cdmlib.git
7 years agoupdate path to dataset.xsd in persistence test data
Andreas Müller [Fri, 21 Oct 2016 14:41:24 +0000 (16:41 +0200)]
update path to dataset.xsd in persistence test data

7 years agoCleanup merge model 4.1/develop
Andreas Müller [Fri, 21 Oct 2016 12:47:10 +0000 (14:47 +0200)]
Cleanup merge model 4.1/develop

7 years agoMerge remote-tracking branch 'origin/develop' into develop
Andreas Müller [Fri, 21 Oct 2016 12:26:11 +0000 (14:26 +0200)]
Merge remote-tracking branch 'origin/develop' into develop

7 years agoref #5972: add service method to get count of referencing objects
Katja Luther [Fri, 21 Oct 2016 12:19:52 +0000 (14:19 +0200)]
ref #5972: add service method to get count of referencing objects

7 years agoenabling http POST for a couple of name catalogue controller methods
Andreas Kohlbecker [Fri, 21 Oct 2016 10:06:19 +0000 (12:06 +0200)]
enabling http POST for a couple of name catalogue controller methods

7 years agoMerge remote-tracking branch 'origin/develop' into develop
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

7 years agochildNode needs to be saved in TestService to fix the editor test
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

7 years agoset test to ignore, create ticket to fix this.
Katja Luther [Thu, 20 Oct 2016 10:11:58 +0000 (12:11 +0200)]
set test to ignore, create ticket to fix this.

7 years agofix failing test
Katja Luther [Thu, 20 Oct 2016 10:10:14 +0000 (12:10 +0200)]
fix failing test

7 years agominor
Katja Luther [Thu, 20 Oct 2016 09:44:51 +0000 (11:44 +0200)]
minor

7 years agoMerge remote-tracking branch 'origin/cdm-4.1' into develop
Andreas Müller [Tue, 18 Oct 2016 17:51:31 +0000 (19:51 +0200)]
Merge remote-tracking branch 'origin/cdm-4.1' into develop

7 years agominor
Andreas Müller [Tue, 18 Oct 2016 17:50:54 +0000 (19:50 +0200)]
minor

7 years agoremaining merge issue for morge develop to cdm4.1 cdm-4.1 origin/cdm-4.1
Andreas Müller [Tue, 18 Oct 2016 17:31:06 +0000 (19:31 +0200)]
remaining merge issue for morge develop to cdm4.1

7 years agoMerge remote-tracking branch 'origin/develop' into cdm-4.1
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

7 years agoupdate remote-webapp test H2 to model 4.1
Andreas Müller [Tue, 18 Oct 2016 15:52:06 +0000 (17:52 +0200)]
update remote-webapp test H2 to model 4.1

7 years agofix #5634 Update excluded/unplaced for TaxonNodes with no taxon_id
Andreas Müller [Tue, 18 Oct 2016 15:51:09 +0000 (17:51 +0200)]
fix #5634 Update excluded/unplaced for TaxonNodes with no taxon_id

7 years agominor
Andreas Müller [Tue, 18 Oct 2016 15:17:16 +0000 (17:17 +0200)]
minor

7 years agofix #5974 fix moving synonym type to TaxonBase and SynonymRelationType label
Andreas Müller [Tue, 18 Oct 2016 14:53:59 +0000 (16:53 +0200)]
fix #5974 fix moving synonym type to TaxonBase and SynonymRelationType label

7 years agofix clone test for Media
Andreas Müller [Tue, 18 Oct 2016 14:07:08 +0000 (16:07 +0200)]
fix clone test for Media

7 years agoremove final from classification.description
Andreas Müller [Tue, 18 Oct 2016 14:00:29 +0000 (16:00 +0200)]
remove final from classification.description

7 years agominor
Andreas Müller [Tue, 18 Oct 2016 13:58:52 +0000 (15:58 +0200)]
minor

7 years agoref #5634 fix clone issue for excludedNote
Andreas Müller [Tue, 18 Oct 2016 13:58:40 +0000 (15:58 +0200)]
ref #5634 fix clone issue for excludedNote

7 years agoCleanup language string handling and cloning
Andreas Müller [Tue, 18 Oct 2016 13:57:48 +0000 (15:57 +0200)]
Cleanup language string handling and cloning

