[med-svn] [mage2tab] 14/15: Update upstream source from tag 'upstream/0.9'
Andreas Tille
tille at debian.org
Sun Dec 10 17:34:36 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mage2tab.
commit 1dd266ff1458a849545b3df820f622747154fbf0
Merge: 77dd50c d47b90c
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 10 18:33:08 2017 +0100
Update upstream source from tag 'upstream/0.9'
Update to upstream version '0.9'
with Debian dir 6652ae9ea0103b1288bfffbe64b60f4773b8525c
README | 62 +
bin/mage-checker.pl | 95 +
bin/mage2graph.pl | 94 +
bin/mage2tab.pl | 91 +
config/config_VoToMageTab.xml | 23 +
config/log4perl.config | 46 +
lib/perl/RAD/MR_T/MageImport/Loggable.pm | 17 +
lib/perl/RAD/MR_T/MageImport/MageImportError.pm | 215 +
.../MageImport/Service/AbstractProcessModule.pm | 23 +
.../MR_T/MageImport/Service/AbstractProcessor.pm | 8 +
.../RAD/MR_T/MageImport/Service/AbstractReader.pm | 80 +
.../MR_T/MageImport/Service/AbstractReporter.pm | 11 +
.../RAD/MR_T/MageImport/Service/AbstractTester.pm | 11 +
.../MR_T/MageImport/Service/AbstractTranslator.pm | 38 +
.../MR_T/MageImport/Service/AbstractValidator.pm | 13 +
.../MageImport/Service/AbstractValidatorRule.pm | 45 +
.../Service/ProcessModule/BlankModule.pm | 25 +
.../Service/ProcessModule/MakeTreatmentSeries.pm | 93 +
.../MergeTreatmentSeriesForSpeciedBiomatAction.pm | 84 +
.../Service/ProcessModule/NamingAcqAndQuan.pm | 58 +
.../Service/ProcessModule/NamingBioSource.pm | 44 +
.../ProcessModule/SetQuanProtocolToGusProtocol.pm | 70 +
lib/perl/RAD/MR_T/MageImport/Service/Processor.pm | 36 +
.../MageImport/Service/Reader/MageTabReader.pm | 1423 ++++
.../MR_T/MageImport/Service/Reader/MagemlReader.pm | 822 ++
.../MR_T/MageImport/Service/Reader/MockReader.pm | 386 +
.../MageImport/Service/Reporter/SqlReporter.pm | 233 +
.../MR_T/MageImport/Service/Tester/SqlTester.pm | 210 +
.../MR_T/MageImport/Service/Translator/VoToDot.pm | 119 +
.../Service/Translator/VoToGusTranslator.pm | 2069 +++++
.../MageImport/Service/Translator/VoToMageTab.pm | 1328 +++
lib/perl/RAD/MR_T/MageImport/Service/Validator.pm | 127 +
.../Service/ValidatorRule/AssayHasContact.pm | 56 +
.../Service/ValidatorRule/AssayHasFactorValue.pm | 66 +
.../ValidatorRule/AssayHasLexAndNoHangingLex.pm | 80 +
.../MageImport/Service/ValidatorRule/BlankRule.pm | 25 +
.../Service/ValidatorRule/CheckDataFiles.pm | 156 +
.../ValidatorRule/CheckExistingGusProtocols.pm | 102 +
.../Service/ValidatorRule/NoHangingBioMaterials.pm | 108 +
.../Service/ValidatorRule/ProtocolHasMgedType.pm | 136 +
.../ValidatorRule/StudyDesignHasMgedType.pm | 166 +
.../StudyHasContactAndNameAndDescription.pm | 62 +
.../ValidatorRule/StudyHasDesignsAndFactors.pm | 60 +
.../Service/ValidatorRule/StudyNameNotInGus.pm | 77 +
lib/perl/RAD/MR_T/MageImport/ServiceFactory.pm | 381 +
.../RAD/MR_T/MageImport/Test/Odom_ChIP_test.xml | 8520 ++++++++++++++++++++
.../RAD/MR_T/MageImport/Test/TestAcquisitionVO.pm | 112 +
.../RAD/MR_T/MageImport/Test/TestAffiliationVO.pm | 93 +
.../MR_T/MageImport/Test/TestAssayHasContact.pm | 53 +
.../Test/TestAssayHasLexAndNoHangingLex.pm | 62 +
lib/perl/RAD/MR_T/MageImport/Test/TestAssayVO.pm | 113 +
.../Test/TestBioMaterialMeasurementVO.pm | 76 +
.../RAD/MR_T/MageImport/Test/TestBioMaterialVO.pm | 118 +
.../RAD/MR_T/MageImport/Test/TestConfigChecking.pm | 75 +
lib/perl/RAD/MR_T/MageImport/Test/TestDocRoot.pm | 183 +
.../RAD/MR_T/MageImport/Test/TestExceptions.pm | 65 +
.../MR_T/MageImport/Test/TestExternalDatabaseVO.pm | 56 +
.../RAD/MR_T/MageImport/Test/TestMageTabReader.pm | 805 ++
.../RAD/MR_T/MageImport/Test/TestMagemlReader.pm | 91 +
