cdmlib.git
8 years agoupdating poms for 3.7.0 branch with snapshot versions
jenkins [Wed, 15 Jul 2015 11:42:39 +0000 (13:42 +0200)]
updating poms for 3.7.0 branch with snapshot versions

8 years agousing localy availabel pre-release build 1.0-m6 of jgitflow-maven-plugin in order...
Andreas Kohlbecker [Wed, 15 Jul 2015 11:34:08 +0000 (13:34 +0200)]
using localy availabel pre-release build 1.0-m6 of jgitflow-maven-plugin in order to be able to use 0 as third digit in version numbers

8 years agoRevert versions back to current
Cherian Mathew [Wed, 15 Jul 2015 09:51:19 +0000 (11:51 +0200)]
Revert versions back to current

8 years agoUpdating develop poms back to pre merge state
jenkins [Wed, 15 Jul 2015 09:39:03 +0000 (11:39 +0200)]
Updating develop poms back to pre merge state

8 years agoMerge branch 'master' into develop
jenkins [Wed, 15 Jul 2015 09:39:02 +0000 (11:39 +0200)]
Merge branch 'master' into develop

8 years agoupdating develop poms to master versions to avoid merge conflicts
jenkins [Wed, 15 Jul 2015 09:39:01 +0000 (11:39 +0200)]
updating develop poms to master versions to avoid merge conflicts

8 years agoMerge branch 'release/3.13' attic/tags/cdmlib/3.13/24840
jenkins [Wed, 15 Jul 2015 09:38:57 +0000 (11:38 +0200)]
Merge branch 'release/3.13'

8 years agoupdating poms for branch'release/3.13' with non-snapshot versions
jenkins [Wed, 15 Jul 2015 09:23:16 +0000 (11:23 +0200)]
updating poms for branch'release/3.13' with non-snapshot versions

8 years agoupdating poms for 3.14-SNAPSHOT development
jenkins [Wed, 15 Jul 2015 08:25:26 +0000 (10:25 +0200)]
updating poms for 3.14-SNAPSHOT development

8 years agoupdating poms for 3.13-SNAPSHOT development
jenkins [Wed, 15 Jul 2015 08:20:50 +0000 (10:20 +0200)]
updating poms for 3.13-SNAPSHOT development

8 years agoupdating poms for 3.12-SNAPSHOT development
jenkins [Wed, 15 Jul 2015 08:06:33 +0000 (10:06 +0200)]
updating poms for 3.12-SNAPSHOT development

8 years agoupdating poms for 3.11-SNAPSHOT development
jenkins [Wed, 15 Jul 2015 07:47:30 +0000 (09:47 +0200)]
updating poms for 3.11-SNAPSHOT development

8 years agoMerge branch 'develop' into abcd attic/branches/cdmlib/abcd/25144
Patrick Plitzner [Wed, 15 Jul 2015 07:12:44 +0000 (09:12 +0200)]
Merge branch 'develop' into abcd

8 years agoAdd new test file
Patrick Plitzner [Tue, 14 Jul 2015 13:55:02 +0000 (15:55 +0200)]
Add new test file

8 years agoAdd two new test files
Patrick Plitzner [Wed, 15 Jul 2015 07:03:27 +0000 (09:03 +0200)]
Add two new test files

8 years agoEnhance name parsing
Patrick Plitzner [Wed, 15 Jul 2015 07:02:47 +0000 (09:02 +0200)]
Enhance name parsing
 - more logging
 - fixed rank assignment

8 years agoError logging for name parsing
Patrick Plitzner [Wed, 15 Jul 2015 05:52:41 +0000 (07:52 +0200)]
Error logging for name parsing

 - advanced readability

8 years agoEnhance name parsing
Patrick Plitzner [Wed, 15 Jul 2015 05:49:16 +0000 (07:49 +0200)]
Enhance name parsing

 - added more error logging
 - avoid creating duplicate taxon names due to parsing problems

8 years agoRemove parseNameAutomatically flag
Patrick Plitzner [Wed, 15 Jul 2015 05:48:26 +0000 (07:48 +0200)]
Remove parseNameAutomatically flag