7 years agominor
Andreas Müller [Tue, 18 Oct 2016 12:16:36 +0000 (14:16 +0200)]
minor

7 years agoref #5952 Add index to identityCache
Andreas Müller [Tue, 18 Oct 2016 12:15:56 +0000 (14:15 +0200)]
ref #5952 Add index to identityCache

7 years agocleanup
Andreas Müller [Tue, 18 Oct 2016 12:14:01 +0000 (14:14 +0200)]
cleanup

7 years agoref #3658 further improvements for NomCode update
Andreas Müller [Tue, 18 Oct 2016 12:13:08 +0000 (14:13 +0200)]
ref #3658 further improvements for NomCode update

7 years ago#5634 Add excludedNote to TaxonNode (still some tests not running)
Andreas Müller [Tue, 18 Oct 2016 12:11:13 +0000 (14:11 +0200)]
#5634 Add excludedNote to TaxonNode (still some tests not running)

7 years agoref #3925 Adapt tests for moving unplaced and excluded
Andreas Müller [Tue, 18 Oct 2016 12:07:27 +0000 (14:07 +0200)]
ref #3925 Adapt tests for moving unplaced and excluded

7 years agoref #6099: removing cascading to child nodes and adapting the service and persistence...
Katja Luther [Tue, 18 Oct 2016 08:29:28 +0000 (10:29 +0200)]
ref #6099: removing cascading to child nodes and adapting the service and persistence layer

7 years agoref #5431: the type designation blocks the name deletion only if it is the type name
Katja Luther [Tue, 18 Oct 2016 07:59:04 +0000 (09:59 +0200)]
ref #5431: the type designation blocks the name deletion only if it is the type name

7 years agoref #5826 adapt update script
Andreas Müller [Fri, 14 Oct 2016 15:10:36 +0000 (17:10 +0200)]
ref #5826 adapt update script

7 years agoCorrect errors in update script
Andreas Müller [Fri, 14 Oct 2016 14:14:00 +0000 (16:14 +0200)]
Correct errors in update script

7 years agoref #3925 Move excluded and unplaced to TaxonNode
Andreas Müller [Fri, 14 Oct 2016 14:13:03 +0000 (16:13 +0200)]
ref #3925 Move excluded and unplaced to TaxonNode

7 years agofix #5952 Add identityCache
Andreas Müller [Thu, 13 Oct 2016 21:54:09 +0000 (23:54 +0200)]
fix #5952 Add identityCache

7 years agocleanup
Andreas Müller [Thu, 13 Oct 2016 21:53:28 +0000 (23:53 +0200)]
cleanup

7 years agofix #6127 handling case the taxon has no LSID, avoid NPE in NameCatalogeController
Andreas Kohlbecker [Thu, 13 Oct 2016 15:46:39 +0000 (17:46 +0200)]
fix #6127 handling case the taxon has no LSID, avoid NPE in NameCatalogeController

7 years agofix #5952 Add fieldNumberCache
Andreas Müller [Thu, 13 Oct 2016 14:59:49 +0000 (16:59 +0200)]
fix #5952 Add fieldNumberCache

7 years agofix #5981 Add abbreviation to Rank "Cultivar"
Andreas Müller [Thu, 13 Oct 2016 14:23:40 +0000 (16:23 +0200)]
fix #5981 Add abbreviation to Rank "Cultivar"

7 years agoref #3658 remove nomenclaturalCode from all datasource related classes
Andreas Müller [Thu, 13 Oct 2016 11:14:34 +0000 (13:14 +0200)]
ref #3658 remove nomenclaturalCode from all datasource related classes

 * and rename NomenclaturalCodeAwareDataSource

7 years agoref #3658 Update nomenclatural code as CdmPreference (most probable value)
Andreas Müller [Thu, 13 Oct 2016 09:57:19 +0000 (11:57 +0200)]
ref #3658 Update nomenclatural code as CdmPreference (most probable value)

7 years agocleanup
Andreas Müller [Thu, 13 Oct 2016 09:52:32 +0000 (11:52 +0200)]
cleanup

7 years agoref #3658 Update nomenclatural code as CdmPreference (most probable value)
Andreas Müller [Thu, 13 Oct 2016 09:52:22 +0000 (11:52 +0200)]
ref #3658 Update nomenclatural code as CdmPreference (most probable value)

