[med-svn] [Git][med-team/python-pbcore][upstream] New upstream version 1.7.1+git20200430.a127b1e+dfsg
Steffen Möller
gitlab at salsa.debian.org
Tue May 5 16:47:41 BST 2020
Steffen Möller pushed to branch upstream at Debian Med / python-pbcore
Commits:
8b1d4422 by Steffen Moeller at 2020-05-05T17:43:01+02:00
New upstream version 1.7.1+git20200430.a127b1e+dfsg
- - - - -
14 changed files:
- bin/updateXSDs.py
- pbcore/io/dataset/DataSetIO.py
- pbcore/io/dataset/DataSetMembers.py
- pbcore/io/dataset/pyxb/DataSetXsd.py
- pbcore/io/dataset/pyxb/__init__.py
- pbcore/io/dataset/pyxb/_pbbase.py
- pbcore/io/dataset/pyxb/_pbmeta.py
- pbcore/io/dataset/pyxb/_pbrk.py
- pbcore/io/dataset/pyxb/_pbsample.py
- pbcore/util/statistics.py
- setup.py
- tests/test_pbcore_util.py
- tests/test_pbdataset.py
- tests/test_pbdataset_subtypes.py
Changes:
=====================================
bin/updateXSDs.py
=====================================
@@ -47,4 +47,3 @@ if __name__ == "__main__":
xsd_name = os.path.basename(args.xsd)
generate_pyxb(os.path.join(tempd, xsd_name), args.outdir, args.mod_name)
shutil.rmtree(tempd)
- print("please view commit b7ef4238b63 for additional diffs required for python3 support")
=====================================
pbcore/io/dataset/DataSetIO.py
=====================================
@@ -544,6 +544,9 @@ class DataSet:
# update counts
if files:
+ # generate indices if requested and needed
+ if _induceIndices:
+ self.induceIndices()
if not self.totalLength or not self.numRecords:
self.updateCounts()
elif self.totalLength <= 0 or self.numRecords <= 0:
@@ -551,10 +554,6 @@ class DataSet:
elif len(files) > 1:
self.updateCounts()
- # generate indices if requested and needed
- if _induceIndices:
- self.induceIndices()
-
def induceIndices(self, force=False):
"""Generate indices for ExternalResources.
@@ -2233,6 +2232,16 @@ class ReadSet(DataSet):
else:
raise
+ @property
+ def numBarcodes(self):
+ self.assertIndexed()
+ self.assertBarcoded()
+ barcodes = set([])
+ for bcTuple in zip(self.index.bcForward,
+ self.index.bcReverse):
+ barcodes.add(bcTuple)
+ return len(barcodes)
+
def _split_barcodes(self, chunks=0):
"""Split a readset into chunks by barcodes.
=====================================
pbcore/io/dataset/DataSetMembers.py
=====================================
@@ -1646,7 +1646,9 @@ class ExternalResource(RecordWrapper):
if current:
return FileIndices(current[0])
else:
- return FileIndices()
+ idx = FileIndices()
+ self.append(idx)
+ return idx
@indices.setter
def indices(self, indexList):
=====================================
pbcore/io/dataset/pyxb/DataSetXsd.py
=====================================
The diff for this file was not included because it is too large.
=====================================
pbcore/io/dataset/pyxb/__init__.py
=====================================
@@ -1,3 +1,3 @@
from __future__ import absolute_import, division, print_function
-XSD_CHANGELIST = "e2bf2c71d32eedc7f85d18c960bfe23d662afdb3"
+XSD_CHANGELIST = "6698a98c0279f26e8f8dc3674a700c747c4ef345"
=====================================
pbcore/io/dataset/pyxb/_pbbase.py
=====================================
The diff for this file was not included because it is too large.
=====================================
pbcore/io/dataset/pyxb/_pbmeta.py
=====================================
The diff for this file was not included because it is too large.
=====================================
pbcore/io/dataset/pyxb/_pbrk.py
=====================================
@@ -1,7 +1,7 @@
# pbcore/io/dataset/pyxb/_pbrk.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:82fd17ff8c81a0cc423cbd13a9167bcda5f96419
-# Generated 2020-02-06 10:10:19.723834 by PyXB version 1.2.6 using Python 3.7.3.final.0
+# Generated 2020-04-28 14:07:08.811256 by PyXB version 1.2.6 using Python 3.7.3.final.0
# Namespace http://pacificbiosciences.com/PacBioReagentKit.xsd [xmlns:pbrk]
from __future__ import unicode_literals
@@ -14,7 +14,7 @@ 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:ef0acb54-490b-11ea-a47b-005056875d19')
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:3866d522-8994-11ea-9798-005056871a22')
# Version of PyXB used to generate the bindings
_PyXBVersion = '1.2.6'
@@ -85,7 +85,7 @@ class TubeLocation (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeratio
"""An atomic simple type."""
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'TubeLocation')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 173, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 173, 2)
_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')
@@ -100,7 +100,7 @@ class TubeSize (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_mi
"""An atomic simple type."""
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'TubeSize')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 179, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 179, 2)
_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')
@@ -115,7 +115,7 @@ class ReagentKey (pyxb.binding.datatypes.string, pyxb.binding.basis.enumeration_
"""An atomic simple type."""
