] = req.operator + req.value
+ script['filters'].append(filtDict)
+ else:
+ names = [rec.qName for rec in filterDset]
+ script = {"filters":[{"name": name} for name in names]}
+ with open(filtScriptName, 'w') as scriptFile:
+ scriptFile.write(json.dumps(script))
+
diff --git a/tests/test_pbcore_io_AlnFileReaders.py b/tests/test_pbcore_io_AlnFileReaders.py
index df5980f..cac5d36 100644
--- a/tests/test_pbcore_io_AlnFileReaders.py
+++ b/tests/test_pbcore_io_AlnFileReaders.py
@@ -409,10 +409,19 @@ class TestBasicBam(_BasicAlnFileReaderTests):
def testSpecVersion(self):
EQ("3.0b7", self.f.version)
+ def testReadScore(self):
+ EQ(0.904, self.fwdAln.readScore)
+
+
class TestIndexedBam(_IndexedAlnFileReaderTests):
READER_CONSTRUCTOR = IndexedBamReader
CONSTRUCTOR_ARGS = (data.getBamAndCmpH5()[0], data.getLambdaFasta())
+ def test_empty_bam(self):
+ fn = data.getEmptyBam()
+ bam = IndexedBamReader(fn)
+ EQ(len(bam), 0)
+
class TestCCSBam(object):
def __init__(self):
diff --git a/tests/test_pbcore_io_GffIO.py b/tests/test_pbcore_io_GffIO.py
index 5f822e7..8144910 100644
--- a/tests/test_pbcore_io_GffIO.py
+++ b/tests/test_pbcore_io_GffIO.py
@@ -1,6 +1,12 @@
-from nose.tools import assert_equal, assert_raises
+
from StringIO import StringIO
+import unittest
+import os.path
+
+from nose.tools import assert_equal, assert_raises
+
from pbcore.io import GffWriter, Gff3Record, GffReader
+from pbcore.io.GffIO import merge_gffs, sort_gff
from pbcore import data
class TestGff3Record:
@@ -98,3 +104,62 @@ class TestGffWriter:
"chr1\t.\tinsertion\t10\t11\t.\t.\t.\tcat=1;dog=2\n" +
"chr1\t.\tsubstitution\t200\t201\t.\t.\t.\tmouse=1;moose=2\n")
assert_equal(expected, self.outfile.getvalue())
+
+
+class TestGffSorting(unittest.TestCase):
+ gff_data = ["""\
+##gff-version 3
+##some random comment here
+chr1\tkinModCall\tmodified_base\t32580\t32580\t32\t-\t.\tcoverage=94;context=AATGGCATCGTTCCGGTGGTGGGCGTTGATGGCTGGTCCCG;IPDRatio=1.75
+chr1\tkinModCall\tmodified_base\t32766\t32766\t42\t-\t.\tcoverage=170;context=GCTGGGAAGCTGGCTGAACGTGTCGGCATGGATTCTGTCGA;IPDRatio=1.70
+chr1\tkinModCall\tmodified_base\t32773\t32773\t54\t-\t.\tcoverage=154;context=AACGCTGGCTGGGAAGCTGGCTGAACGTGTCGGCATGGATT;IPDRatio=2.65""", """\
+##gff-version 3
+chr2\tkinModCall\tmodified_base\t1200\t1200\t47\t-\t.\tcoverage=109;context=ACTTTTCACGGTAGTTTTTTGCCGCTTTACCGCCCAGGCAC;IPDRatio=1.89
+chr2\tkinModCall\tmodified_base\t1786\t1786\t36\t-\t.\tcoverage=153;context=TCCCACGTCTCACCGAGCGTGGTGTTTACGAAGGTTTTACG;IPDRatio=1.67
+chr2\tkinModCall\tmodified_base\t1953\t1953\t39\t+\t.\tcoverage=148;context=AATGCGCGTATGGGGATGGGGGCCGGGTGAGGAAAGCTGGC;IPDRatio=1.86""", """\
+chr1\tkinModCall\tmodified_base\t16204\t16204\t31\t-\t.\tcoverage=119;context=CCCGCGCAGATGATAATTACGGCTCACCTGCTGGCTGCCGA;IPDRatio=1.80
+chr1\tkinModCall\tmodified_base\t16302\t16302\t33\t+\t.\tcoverage=108;context=TGGGACGGAACGTTTAAACCGGCATACAGCAACAACATGGC;IPDRatio=1.81
+chr1\tkinModCall\tmodified_base\t16348\t16348\t42\t-\t.\tcoverage=115;context=CCCCATGCCGTAGCGCGGATGGGTCAGCATATCCCACAGAC;IPDRatio=1.82""",]
+ sorted_start = [
+ ('chr1', 16204), ('chr1', 16302), ('chr1', 16348),
+ ('chr1', 32580), ('chr1', 32766), ('chr1', 32773),
+ ('chr2', 1200), ('chr2', 1786), ('chr2', 1953),
+ ]
+
+ @classmethod
+ def setUpClass(cls):
+ cls.files = []
+ cls.combined = "tmp_pbcore_all.gff"
+ with open(cls.combined, "w") as f_all:
+ for i in range(3):
+ file_name = "tmp_pbcore_%d.gff" % i
+ with open(file_name, "w") as f:
+ f.write(cls.gff_data[i])
+ cls.files.append(file_name)
+ for line in cls.gff_data[i].splitlines():
+ if line.startswith("#"):
+ if i == 0:
+ f_all.write(line+"\n")
+ else:
+ f_all.write(line+"\n")
+
+ @classmethod
+ def tearDownClass(cls):
+ for file_name in cls.files:
+ if os.path.exists(file_name):
+ os.remove(file_name)
+ if os.path.exists(cls.combined):
+ os.remove(cls.combined)
+
+ def test_merge_gffs(self):
+ gff_out = "tmp_pbcore_merged.gff"
+ merge_gffs(self.files, gff_out)
+ with GffReader(gff_out) as f:
+ start = [ (rec.seqid, rec.start) for rec in f ]
+ self.assertEqual(start, self.sorted_start)
+
+ def test_sort_gff(self):
+ gff_out = sort_gff(self.combined)
+ with GffReader(gff_out) as f:
+ start = [ (rec.seqid, rec.start) for rec in f ]
+ self.assertEqual(start, self.sorted_start)
diff --git a/tests/test_pbcore_io_bgzf.py b/tests/test_pbcore_io_bgzf.py
new file mode 100644
index 0000000..f58abfd
--- /dev/null
+++ b/tests/test_pbcore_io_bgzf.py
@@ -0,0 +1,42 @@
+from nose.tools import assert_equal, assert_true, assert_false
+import sys, numpy as np
+
+from tempfile import NamedTemporaryFile
+
+from pbcore.io.align._bgzf import BgzfReader, BgzfWriter
+
+
+# TODO: did Biopython have tests for it?
