EDIT

improve delete configurator for taxa and synonyms

Update test H2 after model update to 4.0

Remove method agentsUsedAsUsers related to #5743

minor

minor

Remove bidirectionality for supplemental data #5743

Add test for bidirectional supplemental data #5743

Clean up AnnotationDao and AnnotationService

Update test data for xxxObj_type #3701

Adapt table and column names to hibernate 5 naming strategy #5369

... and some other changes to table/attribute names

Remove Autoincrement on AuditEvent.revisionnumber on MySQL #5718

• Not yet tested for H2 and PostGreSQL

Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop

smaller changes for fauna europaea import and csvNameExport

Fix order for areas #5677

Fix potential NPE

Reload type designation before deleting it to avoid caching conflicts.

Fix compilation error for Distribution comparator #5677

Implement natural ordering for distributions in data portal #5677

fix move taxonnode and remove null values from childrenlists in several places

Add IEventBaseService to application controller #5403

Adapt test to service method changes

Also return all specimens belonging to sub classes when specifying
SpecimenOrObservationBase as type

minor

Add uuid based method for deleting type designations #5490

minor

minor

TaxonNodeByNameComparator is not a component anymore and add configurable delete method for media

fix move synonym to another accepted taxon

Refactor associated taxa assembly to include uuid #5611

workaround for delete of polytomous keynodes, because of null values in children list

removing all (almost all) spy6 references and dependencies

cosmetics

Fix for DnaSample relation to Identifier, Annotations, etc.

• Add DnaSample to metaDef for Any relation in package-info.java
• added test for SampleDesignation for DnaSample

Fix failing test

Fix et al. for collectors #5568

Adjust specimen delete configurator

• when isDeleteChildren is true then also molecular data will be deleted
• specimen descriptions will always be deleted

Add missing Transactional annotation to delete method

Fix CCE in DefinedTermDaoImpl.getPartOf (#5556) and make deproxy more
generic

Merge branch 'hotfix/3.12.4' into develop

Conflicts:
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeCacheStrategyInjectionTest.java
cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeCacheStrategyInjectionTest.xml

Fix strategy injection test

Fix test for cache strategy loading

Fix javassist error for specimen cache strategy loading #5545

Fix test for cache strategy loading

Fix javassist error for specimen cache strategy loading #5545

Merge branch 'hotfix/3.12.3' into develop

Conflicts:
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTest.java

Implement preliminary Specimen cache strategy using facade cache
strategy

adapt test for searching for name without taxon

adapt test for searching for name without taxon

Revert last commit (taxon node handling is done in taxeditor)

Fix potential NPE when creating a new taxon for a classfication

minor

minor

cherry pick from develeop

new createNewTaxonNode service method

Fix specimen retrieval by assignment status

new createNewTaxonNode service method

Cleanup CdmTermCacher and CdmCacher

Fix failing test in cdmlib-services

Use correct StringUtils class

minor

Fix NPE in DistributionNodeByAreaLabelComparator

#5477 circumventing bug that broke test and creating nwe test to reproduce the issue

Add assignmentStatus as parameter to occurrence retrieval in service
method

Update dependencies to the latest versions (except for lucene) #4716

fixing problems regarding lucene search after merge - one test still failing

resolving conflicts after merge of ticket_4716 into develop

avoiding NPEs in pager

Cleanup description generics (related to #5357)

minor

add null check for delete and minor

organizing imports

organizing imports

#4716 reduicing clutter in the lucene index and solving performance problems which probably fixes #4277 and #3663

Generalize term service method listByTermType()

#4761 performance improvent of massindexer by using new hibernate 5 massindexer, speedup by 3x

#4761 performance improvent of massindexer by using new hibernate 5 massindexer, speedup by 3x

#4761 avoiding deprecations in highlighter api

#4761 updating means to obtain the IndexManager to new hibernate search api and extending according test

#4761 TopDocs adapting to removed IndexSearcher.setDefaultFieldSortScoring(boolean, boolean) method

#4761 TopDocs now supports maxScore, so TopGroupsWithMaxScore has become obsolete

#4761 correcting usage of new paramaters joinQuery parameters ScoreMode and multipleValuesPerDocument

#4761 fixing broken area filter join query, by circumventing a bug in lucene LUCENE-4824 (numeric fields not supported in join queries)

#4716 fixing proplems with testdata by making use of the CleanSweepInsertLoadStrategy.class

#4716 using BooelanQuery added with Occur.FILTER instead of deprecated search method

#4716 removing deprecated usage of new BooleanQuery, using BooleanQuery.Builder instead

index creation without errors, most lucene search test working again

• using TextField instead of StringField to enable tokenization for some fields
• @IndexedEmbedded(includeEmbeddedObjectId=true) added where necessary

Add uuid based method for getAllChildDerivatives()

Specified method signature as type designations are only available for
DerivedUnits

split test for moveDescriptionElements into two tests, on or the correct deletion and the other one for resaving the taxonDescription

changes for #4960 and #4959

Add convenience service methods to occurrence service

#4716 IndexDocValue relates issues solved, indexing now without exceptions, most tests in TaxonServiceSearchTest successful

TaxonServiceSearchTest: assertions no longer unnessecarily doing object comparision, relying on auto boxing is better!

Add load method for uuid lists

Minor

add the missing files

fix the term delete test

#4716 upgrading spring xsd schema version to 4.0

Cleanup

Set failing DescriptionService test preliminary to ignore #4716

Fix issues after rebase #4716