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentKey')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 185, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 185, 2)
_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')
@@ -172,13 +172,13 @@ class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 11, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 11, 4)
_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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 18, 1), )
+ __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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 18, 2), )
ReagentKit = property(__ReagentKit.value, __ReagentKit.set, None, None)
@@ -199,13 +199,13 @@ class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 101, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 101, 12)
_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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 17, 1), )
+ __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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 17, 2), )
Reagent = property(__Reagent.value, __Reagent.set, None, None)
@@ -226,13 +226,13 @@ class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 108, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 108, 12)
_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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 19, 1), )
+ __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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 19, 2), )
ReagentTube = property(__ReagentTube.value, __ReagentTube.set, None, None)
@@ -253,13 +253,13 @@ class CTD_ANON_3 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 115, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 115, 12)
_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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 20, 1), )
+ __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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 20, 2), )
ReagentPlateRow = property(__ReagentPlateRow.value, __ReagentPlateRow.set, None, None)
@@ -280,13 +280,13 @@ class CTD_ANON_4 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 122, 24)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 122, 12)
_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_pbbase, 'ChemistryConfig'), 'ChemistryConfig', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioBaseDataModel_xsdChemistryConfig', True, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 1037, 1), )
+ __ChemistryConfig = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ChemistryConfig'), 'ChemistryConfig', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_4_httppacificbiosciences_comPacBioBaseDataModel_xsdChemistryConfig', True, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 1043, 2), )
ChemistryConfig = property(__ChemistryConfig.value, __ChemistryConfig.set, None, None)
@@ -307,13 +307,13 @@ class CTD_ANON_5 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 133, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 133, 12)
_ElementMap = {}
_AttributeMap = {}
# Base type is pyxb.binding.datatypes.anyType
# Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}Automation uses Python identifier Automation
- __Automation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automation'), 'Automation', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioReagentKit_xsdAutomation', True, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 135, 8), )
+ __Automation = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automation'), 'Automation', '__httppacificbiosciences_comPacBioReagentKit_xsd_CTD_ANON_5_httppacificbiosciences_comPacBioReagentKit_xsdAutomation', True, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 135, 16), )
Automation = property(__Automation.value, __Automation.set, None, None)
@@ -334,7 +334,7 @@ class ReagentType (_ImportedBinding__pbbase.BaseEntityType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 84, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 84, 2)
_ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.BaseEntityType
@@ -359,48 +359,48 @@ class ReagentType (_ImportedBinding__pbbase.BaseEntityType):
# Attribute ReagentKey uses Python identifier ReagentKey
__ReagentKey = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ReagentKey'), 'ReagentKey', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_ReagentKey', _module_typeBindings.ReagentKey, required=True)
- __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 87, 4)
- __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 87, 4)
+ __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 87, 8)
+ __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 87, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 88, 4)
- __PlateColumn._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 88, 4)
+ __PlateColumn._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 88, 8)
+ __PlateColumn._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 88, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 89, 4)
- __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 89, 4)
+ __Volume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 89, 8)
+ __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 89, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 90, 4)
- __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 90, 4)
+ __DeadVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 90, 8)
+ __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 90, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 91, 4)
- __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 91, 4)
+ __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 91, 8)
+ __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 91, 8)
ActiveInHour = property(__ActiveInHour.value, __ActiveInHour.set, None, None)
# Attribute Rows uses Python identifier Rows
__Rows = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Rows'), 'Rows', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentType_Rows', pyxb.binding.datatypes.string, required=True)
- __Rows._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 92, 5)
- __Rows._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 92, 5)
+ __Rows._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 92, 8)
+ __Rows._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 92, 8)
Rows = property(__Rows.value, __Rows.set, None, None)
@@ -426,7 +426,7 @@ class ReagentKitType (_ImportedBinding__pbbase.BaseEntityType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentKitType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 96, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 96, 2)
_ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.BaseEntityType
@@ -434,42 +434,42 @@ class ReagentKitType (_ImportedBinding__pbbase.BaseEntityType):
# Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
# Element {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Defaults uses Python identifier Defaults
- __Defaults = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults'), 'Defaults', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioBaseDataModel_xsdDefaults', False, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 1038, 4), )
+ __Defaults = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults'), 'Defaults', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioBaseDataModel_xsdDefaults', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 1044, 2), )
Defaults = property(__Defaults.value, __Defaults.set, None, 'Default paramaters and filters which may be applied to PartNumber types in order to constrain them via parameterization')
# 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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 100, 5), )
+ __Reagents = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), 'Reagents', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdReagents', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 100, 10), )
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 107, 5), )
+ __ReagentTubes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), 'ReagentTubes', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdReagentTubes', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 107, 10), )
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 114, 5), )
+ __ReagentPlateRows = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), 'ReagentPlateRows', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdReagentPlateRows', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 114, 10), )
ReagentPlateRows = property(__ReagentPlateRows.value, __ReagentPlateRows.set, None, None)
# Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}ChemistryConfigs uses Python identifier ChemistryConfigs
- __ChemistryConfigs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfigs'), 'ChemistryConfigs', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdChemistryConfigs', False, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 121, 20), )
+ __ChemistryConfigs = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfigs'), 'ChemistryConfigs', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdChemistryConfigs', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 121, 10), )
ChemistryConfigs = property(__ChemistryConfigs.value, __ChemistryConfigs.set, None, None)
# Element {http://pacificbiosciences.com/PacBioReagentKit.xsd}Automations uses Python identifier Automations
- __Automations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automations'), 'Automations', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdAutomations', False, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 129, 5), )
+ __Automations = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'Automations'), 'Automations', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentKitType_httppacificbiosciences_comPacBioReagentKit_xsdAutomations', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 129, 10), )
Automations = property(__Automations.value, __Automations.set, None, 'Automations that are deemed compatible with this kit. Parameters specified within an automation will override a parameter with the same name and data type specified in the above Defaults section')
@@ -493,40 +493,40 @@ class ReagentKitType (_ImportedBinding__pbbase.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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 140, 4)
- __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 140, 4)
+ __ProductCode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 140, 8)
+ __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 140, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 141, 4)
- __PlateType._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 141, 4)
+ __PlateType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 141, 8)
+ __PlateType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 141, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 142, 4)
- __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 142, 4)
+ __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 142, 8)
+ __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 142, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 143, 4)
- __BasesPerSecond._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 143, 4)
+ __BasesPerSecond._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 143, 8)
+ __BasesPerSecond._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 143, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 144, 4)
- __AcquisitionCount._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 144, 4)
+ __AcquisitionCount._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 144, 8)