8 years agoupdating poms for 3.10-SNAPSHOT development attic/branches/cdmlib/develop/24823
jenkins [Tue, 14 Jul 2015 16:58:43 +0000 (18:58 +0200)]
updating poms for 3.10-SNAPSHOT development

8 years agoupdating poms for 3.9-SNAPSHOT development
jenkins [Tue, 14 Jul 2015 16:49:02 +0000 (18:49 +0200)]
updating poms for 3.9-SNAPSHOT development

8 years agoupdating poms for 3.8-SNAPSHOT development
jenkins [Tue, 14 Jul 2015 16:13:42 +0000 (18:13 +0200)]
updating poms for 3.8-SNAPSHOT development

8 years agoRevert jgitflow settings to default
Cherian Mathew [Tue, 14 Jul 2015 16:06:22 +0000 (18:06 +0200)]
Revert jgitflow settings to default

8 years agoUpdate all version to next snapshot and remove duplicate version settings
Cherian Mathew [Tue, 14 Jul 2015 15:58:31 +0000 (17:58 +0200)]
Update all version to next snapshot and remove duplicate version settings

8 years agoUpdate version to remove patch number
Cherian Mathew [Tue, 14 Jul 2015 15:48:56 +0000 (17:48 +0200)]
Update version to remove patch number

8 years agoUpdate pom to correct snapshot version
Cherian Mathew [Tue, 14 Jul 2015 15:36:53 +0000 (17:36 +0200)]
Update pom to correct snapshot version

8 years agoAdd jgitflow plugin to pom
Cherian Mathew [Tue, 14 Jul 2015 15:12:06 +0000 (17:12 +0200)]
Add jgitflow plugin to pom

8 years agominor
Katja Luther [Tue, 14 Jul 2015 12:26:38 +0000 (12:26 +0000)]
minor

8 years ago(no commit message)
Katja Luther [Tue, 14 Jul 2015 11:36:53 +0000 (11:36 +0000)]

8 years ago(no commit message)
Katja Luther [Tue, 14 Jul 2015 11:30:49 +0000 (11:30 +0000)]

8 years agoAdd test to @ignore
Patrick Plitzner [Tue, 14 Jul 2015 11:29:11 +0000 (13:29 +0200)]
Add test to @ignore

8 years ago(no commit message)
Katja Luther [Tue, 14 Jul 2015 11:15:46 +0000 (11:15 +0000)]

8 years agoRefactor ABCD import attic/branches/cdmlib/abcd/24801
Patrick Plitzner [Tue, 14 Jul 2015 11:03:53 +0000 (13:03 +0200)]
Refactor ABCD import

 - use association wrapper to store prefix
 - correctly push and pop import state
 - only delete field unit if it has no other links to objects

8 years agoRefactor ABCD import
Patrick Plitzner [Tue, 14 Jul 2015 07:27:46 +0000 (09:27 +0200)]
Refactor ABCD import

 - removed "determination on field unit level" flag
 - parse unit associations recursively
 - removed field unit from import state
 - enhanced unit association handling concerning field units and
ereivation events

8 years agoMerge branch 'master' into abcd
Patrick Plitzner [Mon, 13 Jul 2015 14:51:50 +0000 (16:51 +0200)]
Merge branch 'master' into abcd

8 years agoAdd new GGBN import test
Patrick Plitzner [Mon, 13 Jul 2015 14:49:58 +0000 (16:49 +0200)]
Add new GGBN import test

8 years agoIncrease character limit for titlecaches in test DB attic/trunk/cdmlib/24793
Patrick Plitzner [Mon, 13 Jul 2015 14:48:13 +0000 (16:48 +0200)]
Increase character limit for titlecaches in test DB

8 years agoFix taxon existance check attic/trunk/cdmlib/24792
Patrick Plitzner [Mon, 13 Jul 2015 12:44:22 +0000 (14:44 +0200)]
Fix taxon existance check

8 years agotypo attic/branches/cdmlib/develop/24806
Andreas Kohlbecker [Mon, 13 Jul 2015 08:52:51 +0000 (10:52 +0200)]
typo