+
+class TestBgzf(object):
+
+ def __init__(self):
+ pass
+
+ def roundTripData(self, size, sizeToRead=None):
+ if sizeToRead is None: sizeToRead = size
+ data = (np.sin(np.arange(size))*100).astype(np.int8).tostring()
+ assert size == len(data)
+ with NamedTemporaryFile() as compressionOutput:
+ with BgzfWriter(compressionOutput.name, compresslevel=1) as writer:
+ writer.write(data)
+ with BgzfReader(compressionOutput.name) as reader:
+ decompressionOutput = reader.read(sizeToRead)
+ assert_equal(data[:sizeToRead], decompressionOutput)
+
+ def test_small_data(self):
+ self.roundTripData(0)
+ for i in xrange(8):
+ self.roundTripData(10**i)
+
+ def test_partial_reads(self):
+ self.roundTripData(10**7, (10**7)/2)
+
+ # def test_big_data(self):
+ # # This breaks because of recursion depth limit in
+ # # implementation from Biopython.
+ # self.roundTripData(10**8)
+
+if __name__ == "__main__":
+ size = int(sys.argv[1])
+ TestBgzf().roundTripData(size)
diff --git a/tests/test_pbdataset.py b/tests/test_pbdataset.py
index 9f3739d..66ad971 100644
--- a/tests/test_pbdataset.py
+++ b/tests/test_pbdataset.py
@@ -2,6 +2,7 @@
import os
import re
import logging
+import itertools
import tempfile
import numpy as np
@@ -10,7 +11,7 @@ from unittest.case import SkipTest
from pbcore.io import openIndexedAlignmentFile
from pbcore.io import (DataSet, SubreadSet, ReferenceSet, AlignmentSet,
- openDataSet, DataSetMetaTypes)
+ openDataSet, DataSetMetaTypes, HdfSubreadSet)
from pbcore.io.dataset.DataSetIO import _dsIdToSuffix
from pbcore.io.dataset.DataSetMembers import ExternalResource, Filters
from pbcore.io.dataset.DataSetWriter import toXml
@@ -78,6 +79,44 @@ class TestDataSet(unittest.TestCase):
ds.externalResources[-1].indices[0].resourceId ==
"IdontExist.bam.pbi")
+ def test_split_cli(self):
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ cmd = "dataset.py split --outdir {o} --contigs --chunks 2 {d}".format(
+ o=outdir,
+ d=data.getXml(8))
+ log.debug(cmd)
+ o, r, m = backticks(cmd)
+ self.assertEqual(r, 0)
+ self.assertTrue(os.path.exists(
+ os.path.join(outdir, os.path.basename(data.getXml(15)))))
+ self.assertTrue(os.path.exists(
+ os.path.join(outdir, os.path.basename(data.getXml(16)))))
+
+ def test_create_cli(self):
+ log.debug("Absolute")
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ cmd = "dataset.py create --type AlignmentSet {o} {i1} {i2}".format(
+ o=os.path.join(outdir, 'pbalchemysim.alignmentset.xml'),
+ i1=data.getXml(8), i2=data.getXml(11))
+ log.debug(cmd)
+ o, r, m = backticks(cmd)
+ self.assertEqual(r, 0)
+ self.assertTrue(os.path.exists(
+ os.path.join(outdir, os.path.basename(data.getXml(12)))))
+
+ log.debug("Relative")
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ cmd = ("dataset.py create --relative --type AlignmentSet "
+ "{o} {i1} {i2}".format(
+ o=os.path.join(outdir, 'pbalchemysim.alignmentset.xml'),
+ i1=data.getXml(8),
+ i2=data.getXml(11)))
+ log.debug(cmd)
+ o, r, m = backticks(cmd)
+ self.assertEqual(r, 0)
+ self.assertTrue(os.path.exists(
+ os.path.join(outdir, os.path.basename(data.getXml(12)))))
+
def test_empty_metatype(self):
inBam = data.getBam()
d = DataSet(inBam)
@@ -89,7 +128,7 @@ class TestDataSet(unittest.TestCase):
d = AlignmentSet(inBam)
for extRes in d.externalResources:
self.assertEqual(extRes.metaType,
- "PacBio.SubreadFile.SubreadBamFile")
+ "PacBio.AlignmentFile.AlignmentBamFile")
def test_loading_reference(self):
log.info('Opening Reference')
@@ -110,21 +149,52 @@ class TestDataSet(unittest.TestCase):
self.assertTrue(res.isReferenceLoaded)
def test_factory_function(self):
- bam = data.getBam()
aln = data.getXml(8)
ref = data.getXml(9)
sub = data.getXml(10)
- inTypes = [bam, aln, ref, sub]
- expTypes = [DataSet, AlignmentSet, ReferenceSet, SubreadSet]
+ inTypes = [aln, ref, sub]
+ expTypes = [AlignmentSet, ReferenceSet, SubreadSet]
for infn, exp in zip(inTypes, expTypes):
# TODO enable this for all when simulated subread files can be
# pbi'd
- if exp in [DataSet, ReferenceSet, AlignmentSet]:
+ if exp in [ReferenceSet, AlignmentSet]:
ds = openDataSet(infn, strict=True)
else:
- ds = openDataSet(infn)
+ ds = openDataSet(infn, strict=False)
self.assertEqual(type(ds), exp)
+ def test_type_checking(self):
+ bam = data.getBam()
+ fasta = ReferenceSet(data.getXml(9)).toExternalFiles()[0]
+ bax = HdfSubreadSet(data.getXml(19)).toExternalFiles()[0]
+
+ DataSet(bam, strict=False)
+ DataSet(fasta, strict=False)
+ DataSet(bax, strict=False)
+ with self.assertRaises(Exception):