+ __AcquisitionCount._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 144, 8)
AcquisitionCount = property(__AcquisitionCount.value, __AcquisitionCount.set, None, None)
@@ -556,7 +556,7 @@ class ReagentTubeType (_ImportedBinding__pbbase.BaseEntityType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentTubeType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 148, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 148, 2)
_ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.BaseEntityType
@@ -581,80 +581,80 @@ class ReagentTubeType (_ImportedBinding__pbbase.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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 151, 4)
- __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 151, 4)
+ __ProductCode._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 151, 8)
+ __ProductCode._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 151, 8)
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', _module_typeBindings.ReagentKey, required=True)
- __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 152, 4)
- __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 152, 4)
+ __ReagentKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 152, 8)
+ __ReagentKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 152, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 153, 4)
- __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 153, 4)
+ __Volume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 153, 8)
+ __Volume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 153, 8)
Volume = property(__Volume.value, __Volume.set, None, None)
# Attribute UsageVolume uses Python identifier UsageVolume
__UsageVolume = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'UsageVolume'), 'UsageVolume', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_UsageVolume', pyxb.binding.datatypes.double, required=True)
- __UsageVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 154, 4)
- __UsageVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 154, 4)
+ __UsageVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 154, 8)
+ __UsageVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 154, 8)
UsageVolume = property(__UsageVolume.value, __UsageVolume.set, None, None)
# Attribute UsageKey uses Python identifier UsageKey
__UsageKey = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'UsageKey'), 'UsageKey', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentTubeType_UsageKey', pyxb.binding.datatypes.string, required=True)
- __UsageKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 155, 4)
- __UsageKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 155, 4)
+ __UsageKey._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 155, 8)
+ __UsageKey._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 155, 8)
UsageKey = property(__UsageKey.value, __UsageKey.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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 156, 4)
- __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 156, 4)
+ __DeadVolume._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 156, 8)
+ __DeadVolume._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 156, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 157, 4)
- __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 157, 4)
+ __ActiveInHour._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 157, 8)
+ __ActiveInHour._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 157, 8)
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', _module_typeBindings.TubeSize, required=True)
- __TubeWellType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 158, 4)
- __TubeWellType._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 158, 4)
+ __TubeWellType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 158, 8)
+ __TubeWellType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 158, 8)
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', _module_typeBindings.TubeLocation, required=True)
- __ReagentTubeType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 159, 4)
- __ReagentTubeType._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 159, 4)
+ __ReagentTubeType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 159, 8)
+ __ReagentTubeType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 159, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 160, 4)
- __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 160, 4)
+ __InitialUse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 160, 8)
+ __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 160, 8)
InitialUse = property(__InitialUse.value, __InitialUse.set, None, None)
@@ -684,7 +684,7 @@ class ReagentPlateRowType (_ImportedBinding__pbbase.BaseEntityType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRowType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 164, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 164, 2)
_ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.BaseEntityType
@@ -709,24 +709,24 @@ class ReagentPlateRowType (_ImportedBinding__pbbase.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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 167, 4)
- __PlateRow._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 167, 4)
+ __PlateRow._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 167, 8)
+ __PlateRow._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 167, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 168, 4)
- __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 168, 4)
+ __InitialUse._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 168, 8)
+ __InitialUse._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 168, 8)
InitialUse = property(__InitialUse.value, __InitialUse.set, None, None)
# Attribute Reaction uses Python identifier Reaction
__Reaction = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'Reaction'), 'Reaction', '__httppacificbiosciences_comPacBioReagentKit_xsd_ReagentPlateRowType_Reaction', pyxb.binding.datatypes.int, required=True)
- __Reaction._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 169, 5)
- __Reaction._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 169, 5)
+ __Reaction._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 169, 8)
+ __Reaction._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 169, 8)
Reaction = property(__Reaction.value, __Reaction.set, None, None)
@@ -749,7 +749,7 @@ class SupplyKitSequencing (_ImportedBinding__pbbase.PartNumberType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'SupplyKitSequencing')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 21, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 21, 2)
_ElementMap = _ImportedBinding__pbbase.PartNumberType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.PartNumberType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.PartNumberType
@@ -761,28 +761,28 @@ class SupplyKitSequencing (_ImportedBinding__pbbase.PartNumberType):
# Element Defaults ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Defaults) 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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 28, 5), )
+ __ReagentAutomationName = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName'), 'ReagentAutomationName', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdReagentAutomationName', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 28, 10), )
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 33, 5), )
+ __ReagentTubes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), 'ReagentTubes', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdReagentTubes', True, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 33, 10), )
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 38, 5), )
+ __SequencingChemistry = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), 'SequencingChemistry', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdSequencingChemistry', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 38, 10), )
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 39, 5), )
+ __SequencingKitDefinition = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), 'SequencingKitDefinition', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_httppacificbiosciences_comPacBioReagentKit_xsdSequencingKitDefinition', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 39, 10), )
SequencingKitDefinition = property(__SequencingKitDefinition.value, __SequencingKitDefinition.set, None, None)
@@ -828,64 +828,64 @@ class SupplyKitSequencing (_ImportedBinding__pbbase.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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 41, 4)
- __Location._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 41, 4)
+ __Location._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 41, 8)
+ __Location._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 41, 8)
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 46, 4)
- __MaxCollections._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 46, 4)
+ __MaxCollections._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 46, 8)
+ __MaxCollections._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 46, 8)
MaxCollections = property(__MaxCollections.value, __MaxCollections.set, None, 'The number of collections this supply kit is capable of')
# Attribute ActiveHours uses Python identifier ActiveHours
__ActiveHours = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveHours'), 'ActiveHours', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_ActiveHours', pyxb.binding.datatypes.double, unicode_default='0')
- __ActiveHours._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 51, 4)
- __ActiveHours._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 51, 4)
+ __ActiveHours._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 51, 8)
+ __ActiveHours._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 51, 8)
ActiveHours = property(__ActiveHours.value, __ActiveHours.set, None, 'The number of hours that the kit has been active (i.e. hours since first opened)')
# Attribute ActiveHoursLimit uses Python identifier ActiveHoursLimit
__ActiveHoursLimit = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'ActiveHoursLimit'), 'ActiveHoursLimit', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_ActiveHoursLimit', pyxb.binding.datatypes.int, unicode_default='0')
- __ActiveHoursLimit._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 56, 4)
- __ActiveHoursLimit._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 56, 4)
+ __ActiveHoursLimit._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 56, 8)
+ __ActiveHoursLimit._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 56, 8)
ActiveHoursLimit = property(__ActiveHoursLimit.value, __ActiveHoursLimit.set, None, 'The limit on the number of hours after opening that a kit can be used')
# Attribute MaxRunHours uses Python identifier MaxRunHours
__MaxRunHours = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'MaxRunHours'), 'MaxRunHours', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_MaxRunHours', pyxb.binding.datatypes.double, unicode_default='-1')
- __MaxRunHours._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 61, 8)
- __MaxRunHours._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 61, 8)
+ __MaxRunHours._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 61, 8)
+ __MaxRunHours._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 61, 8)
MaxRunHours = property(__MaxRunHours.value, __MaxRunHours.set, None, 'The maximum run hours for a run using this this kit. A negative value indicates unlimited run time.')
