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
Cherian Mathew [Mon, 29 Jun 2015 14:48:58 +0000 (16:48 +0200)]
#5009 Add service method to update all nodes
Andreas Kohlbecker [Mon, 29 Jun 2015 14:32:45 +0000 (16:32 +0200)]
fixing bug that occurred with empty distributions- #5041
Cherian Mathew [Mon, 29 Jun 2015 12:26:33 +0000 (14:26 +0200)]
Add default delete method for uuid collections and implement update nodes method in polytomouse key service
Andreas Müller [Mon, 29 Jun 2015 11:13:02 +0000 (13:13 +0200)]
Further fix DistributionTree.matchesLevels #5041
Andreas Müller [Sun, 28 Jun 2015 14:51:43 +0000 (16:51 +0200)]
Fix DistributionTree.matchesLevels #5041
Andreas Müller [Sun, 28 Jun 2015 12:32:13 +0000 (14:32 +0200)]
Fix label order marker types in imports
Andreas Müller [Sat, 27 Jun 2015 13:13:57 +0000 (15:13 +0200)]
Fix ClassCastException in call to distributionInfo service #5041
Andreas Müller [Fri, 26 Jun 2015 19:25:05 +0000 (21:25 +0200)]
Add getTermByIdInVoc method to vocabularies
Andreas Müller [Fri, 26 Jun 2015 18:04:23 +0000 (20:04 +0200)]
Improve transmission engine parameters for web service (#5040)
Andreas Müller [Fri, 26 Jun 2015 17:24:03 +0000 (19:24 +0200)]
Fix umlaut bug in parser test
Andreas Müller [Fri, 26 Jun 2015 16:59:20 +0000 (18:59 +0200)]
Fix unparsed sections and subsections #4764
Cherian Mathew [Fri, 26 Jun 2015 14:36:45 +0000 (16:36 +0200)]
#5034 Add methods for testing handler / operations architecture
Andreas Müller [Fri, 26 Jun 2015 10:00:31 +0000 (12:00 +0200)]
Fix updateSortindex test for TaxonNode javassist objects
Cherian Mathew [Fri, 26 Jun 2015 09:23:44 +0000 (11:23 +0200)]
#5032 Add new test service for remoting clients
Andreas Müller [Thu, 25 Jun 2015 21:56:21 +0000 (23:56 +0200)]
Fix possible but in FeatureNode sortindex creation
See similar issue in TaxonNode sortindex creation.
Andreas Müller [Thu, 25 Jun 2015 21:47:14 +0000 (23:47 +0200)]
minor
Andreas Müller [Thu, 25 Jun 2015 21:40:22 +0000 (23:40 +0200)]
minor
Andreas Müller [Thu, 25 Jun 2015 21:35:25 +0000 (23:35 +0200)]
Fix sortindex computation in TaxonNode
After commit from 2015-06-18 the sortindex was computed slightly
different. In some cases the parent was not deproxied anymore and
therefore the parent.childNodes always returned the empty list of the
proxy object instead of returning the actual childrens list.
Andreas Kohlbecker [Thu, 25 Jun 2015 16:39:24 +0000 (18:39 +0200)]
some bugfixes in CondensedDistribution composition code - #3907
Andreas Kohlbecker [Thu, 25 Jun 2015 14:28:47 +0000 (16:28 +0200)]
minor documentation cleaning
Andreas Kohlbecker [Thu, 25 Jun 2015 14:23:41 +0000 (16:23 +0200)]
composition of condensed distribution fully implemented - #3907
Andreas Kohlbecker [Wed, 24 Jun 2015 15:13:43 +0000 (17:13 +0200)]
base framework for condensedDistributions implemented - #4911
Andreas Kohlbecker [Wed, 24 Jun 2015 12:54:18 +0000 (14:54 +0200)]
performance: avoiding second distribution filtering when creating the DistributionServiceRequestParameterString - #4911
Andreas Kohlbecker [Wed, 24 Jun 2015 12:22:58 +0000 (14:22 +0200)]
replacing 'non-java-doc by {@inheritDoc}
Andreas Müller [Thu, 25 Jun 2015 13:07:40 +0000 (15:07 +0200)]
Clean up transmission engine and BerlinModelTransformer
Cherian Mathew [Thu, 25 Jun 2015 12:21:37 +0000 (14:21 +0200)]
#5031 Corrected common service / dao collection methods to use uuid + fieldName