7 years agoref #5974 Replace synonym relationship update scripts (untested)
Andreas Müller [Thu, 13 Oct 2016 09:09:45 +0000 (11:09 +0200)]
ref #5974 Replace synonym relationship update scripts (untested)

7 years agoclean up and java doc
Andreas Müller [Thu, 13 Oct 2016 09:09:03 +0000 (11:09 +0200)]
clean up and java doc

7 years ago#3547 remove not needed dataset.dtd from persistence
Andreas Müller [Thu, 13 Oct 2016 09:07:59 +0000 (11:07 +0200)]
#3547 remove not needed dataset.dtd from persistence

7 years agoref #5974 Replace synonymRelationshipType by SynonymType and replace some other occur...
Andreas Müller [Thu, 13 Oct 2016 07:58:11 +0000 (09:58 +0200)]
ref #5974 Replace synonymRelationshipType by SynonymType and replace some other occurrences of synonym relationship

7 years agoref #5974 Remove synonym relationship first compiling implementation in cdmlib
Andreas Müller [Wed, 12 Oct 2016 19:00:32 +0000 (21:00 +0200)]
ref #5974 Remove synonym relationship first compiling implementation in cdmlib

7 years agoIDE launcher config cdmlib-remote-webapp-unit-test
Andreas Kohlbecker [Wed, 12 Oct 2016 13:04:05 +0000 (15:04 +0200)]
IDE launcher config cdmlib-remote-webapp-unit-test

7 years agorelaxing web service access restrictions
Andreas Kohlbecker [Wed, 12 Oct 2016 13:02:47 +0000 (15:02 +0200)]
relaxing web service access restrictions

7 years agoref #6118 OAuth2 ready for production
Andreas Kohlbecker [Tue, 11 Oct 2016 08:01:18 +0000 (10:01 +0200)]
ref #6118 OAuth2 ready for production
    - removing development setup
    - UserController to return details on the authenticated principal

7 years agoref #6118 working test implementation of OAuth2
Andreas Kohlbecker [Mon, 10 Oct 2016 20:44:46 +0000 (22:44 +0200)]
ref #6118  working test implementation of OAuth2
   - grant types 'implicite', 'authorization_code' tested and working
   - /manage/ service protected (OK for production)
   - /classification/ endpoint restricted for testing only

7 years agoref #6118 OAuth2 AuthorizationServer implemented
Andreas Kohlbecker [Fri, 7 Oct 2016 10:47:43 +0000 (12:47 +0200)]
ref #6118 OAuth2 AuthorizationServer implemented

7 years agorel #6118 switching from xml to java based web security configuration
Andreas Kohlbecker [Thu, 6 Oct 2016 19:07:33 +0000 (21:07 +0200)]
rel #6118 switching from xml to java based web security configuration

7 years agocleaning indent
Andreas Kohlbecker [Wed, 5 Oct 2016 14:18:08 +0000 (16:18 +0200)]
cleaning indent

7 years agoref #3547 remove testDelete-result1 and cleanup and reuse testDelete-result
Andreas Müller [Fri, 7 Oct 2016 17:06:58 +0000 (19:06 +0200)]
ref #3547 remove testDelete-result1 and cleanup and reuse testDelete-result

7 years agoref #3547 Cleanup TaxonDaoHibernateImplTest.xml
Andreas Müller [Fri, 7 Oct 2016 16:30:43 +0000 (18:30 +0200)]
ref #3547 Cleanup TaxonDaoHibernateImplTest.xml

7 years agoref #3547 fix related tests
Andreas Müller [Fri, 7 Oct 2016 14:56:44 +0000 (16:56 +0200)]
ref #3547 fix related tests

7 years agoref #3547 Cleanup TaxonDao.testGetTaxaByNameAndArea.xml test data a bit
Andreas Müller [Fri, 7 Oct 2016 14:06:04 +0000 (16:06 +0200)]
ref #3547 Cleanup TaxonDao.testGetTaxaByNameAndArea.xml test data a bit

7 years agoref #3547 Cleanup TaxonDao.testFindDeleted test data
Andreas Müller [Fri, 7 Oct 2016 13:46:25 +0000 (15:46 +0200)]
ref #3547 Cleanup TaxonDao.testFindDeleted test data