+ DataSet(bam, strict=True)
+ with self.assertRaises(Exception):
+ DataSet(fasta, strict=True)
+ with self.assertRaises(Exception):
+ DataSet(bax, strict=True)
+
+ AlignmentSet(bam, strict=True)
+ with self.assertRaises(Exception):
+ AlignmentSet(fasta, strict=True)
+ with self.assertRaises(Exception):
+ AlignmentSet(bax, strict=True)
+
+ ReferenceSet(fasta, strict=True)
+ with self.assertRaises(Exception):
+ ReferenceSet(bam, strict=True)
+ with self.assertRaises(Exception):
+ ReferenceSet(bax, strict=True)
+
+ HdfSubreadSet(bax, strict=True)
+ with self.assertRaises(Exception):
+ HdfSubreadSet(bam, strict=True)
+ with self.assertRaises(Exception):
+ HdfSubreadSet(fasta, strict=True)
def test_dsIdToSuffix(self):
suffixes = ['subreadset.xml', 'hdfsubreadset.xml', 'alignmentset.xml',
@@ -263,7 +333,7 @@ class TestDataSet(unittest.TestCase):
self.assertTrue(old != ds.uuid)
def test_split(self):
- ds1 = DataSet(data.getXml())
+ ds1 = openDataSet(data.getXml(12))
self.assertTrue(ds1.numExternalResources > 1)
dss = ds1.split()
self.assertTrue(len(dss) == ds1.numExternalResources)
@@ -274,10 +344,10 @@ class TestDataSet(unittest.TestCase):
self.assertFalse(dss[0].uuid == dss[1].uuid)
self.assertTrue(dss[0].name == dss[1].name)
# Lets try merging and splitting on subdatasets
- ds1 = DataSet(data.getXml(8))
+ ds1 = openDataSet(data.getXml(8))
self.assertEquals(ds1.totalLength, 123588)
ds1tl = ds1.totalLength
- ds2 = DataSet(data.getXml(11))
+ ds2 = openDataSet(data.getXml(11))
self.assertEquals(ds2.totalLength, 117086)
ds2tl = ds2.totalLength
dss = ds1 + ds2
@@ -287,8 +357,26 @@ class TestDataSet(unittest.TestCase):
self.assertTrue(ds1.totalLength == ds1tl)
self.assertTrue(ds2.totalLength == ds2tl)
+ @unittest.skipUnless(os.path.isdir("/mnt/secondary-siv/testdata"),
+ "Missing testadata directory")
+ def test_split_zmws(self):
+ test_file = ("/mnt/secondary-siv/testdata/SA3-DS/lambda/2372215/"
+ "0007_micro/Analysis_Results/m150404_101626_42267_c"
+ "100807920800000001823174110291514_s1_p0.all."
+ "subreadset.xml")
+ ds1 = openDataSet(test_file)
+ self.assertEqual(len([r for r in ds1]), 1220)
+ dss = ds1.split(chunks=1, zmws=True)
+ self.assertEqual(sum([len([r for r in ds_]) for ds_ in dss]), 1220)
+ dss = ds1.split(chunks=9, zmws=True)
+ self.assertEqual(sum([len([r for r in ds_]) for ds_ in dss]), 1220)
+ self.assertEqual(
+ dss[0].zmwRanges,
+ [('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
+ 55, 1815)])
+
def test_copy(self):
- ds1 = DataSet(data.getXml())
+ ds1 = DataSet(data.getXml(12))
ds2 = ds1.copy()
self.assertFalse(ds1 == ds2)
self.assertFalse(ds1.uuid == ds2.uuid)
@@ -391,12 +479,12 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(extRef.resourceId, 'test2.bam')
def test_resourceReaders(self):
- ds = DataSet(data.getBam())
+ ds = AlignmentSet(data.getBam())
for seqFile in ds.resourceReaders():
self.assertEqual(len([row for row in seqFile]), 92)
def test_records(self):
- ds = DataSet(data.getXml(8))
+ ds = AlignmentSet(data.getXml(8))
self.assertTrue(len(list(ds.records)), 112)
def test_toFofn(self):
@@ -426,51 +514,43 @@ class TestDataSet(unittest.TestCase):
self.assertTrue(os.path.exists(files[0]))
self.assertTrue(os.path.isabs(files[0]))
- @SkipTest
- def test_checkFilterMatch(self):
- # different resourceIds, compatible filters:
- ds1 = DataSet(data.getXml(no=8))
- ds2 = DataSet(data.getXml(no=11))
- #self.assertTrue(ds1._checkFilterMatch(ds2.filters))
- self.assertTrue(ds1.filters.testCompatibility(ds2.filters))
- # different resourceIds, incompatible filters:
- ds3 = DataSet(data.getXml(no=11))
- ds3.filters.addRequirement(rname=[('=', 'E.faecalis.1')])
- #self.assertFalse(ds1._checkFilterMatch(ds3.filters))
- self.assertFalse(ds1.filters.testCompatibility(ds3.filters))
-
- #def test_filterOk(self):
- ## compatible filters
- #filt1 = {'rq':'>0.85'}
- #filt2 = {'rq':'>0.85'}
- #self.assertTrue(_filterOk(filt1, filt2))
- ## incompatible filters
- #filt1 = {'rq':'>0.85'}
- #filt2 = {'rq':'>0.75'}
- #self.assertFalse(_filterOk(filt1, filt2))
-
def test_chunk_list(self):
test = [1, 2, 3, 4, 5]
chunks = DataSet()._chunkList(test, 3, balanceKey=lambda x: x)
self.assertEqual(chunks, [[5], [4, 1], [3, 2]])
def test_ref_names(self):
- ds = DataSet(data.getBam())
+ ds = AlignmentSet(data.getBam())
refNames = ds.refNames
self.assertEqual(sorted(refNames)[0], 'A.baumannii.1')
self.assertEqual(len(refNames), 59)
def test_reads_in_range(self):
- ds = DataSet(data.getBam())
