Andreas Müller [Fri, 2 Dec 2016 09:04:57 +0000 (10:04 +0100)]
Cleanup and replace int by long in count
Andreas Müller [Thu, 1 Dec 2016 23:53:44 +0000 (00:53 +0100)]
fix #6132 first implementation of parent taxon in TaxonInContextDTO
Andreas Müller [Thu, 1 Dec 2016 14:42:17 +0000 (15:42 +0100)]
add getIdentifierType to IO Transformers
Andreas Müller [Thu, 1 Dec 2016 14:41:43 +0000 (15:41 +0100)]
Cleanup
Andreas Kohlbecker [Thu, 1 Dec 2016 13:18:56 +0000 (14:18 +0100)]
Revert "updating poms for 4.5.0-SNAPSHOT development"
This reverts commit
9ff0eb6731c1b854d6bea082b5bd87e001b202bd.
Andreas Kohlbecker [Thu, 1 Dec 2016 12:31:26 +0000 (13:31 +0100)]
reverting version to 4.4.0-SNAPSHOT
Andreas Kohlbecker [Thu, 1 Dec 2016 12:30:18 +0000 (13:30 +0100)]
ref #2985 portal controller for named areas
jenkins [Thu, 1 Dec 2016 12:20:05 +0000 (13:20 +0100)]
updating poms for 4.5.0-SNAPSHOT development
Andreas Kohlbecker [Thu, 1 Dec 2016 10:42:02 +0000 (11:42 +0100)]
ref #2985 fixing init strategy to add the gateringEvent.collectingAreas
Andreas Kohlbecker [Wed, 30 Nov 2016 17:38:53 +0000 (18:38 +0100)]
ref #2985 controller method to return extensions with type and solving probelm with pagin of sets in generic controller
Andreas Müller [Fri, 25 Nov 2016 16:23:08 +0000 (17:23 +0100)]
ref #6211 cleanup old code
Andreas Müller [Fri, 25 Nov 2016 16:22:40 +0000 (17:22 +0100)]
cleanup
Andreas Müller [Fri, 25 Nov 2016 16:21:38 +0000 (17:21 +0100)]
fix #6122 use StringResultDTO for titleCache service
Andreas Müller [Fri, 25 Nov 2016 15:42:37 +0000 (16:42 +0100)]
doc
Andreas Müller [Fri, 25 Nov 2016 14:42:33 +0000 (15:42 +0100)]
cleanup
Andreas Kohlbecker [Fri, 25 Nov 2016 14:05:55 +0000 (15:05 +0100)]
ref #6211 avoiding to deep initialization of synonym groups
Andreas Müller [Fri, 25 Nov 2016 12:39:58 +0000 (13:39 +0100)]
fix #6211 fix API incompatibility
Andreas Müller [Fri, 25 Nov 2016 12:08:18 +0000 (13:08 +0100)]
cleanup
Andreas Müller [Fri, 25 Nov 2016 12:05:59 +0000 (13:05 +0100)]
fix #6211 reduce initialization for synonymy
Andreas Müller [Thu, 24 Nov 2016 15:35:16 +0000 (16:35 +0100)]
ref #6211 try to fix heap consumption in synonymy service
Andreas Müller [Thu, 24 Nov 2016 14:02:00 +0000 (15:02 +0100)]
minor
Andreas Müller [Thu, 24 Nov 2016 12:44:09 +0000 (13:44 +0100)]
ref #6220 javadoc
Andreas Müller [Thu, 24 Nov 2016 12:33:27 +0000 (13:33 +0100)]
fix #6220 Improve isOrphaned definition for Taxon.