# Attribute NumOilTubes uses Python identifier NumOilTubes
__NumOilTubes = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'NumOilTubes'), 'NumOilTubes', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_NumOilTubes', pyxb.binding.datatypes.int, unicode_default='1')
- __NumOilTubes._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 66, 8)
- __NumOilTubes._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 66, 8)
+ __NumOilTubes._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 66, 8)
+ __NumOilTubes._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 66, 8)
NumOilTubes = property(__NumOilTubes.value, __NumOilTubes.set, None, 'The number of oil tubes required to support this sequencing kit.')
# Attribute NumOseTubes uses Python identifier NumOseTubes
__NumOseTubes = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'NumOseTubes'), 'NumOseTubes', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_NumOseTubes', pyxb.binding.datatypes.int, unicode_default='1')
- __NumOseTubes._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 71, 5)
- __NumOseTubes._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 71, 5)
+ __NumOseTubes._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 71, 8)
+ __NumOseTubes._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 71, 8)
NumOseTubes = property(__NumOseTubes.value, __NumOseTubes.set, None, 'The number of os enzyme tubes required to support this sequencing kit.')
# Attribute SupportsDynamicLoading uses Python identifier SupportsDynamicLoading
__SupportsDynamicLoading = pyxb.binding.content.AttributeUse(pyxb.namespace.ExpandedName(None, 'SupportsDynamicLoading'), 'SupportsDynamicLoading', '__httppacificbiosciences_comPacBioReagentKit_xsd_SupplyKitSequencing_SupportsDynamicLoading', pyxb.binding.datatypes.boolean)
- __SupportsDynamicLoading._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 76, 4)
- __SupportsDynamicLoading._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 76, 4)
+ __SupportsDynamicLoading._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 76, 8)
+ __SupportsDynamicLoading._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 76, 8)
SupportsDynamicLoading = property(__SupportsDynamicLoading.value, __SupportsDynamicLoading.set, None, 'Does this automation support dynamic loading?')
@@ -909,24 +909,24 @@ _module_typeBindings.SupplyKitSequencing = SupplyKitSequencing
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 7, 1))
+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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 7, 2))
Namespace.addCategoryObject('elementBinding', PacBioReagentKit.name().localName(), PacBioReagentKit)
-Reagent = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 17, 1))
+Reagent = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 17, 2))
Namespace.addCategoryObject('elementBinding', Reagent.name().localName(), Reagent)
-ReagentKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 18, 1))
+ReagentKit = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 18, 2))
Namespace.addCategoryObject('elementBinding', ReagentKit.name().localName(), ReagentKit)
-ReagentTube = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 19, 1))
+ReagentTube = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 19, 2))
Namespace.addCategoryObject('elementBinding', ReagentTube.name().localName(), ReagentTube)
-ReagentPlateRow = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 20, 1))
+ReagentPlateRow = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 20, 2))
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 18, 1)))
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit'), ReagentKitType, scope=CTD_ANON, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 18, 2)))
def _BuildAutomaton ():
# Remove this helper function from the namespace after it is invoked
@@ -937,7 +937,7 @@ def _BuildAutomaton ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 13, 4))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentKit')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 13, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -948,7 +948,7 @@ 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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 17, 1)))
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagent'), ReagentType, scope=CTD_ANON_, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 17, 2)))
def _BuildAutomaton_ ():
# Remove this helper function from the namespace after it is invoked
@@ -959,7 +959,7 @@ def _BuildAutomaton_ ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagent')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 103, 8))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagent')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 103, 16))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -972,7 +972,7 @@ 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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 19, 1)))
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube'), ReagentTubeType, scope=CTD_ANON_2, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 19, 2)))
def _BuildAutomaton_2 ():
# Remove this helper function from the namespace after it is invoked
@@ -983,7 +983,7 @@ def _BuildAutomaton_2 ():
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 110, 8))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTube')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 110, 16))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -996,7 +996,7 @@ 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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 20, 1)))
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow'), ReagentPlateRowType, scope=CTD_ANON_3, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 20, 2)))
def _BuildAutomaton_3 ():
# Remove this helper function from the namespace after it is invoked
@@ -1007,7 +1007,7 @@ def _BuildAutomaton_3 ():
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 117, 8))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRow')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 117, 16))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -1020,7 +1020,7 @@ CTD_ANON_3._Automaton = _BuildAutomaton_3()
-CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ChemistryConfig'), _ImportedBinding__pbbase.SequencingChemistryConfig, scope=CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 1037, 1)))
+CTD_ANON_4._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ChemistryConfig'), _ImportedBinding__pbbase.SequencingChemistryConfig, scope=CTD_ANON_4, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 1043, 2)))
def _BuildAutomaton_4 ():
# Remove this helper function from the namespace after it is invoked
@@ -1031,7 +1031,7 @@ def _BuildAutomaton_4 ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ChemistryConfig')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 124, 36))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_4._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'ChemistryConfig')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 124, 16))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -1044,7 +1044,7 @@ CTD_ANON_4._Automaton = _BuildAutomaton_4()
-CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automation'), _ImportedBinding__pbbase.AutomationType, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 135, 8)))
+CTD_ANON_5._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automation'), _ImportedBinding__pbbase.AutomationType, scope=CTD_ANON_5, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 135, 16)))
def _BuildAutomaton_5 ():
