EDIT

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

Adapt log4j.properties to hibernate deprecated logging problem

Fix NPE in DistributionNodeByAreaLabelComparator

Further fix right quotation mark parsing

Add different apostroph to author name parser

Add NomenclaturalStateType 'ined.'

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

Upgrade to spring 4.2.2, spring-security 4.0.2 and latest hibernate
validator #4716 and #4702

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

Revert "accept the change from a number to null in TimePeriod fields #5319"

This reverts commit a3960fa7c279f2aa9fafbefde098c529e269d382.

fix #5341 and fixing deletion of specimen

Return correct match strategy #5337

#5297 Refactor ProgressMonitorController, Add Remoting Progress monitor

#5297 Add progress monitor service, Add test services

#5297 Add monit import method

#5297 Update no. of work units

#5297 Add new thread class for remoting monitors

#5297 Add owner field to monitor thread and user checks in service...

Minor cleanup

Fix test in dataportal with strict bean initalization #5077

Revert "minor"

This reverts commit 64367d007ba404e037ccc2b6794b46c4f1f321bc.

minor

Add some more BeanUtil test to other classes #5307

Fix bean read/write inconsistency in Taxon and TaxonBase #5307

fix #5179 and adapting the tests because the classification argument is needed now

accept the change from a number to null in TimePeriod fields #5319

Merge branch 'ticket-5066' into develop

Conflicts:
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmEntityDaoBase.java
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/hibernate/PostMergeEntityListener.java

minor clean ups

Add cascade merge to members field

#5281 Make SingleReadAlignment.Shift serializable

#5299 Add new entity listener and event firing

minor

#5259 Add method to init defaul terms

#5249 Correct if statements

#5223 Copy utility method from service to derived unit

Implement hasCharacterData and isCharacterData.
And fix characterData semantics.

move specimen.getCharacterData to model

minor

clean up taxon cache strategy

Document new initListener method (#5161)

Simplify getNameTags in Taxon cache strategy (#5229)

Create new tag type for secundum reference (#5229)

#3991 hiding the delegeate boolean properties in TaggedText by making them protected

Deproxy name in taxon cache strategy.

Fix tagged title generation for taxa

Implement taggedTitle for taxon base #5229

Set sequence to null when removing a single read #5200

#5138, #5102 Fix cascade delete orphan error for address list in contact entity

removing System.out.println

minor

adding a convertmergeStrategy because of a different handling of merge and convert

changes for tcs import, fixing taxonnodecomparator, polytomouskey deletion and converting from person to team and team to person

adding a ConvertMergeStrategy

#5161 Add initListener method to CdmBase object

add @Audited to startNumber

changes for deleting polytomous key nodes

Revert final qualifier after discussion in #5102

adding IdInVocabulary to the toString representation of NamedAreas

#5100 Fix default language for remoting