EDIT

• fully implemented deep delete (child derivates)
  • added tests

minor

• implemented isDeletable() and delete()
  • fixed test XML files and tests

• added isDeleteMolecularData flag to configurator

• use labelCache instead of description for amplification labeling

• organized imports

merge-update from trunk

-fixed possible NPE (fixes #4532)

merge-update from trunk

• added isPublish() method to facade

some adaptations after trunk merge to 3.4.1

merge-update from trunk

separate Amplification and AmplificationResult.java #4541

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

• invoke super method in isDeletable()

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

implement SingleReadAlignment.java #4529
not yet ready

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

• commented unused fields of DeleteResult

isDeletable returns DeleteResult

merge-update from trunk

merge PresenceTerm and AbsenceTerm #4521

• 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...

• extended toString() method

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

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

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

removed unwanted service field

whitespace

• when moving derivate also set "derivedFrom" to the new DerivationEvent

ICdmCacher, DefaultTermInitializer : added comments
CdmCacher : added code to disallow null values in cache and moved term initialisation code to specific subclass
CdmDaoCacher : replaced with specialised CdmTermCacher
defaultApplicationContext : removed remoting exception

minor

improve cache update algorithm

• added delete configurator to occurence service

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

• provide contig and read information in portal and webservice

• extende DerivateHierarchyDTO to also show contig and primer info

• removed comma in specimen citation

• added exception throwing to URI assembly in Sequence class
  • handled exception in editor details view

• adapted derivate hierarchy assembly to cdmlib3.4 changes (TissueSample, DnaSample as one class)

fix #4450

• added service method deleteDerivateHierarchy()

merge-update from trunk

allow saving FullDataGenerator data through API (preliminary)

minor

• fixed service method and extended test

merge-update from trunk

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

merge-update from trunk

fix delete taxon nodes with children

merge-update from trunk

bugfix for null rank in #4374

remove generics

generics

handle null name

• fixed case where a DerivedUnit is given as method parameter -> needed also to check for parent FieldUnits

• reverted accidentally removed methods due to merge with trunk

merge-update from trunk

• removed @Cascade for country in GatheringEvent because DefinedTerms should not be cascaded
  • added new service method to occurence service to find all CDM entities that are not saved via cascading
  • added tests for new method
  • added test for concurrent session saving of terms...

typos

merge-update from trunk; added import preference to add media as media specimen

added check for null cdm entity when putting default terms in cache

added possiblity to initialise some specific terms (like default language) which could be called outside a session

merge-update from trunk

fixing prefer specific distributions for #3904 (EuroMed: Implement filtering rules for Distributions), status=null was ereoneously preferred

isDeletable ignores relations of identifiableEntity

• assured image order for images from image galleries #3242

merge-update from trunk

fix jenkins

• replaced using the dao with using the service for taxa

• finished DerivateHierarchyDTO citation

merge-update from trunk

• restructured derivate hierarchy query
  • step 1: get associated field units for a taxon (taxon service)
  • step 2: assemble derivate hierarchy for each field unit (occurrence service)

update abbrevTitleCache in bulk update (Cont.)

update abbrevTitleCache in bulk update

generics

remove deprecated name service getVocabulary methods

minor

implement getNextHigherTerm and getNextLowerTerm #3327

move vocabulary tests to vocabulary service and fix @Ignore, remove deprecated methods from INameService

updated doc

• added type information to DTO
  • enhanced media labeling

• enhanced DerivateHierarchyDTO data

merge-update from trunk

• extended dto assembly

replace LockMode by LockOptions in service layer and persistence

merge-update from trunk

• fixed possible NPEs

return value of delete methods are DeleteResults

• added more parameters to DerivateHierarchyDTO

• added methods to add to DTO arrays
  • check if CDM entity already attached to session before loading it

• added more parameters to DerivateHierarchyDTO

• added more parameters to DerivateHierarchyDTO

• added service for retrieving all "associatied" FieldUnits for a taxon
  • added service for retrieving the "associated derivate hierarchies" for a taxon

• merge update from trunk