# Remove this helper function from the namespace after it is invoked
@@ -1055,7 +1055,7 @@ def _BuildAutomaton_5 ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automation')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 135, 8))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_5._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automation')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 135, 16))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -1075,12 +1075,12 @@ def _BuildAutomaton_6 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
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/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(ReagentType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -1093,17 +1093,17 @@ ReagentType._Automaton = _BuildAutomaton_6()
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults'), _ImportedBinding__pbbase.DefaultsType, nillable=pyxb.binding.datatypes.boolean(1), scope=ReagentKitType, documentation='Default paramaters and filters which may be applied to PartNumber types in order to constrain them via parameterization', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 1038, 4)))
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults'), _ImportedBinding__pbbase.DefaultsType, nillable=pyxb.binding.datatypes.boolean(1), scope=ReagentKitType, documentation='Default paramaters and filters which may be applied to PartNumber types in order to constrain them via parameterization', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 1044, 2)))
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), CTD_ANON_, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 100, 5)))
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Reagents'), CTD_ANON_, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 100, 10)))
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), CTD_ANON_2, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 107, 5)))
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes'), CTD_ANON_2, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 107, 10)))
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), CTD_ANON_3, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 114, 5)))
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows'), CTD_ANON_3, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 114, 10)))
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfigs'), CTD_ANON_4, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 121, 20)))
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfigs'), CTD_ANON_4, scope=ReagentKitType, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 121, 10)))
-ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automations'), CTD_ANON_5, nillable=pyxb.binding.datatypes.boolean(1), scope=ReagentKitType, documentation='Automations that are deemed compatible with this kit. Parameters specified within an automation will override a parameter with the same name and data type specified in the above Defaults section', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 129, 5)))
+ReagentKitType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'Automations'), CTD_ANON_5, nillable=pyxb.binding.datatypes.boolean(1), scope=ReagentKitType, documentation='Automations that are deemed compatible with this kit. Parameters specified within an automation will override a parameter with the same name and data type specified in the above Defaults section', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 129, 10)))
def _BuildAutomaton_7 ():
# Remove this helper function from the namespace after it is invoked
@@ -1112,41 +1112,41 @@ def _BuildAutomaton_7 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 128, 20))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 128, 10))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 129, 5))
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 129, 10))
counters.add(cc_2)
states = []
final_update = None
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 100, 5))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Reagents')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 100, 10))
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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 107, 5))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 107, 10))
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(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 114, 5))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentPlateRows')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 114, 10))
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(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfigs')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 121, 20))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ChemistryConfigs')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 121, 10))
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(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 128, 20))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 128, 10))
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_2, False))
- symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automations')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 129, 5))
+ symbol = pyxb.binding.content.ElementUse(ReagentKitType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'Automations')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 129, 10))
st_6 = fac.State(symbol, is_initial=False, final_update=final_update, is_unordered_catenation=False)
states.append(st_6)
transitions = []
@@ -1196,12 +1196,12 @@ def _BuildAutomaton_8 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
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/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(ReagentTubeType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -1221,12 +1221,12 @@ def _BuildAutomaton_9 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
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/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(ReagentPlateRowType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -1239,13 +1239,13 @@ ReagentPlateRowType._Automaton = _BuildAutomaton_9()
-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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 28, 5)))
+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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 28, 10)))
-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/tmptd_ghkedxsds/PacBioReagentKit.xsd', 33, 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/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 33, 10)))
-SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), _ImportedBinding__pbbase.SequencingChemistry, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 38, 5)))
+SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry'), _ImportedBinding__pbbase.SequencingChemistry, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 38, 10)))
-SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), ReagentKitType, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 39, 5)))
+SupplyKitSequencing._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition'), ReagentKitType, scope=SupplyKitSequencing, location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 39, 10)))
def _BuildAutomaton_10 ():
# Remove this helper function from the namespace after it is invoked
@@ -1254,54 +1254,54 @@ def _BuildAutomaton_10 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 206, 5))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 206, 10))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 457, 5))
+ cc_2 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 457, 10))
counters.add(cc_2)
- cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 28, 5))
+ cc_3 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 28, 10))
counters.add(cc_3)
- cc_4 = fac.CounterCondition(min=0, max=2, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 33, 5))