Cherian Mathew [Thu, 25 Jun 2015 07:35:46 +0000 (09:35 +0200)]
Fix classloading priority of patched hibernate class
Cherian Mathew [Wed, 24 Jun 2015 15:39:50 +0000 (17:39 +0200)]
#5025 : Add new cdm entity identifier object and use case in taxon node service
Andreas Müller [Wed, 24 Jun 2015 23:10:24 +0000 (01:10 +0200)]
Improve E+M post import methods #3979
Andreas Müller [Wed, 24 Jun 2015 23:08:00 +0000 (01:08 +0200)]
Improve distribution transmission engine for E+M import #3979
Andreas Müller [Wed, 24 Jun 2015 16:52:21 +0000 (18:52 +0200)]
Add publisher role uuid and clean up FirstDataInserter #3979
Andreas Müller [Wed, 24 Jun 2015 15:11:32 +0000 (17:11 +0200)]
Add hidden area related UUIDs to BerlinModelImport #3979 .5
Andreas Müller [Wed, 24 Jun 2015 14:39:40 +0000 (16:39 +0200)]
Add E+M vocabulary uuid to E+M-Transformer
Andreas Müller [Wed, 24 Jun 2015 13:30:13 +0000 (15:30 +0200)]
Add isImport request to import configurator
Cherian Mathew [Wed, 24 Jun 2015 12:16:48 +0000 (14:16 +0200)]
#5025 : Add CdmBase id+Class objects to UpdateResult
Andreas Müller [Tue, 23 Jun 2015 15:49:11 +0000 (17:49 +0200)]
Solve merge conflict for CdmTransactionalIntegrationTest
Andreas Müller [Tue, 23 Jun 2015 10:40:02 +0000 (12:40 +0200)]
Cleanup dao test classes
Andreas Müller [Mon, 22 Jun 2015 20:45:00 +0000 (22:45 +0200)]
Rename remaining occurrences of xxxAuthorTeam #4968
Rename remaining occurrences of combinationAuthorTeam and
basionymAuthorTeam in code and other files
Andreas Müller [Mon, 22 Jun 2015 17:16:20 +0000 (19:16 +0200)]
Rename NonViralName.xxxAuthorTeam to xxxAuthorship #4968
Andreas Kohlbecker [Tue, 23 Jun 2015 14:52:41 +0000 (16:52 +0200)]
3.6.2 has just been released, setting version to 3.6.3-SNAPSHOT
Andreas Müller [Tue, 23 Jun 2015 14:40:01 +0000 (16:40 +0200)]
Fix ignored test in TaxonDaoHibernateImplTest #2815
Cherian Mathew [Tue, 23 Jun 2015 10:55:50 +0000 (12:55 +0200)]
#5007 : Correct setting of updated objects when deleting taxon
Andreas Müller [Tue, 23 Jun 2015 10:43:38 +0000 (12:43 +0200)]
Fix ignored test in DescriptionElementDao #2815
Remaining tasks
Andreas Müller [Mon, 22 Jun 2015 15:20:33 +0000 (17:20 +0200)]
Cleanup Identifiable service
Patric Plitzner [Mon, 22 Jun 2015 12:41:32 +0000 (12:41 +0000)]
Copy DeterminationEvent data when moving derivates
Andreas Kohlbecker [Mon, 22 Jun 2015 08:33:10 +0000 (10:33 +0200)]
bumping project version to 3.6.2-SNAPSHOT, 3.6.1 has already been released
Andreas Müller [Fri, 19 Jun 2015 12:51:53 +0000 (14:51 +0200)]
fix titleCache for et al. teams #4967
Andreas Müller [Fri, 19 Jun 2015 11:46:51 +0000 (13:46 +0200)]
add non-absolute test to isServiceAvailable #4587
Andreas Müller [Fri, 19 Jun 2015 10:02:52 +0000 (12:02 +0200)]
fix parsing of names with teams in name and reference #2223
Katja Luther [Thu, 18 Jun 2015 12:59:38 +0000 (12:59 +0000)]
minor
Katja Luther [Thu, 18 Jun 2015 12:50:54 +0000 (12:50 +0000)]
forgot to check in the changes
Katja Luther [Thu, 18 Jun 2015 12:46:20 +0000 (12:46 +0000)]
- add @Audited to all type properties
- add taxonNodeComparator for rank and alphabetical orderedVocabularyDao
- change delete() methods arguments to UUIDs
Andreas Müller [Thu, 18 Jun 2015 11:18:02 +0000 (13:18 +0200)]
Merge branch 'RankSpecificRootNodes-1'
Andreas Müller [Thu, 18 Jun 2015 11:11:45 +0000 (13:11 +0200)]
Fixing test for listRankSpecificRootNodes
Katja Luther [Thu, 18 Jun 2015 09:58:23 +0000 (09:58 +0000)]
add @Audited to the argument type
