Enhance ABCD import report

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

Add support for ABCD 2.0.6 in UnitAssociationParser

WARNING: head commit changed in the meantime¶

Log ignored specimens in import report

Add two new test files

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

Remove parseNameAutomatically flag

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

Catch exception instead of throwing them

Lets the methods return

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

Do not close system.out

Soften association type matching.

Map preparation material to derivation event description

Fix potential NPE

Fix potential NPE

Evaluate unit association type in ABCD import

• added test
• correctly set derivative hierarchy

Check if primer or amplification already exist

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

Parse sample designation in ABCD GGBN import

Move up name parsing

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.

??

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

• 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

• 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