8 years agoMerge branch 'master' into abcd
Patrick Plitzner [Mon, 13 Jul 2015 07:48:47 +0000 (09:48 +0200)]
Merge branch 'master' into abcd

8 years agoAdd import report logging to utility methods
Patrick Plitzner [Mon, 13 Jul 2015 05:03:04 +0000 (07:03 +0200)]
Add import report logging to utility methods

9 years agoFix long running name parser problem #5072 attic/trunk/cdmlib/24767
Andreas Müller [Thu, 9 Jul 2015 14:49:37 +0000 (16:49 +0200)]
Fix long running name parser problem  #5072

9 years agoAvoid NPE in ShiftUserType
Andreas Müller [Wed, 8 Jul 2015 15:12:54 +0000 (17:12 +0200)]
Avoid NPE in ShiftUserType

9 years agoMerge branch 'master' into abcd
Patrick Plitzner [Wed, 8 Jul 2015 17:44:50 +0000 (19:44 +0200)]
Merge branch 'master' into abcd

9 years agoCatch exception instead of throwing them
Patrick Plitzner [Wed, 8 Jul 2015 12:44:36 +0000 (14:44 +0200)]
Catch exception instead of throwing them

Lets the methods return

9 years agoCatch exception instead of throwing them
Patrick Plitzner [Wed, 8 Jul 2015 12:44:36 +0000 (14:44 +0200)]
Catch exception instead of throwing them

Lets the methods return

9 years agoError loggind during import
Patrick Plitzner [Wed, 8 Jul 2015 12:24:16 +0000 (14:24 +0200)]
Error loggind during import

9 years agoMerge branch 'master' into abcd
Patrick Plitzner [Wed, 8 Jul 2015 11:09:24 +0000 (13:09 +0200)]
Merge branch 'master' into abcd

9 years agominor attic/trunk/cdmlib/24755
Katja Luther [Wed, 8 Jul 2015 10:38:36 +0000 (10:38 +0000)]
minor

9 years agoAdd <IDENTIFIER> to clear DB script
Patrick Plitzner [Wed, 8 Jul 2015 09:38:51 +0000 (11:38 +0200)]
Add <IDENTIFIER> to clear DB script

9 years agoClear Terms before starting test
Patrick Plitzner [Wed, 8 Jul 2015 09:22:34 +0000 (11:22 +0200)]
Clear Terms before starting test

9 years agoRemove countries and areas to avoid test failure
Patrick Plitzner [Wed, 8 Jul 2015 08:26:59 +0000 (10:26 +0200)]
Remove countries and areas to avoid test failure

9 years agoAdd exception during import to report
Patrick Plitzner [Wed, 8 Jul 2015 07:40:30 +0000 (09:40 +0200)]
Add exception during import to report

9 years agoFix classification handling for new and exisiting taxa
Patrick Plitzner [Wed, 8 Jul 2015 05:34:38 +0000 (07:34 +0200)]
Fix classification handling for new and exisiting taxa

9 years agoAdd new test for classification handling
Patrick Plitzner [Tue, 7 Jul 2015 15:19:32 +0000 (17:19 +0200)]
Add new test for classification handling

9 years agoException handling
Patrick Plitzner [Tue, 7 Jul 2015 15:19:17 +0000 (17:19 +0200)]
Exception handling

 - moved report printing to finally clause to always have a report.
 - fixed possible NPE

9 years agoMerge branch 'master' into abcd
Patrick Plitzner [Tue, 7 Jul 2015 14:02:40 +0000 (16:02 +0200)]
Merge branch 'master' into abcd

9 years agoTest classification handling
Patrick Plitzner [Tue, 7 Jul 2015 13:38:08 +0000 (15:38 +0200)]
Test classification handling

9 years agoHandle default classification in state object
Patrick Plitzner [Tue, 7 Jul 2015 13:37:46 +0000 (15:37 +0200)]
Handle default classification in state object

9 years agoFix missing protected evaluation for Taxon titleCache #5018 attic/trunk/cdmlib/24749
Andreas Müller [Tue, 7 Jul 2015 12:51:34 +0000 (14:51 +0200)]
Fix missing protected evaluation for Taxon titleCache  #5018