Andreas Müller [Thu, 18 Jun 2015 09:48:16 +0000 (11:48 +0200)]
fix listRankSpecificRootNodes behavior for ranks in between and some
additional tests
Cherian Mathew [Thu, 18 Jun 2015 09:22:48 +0000 (11:22 +0200)]
Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/cdmlib
Cherian Mathew [Thu, 18 Jun 2015 09:14:06 +0000 (11:14 +0200)]
IUserService, UserService : added db check methods
remoting-services : moved database service to be included in security filter
Andreas Müller [Thu, 18 Jun 2015 08:31:49 +0000 (10:31 +0200)]
Merge branch 'RankSpecificRootNodes-1'
Andreas Müller [Wed, 17 Jun 2015 17:31:40 +0000 (19:31 +0200)]
Merge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib
Andreas Müller [Wed, 17 Jun 2015 16:38:34 +0000 (18:38 +0200)]
some additional test for #2778
Andreas Müller [Wed, 17 Jun 2015 16:29:15 +0000 (18:29 +0200)]
add some tests for rankSpecificRootNodes, related to #2778
Andreas Müller [Wed, 17 Jun 2015 15:04:14 +0000 (17:04 +0200)]
Merge branch 'RankSpecificRootNodes-1' of https://dev.e-taxonomy.eu/git/cdmlib into RankSpecificRootNodes-1
Andreas Kohlbecker [Thu, 21 May 2015 09:15:30 +0000 (11:15 +0200)]
avoiding LEFT OUTER JOIN by splitting query in two
Andreas Kohlbecker [Wed, 17 Jun 2015 14:23:38 +0000 (16:23 +0200)]
adding support for https in UriUtils
Andreas Kohlbecker [Thu, 21 May 2015 09:15:30 +0000 (11:15 +0200)]
avoiding LEFT OUTER JOIN by splitting query in two
Andreas Müller [Wed, 17 Jun 2015 13:07:24 +0000 (15:07 +0200)]
cleanup dataset
Andreas Müller [Wed, 17 Jun 2015 12:42:09 +0000 (14:42 +0200)]
fix testdata for #2778
Andreas Müller [Wed, 17 Jun 2015 12:34:25 +0000 (14:34 +0200)]
fixing missing LanguageString in test dataset for #2778. However, test
still fails.
Patric Plitzner [Wed, 17 Jun 2015 11:07:58 +0000 (11:07 +0000)]
test commit
Andreas Kohlbecker [Tue, 16 Jun 2015 16:05:29 +0000 (16:05 +0000)]
only a test
Andreas Kohlbecker [Tue, 16 Jun 2015 16:05:12 +0000 (16:05 +0000)]
only a test
Andreas Müller [Tue, 16 Jun 2015 14:20:04 +0000 (16:20 +0200)]
fix #4976 Titlecache for new vocabularies not filled correctly
Andreas Müller [Tue, 16 Jun 2015 14:16:08 +0000 (16:16 +0200)]
minor cleanup
Andreas Müller [Tue, 16 Jun 2015 14:14:57 +0000 (16:14 +0200)]
minor cleanup
Cherian Mathew [Mon, 15 Jun 2015 13:44:07 +0000 (15:44 +0200)]
merging test file from remote master
Cherian Mathew [Mon, 15 Jun 2015 12:24:14 +0000 (14:24 +0200)]
DescriptionServiceImpl : added dao delete of description
OccurrenceServiceDeepDeleteTest : removed extra delete call
TaxonServiceImplTest : added testing of taxon.removeDescription
Cherian Mathew [Fri, 12 Jun 2015 16:35:51 +0000 (18:35 +0200)]
correcting wrong merge
Cherian Mathew [Fri, 12 Jun 2015 15:39:08 +0000 (17:39 +0200)]
pushing delete to end of method to fix problem with merge
Cherian Mathew [Mon, 15 Jun 2015 12:47:42 +0000 (14:47 +0200)]
Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/cdmlib
Andreas Kohlbecker [Mon, 15 Jun 2015 12:09:30 +0000 (14:09 +0200)]
implementing modifications requested in #2880
Patric Plitzner [Mon, 15 Jun 2015 11:36:53 +0000 (11:36 +0000)]
- correctly cleaned up between test invocations
Patric Plitzner [Mon, 15 Jun 2015 11:33:50 +0000 (11:33 +0000)]
- added missing table column to test DB
Andreas Kohlbecker [Mon, 15 Jun 2015 10:23:22 +0000 (12:23 +0200)]
implementing test to reproduce issue #2778 - the test runs succesfully, so the issue is already solved