7 years agoref #3547 Cleanup TaxonDao.testFind test data
Andreas Müller [Fri, 7 Oct 2016 13:30:54 +0000 (15:30 +0200)]
ref #3547 Cleanup TaxonDao.testFind test data

7 years agoref #5972: add method to count referencing objects
Katja Luther [Fri, 7 Oct 2016 13:11:58 +0000 (15:11 +0200)]
ref #5972: add method to count referencing objects

7 years agofix #6089 Remove taxonomicParentCache and taxonomicChildrenCount, fix Testdata
Andreas Müller [Fri, 7 Oct 2016 13:06:14 +0000 (15:06 +0200)]
fix #6089 Remove taxonomicParentCache and taxonomicChildrenCount, fix Testdata

7 years agofix #6089 Remove taxonomicParentCache and taxonomicChildrenCount from Taxon
Andreas Müller [Fri, 7 Oct 2016 09:22:27 +0000 (11:22 +0200)]
fix #6089 Remove taxonomicParentCache and taxonomicChildrenCount from Taxon

7 years agoremove ImportReport in model branch
Andreas Müller [Fri, 7 Oct 2016 09:17:49 +0000 (11:17 +0200)]
remove ImportReport in model branch

7 years agominor
Andreas Müller [Thu, 6 Oct 2016 14:57:47 +0000 (16:57 +0200)]
minor

7 years agoref #5499 add some markerType methods
Andreas Müller [Thu, 6 Oct 2016 14:57:15 +0000 (16:57 +0200)]
ref #5499 add some markerType methods

7 years agofix #6122 fix signature issue
Andreas Müller [Thu, 6 Oct 2016 14:16:34 +0000 (16:16 +0200)]
fix #6122 fix signature issue

7 years agofix #6122 add titleCache service to remote
Andreas Müller [Thu, 6 Oct 2016 12:51:36 +0000 (14:51 +0200)]
fix #6122 add titleCache service to remote

7 years agoUse abstract controller for identifiable controllers
Andreas Müller [Thu, 6 Oct 2016 12:38:25 +0000 (14:38 +0200)]
Use abstract controller for identifiable controllers

7 years agoCreate and rename Identifiable(List)Controllers
Andreas Müller [Thu, 6 Oct 2016 12:32:23 +0000 (14:32 +0200)]
Create and rename Identifiable(List)Controllers

7 years agofix #6122 add titleCache service
Andreas Müller [Thu, 6 Oct 2016 12:24:32 +0000 (14:24 +0200)]
fix #6122 add titleCache service

7 years agofx #6119 Implement uuidAndTitleCache remote services
Andreas Müller [Thu, 6 Oct 2016 11:24:42 +0000 (13:24 +0200)]
fx #6119 Implement uuidAndTitleCache remote services

7 years agofix #6120 Cleanup uuidAndTitleCache methods
Andreas Müller [Thu, 6 Oct 2016 10:36:53 +0000 (12:36 +0200)]
fix #6120 Cleanup uuidAndTitleCache methods

7 years agoMinor cleanup
Andreas Müller [Tue, 4 Oct 2016 12:26:42 +0000 (14:26 +0200)]
Minor cleanup

7 years agoadd missing changes
Katja Luther [Fri, 30 Sep 2016 19:09:04 +0000 (21:09 +0200)]
add missing changes

7 years agominor
Katja Luther [Fri, 30 Sep 2016 14:34:25 +0000 (16:34 +0200)]
minor

7 years agospecimen import/search changes
Katja Luther [Fri, 30 Sep 2016 14:09:54 +0000 (16:09 +0200)]
specimen import/search changes

7 years agodelete system.out.println from test
Katja Luther [Tue, 27 Sep 2016 06:55:31 +0000 (08:55 +0200)]
delete system.out.println from test

7 years agoUpdating develop poms back to pre merge state
jenkins [Fri, 23 Sep 2016 13:37:31 +0000 (15:37 +0200)]
Updating develop poms back to pre merge state

7 years agoupdating develop poms to master versions to avoid merge conflicts
jenkins [Fri, 23 Sep 2016 13:37:29 +0000 (15:37 +0200)]
updating develop poms to master versions to avoid merge conflicts