+ ds = AlignmentSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
- reads = ds.readsInRange(rn, 10, 100)
- self.assertEqual(len(list(reads)), 10)
+ reads = list(ds.readsInRange(rn, 10, 100))
+ self.assertEqual(len(reads), 10)
+
+ def lengthInWindow(hit, winStart, winEnd):
+ return min(hit.tEnd, winEnd) - max(hit.tStart, winStart)
+
+ reads = list(ds.readsInRange(rn, 10, 100, longest=True))
+ last = None
+ for read in reads:
+ if last is None:
+ last = lengthInWindow(read, 10, 100)
+ else:
+ self.assertTrue(last >= lengthInWindow(read, 10, 100))
+ last = lengthInWindow(read, 10, 100)
+ reads = list(ds._pbiReadsInRange(rn, 10, 100))
+ self.assertEqual(len(reads), 10)
- ds2 = DataSet(data.getBam(0))
- reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
- self.assertEqual(len(list(reads)), 20)
+
+ ds2 = AlignmentSet(data.getBam(0))
+ reads = list(ds2.readsInRange("E.faecalis.1", 0, 1400))
+ self.assertEqual(len(reads), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
@@ -482,8 +562,89 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
+ @unittest.skipUnless(os.path.isdir("/mnt/secondary-siv/testdata"),
+ "Missing testadata directory")
+ def test_reads_in_range_order(self):
+ log.debug("Testing with one file")
+ testFile = ("/mnt/secondary-siv/testdata/SA3-DS/lambda/"
+ "2372215/0007/Alignment_Results/m150404_101"
+ "626_42267_c1008079208000000018231741102915"
+ "14_s1_p0.1.alignmentset.xml")
+ aln = AlignmentSet(testFile)
+ reads1 = aln.readsInRange(aln.refNames[0], 0, 400,
+ usePbi=False)
+ reads2 = aln.readsInRange(aln.refNames[0], 0, 400,
+ usePbi=True)
+ num = 0
+ for r1, r2 in itertools.izip(reads1, reads2):
+ self.assertEqual(r1, r2)
+ num += 1
+ self.assertTrue(num > 2000)
+
+ log.debug("Testing with three files")
+ testFile = ("/mnt/secondary-siv/testdata/SA3-DS/lambda/"
+ "2372215/0007/Alignment_Results/m150404_101"
+ "626_42267_c1008079208000000018231741102915"
+ "14_s1_p0.all.alignmentset.xml")
+ aln = AlignmentSet(testFile)
+ reads1 = aln.readsInRange(aln.refNames[0], 0, 400,
+ usePbi=False)
+ reads2 = aln.readsInRange(aln.refNames[0], 0, 400,
+ usePbi=True)
+ num = 0
+ for r1, r2 in itertools.izip(reads1, reads2):
+ self.assertEqual(r1, r2)
+ num += 1
+ self.assertTrue(num > 2000)
+
+ @unittest.skipUnless(os.path.isdir("/mnt/secondary/Share/Quiver"),
+ "Missing testadata directory")
+ def test_reads_in_range_order_large(self):
+ window = ('Staphylococcus_aureus_subsp_aureus_USA300_TCH1516',
+ 558500,
+ 559005)
+ log.debug("Testing with one file")
+ testFile = ("/mnt/secondary/Share/Quiver/TestData/"
+ "staph/m140911_084715_42139_c100702390"
+ "480000001823141103261514_s1_p0.aligned_subreads.bam")
+ aln = AlignmentSet(testFile)
+ reads1 = aln.readsInRange(*window, usePbi=False)
+ reads2 = aln.readsInRange(*window, usePbi=True)
+ num = 0
+ for r1, r2 in itertools.izip(reads1, reads2):
+ self.assertEqual(r1, r2)
+ num += 1
+ self.assertTrue(num > 100)
+
+
+ winId, winStart, winEnd = window
+ def lengthInWindow(hit):
+ return min(hit.tEnd, winEnd) - max(hit.tStart, winStart)
+
+ log.debug("Testing longest sort vs no pbi")
+ aln = AlignmentSet(testFile)
+ reads1 = aln.readsInRange(*window, usePbi=False)
+ reads2 = aln.readsInRange(*window, usePbi=True, longest=True)
+ reads1 = list(reads1)
+ reads2 = list(reads2)
+ self.assertEqual(len(reads1), len(reads2))
+ reads1 = sorted(reads1, key=lengthInWindow, reverse=True)
+ for r1, r2 in itertools.izip(reads1, reads2):
+ self.assertEqual(r1, r2)
+
+ log.debug("Testing longest sort vs pbi")
+ aln = AlignmentSet(testFile)
+ reads1 = aln.readsInRange(*window, usePbi=True)
+ reads2 = aln.readsInRange(*window, usePbi=True, longest=True)
+ reads1 = list(reads1)
+ reads2 = list(reads2)
+ self.assertEqual(len(reads1), len(reads2))
+ reads1 = sorted(reads1, key=lengthInWindow, reverse=True)
+ for r1, r2 in itertools.izip(reads1, reads2):
+ self.assertEqual(r1, r2)
+
def test_filter(self):
- ds2 = DataSet(data.getXml(8))
+ ds2 = AlignmentSet(data.getXml(8))
ds2.filters.addRequirement(rname=[('=', 'E.faecalis.1')])
self.assertEqual(len(list(ds2.records)), 20)
ds2.disableFilters()
@@ -519,7 +680,7 @@ class TestDataSet(unittest.TestCase):
def test_split_by_contigs_with_split_and_maxChunks(self):
# test to make sure the refWindows work when chunks == # refs
- ds3 = DataSet(data.getBam())
+ ds3 = AlignmentSet(data.getBam())
dss = ds3.split(contigs=True)
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
@@ -527,16 +688,17 @@ class TestDataSet(unittest.TestCase):
