[med-svn] [sra-sdk] 01/01: Try to run test suite but failed. Since I probably need some help here I'm waiting until ncbi-vdb has passed new queue.
Andreas Tille
tille at debian.org
Mon Jul 25 11:06:26 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit a3d8e304389f5195dfcf0efb1333a24060ff9591
Author: Andreas Tille <tille at debian.org>
Date: Mon Jul 25 13:04:59 2016 +0200
Try to run test suite but failed. Since I probably need some help here I'm waiting until ncbi-vdb has passed new queue.
---
debian/patches/series | 1 +
debian/patches/set_explicit_path_to_schemata.patch | 186 +++++++++++++++++++++
debian/rules | 4 +-
3 files changed, 189 insertions(+), 2 deletions(-)
diff --git a/debian/patches/series b/debian/patches/series
index a606f84..029693f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@ link_debian_packaged_libz.patch
link_debian_packaged_lmagic.patch
dont_use_static_lib.patch
fix_tests.patch
+set_explicit_path_to_schemata.patch
diff --git a/debian/patches/set_explicit_path_to_schemata.patch b/debian/patches/set_explicit_path_to_schemata.patch
new file mode 100644
index 0000000..3b0817e
--- /dev/null
+++ b/debian/patches/set_explicit_path_to_schemata.patch
@@ -0,0 +1,186 @@
+--- a/test/fastq-loader/test-fastq-loader.cpp
++++ b/test/fastq-loader/test-fastq-loader.cpp
+@@ -146,7 +146,7 @@ public:
+ string dbName;
+ };
+ const string TempFileFixture::TempDir = "./tmp";
+-const string TempFileFixture::SchemaPath = "align/align.vschema";
++const string TempFileFixture::SchemaPath = "/usr/lib/ncbi-vdb/align/align.vschema";
+ const string TempFileFixture::DbType = "NCBI:align:db:alignment_unsorted";
+
+ ///////////////////////////////////////////////// FASTQ-based tests for CommonWriter
+--- a/test/general-loader/test-general-loader.cpp
++++ b/test/general-loader/test-general-loader.cpp
+@@ -488,7 +488,7 @@ FIXTURE_TEST_CASE ( BadSchemaFileName_Lo
+
+ FIXTURE_TEST_CASE ( BadSchemaName, GeneralLoaderFixture )
+ {
+- SetUpStream ( GetName(), "align/align.vschema", "bad schema name" );
++ SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", "bad schema name" );
+ m_source . OpenStreamEvent();
+
+ REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );
+@@ -496,7 +496,7 @@ FIXTURE_TEST_CASE ( BadSchemaName, Gener
+
+ FIXTURE_TEST_CASE ( BadSchemaName_Long, GeneralLoaderFixture )
+ {
+- SetUpStream ( GetName(), "align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) );
++ SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) );
+ m_source . OpenStreamEvent();
+
+ REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );
+--- a/test/general-loader/makeinputs.cpp
++++ b/test/general-loader/makeinputs.cpp
+@@ -69,7 +69,7 @@ OneTableOneColumnWithDefaults( const str
+ TestSource source;
+ TestSource::packed = p_packed;
+
+- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
+ source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
+
+ source . NewTableEvent ( 1, tableName );
+@@ -104,7 +104,7 @@ ErrorMessage( const string& p_caseId, bo
+ TestSource source;
+ TestSource::packed = p_packed;
+
+- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
+ source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
+
+ source . NewTableEvent ( 1, tableName );
+@@ -123,7 +123,7 @@ EmptyDefaultValue( const string& p_caseI
+ TestSource source;
+ TestSource::packed = p_packed;
+
+- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
+ source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
+
+ source . NewTableEvent ( 1, tableName );
+@@ -143,7 +143,7 @@ MoveAhead( const string& p_caseId, bool
+ TestSource source;
+ TestSource::packed = p_packed;
+
+- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
+ source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
+
+ source . NewTableEvent ( 1, tableName );
+@@ -172,7 +172,7 @@ IntegerCompression( const string& p_case
+ TestSource source;
+ TestSource::packed = true;
+
+- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
+ source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
+
+ source . NewTableEvent ( 1, tableName );
+@@ -194,7 +194,7 @@ SoftwareIdString( const string& p_caseId