+ cc_4 = fac.CounterCondition(min=0, max=2, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 33, 10))
counters.add(cc_4)
- cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 38, 5))
+ cc_5 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 38, 10))
counters.add(cc_5)
- cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 39, 5))
+ cc_6 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 39, 10))
counters.add(cc_6)
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/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 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(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 206, 5))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'CheckSum')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 206, 10))
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, 'Defaults')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 457, 5))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Defaults')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 457, 10))
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, 'ReagentAutomationName')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 28, 5))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentAutomationName')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 28, 10))
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, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 33, 5))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'ReagentTubes')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 33, 10))
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, 'SequencingChemistry')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 38, 5))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingChemistry')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 38, 10))
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, 'SequencingKitDefinition')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioReagentKit.xsd', 39, 5))
+ symbol = pyxb.binding.content.ElementUse(SupplyKitSequencing._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'SequencingKitDefinition')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioReagentKit.xsd', 39, 10))
st_6 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_6)
transitions = []
=====================================
pbcore/io/dataset/pyxb/_pbsample.py
=====================================
@@ -1,7 +1,7 @@
# pbcore/io/dataset/pyxb/_pbsample.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:a7c0866985dba806fe3112e9fbc4707c9f978443
-# Generated 2020-02-06 10:10:19.700747 by PyXB version 1.2.6 using Python 3.7.3.final.0
+# Generated 2020-04-28 14:07:08.787121 by PyXB version 1.2.6 using Python 3.7.3.final.0
# Namespace http://pacificbiosciences.com/PacBioSampleInfo.xsd [xmlns:pbsample]
from __future__ import unicode_literals
@@ -14,7 +14,7 @@ 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:ef0acb54-490b-11ea-a47b-005056875d19')
+_GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:3866d522-8994-11ea-9798-005056871a22')
# Version of PyXB used to generate the bindings
_PyXBVersion = '1.2.6'
@@ -86,20 +86,20 @@ class CTD_ANON (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 96, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 96, 4)
_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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 103, 5), )
+ __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/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 103, 10), )
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 112, 1), )
+ __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/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 112, 2), )
BarcodedSamplePointers = property(__BarcodedSamplePointers.value, __BarcodedSamplePointers.set, None, 'Back references to other BarcodedSampleType object UniqueIds which utilize this sample')
@@ -121,13 +121,13 @@ class CTD_ANON_ (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 116, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 116, 4)
_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__httppacificbiosciences_comPacBioSampleInfo_xsdBarcodedSamplePointer', True, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 118, 4), )
+ __BarcodedSamplePointer = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), 'BarcodedSamplePointer', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON__httppacificbiosciences_comPacBioSampleInfo_xsdBarcodedSamplePointer', True, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 118, 8), )
BarcodedSamplePointer = property(__BarcodedSamplePointer.value, __BarcodedSamplePointer.set, None, 'Pointer to a group of barcoded samples')
@@ -148,13 +148,13 @@ class CTD_ANON_2 (pyxb.binding.basis.complexTypeDefinition):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 130, 2)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 130, 4)
_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_2_httppacificbiosciences_comPacBioSampleInfo_xsdBioSample', True, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 136, 1), )
+ __BioSample = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), 'BioSample', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON_2_httppacificbiosciences_comPacBioSampleInfo_xsdBioSample', True, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 136, 2), )
BioSample = property(__BioSample.value, __BioSample.set, None, 'An individual biological sample.')
@@ -175,7 +175,7 @@ class BioSampleType (_ImportedBinding__pbbase.BaseEntityType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = pyxb.namespace.ExpandedName(Namespace, 'BioSampleType')
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 8, 1)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 8, 2)
_ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.BaseEntityType
@@ -183,7 +183,7 @@ class BioSampleType (_ImportedBinding__pbbase.BaseEntityType):
# Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
# Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}DNABarcodes uses Python identifier DNABarcodes
- __DNABarcodes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DNABarcodes'), 'DNABarcodes', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_httppacificbiosciences_comPacBioSampleInfo_xsdDNABarcodes', False, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 15, 5), )
+ __DNABarcodes = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DNABarcodes'), 'DNABarcodes', '__httppacificbiosciences_comPacBioSampleInfo_xsd_BioSampleType_httppacificbiosciences_comPacBioSampleInfo_xsdDNABarcodes', False, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 15, 10), )
DNABarcodes = property(__DNABarcodes.value, __DNABarcodes.set, None, 'A list of barcodes associated with the biological sample')
@@ -207,88 +207,88 @@ class BioSampleType (_ImportedBinding__pbbase.BaseEntityType):
# 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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 34, 4)
- __DateReceived._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 34, 4)
+ __DateReceived._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 34, 8)
+ __DateReceived._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 34, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 39, 4)
- __Organism._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 39, 4)
+ __Organism._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 39, 8)
+ __Organism._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 39, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 44, 4)
- __Reference._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 44, 4)
+ __Reference._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 44, 8)
+ __Reference._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 44, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 49, 4)
