ref #8162 adapt cdmlip to new term package structure

fix exception if biocase provider is not available

smaller changes in abcd import

fix bugs in abcd import

adapt abcd import to changes in derivedUnitFacade

kindOfUnit for all derivates not only for field units

fix collector import if it is a single string value in gatheringAgentsText

smaller changes in ABCD import

ref #7434: remember sequence uris for downloading the files at the end of the import

adapt source reference in ABCD import

smaller changes in ABCD import

ref #6241 replaced @created by @since in cdmlib

ref #7095 Add property paths to some methods

adapted deleteResult

fix gatheringAgent import in ABCD Import

add the new created namedArea for gathering event to a vocabulary in specimen import

fix abcd import for associated units

ABCD import:set fieldUnit in derivedUnitFace after creation to avoid new creation of fieldUnit

cleanup and adapt export hierarchie (add destination generics)

smaller changes in specimen import

revert the last change in AbcdImport

cleanup

reload default classification after commit

adapt Abcd206Import for gbol

fix siblings import and source reference import

some code cleaning and improvement of siblings search

minor

ref #6166: parsing of siblings and search for siblings in different accessPoints

adapt ABCD and GBIF imports to requirements of algae specimen and obeservation imports

Cleanup

ref #6419 renaming ICdmApplicationDefaultConfiguration to ICdmRepository

changes in specimen import

ref #6190 removing svn property place holder in first line of code

extend biocase import

ref #6166: import siblings if an specimen and smaller changes in ABCD
import

abcd import: association type living culture is a parent child relation

specimen import/search changes

Remove duplicate method

Fix merge problems

fix #6001 Clean up multiple sourceNotLinked() methods

specimen import changes

Import specimen scans with StillImage type

Remove unneccesary casts

#5251 Fix Incorrect taxon source attachments

fix merge problems

Remove generics from Reference in cdmlib (except for cdmlib-model) #5830

Fix potential NPE

Parse spatial data for gathering event in ABCD import #5169

Set Unit/Notes and Gathering/Notes in ABCD import #5168

Import missing parameters for ggbn ABCD import

• some refactoring

Refactored import return type from boolean to ImportResult

Move import report to import state super class

#5297 Add cancel and waitForFeedback functionality

Correct work units

#5297 Refactor ProgressMonitorController, Add Remoting Progress monitor

#5297 Add progress monitor service, Add test services

#5297 Add monit import method

#5297 Update no. of work units

#5297 Add new thread class for remoting monitors

#5297 Add owner field to monitor thread and user checks in service...

Fix NPE in ABCD import collection matching

• also added for-loop break

Refine rank parsing

• if rank cannot be parsed the taxon will be created as is with a single taxon node without any parent taxon node but the classification itself
• some code refactoring
• avoid NPEs

Enhance ignored import due to already existing specimens

#5130 Extend cdmlib import architecture to allow for remoting and Add import methods to IOService

WARNING: head commit changed in the meantime¶

Log ignored specimens in import report

Enhance name parsing

• more logging
• fixed rank assignment

Error logging for name parsing

• advanced readability

Enhance name parsing

• added more error logging
• avoid creating duplicate taxon names due to parsing problems

Refactor ABCD import

• use association wrapper to store prefix
• correctly push and pop import state
• only delete field unit if it has no other links to objects

Refactor ABCD import

• removed "determination on field unit level" flag
• parse unit associations recursively
• removed field unit from import state
• enhanced unit association handling concerning field units and ereivation events

Fix taxon existance check

Add import report logging to utility methods

Error loggind during import

Add exception during import to report

Fix classification handling for new and exisiting taxa

Exception handling

• moved report printing to finally clause to always have a report.
• fixed possible NPE

Handle default classification in state object

Fix classification handling in ABCD import

Log exceptions during import in the report file

Reset prefix after importing associated units

Soften association type matching.

Evaluate unit association type in ABCD import

• added test
• correctly set derivative hierarchy

Evaluate UnitAssociationType during import

Current rule for the relation between the imported unit and its
associated units:

• "same population" => sibling relation
• "same individual" => parent-child

Fix potential NPE

Import associated units

• Set derivation event correctly
• adapted test

Import associated units via BioCase query

Move prefix parsing to utility method and import state

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.

Import associated units in ABCD import

First changes

Refactor ABCD import

Moved class variables to import state

• added preservation/preparation parameters
  • fixed parsing of unitID

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

Rename NonViralName.xxxAuthorTeam to xxxAuthorship #4968

• 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

• 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