9 years ago#5054 Add delete method call with uuid
Cherian Mathew [Tue, 7 Jul 2015 12:08:06 +0000 (14:08 +0200)]
#5054 Add delete method call with uuid

9 years agoAdd tests for classification handling
Patrick Plitzner [Tue, 7 Jul 2015 07:18:44 +0000 (09:18 +0200)]
Add tests for classification handling

9 years agoFix classification handling in ABCD import
Patrick Plitzner [Tue, 7 Jul 2015 07:18:27 +0000 (09:18 +0200)]
Fix classification handling in ABCD import

9 years agoCheck ignoreAuthorship flag with different authors in test data
Patrick Plitzner [Tue, 7 Jul 2015 05:44:10 +0000 (07:44 +0200)]
Check ignoreAuthorship flag with different authors in test data

9 years agominor
Katja Luther [Mon, 6 Jul 2015 18:54:17 +0000 (18:54 +0000)]
minor

9 years agocacheUpdater Caryophyllales
Katja Luther [Mon, 6 Jul 2015 16:34:14 +0000 (16:34 +0000)]
cacheUpdater Caryophyllales

9 years agocacheUpdater for caryophyllales
Katja Luther [Mon, 6 Jul 2015 15:48:00 +0000 (15:48 +0000)]
cacheUpdater for caryophyllales

9 years agoRemove unneccessary check
Patrick Plitzner [Mon, 6 Jul 2015 13:59:16 +0000 (15:59 +0200)]
Remove unneccessary check

9 years agoLog exceptions during import in the report file
Patrick Plitzner [Mon, 6 Jul 2015 13:49:26 +0000 (15:49 +0200)]
Log exceptions during import in the report file

9 years agoImprove DwC-A import for large datasets
Andreas Müller [Mon, 6 Jul 2015 13:41:23 +0000 (15:41 +0200)]
Improve DwC-A import for large datasets

9 years agoExtend tests for GGBN import.
Patrick Plitzner [Mon, 6 Jul 2015 11:39:35 +0000 (13:39 +0200)]
Extend tests for GGBN import.

Checking field unit data.

9 years agoMerge branch 'master' into abcd
Patrick Plitzner [Mon, 6 Jul 2015 08:04:04 +0000 (10:04 +0200)]
Merge branch 'master' into abcd

9 years agominor
Katja Luther [Sat, 4 Jul 2015 00:06:24 +0000 (00:06 +0000)]
minor

9 years agoCaryophyllales stuff
Katja Luther [Fri, 3 Jul 2015 20:29:42 +0000 (20:29 +0000)]
Caryophyllales stuff

9 years agoAllow to split DwCA imports in parts (first steps)
Andreas Müller [Fri, 3 Jul 2015 10:47:56 +0000 (12:47 +0200)]
Allow to split DwCA imports in parts (first steps)

9 years ago#5056 Refactored 'save' call to return saved entity
Cherian Mathew [Fri, 3 Jul 2015 10:01:33 +0000 (12:01 +0200)]
#5056 Refactored 'save' call to return saved entity

9 years ago#5012 Add service layer updates for remoting calls from the Bulk Editor
Cherian Mathew [Thu, 2 Jul 2015 08:56:55 +0000 (10:56 +0200)]
#5012 Add service layer updates for remoting calls from the Bulk Editor

9 years agoremoved named areas to avoid test failure
Patrick Plitzner [Thu, 2 Jul 2015 08:16:57 +0000 (10:16 +0200)]
removed named areas to avoid test failure

9 years agoAdd test for importing two dna units with associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:49:23 +0000 (09:49 +0200)]
Add test for importing two dna units with associated units

9 years agoReset prefix after importing associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:47:14 +0000 (09:47 +0200)]
Reset prefix after importing associated units

9 years agoDo not close system.out
Patrick Plitzner [Thu, 2 Jul 2015 07:46:40 +0000 (09:46 +0200)]
Do not close system.out

