EDIT

add update script and JAXB annotation for sequence positions #4743

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

code conventions for NVNParserRegEx

implement cache strategy for "et al." #4791

Create updater for cdm36 and update schema/term version

Add hasMoreMembers to Team, update script still missing #4791

quick fix for cache strategy exception. Cache strategy not yet correctly created. #4773

first implementation of team->person->team conversion #4769, #4770

minor

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

add O'Connor and zur Strassen as parsable authors. #4759

implement clone for SingleReadAlignment

no null return type even safer

get Shift always returns empty array instead of null #4734

handle empty Shift #4734

merge r23161 into trunk

merge r23145 into trunk

add Transient to getNullSafe methods and make MarkerType not null Level2 rule

Improved parser for zoological names...

further fixes for collectorTitle #4311

add collectorTitle and protectedCollectorTitleCache to Team(orPersonBase) #4311

make identifier annotatable #4673

merge validation2 and model 3.5 into trunk

merge validation2 and model 3.5 into trunk

fix search for common names in editor and minor

add LSID and Alternative field number to Identifier Type vocabulary #4708, #4674

type removed from SpecimenTypeParser

add NewInstance for Names in Determination Event

adadpt TimePeriodParser to include lifespan

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

activating the swagger rest service documentation by reverting the revertion of the premature committed experimental branch (swagger) svn: r21387, git: be528c1edf

• fixed typo

adding ISelfDescriptive from validation branch

VocEnum

factory method for Identifier Type

labels for some TermTypes

minor

add getter and setter for reverse complement

minor

refactor validation classes

minor

javadoc for Amplification and AmplificationResult

test for Amplification labelCache

implement Amplification.labelCache generation

• added cascade saving for amplification result
  • made constructor protected to avoid JavaAssistEnhancementException

doc

handle duplicates in identifier list

solve identifier conflict

Bidirectional identifier handling

latest changes to AmplificationResult and DnaQuality

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

JAXB annotations for amplification results

latest changes for AmplificationResult

add labelCache to Amplification #4542

some bugfixes to new Amplification modelling #4541

some adaptations after trunk merge to 3.4.1

merge-update from trunk

dna Quality purification method

separate Amplification and AmplificationResult.java #4541

• re-added hibernate annotation

-removed hibernate search annotation (copy&paste error)

• fixed bidriectionality for DnaSample<->Amplification

fixing test for SingleReadAlignment and removal of SpecAndObs_Sequence

implement SingleReadAlignment.java #4529
not yet ready

minor changes

• implemented bidirectionality for derivation events

some fixes after trunk integration to 341branch

merge-update from trunk

add first version of BigDecimal (still unclear if we want to keep the UserType) #4499

merge PresenceTerm and AbsenceTerm #4521

remove TODO

• fixed bidirectional mapping

remove FIMXE on protected constructor

creationi fo PresenceAbsence Terms

make all defined terms comparable

• converted dnaQuality from DefinedTerm to OrderedTerm (#4434)

Add institution to DerivationEvent and Amplification

add DnaMarker to Primer #4470

add DNA Quality Type vocabulary

Add DnaQuality.csv (not fully ready)

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

cleanup javadoc

update JaxbImportActivator

• fixed possible NPE

• fixed typo with semantic meaning

• used ImageFile instead of more generic MediaRepresentationPart when creating the Media (fixes #4402)
  • fixed a typo

• fixed typo

• provide contig and read information in portal and webservice

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

• made constructor protected to avoid JavaAssistEnhancementException

revert contact URLs #3920, #4444

workaround for Contact.urls to solve #4444 preliminary

reduce size of contact URI due to key length problems

• removed accidentally committed class

• merge-update from trunk