EDIT

Fix Jaxb for SpecimenOrObservationBase #5606

Add secundum micro reference to TaxonBase #5717

Add secMicroReference #5717

Add preferred stable URI to SpecimenOrObservation #5606

Add base structure for model update to 4.0

Fix sort order for nom illeg with date #3338

Include nom. illeg. in homotypic group ordering #3338

Allow parsing of accent acute for coordinates #5716

fix #5669

#5679 catching and ignoring LIEs during the attempt to clean up NULL items in sets

Fix label for taxon description #5547

fixing LIE in webservice: taxonNode.sortIndex needs to be @Transient

Update javadoc and illegitimate status for
NomenclaturalStatusType.CONS_DESIG #5662

Minor change in order

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

Remove nomenclatural status type ined. as it is a duplicate for nom.
provis. (related to Cuba #5443)

Added nom. cons. des. status #5662

Add nom. cons. des. to parser #5662

Add orth. rej. to parsing #5649 and clean up test

#5659 fixing hibernate search indexing annotation

Some additional tests for sorting homotypical groups #3338

Add circular check for homotypicgouptaxon comparator #3338

#5635 indexing : skipping MultilanguageText entities with text == null

Include rank comparison in HomotypicGroupTaxonComparator #3338

minor

Fix bug in HomotypicGroupTaxonComparator #3338

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

Ordering of multiple Homotypic Groups #3338

Some cleanup for HGTaxonComparator #3338

Apply HomotypicGroupTaxonComparator to all existing uses of old
TaxonComparator #3338

Cleanup

Add Orthography Rejected to NomenclaturalStatusType #5649

Improve sort order within a homotypic group (new Comparator) #3338

Fix formatter bug

Fix deduplication problem with list order #5652

minor

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

Add cultivated, presence questionable to PresenceAbsenceTerms #5443

Fix combination author without space parsing #5618

Implement notho rank recognition #3868

workaround for #5590

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

Add post-separator to better handle tagged text

Refactor format method of cdm formatter

Refactor formatter framework

• Simplify interface
• added javadoc
• added static methods

Add reported in error static method

Fix cache strategy for taxon base with appended name #5586 and #5577

Fix bug in TextData factory method.

Minor

Add separator after nom status in taxon titleCache #5576

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 et al. for collectors #5568

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

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

Allow recognizing forma in ranks

Use correct column length annotation #5535

minor

Fix volume range bug in name parser #5518

Javadoc

Fix NPE in HibernateProxyHelper for null objects

Minor

Fix NPE in DistributionNodeByAreaLabelComparator

Further fix right quotation mark parsing

Add different apostroph to author name parser

Add commented base code for guessBasionym function to Homotypical group

• and cleanup

Cleanup

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

resolving conflicts after merge of ticket_4716 into develop

Some minor markup routine updates

add null check for delete and minor

organizing imports

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

#4761 removing @Indexed from abstract base classes since hibernate now fully supports polymorph class hierarchies

#4761 removing @Field annotation from CdmBase.id which has become obsolete

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

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 missing formatter to factory method

• Fix possible NPEs

Implement FormatKeys for all currently used occurrences parameters

Implement first take on formatter framework

A formatter provides a string representation of an object based on the
selected FormatKeys

changes for #4960 and #4959

#4716 IndexDocValue related issues solved, indexing now without exceptions, most tests in TaxonServiceSearchTest successful - commit of missing file

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

first steps to make lucene working again

#4716 temporarily making 3 fieldnames lowercase to prevent from trouble with new hibernate naming strategy, needs to be reverted later, see #5369

Update some more hibernate mapping nameings #4716 and #5369

Fix upgrade issues after rebase #4716

Fix issues after rebase #4716

Fix compile issues after rebase #4716

migrate to hibernate 5 for cdmlib-services and cdmlib-ext #4716

• (except for hibernate search tests)
• including new spring-config structure

Upgrade to hibernate 5 with persistence tests running #4716

Some cleanups in hibernate user types

Fix bug for embeddable classes in AdvancedBeanInitializer #5383

Fix bug for embeddable classes in AdvancedBeanInitializer #5383

fixing #4878

Add orphanRemoval to SingleReadAlignment set of Sequence #5200

fixing #5303

fixing #5303

Set singleRead to null when removing SingleReadAlignment from sequence
to avoid "object would be re-saved" #5200