# not all references have something mapped to them, refWindows doesn't
# care...
self.assertNotEqual(refWindows, sorted(ds3.refWindows))
+ self.assertEqual(refWindows,
+ [('B.vulgatus.4', 0, 1449), ('B.vulgatus.5', 0, 1449),
+ ('C.beijerinckii.13', 0, 1433), ('C.beijerinckii.14', 0, 1433),
+ ('C.beijerinckii.9', 0, 1433), ('E.coli.6', 0, 1463),
+ ('E.faecalis.1', 0, 1482), ('E.faecalis.2', 0, 1482),
+ ('R.sphaeroides.1', 0, 1386), ('S.epidermidis.2', 0, 1472),
+ ('S.epidermidis.3', 0, 1472), ('S.epidermidis.4', 0, 1472)])
+ old_refWindows = refWindows
random_few = [('C.beijerinckii.13', 0, 1433),
('B.vulgatus.4', 0, 1449),
('E.faecalis.1', 0, 1482)]
- for reference in random_few:
- found = False
- for ref in refWindows:
- if ref == reference:
- found = True
- self.assertTrue(found)
- old_refWindows = refWindows
dss = ds3.split(contigs=True, maxChunks=1)
self.assertEqual(len(dss), 1)
@@ -561,6 +723,7 @@ class TestDataSet(unittest.TestCase):
log.debug(ref)
self.assertTrue(found)
+ # test with maxchunks but no breaking contigs
dss = ds3.split(contigs=True, maxChunks=36)
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
@@ -572,6 +735,8 @@ class TestDataSet(unittest.TestCase):
found = True
self.assertTrue(found)
+ # test with maxchunks and breaking contigs is allowed (triggers
+ # targetsize, may result in fewer chunks)
dss = ds3.split(contigs=True, maxChunks=36, breakContigs=True)
self.assertEqual(len(dss), 2)
refWindows = sorted(reduce(lambda x, y: x + y,
@@ -583,9 +748,82 @@ class TestDataSet(unittest.TestCase):
found = True
self.assertTrue(found)
+ # test with previous setup and smaller targetSize, resulting in more
+ # chunks
+ dss = ds3.split(contigs=True, maxChunks=36, breakContigs=True,
+ targetSize=10)
+ self.assertEqual(len(dss), 9)
+ refWindows = sorted(reduce(lambda x, y: x + y,
+ [ds.refWindows for ds in dss]))
+ for ref in random_few:
+ found = False
+ for window in refWindows:
+ if ref == window:
+ found = True
+ self.assertTrue(found)
+
+ # test with byRecords and fewer chunks than atoms
+ dss = ds3.split(contigs=True, chunks=3, byRecords=True)
+ self.assertEqual(len(dss), 3)
+ refWindows = sorted(reduce(lambda x, y: x + y,
+ [ds.refWindows for ds in dss]))
+ for ref in random_few:
+ found = False
+ for window in refWindows:
+ if ref == window:
+ found = True
+ self.assertTrue(found)
+
+ # test with byRecords and more chunks than atoms
+ orf = random_few
+ random_few = [('C.beijerinckii.13', 0, 747),
+ ('B.vulgatus.4', 0, 1449),
+ ('E.faecalis.1', 0, 742)]
+ dss = ds3.split(contigs=True, chunks=16, byRecords=True)
+ self.assertEqual(len(dss), 16)
+ refWindows = sorted(reduce(lambda x, y: x + y,
+ [ds.refWindows for ds in dss]))
+ for ref in random_few:
+ found = False
+ for window in refWindows:
+ if ref == window:
+ found = True
+ self.assertTrue(found)
+
+ # test with byRecords and updateCounts
+ random_few = orf
+ dss = ds3.split(contigs=True, chunks=3, byRecords=True,
+ updateCounts=True)
+ self.assertEqual(len(dss), 3)
+ sizes = sorted([dset.numRecords for dset in dss])
+ self.assertListEqual(sizes, [30, 31, 31])
+ refWindows = sorted(reduce(lambda x, y: x + y,
+ [ds.refWindows for ds in dss]))
+ for ref in random_few:
+ found = False
+ for window in refWindows:
+ if ref == window:
+ found = True
+ self.assertTrue(found)
+
+ # test with byRefLength and updateCounts
+ random_few = orf
+ dss = ds3.split(contigs=True, chunks=3, updateCounts=True)
+ self.assertEqual(len(dss), 3)
+ sizes = sorted([dset.numRecords for dset in dss])
+ self.assertListEqual(sizes, [22, 31, 39])
+ refWindows = sorted(reduce(lambda x, y: x + y,
+ [ds.refWindows for ds in dss]))
+ for ref in random_few:
+ found = False
+ for window in refWindows:
+ if ref == window:
+ found = True
+ self.assertTrue(found)
+
def test_split_by_contigs_with_split(self):
# test to make sure the refWindows work when chunks == # refs
- ds3 = DataSet(data.getBam())
+ ds3 = AlignmentSet(data.getBam())
dss = ds3.split(contigs=True)
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
@@ -643,6 +881,7 @@ class TestDataSet(unittest.TestCase):
def test_filter_reference_contigs(self):
ds2 = ReferenceSet(data.getRef())
self.assertEqual(len(list(ds2.refNames)), 59)
+ self.assertEqual(len(list(ds2.records)), len(ds2.index))
filt = Filters()
filt.addRequirement(id=[('==', 'E.faecalis.1')])
ds2.addFilters(filt)
@@ -650,12 +889,15 @@ class TestDataSet(unittest.TestCase):
"( id == E.faecalis.1 )")
self.assertEqual(len(ds2.refNames), 1)
self.assertEqual(len(list(ds2.records)), 1)
+ self.assertEqual(len(list(ds2.records)), len(ds2.index))
ds2.disableFilters()
self.assertEqual(len(list(ds2.refNames)), 59)
self.assertEqual(len(list(ds2.records)), 59)
+ self.assertEqual(len(list(ds2.records)), len(ds2.index))
ds2.enableFilters()
self.assertEqual(len(list(ds2.refNames)), 1)
self.assertEqual(len(list(ds2.records)), 1)
+ self.assertEqual(len(list(ds2.records)), len(ds2.index))
# TODO: get this working again when adding manual subdatasets is good to go
@SkipTest
@@ -685,7 +927,7 @@ class TestDataSet(unittest.TestCase):
#self.assertEqual(len(list(ds3.readsInSubDatasets())), 2)
def test_refWindows(self):
- ds = DataSet(data.getBam())
+ ds = AlignmentSet(data.getBam())
dss = ds.split(chunks=2, contigs=True)
self.assertEqual(len(dss), 2)
