Katja Luther [Tue, 14 Jul 2015 11:36:53 +0000 (11:36 +0000)]
Katja Luther [Tue, 14 Jul 2015 11:30:49 +0000 (11:30 +0000)]
Patrick Plitzner [Tue, 14 Jul 2015 11:29:11 +0000 (13:29 +0200)]
Add test to @ignore
Katja Luther [Tue, 14 Jul 2015 11:15:46 +0000 (11:15 +0000)]
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
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
Patrick Plitzner [Mon, 13 Jul 2015 14:51:50 +0000 (16:51 +0200)]
Merge branch 'master' into abcd
Patrick Plitzner [Mon, 13 Jul 2015 14:49:58 +0000 (16:49 +0200)]
Add new GGBN import test
Patrick Plitzner [Mon, 13 Jul 2015 14:48:13 +0000 (16:48 +0200)]
Increase character limit for titlecaches in test DB
Patrick Plitzner [Mon, 13 Jul 2015 12:44:22 +0000 (14:44 +0200)]
Fix taxon existance check
Andreas Kohlbecker [Mon, 13 Jul 2015 08:52:51 +0000 (10:52 +0200)]
typo
Patrick Plitzner [Mon, 13 Jul 2015 07:48:47 +0000 (09:48 +0200)]
Merge branch 'master' into abcd
Patrick Plitzner [Mon, 13 Jul 2015 05:03:04 +0000 (07:03 +0200)]
Add import report logging to utility methods
Andreas Müller [Thu, 9 Jul 2015 14:49:37 +0000 (16:49 +0200)]
Fix long running name parser problem #5072
Andreas Müller [Wed, 8 Jul 2015 15:12:54 +0000 (17:12 +0200)]
Avoid NPE in ShiftUserType
Patrick Plitzner [Wed, 8 Jul 2015 17:44:50 +0000 (19:44 +0200)]
Merge branch 'master' into abcd
Patrick Plitzner [Wed, 8 Jul 2015 12:44:36 +0000 (14:44 +0200)]
Catch exception instead of throwing them
Lets the methods return
Patrick Plitzner [Wed, 8 Jul 2015 12:44:36 +0000 (14:44 +0200)]
Catch exception instead of throwing them
Lets the methods return
Patrick Plitzner [Wed, 8 Jul 2015 12:24:16 +0000 (14:24 +0200)]
Error loggind during import
Patrick Plitzner [Wed, 8 Jul 2015 11:09:24 +0000 (13:09 +0200)]
Merge branch 'master' into abcd
Katja Luther [Wed, 8 Jul 2015 10:38:36 +0000 (10:38 +0000)]
minor
Patrick Plitzner [Wed, 8 Jul 2015 09:38:51 +0000 (11:38 +0200)]
Add <IDENTIFIER> to clear DB script
Patrick Plitzner [Wed, 8 Jul 2015 09:22:34 +0000 (11:22 +0200)]
Clear Terms before starting test
Patrick Plitzner [Wed, 8 Jul 2015 08:26:59 +0000 (10:26 +0200)]
Remove countries and areas to avoid test failure
Patrick Plitzner [Wed, 8 Jul 2015 07:40:30 +0000 (09:40 +0200)]
Add exception during import to report
Patrick Plitzner [Wed, 8 Jul 2015 05:34:38 +0000 (07:34 +0200)]
Fix classification handling for new and exisiting taxa
Patrick Plitzner [Tue, 7 Jul 2015 15:19:32 +0000 (17:19 +0200)]
Add new test for classification 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
Patrick Plitzner [Tue, 7 Jul 2015 14:02:40 +0000 (16:02 +0200)]
Merge branch 'master' into abcd
Patrick Plitzner [Tue, 7 Jul 2015 13:38:08 +0000 (15:38 +0200)]
Test classification handling
Patrick Plitzner [Tue, 7 Jul 2015 13:37:46 +0000 (15:37 +0200)]
Handle default classification in state object
Andreas Müller [Tue, 7 Jul 2015 12:51:34 +0000 (14:51 +0200)]
Fix missing protected evaluation for Taxon titleCache #5018
Cherian Mathew [Tue, 7 Jul 2015 12:08:06 +0000 (14:08 +0200)]
#5054 Add delete method call with uuid
Patrick Plitzner [Tue, 7 Jul 2015 07:18:44 +0000 (09:18 +0200)]
Add tests for classification handling
Patrick Plitzner [Tue, 7 Jul 2015 07:18:27 +0000 (09:18 +0200)]
Fix classification handling in ABCD import
Patrick Plitzner [Tue, 7 Jul 2015 05:44:10 +0000 (07:44 +0200)]
Check ignoreAuthorship flag with different authors in test data
Katja Luther [Mon, 6 Jul 2015 18:54:17 +0000 (18:54 +0000)]
minor
Katja Luther [Mon, 6 Jul 2015 16:34:14 +0000 (16:34 +0000)]
cacheUpdater Caryophyllales
Katja Luther [Mon, 6 Jul 2015 15:48:00 +0000 (15:48 +0000)]
cacheUpdater for caryophyllales
Patrick Plitzner [Mon, 6 Jul 2015 13:59:16 +0000 (15:59 +0200)]
Remove unneccessary check
Patrick Plitzner [Mon, 6 Jul 2015 13:49:26 +0000 (15:49 +0200)]
Log exceptions during import in the report file
Andreas Müller [Mon, 6 Jul 2015 13:41:23 +0000 (15:41 +0200)]
Improve DwC-A import for large datasets
Patrick Plitzner [Mon, 6 Jul 2015 11:39:35 +0000 (13:39 +0200)]
Extend tests for GGBN import.