- __DNAType._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 49, 4)
+ __DNAType._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 49, 8)
+ __DNAType._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 49, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 54, 4)
- __Concentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 54, 4)
+ __Concentration._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 54, 8)
+ __Concentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 54, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 59, 4)
- __QuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 59, 4)
+ __QuantificationMethod._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 59, 8)
+ __QuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 59, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 64, 4)
- __SMRTBellConcentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 64, 4)
+ __SMRTBellConcentration._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 64, 8)
+ __SMRTBellConcentration._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 64, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 69, 4)
- __SMRTBellQuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 69, 4)
+ __SMRTBellQuantificationMethod._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 69, 8)
+ __SMRTBellQuantificationMethod._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 69, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 74, 4)
- __BufferName._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 74, 4)
+ __BufferName._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 74, 8)
+ __BufferName._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 74, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 79, 4)
- __SamplePrepKit._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 79, 4)
+ __SamplePrepKit._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 79, 8)
+ __SamplePrepKit._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 79, 8)
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 84, 4)
- __TargetLibrarySize._UseLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 84, 4)
+ __TargetLibrarySize._DeclarationLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 84, 8)
+ __TargetLibrarySize._UseLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 84, 8)
TargetLibrarySize = property(__TargetLibrarySize.value, __TargetLibrarySize.set, None, '2000, 10000, 20000')
@@ -319,7 +319,7 @@ class CTD_ANON_3 (_ImportedBinding__pbbase.BaseEntityType):
_ContentTypeTag = pyxb.binding.basis.complexTypeDefinition._CT_ELEMENT_ONLY
_Abstract = False
_ExpandedName = None
- _XSDLocation = pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 19, 6)
+ _XSDLocation = pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 19, 12)
_ElementMap = _ImportedBinding__pbbase.BaseEntityType._ElementMap.copy()
_AttributeMap = _ImportedBinding__pbbase.BaseEntityType._AttributeMap.copy()
# Base type is _ImportedBinding__pbbase.BaseEntityType
@@ -327,7 +327,7 @@ class CTD_ANON_3 (_ImportedBinding__pbbase.BaseEntityType):
# Element Extensions ({http://pacificbiosciences.com/PacBioBaseDataModel.xsd}Extensions) inherited from {http://pacificbiosciences.com/PacBioBaseDataModel.xsd}BaseEntityType
# Element {http://pacificbiosciences.com/PacBioSampleInfo.xsd}DNABarcode uses Python identifier DNABarcode
- __DNABarcode = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DNABarcode'), 'DNABarcode', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioSampleInfo_xsdDNABarcode', True, pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 23, 10), )
+ __DNABarcode = pyxb.binding.content.ElementDeclaration(pyxb.namespace.ExpandedName(Namespace, 'DNABarcode'), 'DNABarcode', '__httppacificbiosciences_comPacBioSampleInfo_xsd_CTD_ANON_3_httppacificbiosciences_comPacBioSampleInfo_xsdDNABarcode', True, pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 23, 20), )
DNABarcode = property(__DNABarcode.value, __DNABarcode.set, None, 'A sequence of barcodes associated with the biological sample')
@@ -357,23 +357,23 @@ class CTD_ANON_3 (_ImportedBinding__pbbase.BaseEntityType):
_module_typeBindings.CTD_ANON_3 = CTD_ANON_3
-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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 92, 1))
+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/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 92, 2))
Namespace.addCategoryObject('elementBinding', BioSamplePointers.name().localName(), BioSamplePointers)
-BarcodedSamplePointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 112, 1))
+BarcodedSamplePointers = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 112, 2))
Namespace.addCategoryObject('elementBinding', BarcodedSamplePointers.name().localName(), BarcodedSamplePointers)
-BioSamples = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_2, documentation='List of biological samples.', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 126, 1))
+BioSamples = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSamples'), CTD_ANON_2, documentation='List of biological samples.', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 126, 2))
Namespace.addCategoryObject('elementBinding', BioSamples.name().localName(), BioSamples)
-BioSample = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, documentation='An individual biological sample.', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 136, 1))
+BioSample = pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, documentation='An individual biological sample.', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 136, 2))
Namespace.addCategoryObject('elementBinding', BioSample.name().localName(), BioSample)
-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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 103, 5)))
+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/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 103, 10)))
-CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_, scope=CTD_ANON, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 112, 1)))
+CTD_ANON._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers'), CTD_ANON_, scope=CTD_ANON, documentation='Back references to other BarcodedSampleType object UniqueIds which utilize this sample', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 112, 2)))
def _BuildAutomaton ():
# Remove this helper function from the namespace after it is invoked
@@ -384,11 +384,11 @@ def _BuildAutomaton ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 102, 5))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointers')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 102, 10))
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/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 103, 5))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSamplePointer')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 103, 10))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
transitions = []
@@ -401,7 +401,7 @@ CTD_ANON._Automaton = _BuildAutomaton()
-CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_, documentation='Pointer to a group of barcoded samples', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 118, 4)))
+CTD_ANON_._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer'), pyxb.binding.datatypes.IDREF, scope=CTD_ANON_, documentation='Pointer to a group of barcoded samples', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 118, 8)))
def _BuildAutomaton_ ():
# Remove this helper function from the namespace after it is invoked
@@ -412,7 +412,7 @@ def _BuildAutomaton_ ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 118, 4))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BarcodedSamplePointer')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 118, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -425,7 +425,7 @@ CTD_ANON_._Automaton = _BuildAutomaton_()
-CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, scope=CTD_ANON_2, documentation='An individual biological sample.', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 136, 1)))
+CTD_ANON_2._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'BioSample'), BioSampleType, scope=CTD_ANON_2, documentation='An individual biological sample.', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 136, 2)))
def _BuildAutomaton_2 ():
# Remove this helper function from the namespace after it is invoked
@@ -436,7 +436,7 @@ def _BuildAutomaton_2 ():
counters = set()
states = []
final_update = set()
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSample')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 132, 4))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_2._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'BioSample')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 132, 8))
st_0 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_0)
transitions = []
@@ -449,7 +449,7 @@ CTD_ANON_2._Automaton = _BuildAutomaton_2()
-BioSampleType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DNABarcodes'), CTD_ANON_3, scope=BioSampleType, documentation='A list of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 15, 5)))
+BioSampleType._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DNABarcodes'), CTD_ANON_3, scope=BioSampleType, documentation='A list of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 15, 10)))
def _BuildAutomaton_3 ():
# Remove this helper function from the namespace after it is invoked
@@ -458,19 +458,19 @@ def _BuildAutomaton_3 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 15, 5))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 15, 10))
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/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 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(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DNABarcodes')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 15, 5))
+ symbol = pyxb.binding.content.ElementUse(BioSampleType._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DNABarcodes')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 15, 10))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
transitions = []
@@ -489,7 +489,7 @@ BioSampleType._Automaton = _BuildAutomaton_3()
-CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DNABarcode'), _ImportedBinding__pbbase.DNABarcode, scope=CTD_ANON_3, documentation='A sequence of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 23, 10)))
+CTD_ANON_3._AddElement(pyxb.binding.basis.element(pyxb.namespace.ExpandedName(Namespace, 'DNABarcode'), _ImportedBinding__pbbase.DNABarcode, scope=CTD_ANON_3, documentation='A sequence of barcodes associated with the biological sample', location=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 23, 20)))
def _BuildAutomaton_4 ():
# Remove this helper function from the namespace after it is invoked
@@ -498,23 +498,23 @@ def _BuildAutomaton_4 ():
import pyxb.utils.fac as fac
counters = set()
- cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 19, 6))
+ cc_0 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 19, 12))
counters.add(cc_0)
- cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ cc_1 = fac.CounterCondition(min=0, max=1, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 6))
counters.add(cc_1)
- cc_2 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 23, 10))
+ cc_2 = fac.CounterCondition(min=0, max=None, metadata=pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 23, 20))
counters.add(cc_2)
states = []
final_update = set()
final_update.add(fac.UpdateInstruction(cc_0, False))
final_update.add(fac.UpdateInstruction(cc_1, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioBaseDataModel.xsd', 98, 3))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(_Namespace_pbbase, 'Extensions')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioBaseDataModel.xsd', 98, 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_0, False))
final_update.add(fac.UpdateInstruction(cc_2, False))
- symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DNABarcode')), pyxb.utils.utility.Location('/tmp/tmptd_ghkedxsds/PacBioSampleInfo.xsd', 23, 10))
+ symbol = pyxb.binding.content.ElementUse(CTD_ANON_3._UseForTag(pyxb.namespace.ExpandedName(Namespace, 'DNABarcode')), pyxb.utils.utility.Location('/tmp/tmpr3ccwhurxsds/PacBioSampleInfo.xsd', 23, 20))
st_1 = fac.State(symbol, is_initial=True, final_update=final_update, is_unordered_catenation=False)
states.append(st_1)
transitions = []
=====================================
pbcore/util/statistics.py
=====================================
@@ -5,6 +5,9 @@ import numpy as np
class Constants:
MAX_QV = 60
+ # (identical) cutoffs for RQ and QV for "High-Fidelity" reads
+ HIFI_QV = 20
+ HIFI_RQ = 0.99
def accuracy_as_phred_qv(accuracy, max_qv=Constants.MAX_QV):
@@ -26,3 +29,12 @@ def accuracy_as_phred_qv(accuracy, max_qv=Constants.MAX_QV):
zero_error = error_rate < min_error_rate
error_rate[zero_error] = min_error_rate
return -10 * np.log10(error_rate)
+
+
+def phred_qv_as_accuracy(qv):
+ if qv == 0:
+ return 0
+ elif qv < 0:
+ raise ValueError("Negative Phred scores not allowed")
+ else:
+ return 1.0 - 10**(-qv/10)
=====================================
setup.py
=====================================
@@ -16,7 +16,7 @@ test_deps = [
setup(
name='pbcore',
- version='2.0.1',
+ version='2.0.8',
author='Pacific Biosciences',
author_email='devnet at pacificbiosciences.com',
description='A Python library for reading and writing PacBio® data files',
=====================================
tests/test_pbcore_util.py
=====================================
@@ -1,7 +1,7 @@
import pytest
import sys
-from pbcore.util.statistics import accuracy_as_phred_qv
+from pbcore.util.statistics import accuracy_as_phred_qv, phred_qv_as_accuracy
class TestStatistics:
@@ -14,3 +14,11 @@ class TestStatistics:
qv = accuracy_as_phred_qv([0.95, 1.0, 0.99999])
qvs = [int(round(x)) for x in qv]
assert qvs == [13, 60, 50]
+
+ def test_phred_qv_as_accuracy(self):
+ assert phred_qv_as_accuracy(20) == 0.99
+ assert phred_qv_as_accuracy(30) == 0.999
+ assert phred_qv_as_accuracy(10) == 0.9
+ assert phred_qv_as_accuracy(0) == 0
+ with pytest.raises(ValueError):
+ x = phred_qv_as_accuracy(-1)
=====================================
tests/test_pbdataset.py
=====================================
@@ -1189,6 +1189,12 @@ class TestDataSet:
assert ds.isIndexed
assert not ds.isMapped
+ def test_numbarcodes(self):
+ import pbtestdata
+ inp = pbtestdata.get_file("barcoded-subreadset")
+ ds = SubreadSet(inp, strict=True)
+ assert ds.numBarcodes == 3
+
@pytest.mark.internal_data
@pytest.mark.constools
def test_copyTo_same_base_names(self):
=====================================
tests/test_pbdataset_subtypes.py
=====================================
@@ -1044,3 +1044,17 @@ class TestDataSet:
fn = upstreamData.getEmptyBam2()
ds = AlignmentSet(fn)
assert len(ds) == 0
+
+ @pytest.mark.constools
+ def test_generate_indices(self):
+ import pbtestdata
+ tmp_bam = tempfile.NamedTemporaryFile(suffix=".subreads.bam").name
+ tmp_pbi = tmp_bam + ".pbi"
+ tmp_bai = tmp_bam + ".bai"
+ shutil.copyfile(pbtestdata.get_file("subreads-bam"), tmp_bam)
+ ds = openDataFile(tmp_bam, strict=False, generateIndices=True)
+ assert ds.externalResources[0].pbi == tmp_pbi
+ assert ds.externalResources[0].bai == tmp_bai
+ assert os.path.isfile(tmp_pbi)
+ assert os.path.isfile(tmp_bai)
+ assert len(ds) == 117
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/commit/8b1d4422b64482dafa1885475576c388214b36d3
--
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/commit/8b1d4422b64482dafa1885475576c388214b36d3
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