log.debug(dss[0].filters)
@@ -696,7 +938,7 @@ class TestDataSet(unittest.TestCase):
or
'( rname = E.faecalis.2 ) '
in str(dss[1].filters))
- ds = DataSet(data.getBam())
+ ds = AlignmentSet(data.getBam())
ds.filters.addRequirement(rname=[('=', 'lambda_NEB3011'),
('=', 'lambda_NEB3011')],
tStart=[('<', '0'),
@@ -713,7 +955,7 @@ class TestDataSet(unittest.TestCase):
def test_refLengths(self):
- ds = DataSet(data.getBam(0))
+ ds = AlignmentSet(data.getBam(0))
random_few = {'B.cereus.6': 1472, 'S.agalactiae.1': 1470,
'B.cereus.4': 1472}
for key, value in random_few.items():
@@ -738,7 +980,7 @@ class TestDataSet(unittest.TestCase):
def test_reads_in_contig(self):
log.info("Testing reads in contigs")
- ds = DataSet(data.getXml(8))
+ ds = AlignmentSet(data.getXml(8))
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 12)
efaec1TimesFound = 0
@@ -759,7 +1001,7 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 3)
- ds = DataSet(data.getXml(8))
+ ds = AlignmentSet(data.getXml(8))
filt = Filters()
filt.addRequirement(length=[('>', '100')])
ds.addFilters(filt)
@@ -783,7 +1025,7 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 3)
- ds = DataSet(data.getXml(8))
+ ds = AlignmentSet(data.getXml(8))
filt = Filters()
filt.addRequirement(length=[('>', '1000')])
ds.addFilters(filt)
@@ -807,8 +1049,23 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 1)
+ def test_get_item(self):
+ # Indexed files only for now:
+ # XXX Reactivate subreadsets when pbindex works for them
+ #toTest = [8, 10, 11, 12, 13, 15, 16]
+ toTest = [8, 11, 12, 15, 16]
+ for fileNo in toTest:
+ aln = openDataSet(data.getXml(fileNo))
+ items1 = [aln[i] for i in range(len(aln))]
+ aln = openDataSet(data.getXml(fileNo))
+ items2 = [aln[i] for i in range(len(aln))]
+ self.assertListEqual(items1, items2)
+ aln = openDataSet(data.getXml(fileNo))
+ for i, item in enumerate(aln):
+ self.assertEqual(item, aln[i])
+
def test_reads_in_reference(self):
- ds = DataSet(data.getBam())
+ ds = AlignmentSet(data.getBam())
refNames = ds.refNames
# See test_ref_names for why this is expected:
@@ -816,14 +1073,14 @@ class TestDataSet(unittest.TestCase):
reads = ds.readsInReference(rn)
self.assertEqual(len(list(reads)), 11)
- ds2 = DataSet(data.getBam(0))
+ ds2 = AlignmentSet(data.getBam(0))
reads = ds2.readsInReference("E.faecalis.1")
self.assertEqual(len(list(reads)), 20)
reads = ds2.readsInReference("E.faecalis.2")
self.assertEqual(len(list(reads)), 3)
- ds2 = DataSet(data.getXml(8))
+ ds2 = AlignmentSet(data.getXml(8))
reads = ds2.readsInReference("E.faecalis.1")
self.assertEqual(len(list(reads)), 20)
@@ -834,15 +1091,17 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(len(list(reads)), 0)
def test_staggered_reads_in_range(self):
- ds = DataSet(data.getXml(8))
+ ds = AlignmentSet(data.getXml(8))
refNames = ds.refNames
rn = 'B.vulgatus.5'
reads = list(ds.readsInRange(rn, 0, 10000))
- ds2 = DataSet(data.getXml(11))
+ ds2 = AlignmentSet(data.getXml(11))
reads2 = list(ds2.readsInRange(rn, 0, 10000))
- dsBoth = DataSet(data.getXml(8), data.getXml(11))
+ dsBoth = AlignmentSet(data.getXml(8), data.getXml(11))
readsBoth = list(dsBoth.readsInRange(rn, 0, 10000))
+ readsBothNoPbi = list(dsBoth.readsInRange(rn, 0, 10000, usePbi=False))
+ self.assertListEqual(readsBoth, readsBothNoPbi)
self.assertEqual(len(reads), 2)
self.assertEqual(len(reads2), 5)
self.assertEqual(len(readsBoth), 7)
diff --git a/tests/test_pbdataset_subtypes.py b/tests/test_pbdataset_subtypes.py
index 3344cdc..71d2869 100644
--- a/tests/test_pbdataset_subtypes.py
+++ b/tests/test_pbdataset_subtypes.py
@@ -4,12 +4,15 @@ from urlparse import urlparse
import unittest
import tempfile
import os
+import itertools
from pbcore.util.Process import backticks
+from pbcore.io.dataset.utils import consolidateBams, _infixFname
from pbcore.io import (DataSet, SubreadSet, ConsensusReadSet,
ReferenceSet, ContigSet, AlignmentSet,
FastaReader, FastaWriter, IndexedFastaReader,
- HdfSubreadSet)
+ HdfSubreadSet, ConsensusAlignmentSet,
+ openDataFile)
import pbcore.data as upstreamData
import pbcore.data.datasets as data
from pbcore.io.dataset.DataSetValidator import validateXml
@@ -17,6 +20,28 @@ import xml.etree.ElementTree as ET
log = logging.getLogger(__name__)
+def _check_constools():
+ cmd = "bamtools"
+ o, r, m = backticks(cmd)
+ if r != 0:
+ return False
+
+ cmd = "pbindex"
+ o, r, m = backticks(cmd)
+ if r != 1:
+ return False
+
+ cmd = "samtools"
+ o, r, m = backticks(cmd)
+ if r != 1:
+ return False
+ return True
+
+def _internal_data():
+ if os.path.exists("/mnt/secondary-siv/testdata"):
+ return True
+ return False
+
class TestDataSet(unittest.TestCase):
"""Unit and integrationt tests for the DataSet class and \
associated module functions"""
@@ -43,6 +68,11 @@ class TestDataSet(unittest.TestCase):
def test_valid_referencesets(self):
validateXml(ET.parse(data.getXml(9)).getroot(), skipResources=True)
+ def test_valid_hdfsubreadsets(self):
+ validateXml(ET.parse(data.getXml(17)).getroot(), skipResources=True)
+ validateXml(ET.parse(data.getXml(18)).getroot(), skipResources=True)
+ validateXml(ET.parse(data.getXml(19)).getroot(), skipResources=True)
+
def test_autofilled_metatypes(self):
ds = ReferenceSet(data.getXml(9))
for extRes in ds.externalResources:
@@ -107,6 +137,38 @@ class TestDataSet(unittest.TestCase):
