EDIT

ref #9349 rename newClassificationName method

ref #9349 deprecate setReuseNames(false)

ref #9228 , ref #4866 some fixes for subtree cloning

cleanup

ref #4866, ref #9228 implement subtree clone

ref #4866, ref #9228 implement subtree clone in branch

cleanup

ref #9322 remove invalid designation relationship from cdmlib

ref #8785: reuse compatible description when adding specimen to character matrix

ref #8754: add deleteConfig for descriptiveDataset

cleanup

cleanup

fix delete problems of taxa used in multiple classifications

typo

ref #8651, #8467 Use unified aggregation class for matrix aggregation

• Link specimen descriptions as sources as direct CDM entities

cleanup

cleanup

cleanup

setters of subtreeConfigurator should be void again, adapt tests

minor

ref #7597 Add configuration to data set aggregation

• implement recursive aggregation

fix #8446 Allow setPublish for subtree to filter for hybrids

fix #7450 allow setPublish for subtree to include misapplied names and pro parte synonyms

cleanup and stream API for ForSubtreeConfigurator

ref #7450 implement interfaces and signatures for setPublishForSubtree for misapplications and ppSyns (not yet implemented)

ref #7450 use PublishForSubtreeConfigurator in TaxonNodeService

cleanup

ref #6794 rename some parameters, methods and classes

ref #8096: move cache updater and service methods return updateResult

ref #7745 add subtree filter to taxon search (not yet tested for subtree != null)

cleanup

ref #7664 adapt return type for many methods with defined typification

cleanup

ref #7528 ref #6655 introducing RegistrationStatusTransitions to provide a matrix of allowed RegistrationStatus transitions

ref #7525 restoring all previously removed Criteria methods

fix #7525 replacing Criteria lists by cdm Restrictions in CdmEntityDaoBase.*ByTitle() methods

fix NPE in IdentifiableServiceBase.getTitleSearchStringSqlized

cleanup

cleanup

cleanup

ref #3560 set includeUnpublished as default for FindTaxaAndNames configurator

ref #3560 implement publish in taxon service by name search

cleanup

ref #3560 implement publish filter for TaxonNodeDao.listChildrenOf and .countChildrenOf

ref #6241 replaced @created by @since in cdmlib

ref #6241 change @date to @since (fix)

ref #6241 change @date to @since

ref #6484 Move enum AssignmentStatus to cdm-persistence

smaller changes in ForSubtreeConfigurator

smaller changes in ForSubtreeConfigurator

remove setSecundum in io package

ref #6730: fix delete of media

ref #6730: first quick fix, to avoid deleting media referenced somewhere else.

fix #6368 rename table and class TaxonNameBase

ref #6527: define default for media deletion

cleanup

use remotingProgressMonitor for setSecundumReferenceForSubtree

ref #6315: minor changes for the implementing setSecundum for subtree in editor

fix #3465 Progressmonitor API and better UpdateResult handling for setSecundumForSubtree

fix #3465 implement setSecundumForSubtree

ref #6190 removing svn property place holder in first line of code

Cleanup and new Rights Factory method

fix #6236 add alphabetic length ordering to name search

fix #6128 include authorship option in taxon and name search

ref #5974 Replace synonymRelationshipType by SynonymType and replace some other occurrences of synonym relationship

ref #5974 Remove synonym relationship first compiling implementation in cdmlib

advanced MediaDeletionConfigurator

improve delete configurator for taxa and synonyms

minor

Adjust specimen delete configurator

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

Add assignmentStatus as parameter to occurrence retrieval in service
method

organizing imports

Remove unused parameters

Extend service methods to retrieve specimens that are determiined as a
taxon name

Add javadoc

fixing cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/FeatureNodeDeletionConfigurator.java

fix #5341 and fixing deletion of specimen

new nodeDeletionConfiguator to fit for taxonnode and feature node deletion

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

#5012 Add service layer updates for remoting calls from the Bulk Editor

Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/cdmlib into remoting-4.0

Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTerm.java
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/INameService.java...

minor

Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/cdmlib into remoting-4.0

Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTerm.java
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/Reference.java...

• added option to retrieve indirectly associated specimen
  • added service method to retrieve the completete derivative hierarchy for a given specimen
  • added test

• added significantIdentifer as search parameter to occurrenceService.findByTitle()

• added findOccurrences() and countOccurrences() to service layer
  • added configurator for these methods
  • optimized retrieval with HQL query
  • made use of service method in DerivateSearchView

remove import

ConversationHolderMock : overriding all methods
DeleteConfiguratorBase : now implements serializable

created new service in classificationService

it is a first draft of the createHierarchyService
based on taxonNames and until genus level.

• added isDeleteMolecularData flag to configurator

• commented unused field from SpecimenDeleteConfigurator
  • added TODOs for deletion checking for specimens
  • added emtpy isDeletable() method

• added isDeleteFromIndividualsAssociation and isDeleteFromTypeDesignation to SpecimenDeleteConfigurator
  • implemented deletion for above mentioned flags
  • added more information to delete result when deleting specimens
  • added tests for above mentioned flags...

• added delete configurator to occurence service

adapted tcs rdf and xml import, using apache jena for rdf import
tcs import for caryophylales
minor

update listIncludedTaxa #4045

delete terms