9 years agoAdd test for importing two dna units with associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:49:23 +0000 (09:49 +0200)]
Add test for importing two dna units with associated units

9 years agoReset prefix after importing associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:47:14 +0000 (09:47 +0200)]
Reset prefix after importing associated units

9 years agoDo not close system.out
Patrick Plitzner [Thu, 2 Jul 2015 07:46:40 +0000 (09:46 +0200)]
Do not close system.out

9 years agotest for fallbackArea rule in DescriptionUtility.filterDistrubution for EuroPlusMed...
Andreas Kohlbecker [Wed, 1 Jul 2015 13:45:42 +0000 (15:45 +0200)]
test for fallbackArea rule in DescriptionUtility.filterDistrubution for EuroPlusMed - #4408

9 years agoimplementing fallbackArea rule into DescriptionUtility.filterDistrubution for EuroPlu...
Andreas Kohlbecker [Wed, 1 Jul 2015 13:01:22 +0000 (15:01 +0200)]
implementing fallbackArea rule into DescriptionUtility.filterDistrubution for EuroPlusMed - #4408

9 years agoadapting tests to changes in EuroPlusMedCondensedDistributionComposer and Description...
Andreas Kohlbecker [Wed, 1 Jul 2015 12:59:41 +0000 (14:59 +0200)]
adapting tests to changes in EuroPlusMedCondensedDistributionComposer and DescriptionUtils
    - testGetWebServiceUrlCountry() : removing restriction on specific order of area status parameters
    - testGetCondensedDistribution() : fixing unappropriate test data

9 years agoIgnore createTestData()
Patrick Plitzner [Wed, 1 Jul 2015 09:42:07 +0000 (11:42 +0200)]
Ignore createTestData()

9 years agoAdd accidentally removed test file
Patrick Plitzner [Wed, 1 Jul 2015 09:38:44 +0000 (11:38 +0200)]
Add accidentally removed test file

9 years agoExtend step-by-step deletion test
Patrick Plitzner [Wed, 1 Jul 2015 08:42:19 +0000 (10:42 +0200)]
Extend step-by-step deletion test

 - Used correct single read deletion method.
 - Created test file

9 years agoSoften association type matching. attic/shelves/cdmlib/p.plitzner/24641
Patrick Plitzner [Wed, 1 Jul 2015 07:22:54 +0000 (09:22 +0200)]
Soften association type matching.

9 years agoMap preparation material to derivation event description
Patrick Plitzner [Wed, 1 Jul 2015 07:22:25 +0000 (09:22 +0200)]
Map preparation material to derivation event description

9 years agoTest import of sparse ABCD file
Patrick Plitzner [Tue, 30 Jun 2015 13:36:15 +0000 (15:36 +0200)]
Test import of sparse ABCD file

9 years agoFix potential NPE
Patrick Plitzner [Tue, 30 Jun 2015 13:22:36 +0000 (15:22 +0200)]
Fix potential NPE

9 years agoAdd method for single read deletion
Patrick Plitzner [Wed, 1 Jul 2015 07:25:34 +0000 (09:25 +0200)]
Add method for single read deletion

9 years agoFix singleton constructor with specimen types
Patrick Plitzner [Wed, 1 Jul 2015 07:15:07 +0000 (09:15 +0200)]
Fix singleton constructor with specimen types

9 years agoDo not set consensus sequence of single read alignment to null when
Patrick Plitzner [Wed, 1 Jul 2015 07:13:47 +0000 (09:13 +0200)]
Do not set consensus sequence of single read alignment to null when
deleting the alignment

9 years agoAdd delete method for SingleReads
Patrick Plitzner [Wed, 1 Jul 2015 07:10:15 +0000 (09:10 +0200)]
Add delete method for SingleReads

9 years agoRemove comments
Patrick Plitzner [Wed, 1 Jul 2015 07:07:25 +0000 (09:07 +0200)]
Remove comments

9 years agocorrecting the cleanup of sub areas labes in condensed distributions
Andreas Kohlbecker [Tue, 30 Jun 2015 14:04:43 +0000 (16:04 +0200)]
correcting the cleanup of sub areas labes in condensed distributions