EDIT

upgrade unitils 3.3->3.4.2 #4636

adding first implementation for getting a csv file with all name informations

• fixed parameter assignment with no effect

• reverted temporary changes for titleCache generation

• temporarily disabled test

[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 test environment for Identifier being Annotatable #4673

fixing persistence tests on AgentBase.collectorTitle #4311

add collectorTitle and protectedCollectorTitleCache to Team(orPersonBase) #4311

update cdmlib poms from 3.4.1-SNAPSHOT to 3.5.0-SNAPSHOT

merge validation2 and model 3.5 into trunk

• added option to cancel import

• avoid duplicate taxon nodes in default classification

• added test file

• refactored code

• enhanced progress monitor

• enhanced progress monitor
  • fixed multiple default classification creation

• fixed potential NPE

• fixed taxon node matching for default classification

• added new test cases (still temporarily @Ignore)

• fixed potential NPE

• fixed potential NPE when adding taxon nodes for infra species

• some code speed up
  • better default classification handling

• fixed adding to default classification

• temporarily added test to ignore

• implemented new config option "Move new taxa to default classification"

• added new config option "Move new taxa to default classification"
  • do not add associations for identifications with preferredFlag=false

• enhanced report

• enhanced ggbn parsing
  • enhanced report

• added test to ignore temporarily

• added test to ignore temporarily

• fixed rank parsing
  • added deprecate annotation to config option

last updates to eFlora import

• temp changes for name matching

• some name matching enhancements

• added info messages to report
  • enhanced taxon name matching

latest updates to FotG import

update to Markup import

• fixed name matching when ignoring authorship

• fixed getTaxonForName()

• added removeCountryFromLocalityText option to configurator (basically implementing the hack #4677)

• shortened regex

• fixed temporary geolocation hack

• fixed name matching when ignoring author

• re-added temporary hack

• removed temporary hack

• fixed mapUnitIdToBarcode
  • fixed NPE for name parsing

• added config option to choose mapping of ABCD UnitID
  • added config option to ignore authorship when matching taxa
  • added first draft of ggbn extension parsing

• added ignoreAuthorship flag to ABCD import
  • when set to true taxon name matching will be done without the the authorship just on the nameCache of the NonViralName

• reset all relevant dataholder fields for every unit

latest changes for Markup import

latest changes for Markup import

add some doubtful taxon relationships tom BM transformer

minor

latest changes to Markup import

extended controller to enable feature export

• error handling for report file

• added @Ignore to failing test -_-

• added ABCD import test for subspecies

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

• fixed potential NPE

• added option to specify a URI for the import report to write it to a file

• add taxon name instead of taxon for determination
  • refactored taxon search
  • 1. search for taxon name (create if not found)
  • 2. search with taxon name for taxon (create if not found)
  • added basic reporting functionality to import

• added two methods to find/create names and taxa
  • fixed double creation of sub species

• added "else if" to avoid unnecessary checking

• increased code readability

• added parameter for each deduplication (references, classifications)

• added ABCD import paramater "skipDeduplication"

• avoid duplicating the default "ABCD classic" reference for every single imported unit

• added gathering date and elevation to ABCD import

• use classification uuid to load classification if it exists in the data source

• cleaned up code

merge cdmlib-io from validation branch to trunk

add xslx test in io

minor

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

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

add poi-ooxml and upgrade to 3.10-FINAL

• change visibility of createTestDataSet to public

merge-update from trunk

• 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

use saveOrUpdate in JaxbImport

fixing test for SingleReadAlignment and removal of SpecAndObs_Sequence

merge-update from trunk

merge PresenceTerm and AbsenceTerm #4521

Add institution to DerivationEvent and Amplification

add DnaMarker to Primer #4470

add DNA Quality Type vocabulary

made changes to be compliant with TaxonomicEditor Export

• extended init test