+ TestSource source;
+ TestSource::packed = true;
+
+- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
+ source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
+
+ source . SoftwareNameEvent ( string ( "some software" ), string ( "9.8.7654" ) );
+--- a/tools/fastq-loader/fastq-loader.c
++++ b/tools/fastq-loader/fastq-loader.c
+@@ -253,7 +253,7 @@ rc_t CC Usage (const Args * args)
+
+ /* MARK: Definitions and Globals */
+
+-#define SCHEMAFILE "align/align.vschema"
++#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema"
+
+ CommonWriterSettings G;
+
+--- a/tools/bam-loader/bam-loader.c
++++ b/tools/bam-loader/bam-loader.c
+@@ -553,7 +553,7 @@ rc_t CC Usage (const Args * args)
+
+ /* MARK: Definitions and Globals */
+
+-#define SCHEMAFILE "align/align.vschema"
++#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema"
+
+ Globals G;
+
+--- a/tools/sra-sort/run.c
++++ b/tools/sra-sort/run.c
+@@ -78,7 +78,7 @@ bool map_typename_builtin ( const ctx_t
+
+ #define ALIGN_EVIDENCE_MAP "NCBI:align:db:alignment_evidence_sorted"
+ #define ALIGN_UNSORTED_MAP "NCBI:align:db:alignment_sorted"
+-#define ALIGN_SRC "align/align.vschema"
++#define ALIGN_SRC "/usr/lib/ncbi-vdb/align/align.vschema"
+
+ if ( strcmp ( out, "NCBI/align/db/alignment_evidence" ) == 0 )
+ copied = string_copy ( out, size, ALIGN_EVIDENCE_MAP, sizeof ALIGN_EVIDENCE_MAP - 1 );
+--- a/tools/cg-load/cg-load.c
++++ b/tools/cg-load/cg-load.c
+@@ -1073,7 +1073,7 @@ rc_t CC KMain( int argc, char* argv[] )
+ const XMLLogger* xml_logger = NULL;
+ SParam params;
+ memset(¶ms, 0, sizeof(params));
+- params.schema = "align/align.vschema";
++ params.schema = "/usr/lib/ncbi-vdb/align/align.vschema";
+
+ params.argv0 = argv[0];
+
+--- a/tools/util/sortreadtest.c
++++ b/tools/util/sortreadtest.c
+@@ -21,11 +21,11 @@
+
+ /*
+
+- default file is "ncbi/seq.vschema"
++ default file is "/usr/lib/ncbi-vdb/ncbi/seq.vschema"
+ default table-spec "NCBI:tbl:base_space#2"
+
+ */
+-#define SCHEMASPEC "ncbi/seq.vschema"
++#define SCHEMASPEC "/usr/lib/ncbi-vdb/ncbi/seq.vschema"
+ #define TYPESPEC "NCBI:tbl:base_space#2"
+
+ const char UsageDefaultName[] = "sortreadtest";
+--- a/tools/vdb-copy/vdb-copy.kfg
++++ b/tools/vdb-copy/vdb-copy.kfg
+@@ -25,11 +25,11 @@
+ # matching legacy-tables with schema's to write to for vdb-copy
+
+ # ILLUMINA
+-/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/schema = "sra/illumina.vschema"
++/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/schema = "/usr/lib/ncbi-vdb/sra/illumina.vschema"
+ #/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:q4:v2"
+ #/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:q1:v2"
+ /VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:phred:v2"
+-/VDBCOPY/_ILLUMINA_/schema = "sra/illumina.vschema"
++/VDBCOPY/_ILLUMINA_/schema = "/usr/lib/ncbi-vdb/sra/illumina.vschema"
+ /VDBCOPY/_ILLUMINA_/tab = "NCBI:SRA:Illumina:tbl:phred:v2"
+
+
+@@ -41,9 +41,9 @@
+
+
+ # ABSOLID
+-/VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/schema = "sra/abi.vschema"
++/VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/schema = "/usr/lib/ncbi-vdb/sra/abi.vschema"
+ /VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/tab = "NCBI:SRA:ABI:tbl:v2"
+-/VDBCOPY/_ABSOLID_/schema = "sra/abi.vschema"
++/VDBCOPY/_ABSOLID_/schema = "/usr/lib/ncbi-vdb/sra/abi.vschema"
+ /VDBCOPY/_ABSOLID_/tab = "NCBI:SRA:ABI:tbl:v2"
+
+
+--- a/tools/pacbio-load/pl-context.h
++++ b/tools/pacbio-load/pl-context.h
+@@ -52,7 +52,7 @@ extern "C" {
+ #define ALIAS_WITH_PROGRESS "p"
+ #define ALIAS_OUTPUT "o"
+
+-#define DFLT_SCHEMA "sra/pacbio.vschema"
++#define DFLT_SCHEMA "/usr/lib/ncbi-vdb/sra/pacbio.vschema"
+ #define PACBIO_SCHEMA_DB "NCBI:SRA:PacBio:smrt:db"
+
+
diff --git a/debian/rules b/debian/rules
index cccbb2b..dfad0a0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -33,8 +33,8 @@ override_dh_install:
done
dh_install
-override_dh_auto_test:
- echo "FIXME: try activating tests!!!!!!!!!!!!!!!!!!!!!!!!"
+#override_dh_auto_test:
+# echo "FIXME: try activating tests!!!!!!!!!!!!!!!!!!!!!!!!"
override_dh_prep:
dh_prep -X debian/tmp
--
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