7 years agoupdating poms for branch'release/4.3.0' with non-snapshot versions
jenkins [Fri, 23 Sep 2016 13:19:49 +0000 (15:19 +0200)]
updating poms for branch'release/4.3.0' with non-snapshot versions

7 years agoupdating poms for 4.4.0-SNAPSHOT development
jenkins [Fri, 23 Sep 2016 13:09:41 +0000 (15:09 +0200)]
updating poms for 4.4.0-SNAPSHOT development

7 years agoRename doPageChildNodes
Andreas Müller [Fri, 23 Sep 2016 12:48:37 +0000 (14:48 +0200)]
Rename doPageChildNodes

7 years agoref #6065 improved Pager handling
Andreas Müller [Fri, 23 Sep 2016 09:40:44 +0000 (11:40 +0200)]
ref #6065 improved Pager handling

7 years agoref #6065 improved Pager handling and pager exception handling
Andreas Müller [Fri, 23 Sep 2016 09:04:26 +0000 (11:04 +0200)]
ref #6065 improved Pager handling and pager exception handling

7 years agoref #6065 Handle synonyms in taxonInContext
Andreas Müller [Fri, 23 Sep 2016 09:03:05 +0000 (11:03 +0200)]
ref #6065 Handle synonyms in taxonInContext

7 years agoCleanup
Andreas Müller [Fri, 23 Sep 2016 09:00:49 +0000 (11:00 +0200)]
Cleanup

7 years agoref #6065 fix NPEs in classification service
Andreas Müller [Thu, 22 Sep 2016 12:10:54 +0000 (14:10 +0200)]
ref #6065 fix NPEs in classification service

7 years agoref #6065 fix NPE in pageSize/limit
Andreas Müller [Thu, 22 Sep 2016 11:25:20 +0000 (13:25 +0200)]
ref #6065 fix NPE in pageSize/limit

7 years agoref #6065 fix NPE in pageSize
Andreas Müller [Thu, 22 Sep 2016 10:27:27 +0000 (12:27 +0200)]
ref #6065 fix NPE in pageSize

7 years agoref #6065 fix page size and add marked ancestors
Andreas Müller [Thu, 22 Sep 2016 09:20:16 +0000 (11:20 +0200)]
ref #6065 fix page size and add marked ancestors

7 years agoref #6065 fix missing taxonUuid in URL
Andreas Müller [Thu, 22 Sep 2016 08:37:00 +0000 (10:37 +0200)]
ref #6065  fix missing taxonUuid in URL

7 years agoref #6065 first implementation of taxonInContext service
Andreas Müller [Wed, 21 Sep 2016 15:49:13 +0000 (17:49 +0200)]
ref #6065  first implementation of taxonInContext service

7 years agocleanup
Andreas Müller [Wed, 21 Sep 2016 15:47:07 +0000 (17:47 +0200)]
cleanup

7 years agofurther refactor FindByIdentifierDTO and FindByMarkerDTO
Andreas Müller [Wed, 21 Sep 2016 13:11:48 +0000 (15:11 +0200)]
further refactor FindByIdentifierDTO and FindByMarkerDTO

7 years agorename FindByIdentifierDTO and FindByMarkerDTO
Andreas Müller [Wed, 21 Sep 2016 12:48:45 +0000 (14:48 +0200)]
rename FindByIdentifierDTO and FindByMarkerDTO

7 years agoRevert "fix #6037 per batch transction commit implemented for excel imports"
Andreas Kohlbecker [Wed, 21 Sep 2016 09:24:49 +0000 (11:24 +0200)]
Revert "fix #6037 per batch transction commit implemented for excel imports"

This reverts commit 53067226137bd8528e6bc26f21edbf98aebe26a9.

7 years agoref #6066 rename childNodes to childNodesByTaxon in ClassificationController
Andreas Müller [Wed, 21 Sep 2016 08:51:19 +0000 (10:51 +0200)]
ref #6066 rename childNodes to childNodesByTaxon in ClassificationController

7 years agoref #6066 add getChildNodes to classification service
Andreas Müller [Wed, 21 Sep 2016 08:07:46 +0000 (10:07 +0200)]
ref #6066 add getChildNodes to classification service