Checking field unit data.
Patrick Plitzner [Mon, 6 Jul 2015 08:04:04 +0000 (10:04 +0200)]
Merge branch 'master' into abcd
Katja Luther [Sat, 4 Jul 2015 00:06:24 +0000 (00:06 +0000)]
minor
Katja Luther [Fri, 3 Jul 2015 20:29:42 +0000 (20:29 +0000)]
Caryophyllales stuff
Andreas Müller [Fri, 3 Jul 2015 10:47:56 +0000 (12:47 +0200)]
Allow to split DwCA imports in parts (first steps)
Cherian Mathew [Fri, 3 Jul 2015 10:01:33 +0000 (12:01 +0200)]
#5056 Refactored 'save' call to return saved entity
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
Patrick Plitzner [Thu, 2 Jul 2015 08:16:57 +0000 (10:16 +0200)]
removed named areas to avoid test failure
Patrick Plitzner [Thu, 2 Jul 2015 07:49:23 +0000 (09:49 +0200)]
Add test for importing two dna units with associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:47:14 +0000 (09:47 +0200)]
Reset prefix after importing associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:46:40 +0000 (09:46 +0200)]
Do not close system.out
Patrick Plitzner [Thu, 2 Jul 2015 07:49:23 +0000 (09:49 +0200)]
Add test for importing two dna units with associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:47:14 +0000 (09:47 +0200)]
Reset prefix after importing associated units
Patrick Plitzner [Thu, 2 Jul 2015 07:46:40 +0000 (09:46 +0200)]
Do not close system.out
Andreas Kohlbecker [Wed, 1 Jul 2015 13:45:42 +0000 (15:45 +0200)]
test for fallbackArea rule in DescriptionUtility.filterDistrubution for EuroPlusMed - #4408
Andreas Kohlbecker [Wed, 1 Jul 2015 13:01:22 +0000 (15:01 +0200)]
implementing fallbackArea rule into DescriptionUtility.filterDistrubution for EuroPlusMed - #4408
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
Patrick Plitzner [Wed, 1 Jul 2015 09:42:07 +0000 (11:42 +0200)]
Ignore createTestData()
Patrick Plitzner [Wed, 1 Jul 2015 09:38:44 +0000 (11:38 +0200)]
Add accidentally removed test file
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
Patrick Plitzner [Wed, 1 Jul 2015 07:22:54 +0000 (09:22 +0200)]
Soften association type matching.
