EDIT

add update script and JAXB annotation for sequence positions #4743

Adding firstSeqPosition, leftCutPosition and rightCutPosition to SingleReadAlignment #4743 , Update script still missing

update script for removing unique key on supportedCategoricalEnums and recommendedModifierEnums #4843

add update script for hasMoreMembers #4791

merge trunk into 36 branch

Create updater for cdm36 and update schema/term version

Add hasMoreMembers to Team, update script still missing #4791

Fix merging of names of different types test

allow different type merging not only for reallocation of links

remove onlyReallocate links as this is not yet implemented #4768

Make deduplication of TeamOrPersonBase possible in cdmlib #4768 and solve test problem in CdmGenericDaoImplTest #2096, finding some bugs in between

correct handling of terms with multiple representations

implementing better namedAreasInUse service for #3994 (Select widget to choose the filter areas for the advanced search)

minor

first implementation of WrappedCdmDataSource #3910

minor cleanup

add tests to avoid inconsistencies in recursive cdm updater calls

bugfix for 34_341 Updater

merge validation commits r23146, r23162, r23163 into trunk

[maven-release-plugin] prepare for next development iteration

[maven-release-plugin] prepare release cdmlib-parent-3.5.0

[maven-release-plugin] prepare for next development iteration

[maven-release-plugin] prepare release cdmlib-commons-3.5.0

fix bug in update script

add listener for taxon name in determination event and run update script again

fix test environment for Identifier being Annotatable #4673

fixing persistence tests on AgentBase.collectorTitle #4311

add collectorTitle and protectedCollectorTitleCache to Team(orPersonBase) #4311

update named area idInVocabularies if necessary #4140

make identifier annotatable #4673

minor

update script for orphaned taxon node removal #2341

update cdmlib poms from 3.4.1-SNAPSHOT to 3.5.0-SNAPSHOT

merge validation2 and model 3.5 into trunk

fix search for common names in editor and minor

for infrageneric unranked rank adding unranked
fixing bug with deletion of names and homotypicalGroups

• fixed java doc

minor

add amplification cache test

for testing

add taxonNode to session in countByIdentifier

improve byIdentifer service

missing persistence changes for findByIdentifier

latest changes for findByIdentifier service

improve and rename findByIdentifier service

fix MatchMode.prepend bug

switch off validation

rename abstract class

rename abstract class

merge cdmlib-persistence from validation branch to trunk

first tests for listByIdentifier

first untested version for findByIdentifier #4594

[maven-release-plugin] prepare for next development iteration

[maven-release-plugin] prepare release cdmlib-parent-3.4.0

minor

add username, groupname and GrantedAuthority deduplication #4102

more logging output

• use labelCache instead of description for amplification labeling

• change visibility of createTestDataSet to public

• change visibility of createTestDataSet to public

implement Amplification.labelCache generation

updating DnaQuality with typedPurificationMethod to allow both #4434 , #4552

merge-update from trunk

update scripts for splitting Amplification and adding labelCache and reversecomplement

• added abstract method createTestData() to CdmIntegrationalTest
  • method should be used for generatin test XML data sets
  • making it abstract and enforcing implementation in sub classes ensures that the same structure is used thus making it easier for the developer to find similar examples....

some bugfixes to new Amplification modelling #4541

merge-update from trunk

separate Amplification and AmplificationResult.java #4541

bug fix

CdmUpdater can run on multiple databases supplied as comma separated list

• added service method to get descriptions which have a specimen set as describedSpecimen
  • added test which fails because the XML is loaded incorrectly

• changed service method to retrieve the directly related objects
  • adapted tests

fixing test for SingleReadAlignment and removal of SpecAndObs_Sequence

implement SingleReadAlignment.java #4529
not yet ready

minor changes

remove Specimen_Sequence table from ddl

add nextUpdater to 331_34 updater

some fixes after trunk integration to 341branch

merge-update from trunk

merge PresenceTerm and AbsenceTerm #4521

• added DISTINCT to HQL query for associated taxa
  • created and used XML data source in occurrence service test

• added occurrence service methods to retrieve all taxa that are associated with a specimen:
  • via IndividualsAssociation
  • via TypeDesignation
  • added test

minor

• added TODO comment

• removed unused code

• implemented service method (and test for it) to get all taxa associated with a single specimen

• added listAssociatedTaxa() method to occurrence service (non functional)

whitespace

Add institution to DerivationEvent and Amplification

add DnaMarker to Primer #4470

fix bug, add OrederedTerm to hibernate cfg

add DNA Quality Type vocabulary

changes in service layer for fixes in bulg editor and search for misapplied names and common names in editor

fix #4450

remove NOT NULL on OriginalSourceType_AUD.sourceType on existing data #4445

last update to schema updater 34.

fix uuid as UniqueKey problem

update fullCoverageDataGenerator