lib/perl/RAD/MR_T/MageImport/Test/TestMain.pm | 167 +
.../MageImport/Test/TestMakeTreatmentSeries.pm | 76 +
...stMergeTreatmentSeriesForSpeciedBiomatAction.pm | 63 +
.../MR_T/MageImport/Test/TestNamingAcqAndQuan.pm | 44 +
.../MageImport/Test/TestNoHangingBioMaterials.pm | 63 +
.../MR_T/MageImport/Test/TestOntologyEntryVO.pm | 54 +
.../MR_T/MageImport/Test/TestParameterValueVO.pm | 43 +
lib/perl/RAD/MR_T/MageImport/Test/TestPersonVO.pm | 107 +
.../RAD/MR_T/MageImport/Test/TestProcessModule.pm | 105 +
.../MageImport/Test/TestProtocolHasMgedType.pm | 72 +
.../MR_T/MageImport/Test/TestProtocolParamVO.pm | 88 +
.../RAD/MR_T/MageImport/Test/TestProtocolVO.pm | 168 +
.../MR_T/MageImport/Test/TestQuantificationVO.pm | 74 +
.../RAD/MR_T/MageImport/Test/TestServiceFactory.pm | 62 +
.../Test/TestSetQuanProtocolToGusProtocol.pm | 48 +
.../RAD/MR_T/MageImport/Test/TestSqlReporter.pm | 93 +
lib/perl/RAD/MR_T/MageImport/Test/TestSqlTester.pm | 156 +
.../MageImport/Test/TestStudyDesignHasMgedType.pm | 82 +
.../RAD/MR_T/MageImport/Test/TestStudyDesignVO.pm | 83 +
.../RAD/MR_T/MageImport/Test/TestStudyFactorVO.pm | 55 +
.../MR_T/MageImport/Test/TestStudyNameNotInGus.pm | 80 +
lib/perl/RAD/MR_T/MageImport/Test/TestStudyVO.pm | 76 +
.../RAD/MR_T/MageImport/Test/TestTreatmentVO.pm | 127 +
lib/perl/RAD/MR_T/MageImport/Test/TestUtil.pm | 91 +
lib/perl/RAD/MR_T/MageImport/Test/TestValidator.pm | 115 +
.../RAD/MR_T/MageImport/Test/TestValidatorRule.pm | 111 +
.../MR_T/MageImport/Test/TestVoGusTranslator.pm | 1431 ++++
.../RAD/MR_T/MageImport/Test/TestVoToMageTab.pm | 60 +
lib/perl/RAD/MR_T/MageImport/Test/VOTestSuite.pm | 48 +
lib/perl/RAD/MR_T/MageImport/Test/config.xml | 44 +
.../MR_T/MageImport/Test/config_VoToMageTab.xml | 23 +
.../RAD/MR_T/MageImport/Test/config_forOdom.xml | 48 +
.../MR_T/MageImport/Test/config_fortestmain.xml | 45 +
.../RAD/MR_T/MageImport/Test/config_not_good.xml | 27 +
.../RAD/MR_T/MageImport/Test/config_not_good2.xml | 27 +
.../MR_T/MageImport/Test/config_testMageTab.xml | 22 +
.../RAD/MR_T/MageImport/Test/mageTabExample.tab | 51 +
lib/perl/RAD/MR_T/MageImport/Test/sqlReporter.txt | 92 +
.../MR_T/MageImport/Test/sqlTest_fortestmain.txt | 28 +
lib/perl/RAD/MR_T/MageImport/Test/test.xml | 1437 ++++
lib/perl/RAD/MR_T/MageImport/Test/toxoTemplate.tab | 48 +
lib/perl/RAD/MR_T/MageImport/Util.pm | 160 +
lib/perl/RAD/MR_T/MageImport/VO/AcquisitionVO.pm | 139 +
lib/perl/RAD/MR_T/MageImport/VO/AffiliationVO.pm | 18 +
lib/perl/RAD/MR_T/MageImport/VO/AssayVO.pm | 158 +
.../MR_T/MageImport/VO/BioMaterialMeasurementVO.pm | 51 +
lib/perl/RAD/MR_T/MageImport/VO/BioMaterialVO.pm | 83 +
lib/perl/RAD/MR_T/MageImport/VO/ContactVO.pm | 50 +
lib/perl/RAD/MR_T/MageImport/VO/DocRoot.pm | 224 +
.../RAD/MR_T/MageImport/VO/ExternalDatabaseVO.pm | 50 +
lib/perl/RAD/MR_T/MageImport/VO/FactorValueVO.pm | 51 +
lib/perl/RAD/MR_T/MageImport/VO/OntologyEntryVO.pm | 51 +
.../RAD/MR_T/MageImport/VO/ParameterValueVO.pm | 51 +
lib/perl/RAD/MR_T/MageImport/VO/PersonVO.pm | 42 +
lib/perl/RAD/MR_T/MageImport/VO/ProcessVO.pm | 95 +
lib/perl/RAD/MR_T/MageImport/VO/ProtocolParamVO.pm | 68 +
lib/perl/RAD/MR_T/MageImport/VO/ProtocolVO.pm | 123 +
.../RAD/MR_T/MageImport/VO/QuantificationVO.pm | 93 +
lib/perl/RAD/MR_T/MageImport/VO/StudyDesignVO.pm | 87 +
lib/perl/RAD/MR_T/MageImport/VO/StudyFactorVO.pm | 43 +
lib/perl/RAD/MR_T/MageImport/VO/StudyVO.pm | 83 +
lib/perl/RAD/MR_T/MageImport/VO/TreatmentVO.pm | 88 +
lib/perl/RAD/MR_T/MageImport/VO/VOBase.pm | 114 +
lib/xml/mage.xslt | 28 +
123 files changed, 27580 insertions(+)
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