Patrick Plitzner [Wed, 1 Jul 2015 07:22:25 +0000 (09:22 +0200)]
Map preparation material to derivation event description
Patrick Plitzner [Tue, 30 Jun 2015 13:36:15 +0000 (15:36 +0200)]
Test import of sparse ABCD file
Patrick Plitzner [Tue, 30 Jun 2015 13:22:36 +0000 (15:22 +0200)]
Fix potential NPE
Patrick Plitzner [Wed, 1 Jul 2015 07:25:34 +0000 (09:25 +0200)]
Add method for single read deletion
Patrick Plitzner [Wed, 1 Jul 2015 07:15:07 +0000 (09:15 +0200)]
Fix singleton constructor with specimen types
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
Patrick Plitzner [Wed, 1 Jul 2015 07:10:15 +0000 (09:10 +0200)]
Add delete method for SingleReads
Patrick Plitzner [Wed, 1 Jul 2015 07:07:25 +0000 (09:07 +0200)]
Remove comments
Andreas Kohlbecker [Tue, 30 Jun 2015 14:04:43 +0000 (16:04 +0200)]
correcting the cleanup of sub areas labes in condensed distributions
Andreas Kohlbecker [Tue, 30 Jun 2015 13:40:10 +0000 (15:40 +0200)]
applying subAreaPreference exclusively for maps
Andreas Kohlbecker [Tue, 30 Jun 2015 10:44:47 +0000 (12:44 +0200)]
subAreaPreference Rule can be run completely separately
- also reoving old unused code
- removing documentation on osoltete rule
- removing all missleading errors on the subAreaPreference in documentation an comments
Patrick Plitzner [Tue, 30 Jun 2015 13:17:28 +0000 (15:17 +0200)]
Fix potential NPE
Patrick Plitzner [Tue, 30 Jun 2015 11:20:12 +0000 (13:20 +0200)]
Evaluate unit association type in ABCD import
- added test
- correctly set derivative hierarchy
Patrick Plitzner [Tue, 30 Jun 2015 05:54:00 +0000 (07:54 +0200)]
Check if primer or amplification already exist
Patrick Plitzner [Tue, 30 Jun 2015 05:52:57 +0000 (07:52 +0200)]
Evaluate UnitAssociationType during import
Current rule for the relation between the imported unit and its
associated units:
- "same population" => sibling relation
- "same individual" => parent-child
Patrick Plitzner [Mon, 29 Jun 2015 17:09:25 +0000 (19:09 +0200)]
Add find- and countByTitle() methods to primer and amplification service
Patrick Plitzner [Mon, 29 Jun 2015 16:27:32 +0000 (18:27 +0200)]
Split up test for unit associations
Patrick Plitzner [Mon, 29 Jun 2015 16:27:01 +0000 (18:27 +0200)]
Fix potential NPE
Patrick Plitzner [Mon, 29 Jun 2015 14:50:17 +0000 (16:50 +0200)]
Parse sample designation in ABCD GGBN import
Patrick Plitzner [Mon, 29 Jun 2015 13:28:52 +0000 (15:28 +0200)]
Move up name parsing
Patrick Plitzner [Wed, 24 Jun 2015 12:37:09 +0000 (14:37 +0200)]
Import associated units
- Set derivation event correctly
- adapted test
Patrick Plitzner [Wed, 24 Jun 2015 07:14:35 +0000 (09:14 +0200)]
Import associated units via BioCase query
Patrick Plitzner [Tue, 23 Jun 2015 16:48:08 +0000 (18:48 +0200)]
Move prefix parsing to utility method and import state
Patrick Plitzner [Tue, 23 Jun 2015 14:40:59 +0000 (16:40 +0200)]
Move unit parsing to utility class
Patrick Plitzner [Tue, 23 Jun 2015 13:38:16 +0000 (15:38 +0200)]
Import associated units in ABCD import
Worked on the order of importing units especially when associated units
are present.
Adapted test.
Patrick Plitzner [Tue, 23 Jun 2015 13:22:22 +0000 (15:22 +0200)]
- added missing columns for derivative import
Patrick Plitzner [Tue, 23 Jun 2015 09:48:47 +0000 (11:48 +0200)]
??
Patrick Plitzner [Tue, 23 Jun 2015 09:48:08 +0000 (11:48 +0200)]
Adapt to method parameter change
Patrick Plitzner [Tue, 23 Jun 2015 09:09:43 +0000 (11:09 +0200)]
Import associated units in ABCD import
First changes
Patrick Plitzner [Tue, 23 Jun 2015 08:46:22 +0000 (10:46 +0200)]
Refactor ABCD import
Moved class variables to import state
Patrick Plitzner [Wed, 17 Jun 2015 14:06:04 +0000 (16:06 +0200)]
- fixed date parsing
- fixed primer saving
- added new parameters to test
Patrick Plitzner [Wed, 17 Jun 2015 12:58:15 +0000 (14:58 +0200)]
- added preservation/preparation parameters
- fixed parsing of unitID
Patrick Plitzner [Wed, 17 Jun 2015 12:56:31 +0000 (14:56 +0200)]
- correctly connected primer, amplification, single reads and sequences
- parsed UnitAssociation to correctly set specimen data
- added UnitAssociationParser
Patrick Plitzner [Tue, 16 Jun 2015 15:41:11 +0000 (17:41 +0200)]
- refactored dna parsing
- added utility classes and person parser
- adapted test
- added parsing of more molecular parameters
Andreas Kohlbecker [Mon, 29 Jun 2015 19:06:02 +0000 (21:06 +0200)]
correctly assigning INTRODUCED_NATURALIZED to n=naturalizes for condensed distribution - #3907
Andreas Kohlbecker [Mon, 29 Jun 2015 15:43:29 +0000 (17:43 +0200)]
fixing sort order in condensed distribution - #3907
Andreas Kohlbecker [Mon, 29 Jun 2015 15:42:16 +0000 (17:42 +0200)]
removing obsolete warning from log - #3907