EDIT

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

• fixed potential LIE

• fixed potential null values
  • added uuid to preserved specimen dto

• refactored DTO assembly for compressed specimen table in the data portal
  • now data is assembled for each individual preserved specimen and the for the parent field unit

make indexing type collection a list (was Set before)

adapt CommonService to allow collection save and add remotewebapp test H2 udpate

merge validation2 and model 3.5 into trunk

remove import

fix search for common names in editor and minor

moveTaxon() with uuids instead of objects as arguments

minor

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

• added methods to handle identifiers

• fixed paging for compressed specimen table

• added pager to associated field units service method

add UpdateResult and make DeleteResult a subclass

DeleteResult : made serializable
remote-security : added remoting url intercept
remoting-services : made user service public
web.xml : added filter chain for securing remoting services

fix #4613

created new service in classificationService

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

• check related objects for DeterminationEvents

• fixed deletion result relates objects
  • removed @Ignore from tests

• replaced instanceof with isInstanceOf()
  • replaced class cast expressions with deproxy

• only add the conflicting related objects to the DeleteResults

PolytomousKey, PolytomousKeyNode : Added merge to cascade annotation
cdmlib-remote-servlet.xml, ConcurrentSessionTest.java : spelling checks
CdmCacher : made cache lement getter methods public
remoting-services.xml, httpInvokerServices : added new services

null handling for find(UUID) and load(UUID) methods

latest changes for findByIdentifier service

improve and rename findByIdentifier service

remove some javadocs

• refactored getFieldUnits()

add transactional to listByIdentifier service

remove imports

minor

merge cdmlib-service from validation branch to trunk

first tests for listByIdentifier

first untested version for findByIdentifier #4594

update javadoc and Override in IdentifiableServiceBase

• fixed deep delete recursion bug
  • fixed tests

• extracted deepDelete tests to own java class
  • reduced exception logged in DeleteResult

add original label info to specimen facade #4218, #4565

• 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