self.assertEquals(type(ds2).__name__, 'ConsensusReadSet')
self.assertEquals(type(ds2._metadata).__name__, 'SubreadSetMetadata')
+ def test_ccsalignment_build(self):
+ ds1 = ConsensusAlignmentSet(data.getXml(20), strict=False)
+ self.assertEquals(type(ds1).__name__, 'ConsensusAlignmentSet')
+ self.assertEquals(type(ds1._metadata).__name__, 'SubreadSetMetadata')
+ # XXX strict=True requires actual existing .bam files
+ #ds2 = ConsensusAlignmentSet(data.getXml(20), strict=True)
+ #self.assertEquals(type(ds2).__name__, 'ConsensusAlignmentSet')
+ #self.assertEquals(type(ds2._metadata).__name__, 'SubreadSetMetadata')
+
+ def test_file_factory(self):
+ # TODO: add ConsensusReadSet, cmp.h5 alignmentSet
+ types = [AlignmentSet(data.getXml(8)),
+ ReferenceSet(data.getXml(9)),
+ SubreadSet(data.getXml(10)),
+ #ConsensusAlignmentSet(data.getXml(20)),
+ HdfSubreadSet(data.getXml(19))]
+ for ds in types:
+ mystery = openDataFile(ds.toExternalFiles()[0])
+ self.assertEqual(type(mystery), type(ds))
+
+ def test_file_factory_fofn(self):
+ mystery = openDataFile(data.getFofn())
+ self.assertEqual(type(mystery), AlignmentSet)
+
+ @unittest.skipUnless(os.path.isdir("/mnt/secondary-siv/testdata/ccs/tiny"),
+ "Missing testadata directory")
+ def test_file_factory_css(self):
+ fname = "/mnt/secondary-siv/testdata/ccs/tiny/little.ccs.bam"
+ myster = openDataFile(fname)
+ self.assertEqual(type(myster), ConsensusReadSet)
+
+
def test_contigset_build(self):
ds1 = ContigSet(data.getXml(3))
self.assertEquals(type(ds1).__name__, 'ContigSet')
@@ -117,6 +179,167 @@ class TestDataSet(unittest.TestCase):
for contigmd in ds2.metadata.contigs:
self.assertEquals(type(contigmd).__name__, 'ContigMetadata')
+ @unittest.skipIf(not _check_constools(),
+ "bamtools or pbindex not found, skipping")
+ def test_alignmentset_consolidate(self):
+ log.debug("Test methods directly")
+ aln = AlignmentSet(data.getXml(12))
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ consolidateBams(aln.toExternalFiles(), outfn, filterDset=aln)
+ self.assertTrue(os.path.exists(outfn))
+ consAln = AlignmentSet(outfn)
+ self.assertEqual(len(consAln.toExternalFiles()), 1)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(consAln))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(aln), len(consAln))
+
+ log.debug("Test through API")
+ aln = AlignmentSet(data.getXml(12))
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ aln.consolidate(outfn)
+ self.assertTrue(os.path.exists(outfn))
+ self.assertEqual(len(aln.toExternalFiles()), 1)
+ nonCons = AlignmentSet(data.getXml(12))
+ self.assertEqual(len(nonCons.toExternalFiles()), 2)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(aln), len(nonCons))
+
+ log.debug("Test with cheap filter")
+ aln = AlignmentSet(data.getXml(12))
+ self.assertEqual(len(list(aln)), 177)
+ aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
+ self.assertEqual(len(list(aln)), 7)
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ aln.consolidate(outfn)
+ self.assertTrue(os.path.exists(outfn))
+ self.assertEqual(len(aln.toExternalFiles()), 1)
+ nonCons = AlignmentSet(data.getXml(12))
+ nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
+ self.assertEqual(len(nonCons.toExternalFiles()), 2)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(list(aln)), len(list(nonCons)))
+
+ log.debug("Test with not refname filter")
+ # This isn't trivial with bamtools
+ """
+ aln = AlignmentSet(data.getXml(12))
+ self.assertEqual(len(list(aln)), 177)
+ aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
+ self.assertEqual(len(list(aln)), 7)
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ aln.consolidate(outfn)
+ self.assertTrue(os.path.exists(outfn))
+ self.assertEqual(len(aln.toExternalFiles()), 1)
+ nonCons = AlignmentSet(data.getXml(12))
+ nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
+ self.assertEqual(len(nonCons.toExternalFiles()), 2)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(list(aln)), len(list(nonCons)))
+ """
+
+ log.debug("Test with expensive filter")
+ aln = AlignmentSet(data.getXml(12))
+ self.assertEqual(len(list(aln)), 177)
+ aln.filters.addRequirement(accuracy=[('>', '.85')])
+ self.assertEqual(len(list(aln)), 174)
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ aln.consolidate(outfn)
+ self.assertTrue(os.path.exists(outfn))
+ self.assertEqual(len(aln.toExternalFiles()), 1)
+ nonCons = AlignmentSet(data.getXml(12))
+ nonCons.filters.addRequirement(accuracy=[('>', '.85')])
+ self.assertEqual(len(nonCons.toExternalFiles()), 2)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(list(aln)), len(list(nonCons)))
+
+ log.debug("Test cli")
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ datafile = os.path.join(outdir, "merged.bam")
+ xmlfile = os.path.join(outdir, "merged.xml")
+ cmd = "dataset.py consolidate {i} {d} {x}".format(i=data.getXml(12),
+ d=datafile,
+ x=xmlfile)
+ log.debug(cmd)
+ o, r, m = backticks(cmd)
+ self.assertEqual(r, 0)
+
+ @unittest.skipIf(not _check_constools() or not _internal_data(),
+ "bamtools, pbindex or data not found, skipping")
+ def test_alignmentset_partial_consolidate(self):
+ testFile = ("/mnt/secondary-siv/testdata/SA3-DS/"
+ "lambda/2372215/0007_tiny/Alignment_"
+ "Results/m150404_101626_42267_c10080"
+ "7920800000001823174110291514_s1_p0."
