Activity for Elvira
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isingh committed [c8af32]
Merge remote-tracking branch 'origin/master' into PBI_112061_Elvira
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James Christensen committed [e2cd95]
add not null assertion for regionNumber in numberLookup test
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flumb database has been retired
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fluutr database is retired
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remove retired database flumb
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removed 2 tests for retired databases
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Paolo Amedeo committed [bcc09b]
Modified queries pulling database names and usage from
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Introduced changes in Perl scripts to accommodate for archived
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remove double entry from Larus glaucescens and add Larus hyperboreus -> Glaucous Gull
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Added a number of avian mappings
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Fixed a typo in query in TIGR::GLKLib.pm and cleaned up code in two Perl
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GLKLib.pm - changed query for getting all VGD databases to check in
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A few more changes to archiveSamples.pl to make it working independently
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Added option for archiving also samples having a sample ID not found in
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VA-996. Add separate STRAIN_CODE. VIRUS_NAME alone is now preferred over SPECIES_CODE (see VA-668)
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add black-bellied tree duck to host map
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Lihui Hu committed [808bf8]
modify ProjectAgreementRecordStatistics to print out tuples with emtpy jira status instead of throwing exceptions
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just for testing
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resolve conflict
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test version
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classpath and gitignore
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First version of using primer mapping file.
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modify test on ElviraSeuqenceMigrationService
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first save, not working yet
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testing
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remove temp test cleanup file
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clean up testing data first working version
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Merge branch 'primerMapNoExtraClass'
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modify IdtTubeOrder to sort the output excel rows, change number cell datatype in picklist and Genewiz order form
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preserve the input order in genewiz form
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put empty strings in the new columns in the CustomClosure3130SequencePicklistWriter class.
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Remove tests on obsoleted sanger form templates
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Add autoColumnSize
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adjust excel columns
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Remove sigma option
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modify sanger order forms basic working version
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First version of using primer mapping file.
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Modify EUID class for application programs.
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Merge branch 'master' of ssh://git.code.sf.net/p/elvira/git
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runDeepSequencingAnalysis.pl - Modified code not to hang in the case
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findVariants.pl - Corrected bug in frequency on call to CLC
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runDeepSequencingAnalysis.pl - fixed bug causing infinite loop on
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findVariants.pl - modified to allow handling "extended BAC ID" (i.e.
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Added wait time between grid job submissions, in order to minimize
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Add back default option to RunFluValidator2.
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Modify BioSampleDTO.java to generate more detailed error message.
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Modify error return in RanFluValidator2.
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Start working on produce both validatioin report and tbl output.
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Modify fluValidator2 so that users get both validation report and tbl info.
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Merge branch 'fluValidator2'
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Corrected CLC scratch path in DSA scripts
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fix error id for BLINDED-WRONG
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move errorFilter to method
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change message filter to function to allow up-leveling errors as well as down leveling errors
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use LocalDate rather than Date objects for comparison
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set default levels for validations
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allow setting message levels for validations, changing ignoreErrors to setMessageLevel
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Added --include_pending_sra option to
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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set source and target for javac
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Merge branch 'master' into sf/trunk/vhtngs-1027
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Remove ctm related options in CreateClosureOrder
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Modify testEUID unit test.
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Modify import
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Move hibernate mapping class
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Modify import for mapping class
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Debuging the unit test: TestLoadCustomPrimersIntoGLK.
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Unit test for LoadCustomPrimerIntoGLK
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Basic working version, will add more details and clean up.
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Merge branch 'primer'
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Merge branch 'memDB'
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Modify AutoPopulate concordion test to catch the exception.
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Modify assertEquals for doubles in TestBasecalls.
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Add consistency check on blinded number set on input spreadsheet.
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Modify deprecated junit headers to junit 4 version
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Modify junit assertion import to junit 4 verson in TestHsqlDbTest.
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Merge branch 'master' of ssh://git.code.sf.net/p/elvira/git
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Modify email address.
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Added script Extract_Low_Coverage_Areas.pl which parses autoTasker2
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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Lihui Hu committed [745be2]
Remove premature unit test of TestLoadCustomPrimersIntoGLK
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Lihui Hu committed [be1322]
Add date check in MarkNextGenSampleAsSubmitted and ElviraUtil.
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Fix several options in Prepare_SRA_Submission_Template.pl
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Create_Tuples_For_SRA_Submission.pl - Corrected bug (tuples of samples
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Create_Tuples_For_SRA_Submission.pl - Implemented splitting
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Added Create_Tuples_For_SRA_Submission.pl - Script that creates tuple
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TIGR::GLKLib.pm - fixed bug in call to isValidBioProject()
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Lihui Hu committed [782caf]
Modify unit test for TestMoveSamplesInJira.
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Lihui Hu committed [d021d2]
Modify updateSamplesInJira to fix the errors of deprecate samples.
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TIGR::GLKLib.pm Updated list of attributes where Missing and Unknown are
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TIGR::GLKLib.pm - Changed signature of isValidBioProject() as part of
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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TIGR::GLKLib.pm Updated lists of attributes accepting "Unknown" and
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Restored file deleted by mistake
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Older files deleted for new deployment process
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Added new property
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Property file for DPCC
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changes for DPCC
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Changes for DPCC
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Lihui Hu committed [10ccd1]
Temporally disable queryCtm, will make modifications through out the
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