cleanup
ref #6241 replaced @created by @since in cdmlib
ref #6158 avoid URL redirects
ref #7080 fix potential other isEmpty issues for @Embeddable classes
Merge branch 'develop' into feature/cdm-4.7
Conflicts: cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/distribution/excelupdate/ExcelDistributionUpdate.java cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/MnTableCreator.java
Avoid dependency to org.codehaus.plexus.util.StringUtils
ref #6190 removing svn property place holder in first line of code
Remove generics from Reference in cdmlib-model #5830
Adapt table and column names to hibernate 5 naming strategy #5369
... and some other changes to table/attribute names
Use correct column length annotation #5535
#4716 reduicing clutter in the lucene index and solving performance problems which probably fixes #4277 and #3663
index creation without errors, most lucene search test working again
Upgrade to hibernate 5 with persistence tests running #4716
Add orphanRemoval to SingleReadAlignment set of Sequence #5200
Set singleRead to null when removing SingleReadAlignment from sequence to avoid "object would be re-saved" #5200
#5281 Make SingleReadAlignment.Shift serializable
Set sequence to null when removing a single read #5200
Do not set consensus sequence of single read alignment to null when deleting the alignment
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...
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...
add update script and JAXB annotation for sequence positions #4743
Adding firstSeqPosition, leftCutPosition and rightCutPosition to SingleReadAlignment #4743 , Update script still missing
implement clone for SingleReadAlignment
no null return type even safer
get Shift always returns empty array instead of null #4734
added Cascade.MERGE to all fields with annotation Cascade.SAVE_UPDATE
add getter and setter for reverse complement
javadoc for Amplification and AmplificationResult
test for Amplification labelCache
implement Amplification.labelCache generation
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
-removed hibernate search annotation (copy&paste error)
fixing test for SingleReadAlignment and removal of SpecAndObs_Sequence
implement SingleReadAlignment.java #4529 not yet ready
merge PresenceTerm and AbsenceTerm #4521
remove FIMXE on protected constructor
Add institution to DerivationEvent and Amplification
add DnaMarker to Primer #4470
fix init problem for DnaSample
bugfix for clone and setDnaSample
add a bit more bidirectionality to DnaSample/Sequence
cascade SingleRead.materialOrMethod
further changes to DnaQuality #4434 and update script for ValidationFramework alpha version
make primer.sequence a SequenceString #4139
first implementation for DnaQuality #4434
minor
again bugfix for DNA URLs
fix bug for getBoldUri
Bug fix for DnaSample record basis
add "part" to sequence setter
javadoc for amplification
Javadoc for molecular classes
rename materialMethodTerm -> definedMaterialOrMethod
final implementation of MaterialOrMethodEvent, Cloning, PreservationMethod, ... #3360
persist Sequence direction via enum key #3686
adding FactoryMethods and Constructor to DNA classes and uuid/key for SequenceDirection
some javadoc and factory methods
fix all compilation errors for app-import 3.3
update update script such that no validation errors exist anymore
change some names in molecular and update the update script
first implementation of new molecular package #3360
make Sequence-PhylogeneticTree ManyToMany (#2540)
remove ReferencedMediaBase and Figure, let PhylogeneticTree inherit from Media, remove citation and microcitation columns from DB
adding recordBasis to SpecimenOrObservationBase and removing some DerivedUnit classes (all #3378) and adding kindOfUnit to SpecimenOrObservationBase (except for according termType and vocabulary) #3568.
Remove GenBankAccession class, Spatium for EN_DASH and some minor stuff for v3.3
make Sequence.sequence a clob (#3325)
remove model changing validations fix Delete_Orphan #3379