+ "all.alignmentset.xml")
+ aln = AlignmentSet(testFile)
+ nonCons= AlignmentSet(testFile)
+ self.assertEqual(len(aln.toExternalFiles()), 3)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ aln.consolidate(outfn, numFiles=2)
+ self.assertFalse(os.path.exists(outfn))
+ self.assertTrue(os.path.exists(_infixFname(outfn, "0")))
+ self.assertTrue(os.path.exists(_infixFname(outfn, "1")))
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ self.assertEqual(len(nonCons.toExternalFiles()), 3)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(aln), len(nonCons))
+
+ log.debug("Test cli")
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ datafile = os.path.join(outdir, "merged.bam")
+ xmlfile = os.path.join(outdir, "merged.xml")
+ cmd = "dataset.py consolidate --numFiles 2 {i} {d} {x}".format(
+ i=testFile, d=datafile, x=xmlfile)
+ log.debug(cmd)
+ o, r, m = backticks(cmd)
+ self.assertEqual(r, 0)
+
+ @unittest.skipIf(not _check_constools(),
+ "bamtools or pbindex not found, skipping")
+ def test_subreadset_consolidate(self):
+ log.debug("Test methods directly")
+ aln = SubreadSet(data.getXml(10), data.getXml(13))
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ consolidateBams(aln.toExternalFiles(), outfn, filterDset=aln)
+ self.assertTrue(os.path.exists(outfn))
+ consAln = SubreadSet(outfn)
+ self.assertEqual(len(consAln.toExternalFiles()), 1)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(consAln))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(aln), len(consAln))
+
+ log.debug("Test through API")
+ aln = SubreadSet(data.getXml(10), data.getXml(13))
+ self.assertEqual(len(aln.toExternalFiles()), 2)
+ outdir = tempfile.mkdtemp(suffix="dataset-unittest")
+ outfn = os.path.join(outdir, 'merged.bam')
+ aln.consolidate(outfn)
+ self.assertTrue(os.path.exists(outfn))
+ self.assertEqual(len(aln.toExternalFiles()), 1)
+ nonCons = SubreadSet(data.getXml(10), data.getXml(13))
+ self.assertEqual(len(nonCons.toExternalFiles()), 2)
+ for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
+ self.assertEqual(read1, read2)
+ self.assertEqual(len(aln), len(nonCons))
+
def test_contigset_consolidate(self):
#build set to merge
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
@@ -171,6 +394,94 @@ class TestDataSet(unittest.TestCase):
self.assertEqual(len(hdfdss[1].toExternalFiles()), 1)
+ def test_len(self):
+ # AlignmentSet
+ aln = AlignmentSet(data.getXml(8), strict=True)
+ self.assertEqual(len(aln), 92)
+ self.assertEqual(aln._length, (92, 123588))
+ self.assertEqual(aln.totalLength, 123588)
+ self.assertEqual(aln.numRecords, 92)
+ aln.totalLength = -1
+ aln.numRecords = -1
+ self.assertEqual(aln.totalLength, -1)
+ self.assertEqual(aln.numRecords, -1)
+ aln.updateCounts()
+ self.assertEqual(aln.totalLength, 123588)
+ self.assertEqual(aln.numRecords, 92)
+
+ # AlignmentSet with filters
+ aln = AlignmentSet(data.getXml(15), strict=True)
+ self.assertEqual(len(aln), 40)
+ self.assertEqual(aln._length, (40, 52023))
+ self.assertEqual(aln.totalLength, 52023)
+ self.assertEqual(aln.numRecords, 40)
+ aln.totalLength = -1
+ aln.numRecords = -1
+ self.assertEqual(aln.totalLength, -1)
+ self.assertEqual(aln.numRecords, -1)
+ aln.updateCounts()
+ self.assertEqual(aln.totalLength, 52023)
+ self.assertEqual(aln.numRecords, 40)
+
+ # NO LONGER SUPPORTED AlignmentSet with cmp.h5
+ #aln = AlignmentSet(upstreamData.getCmpH5(), strict=True)
+ #self.assertEqual(len(aln), 84)
+ #self.assertEqual(aln._length, (84, 26103))
+ #self.assertEqual(aln.totalLength, 26103)
+ #self.assertEqual(aln.numRecords, 84)
+ #aln.totalLength = -1
+ #aln.numRecords = -1
+ #self.assertEqual(aln.totalLength, -1)
+ #self.assertEqual(aln.numRecords, -1)
+ #aln.updateCounts()
+ #self.assertEqual(aln.totalLength, 26103)
+ #self.assertEqual(aln.numRecords, 84)
+
+
+ # SubreadSet
+ # TODO Turn this back on when pbi's are fixed for subreadsets
+ #sset = SubreadSet(data.getXml(10), strict=True)
+ #self.assertEqual(len(sset), 92)
+ #self.assertEqual(sset._length, (92, 123588))
+ #self.assertEqual(sset.totalLength, 123588)
+ #self.assertEqual(sset.numRecords, 92)
+ #sset.totalLength = -1
+ #sset.numRecords = -1
+ #self.assertEqual(sset.totalLength, -1)
+ #self.assertEqual(sset.numRecords, -1)
+ #sset.updateCounts()
+ #self.assertEqual(sset.totalLength, 123588)
+ #self.assertEqual(sset.numRecords, 92)
+
+ # HdfSubreadSet
+ # len means something else in bax/bas land. These numbers may actually
+ # be correct...
+ sset = HdfSubreadSet(data.getXml(17), strict=True)
+ self.assertEqual(len(sset), 9)
+ self.assertEqual(sset._length, (9, 128093))
+ self.assertEqual(sset.totalLength, 128093)
+ self.assertEqual(sset.numRecords, 9)
+ sset.totalLength = -1
+ sset.numRecords = -1
+ self.assertEqual(sset.totalLength, -1)
+ self.assertEqual(sset.numRecords, -1)
+ sset.updateCounts()
+ self.assertEqual(sset.totalLength, 128093)
+ self.assertEqual(sset.numRecords, 9)
+
+ # ReferenceSet
+ sset = ReferenceSet(data.getXml(9), strict=True)
+ self.assertEqual(len(sset), 59)
+ self.assertEqual(sset.totalLength, 85774)
+ self.assertEqual(sset.numRecords, 59)
+ sset.totalLength = -1
+ sset.numRecords = -1
+ self.assertEqual(sset.totalLength, -1)
+ self.assertEqual(sset.numRecords, -1)
+ sset.updateCounts()
+ self.assertEqual(sset.totalLength, 85774)
+ self.assertEqual(sset.numRecords, 59)
+
def test_alignment_reference(self):
rs1 = ReferenceSet(data.getXml(9))
fasta_res = rs1.externalResources[0]
@@ -264,5 +575,7 @@ class TestDataSet(unittest.TestCase):
# 'PacBio.ReferenceFile.ReferenceFastaFile')
-
-
+ def test_contigset_index(self):
+ fasta = upstreamData.getLambdaFasta()
+ ds = ContigSet(fasta)
+ self.assertEqual(ds[0].name, "lambda_NEB3011")
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git
More information about the debian-med-commit
mailing list