Andreas Müller [Thu, 24 Nov 2016 11:00:27 +0000 (12:00 +0100)]
ref #6199 test for reading excluded, unplaced and excludedNote
Andreas Müller [Wed, 23 Nov 2016 12:20:28 +0000 (13:20 +0100)]
Fix proparte is null in update script
Andreas Müller [Wed, 23 Nov 2016 12:19:50 +0000 (13:19 +0100)]
cleanup
Andreas Müller [Tue, 22 Nov 2016 16:32:30 +0000 (17:32 +0100)]
fix sortindex updater and SynonymDeduplicator
Andreas Kohlbecker [Mon, 21 Nov 2016 10:51:47 +0000 (11:51 +0100)]
ref #5974 fixing LIE in controller
Andreas Müller [Fri, 18 Nov 2016 21:22:11 +0000 (22:22 +0100)]
Cleanup
Andreas Müller [Fri, 18 Nov 2016 21:21:56 +0000 (22:21 +0100)]
ref #3934 update Salvador import for facts
Katja Luther [Fri, 18 Nov 2016 18:36:00 +0000 (19:36 +0100)]
solving polytomouskey node sort index problems
Andreas Müller [Fri, 18 Nov 2016 15:40:36 +0000 (16:40 +0100)]
Latest BM import updates for Salvador
Patrick Plitzner [Tue, 15 Nov 2016 16:33:49 +0000 (17:33 +0100)]
ref #4867 Set sec reference for taxa in cloned classification
Andreas Müller [Tue, 15 Nov 2016 11:23:18 +0000 (12:23 +0100)]
fix #6200 Change order of NomenclaturalCodeUpdater and allowOverride adder to avoid null values
Andreas Müller [Tue, 15 Nov 2016 10:37:58 +0000 (11:37 +0100)]
Remove deprecated adder methods for multilanguage text
Andreas Müller [Tue, 15 Nov 2016 10:34:16 +0000 (11:34 +0100)]
ref #5634 add getter and putter for excluded note
Andreas Müller [Tue, 15 Nov 2016 10:07:19 +0000 (11:07 +0100)]
cleanup and javadoc
Andreas Müller [Tue, 15 Nov 2016 10:07:02 +0000 (11:07 +0100)]
ref #5976 add PKNode sortindex update
Andreas Müller [Tue, 15 Nov 2016 07:45:06 +0000 (08:45 +0100)]
ref #5974 fix update script for synonym duplicates
Andreas Müller [Tue, 15 Nov 2016 07:43:19 +0000 (08:43 +0100)]
cleanup
Andreas Müller [Fri, 11 Nov 2016 12:12:00 +0000 (13:12 +0100)]
ref #3925 and #5974 Improve update script for non unique subqueries
Andreas Müller [Fri, 11 Nov 2016 10:23:46 +0000 (11:23 +0100)]
ref #5970 remove transient from allowOverride
Andreas Müller [Thu, 10 Nov 2016 15:30:57 +0000 (16:30 +0100)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Katja Luther [Thu, 10 Nov 2016 13:48:55 +0000 (14:48 +0100)]
delete TestCase from BioCaseQueryServiceWrapper
Andreas Müller [Thu, 10 Nov 2016 12:09:16 +0000 (13:09 +0100)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TaxonInteraction.java
cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestModelUpdate.java
Andreas Müller [Thu, 10 Nov 2016 11:48:13 +0000 (12:48 +0100)]
cleanup
Andreas Müller [Tue, 8 Nov 2016 13:23:00 +0000 (14:23 +0100)]
Minor changes to classification clone method
Andreas Müller [Tue, 8 Nov 2016 13:22:29 +0000 (14:22 +0100)]
Clean up
Andreas Müller [Tue, 8 Nov 2016 13:21:16 +0000 (14:21 +0100)]
Clean up deprecated methods in name service
Andreas Müller [Fri, 4 Nov 2016 14:05:41 +0000 (15:05 +0100)]
Cleanup
Patrick Plitzner [Tue, 8 Nov 2016 09:23:26 +0000 (10:23 +0100)]
ref #4866 Set sec reference for taxa when cloning classification
Katja Luther [Tue, 8 Nov 2016 08:48:25 +0000 (09:48 +0100)]
minor
Katja Luther [Tue, 8 Nov 2016 08:32:37 +0000 (09:32 +0100)]
missed to add the adapted test
Katja Luther [Mon, 7 Nov 2016 14:33:52 +0000 (15:33 +0100)]
fix #5680: get method needs to be named like the attribute
Andreas Kohlbecker [Mon, 7 Nov 2016 12:04:05 +0000 (13:04 +0100)]
