EDIT

Move unit parsing to utility class

Import associated units in ABCD import

Worked on the order of importing units especially when associated units
are present.
Adapted test.

??

Adapt to method parameter change

Import associated units in ABCD import

First changes

Refactor ABCD import

Moved class variables to import state

• fixed date parsing
  • fixed primer saving
  • added new parameters to test

• added preservation/preparation parameters
  • fixed parsing of unitID

• correctly connected primer, amplification, single reads and sequences
  • parsed UnitAssociation to correctly set specimen data
  • added UnitAssociationParser

• refactored dna parsing
  • added utility classes and person parser
  • adapted test
  • added parsing of more molecular parameters

Rename NonViralName.xxxAuthorTeam to xxxAuthorship #4968

• text formatting

• re-enabled dna quality parsing

• added more ggbn ABCD parameters to import and test

• added more parameters to GGBN parser and test

moving UuidAndTitleCache from model to persistence. #4799

• implemented importing of DNA ABCD units
  • DNA sampled will be attached to already existing specimens
  • re-enabled tests

• added null check

• improved name matching for NamedAreas (continents) in ABCD import (#4910)
  • added null check
  • fixed ggbn extension check

• optimized name matching for terms in ABCD import

• added config option to ignore already existing specimens during import
  • for ggbn import already existing specimens are searched and attached if associated to the dna unit
  • refactored AbcdReport to also display the unitId

• added option to cancel import

• avoid duplicate taxon nodes in default classification

• refactored code

• enhanced progress monitor

• enhanced progress monitor
  • fixed multiple default classification creation

• fixed potential NPE

• fixed taxon node matching for default classification

• 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

• 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

• fixed rank parsing
  • added deprecate annotation to config option

• temp changes for name matching

• some name matching enhancements

• added info messages to report
  • enhanced taxon name matching

• 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

• error handling for report file

• 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

add poi-ooxml and upgrade to 3.10-FINAL

rename Reference.authorTeam -> authorship #4432

• added additional ABCD path to search for gathering agents

merge-update from trunk

merge-update from trunk

• add determination to field unit when importing via SpecimenImportView
  • do not add IndividualAssociation between taxon and field unit

merge-update from trunk

• fixed multiple creation of subspecies nodes

merge-update from trunk

• fixed the unnecessary creation of multiple references and taxon nodes in ABCD import
  • added new ABCD import test

• refactored data structure for taxon identifications in ABCD import
  • trimming scientific names avoids creation of multiple taxa/taxon nodes
  • added check for number of taxon nodes to test

• cleaned up code

• fixed typo

merge-update from trunk

• added resetFields() method to avoid NonUniqueObjectExceptions

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

• fixed possible NPE

• adapted some save method to allow transient services (#3726)

updates to taxonX import

better handling of countries in gathering unit

better use of generics in service layer and persistence list methods

adding map to ReferenceSystem

fix AccessionNumber->Locality bug in Specimen Excel Import

Latest updates to Specimen Excel import

determination abbrev

remove isFigure from getImageMedia

debug collection and institution for excel import

latest changes to Specimen Excel Import

• replaced saveOrUpdate() with "bundle" method save()

make description.setTaxon protected and cleanup cyprus altitudes and destinations

reverting back the cdm application configuration refatoring

renaming ICdmApplicationConfiguration to ICdmApplicationDefaultConfiguration

NPE bugfix in Specimen import

reintegrate ABCD import improvements