EDIT

Fix classification handling for new and exisiting taxa

Add new test for classification handling

Exception handling

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

Merge branch 'master' into abcd

Test classification handling

Handle default classification in state object

Fix missing protected evaluation for Taxon titleCache #5018

#5054 Add delete method call with uuid

Add tests for classification handling

Fix classification handling in ABCD import

Check ignoreAuthorship flag with different authors in test data

minor

cacheUpdater Caryophyllales

cacheUpdater for caryophyllales

Remove unneccessary check

Log exceptions during import in the report file

Improve DwC-A import for large datasets

Extend tests for GGBN import.

Checking field unit data.

Merge branch 'master' into abcd

minor

Caryophyllales stuff

Allow to split DwCA imports in parts (first steps)

#5056 Refactored 'save' call to return saved entity

#5012 Add service layer updates for remoting calls from the Bulk Editor

removed named areas to avoid test failure

Add test for importing two dna units with associated units

Reset prefix after importing associated units

Do not close system.out

Add test for importing two dna units with associated units

Reset prefix after importing associated units

Do not close system.out

test for fallbackArea rule in DescriptionUtility.filterDistrubution for EuroPlusMed - #4408

implementing fallbackArea rule into DescriptionUtility.filterDistrubution for EuroPlusMed - #4408

adapting tests to changes in EuroPlusMedCondensedDistributionComposer and DescriptionUtils
- testGetWebServiceUrlCountry() : removing restriction on specific order of area status parameters
- testGetCondensedDistribution() : fixing unappropriate test data

Ignore createTestData()

Add accidentally removed test file

Extend step-by-step deletion test

• Used correct single read deletion method.
• Created test file

Soften association type matching.

Map preparation material to derivation event description

Test import of sparse ABCD file

Fix potential NPE

Add method for single read deletion

Fix singleton constructor with specimen types

Do not set consensus sequence of single read alignment to null when
deleting the alignment

Add delete method for SingleReads

Remove comments

correcting the cleanup of sub areas labes in condensed distributions

applying subAreaPreference exclusively for maps

subAreaPreference Rule can be run completely separately
- also reoving old unused code
- removing documentation on osoltete rule
- removing all missleading errors on the subAreaPreference in documentation an comments

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

Add find- and countByTitle() methods to primer and amplification service

Split up test for unit associations

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.

• added missing columns for derivative import

??

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

correctly assigning INTRODUCED_NATURALIZED to n=naturalizes for condensed distribution - #3907

fixing sort order in condensed distribution - #3907

removing obsolete warning from log - #3907

#5009 Add service method to update all nodes

fixing bug that occurred with empty distributions- #5041

Add default delete method for uuid collections and implement update nodes method in polytomouse key service

Further fix DistributionTree.matchesLevels #5041

Fix DistributionTree.matchesLevels #5041

Fix label order marker types in imports

Fix ClassCastException in call to distributionInfo service #5041

Add getTermByIdInVoc method to vocabularies

Improve transmission engine parameters for web service (#5040)

Fix umlaut bug in parser test

Fix unparsed sections and subsections #4764

#5034 Add methods for testing handler / operations architecture

Fix updateSortindex test for TaxonNode javassist objects

#5032 Add new test service for remoting clients

Fix possible but in FeatureNode sortindex creation

See similar issue in TaxonNode sortindex creation.

minor

minor

Fix sortindex computation in TaxonNode

After commit from 2015-06-18 the sortindex was computed slightly
different. In some cases the parent was not deproxied anymore and
therefore the parent.childNodes always returned the empty list of the
proxy object instead of returning the actual childrens list.

some bugfixes in CondensedDistribution composition code - #3907

minor documentation cleaning

composition of condensed distribution fully implemented - #3907

base framework for condensedDistributions implemented - #4911

performance: avoiding second distribution filtering when creating the DistributionServiceRequestParameterString - #4911

replacing 'non-java-doc by {@inheritDoc}

Clean up transmission engine and BerlinModelTransformer