switching maven-jetty plugin back to jdk 1.7 compatible version
Andreas Kohlbecker [Mon, 7 Nov 2016 11:16:44 +0000 (12:16 +0100)]
fix #6023 solving compatibility problems of aspectj with java 1.8 and fixing invalid path reference
Andreas Kohlbecker [Mon, 7 Nov 2016 10:28:59 +0000 (11:28 +0100)]
updating maven-jetty plugin
Katja Luther [Mon, 7 Nov 2016 08:52:48 +0000 (09:52 +0100)]
smaller changes for abcd import
Katja Luther [Mon, 7 Nov 2016 08:51:21 +0000 (09:51 +0100)]
revert adding error log
Katja Luther [Mon, 7 Nov 2016 08:43:21 +0000 (09:43 +0100)]
minor
Katja Luther [Mon, 7 Nov 2016 08:42:10 +0000 (09:42 +0100)]
minor
Katja Luther [Mon, 7 Nov 2016 08:28:57 +0000 (09:28 +0100)]
ref #6166: import siblings if an specimen and smaller changes in ABCD
import
Patrick Plitzner [Sun, 6 Nov 2016 13:22:02 +0000 (14:22 +0100)]
ref #4866 Fix transient object exception
- fixed typo
Patrick Plitzner [Sat, 5 Nov 2016 14:15:34 +0000 (15:15 +0100)]
ref #5449 Imporvements for CSV export
- Fix initialization problems
- Correctly match taxon name to chosen classification
- allow export for single leaf node
Patrick Plitzner [Fri, 4 Nov 2016 12:14:27 +0000 (13:14 +0100)]
ref #4866 Test for first implementation for clone classification
Patrick Plitzner [Fri, 4 Nov 2016 12:13:59 +0000 (13:13 +0100)]
ref #4866 Create new description set when cloning taxon (avoid
HibernateException)
Patrick Plitzner [Fri, 4 Nov 2016 12:13:23 +0000 (13:13 +0100)]
ref #4866 First implementation for clone classification (including test)
Andreas Müller [Fri, 4 Nov 2016 16:01:04 +0000 (17:01 +0100)]
adapt gestGetUuidAndTitleCache data to new model
Andreas Müller [Fri, 4 Nov 2016 15:12:11 +0000 (16:12 +0100)]
fix compile error in ITaxonNodeService
Andreas Müller [Fri, 4 Nov 2016 13:08:34 +0000 (14:08 +0100)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Conflicts:
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ITaxonNodeService.java
Katja Luther [Thu, 3 Nov 2016 13:03:41 +0000 (14:03 +0100)]
fix #6174: isDeletable needs to be called with UUID and the objects is
loaded on server side
Patrick Plitzner [Thu, 3 Nov 2016 09:12:11 +0000 (10:12 +0100)]
ref #5458 Add classification filter to service method
Katja Luther [Thu, 3 Nov 2016 08:48:06 +0000 (09:48 +0100)]
fix media deletion
Patrick Plitzner [Tue, 1 Nov 2016 15:09:26 +0000 (16:09 +0100)]
ref #5458 Added find-by-titleCache method for taxon node service
Katja Luther [Fri, 28 Oct 2016 08:34:08 +0000 (10:34 +0200)]
abcd import: association type living culture is a parent child relation
Patrick Plitzner [Wed, 26 Oct 2016 09:07:15 +0000 (11:07 +0200)]
ref #2380 Implement service for getting parent of
UuidAndTitleCache<TaxonNode>
- parent of either ITaxonTree or UuidAndTitleCache<TaxonNode>
can be retrieved
- added JUnit test and test file
Patrick Plitzner [Tue, 25 Oct 2016 14:37:28 +0000 (16:37 +0200)]
ref #2380 Implement service for getting children of
UuidAndTitleCache<TaxonNode>
- direct children of either ITaxonTree or UuidAndTitleCache<TaxonNode>
can be retrieved
- added JUnit test
Patrick Plitzner [Mon, 24 Oct 2016 10:59:59 +0000 (12:59 +0200)]
fix #4453 Enhance portal visualization of molecular data
- used DefinedTerm constants for UUIDS
- used titleCache for all DerivedUnits
- move string representations to portal code
Katja Luther [Mon, 24 Oct 2016 11:01:23 +0000 (13:01 +0200)]
add test for ermIdInVocabularyComparator
Katja Luther [Mon, 24 Oct 2016 10:54:47 +0000 (12:54 +0200)]
fix TermIdInVocabularyComparator
Katja Luther [Mon, 24 Oct 2016 08:33:09 +0000 (10:33 +0200)]
move taxonnode needs to save old parent and child node
Andreas Müller [Fri, 21 Oct 2016 14:45:30 +0000 (16:45 +0200)]
Improve taxon delete test
Andreas Müller [Fri, 21 Oct 2016 14:45:04 +0000 (16:45 +0200)]
ref #5974 implement substitute method for TaxonService.getAllRelationships
Andreas Müller [Fri, 21 Oct 2016 14:41:24 +0000 (16:41 +0200)]
update path to dataset.xsd in persistence test data
Andreas Müller [Fri, 21 Oct 2016 12:47:10 +0000 (14:47 +0200)]
Cleanup merge model 4.1/develop
Andreas Müller [Fri, 21 Oct 2016 12:26:11 +0000 (14:26 +0200)]
Merge remote-tracking branch 'origin/develop' into develop
Katja Luther [Fri, 21 Oct 2016 12:19:52 +0000 (14:19 +0200)]
ref #5972: add service method to get count of referencing objects
Andreas Kohlbecker [Fri, 21 Oct 2016 10:06:19 +0000 (12:06 +0200)]
enabling http POST for a couple of name catalogue controller methods
Andreas Müller [Thu, 20 Oct 2016 14:04:04 +0000 (16:04 +0200)]
Merge remote-tracking branch 'origin/develop' into develop
Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest.java
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.java
cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTest.xml
Katja Luther [Thu, 20 Oct 2016 11:04:09 +0000 (13:04 +0200)]
childNode needs to be saved in TestService to fix the editor test
Katja Luther [Thu, 20 Oct 2016 10:11:58 +0000 (12:11 +0200)]
set test to ignore, create ticket to fix this.
Katja Luther [Thu, 20 Oct 2016 10:10:14 +0000 (12:10 +0200)]
fix failing test
Katja Luther [Thu, 20 Oct 2016 09:44:51 +0000 (11:44 +0200)]
minor
Andreas Müller [Tue, 18 Oct 2016 17:51:31 +0000 (19:51 +0200)]
Merge remote-tracking branch 'origin/cdm-4.1' into develop
Andreas Müller [Tue, 18 Oct 2016 17:50:54 +0000 (19:50 +0200)]
minor
Andreas Müller [Tue, 18 Oct 2016 17:31:06 +0000 (19:31 +0200)]
remaining merge issue for morge develop to cdm4.1
Andreas Müller [Tue, 18 Oct 2016 16:52:09 +0000 (18:52 +0200)]
Merge remote-tracking branch 'origin/develop' into cdm-4.1
Conflicts:
cdmlib-db/pom.xml
cdmlib-ext/pom.xml
cdmlib-io/pom.xml
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java
cdmlib-model/pom.xml
cdmlib-model/src/test/java/eu/etaxonomy/cdm/datagenerator/TaxonGenerator.java
cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonTest.java
cdmlib-persistence/pom.xml
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmEntityDaoBase.java
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dto/TaxonNodeDto.java
cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.xml
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ITaxonService.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java
cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/Datasource.java
cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml
cdmlib-test/pom.xml
Andreas Müller [Tue, 18 Oct 2016 15:52:06 +0000 (17:52 +0200)]
update remote-webapp test H2 to model 4.1
Andreas Müller [Tue, 18 Oct 2016 15:51:09 +0000 (17:51 +0200)]
fix #5634 Update excluded/unplaced for TaxonNodes with no taxon_id
Andreas Müller [Tue, 18 Oct 2016 15:17:16 +0000 (17:17 +0200)]
minor