cdmlib.git
3 years agoadd missing reported in error term to test terms (to fix failing CubaCondensedDistrib...
Andreas Müller [Mon, 8 Feb 2021 21:18:42 +0000 (22:18 +0100)]
add missing reported in error term to test terms (to fix failing CubaCondensedDistributionTest

3 years agorevert removing UTF-8 from EuroPlusMedCondensedDistributionComposer
Andreas Müller [Mon, 8 Feb 2021 20:13:03 +0000 (21:13 +0100)]
revert removing UTF-8 from EuroPlusMedCondensedDistributionComposer

3 years agosimplify grouping in EuroPlusMedCondensedDistributionComposer
Andreas Müller [Mon, 8 Feb 2021 16:04:17 +0000 (17:04 +0100)]
simplify grouping in EuroPlusMedCondensedDistributionComposer

3 years agocleanup
Andreas Müller [Mon, 8 Feb 2021 16:01:49 +0000 (17:01 +0100)]
cleanup

3 years agoref #7287 unignore tests on CondensedDistributionComposerBase subclasses
Andreas Müller [Mon, 8 Feb 2021 15:53:34 +0000 (16:53 +0100)]
ref #7287 unignore tests on CondensedDistributionComposerBase subclasses

3 years agocleanup
Andreas Müller [Mon, 8 Feb 2021 15:52:24 +0000 (16:52 +0100)]
cleanup

3 years agofix #7529 adding PUBLISH group to FirstDataInserter
Andreas Kohlbecker [Mon, 8 Feb 2021 14:21:55 +0000 (15:21 +0100)]
fix #7529 adding PUBLISH group to FirstDataInserter

3 years agocleanup
Andreas Müller [Mon, 8 Feb 2021 10:11:21 +0000 (11:11 +0100)]
cleanup

3 years agoref #9457 fix missing space in HQL (cont.)
Andreas Müller [Mon, 8 Feb 2021 10:11:10 +0000 (11:11 +0100)]
ref #9457 fix missing space in HQL (cont.)

3 years agofix #9457 fix missing space in HQL
Andreas Müller [Mon, 8 Feb 2021 09:47:30 +0000 (10:47 +0100)]
fix #9457 fix missing space in HQL

3 years agorename method
Andreas Müller [Sat, 6 Feb 2021 20:33:22 +0000 (21:33 +0100)]
rename method

3 years agofix compilation issue in SetMap
Andreas Müller [Sat, 6 Feb 2021 20:32:49 +0000 (21:32 +0100)]
fix compilation issue in SetMap

3 years agocleanup
Andreas Müller [Sat, 6 Feb 2021 20:11:26 +0000 (21:11 +0100)]
cleanup

3 years agoref #9143 rename variable name for preferComputed->preferAggregated and update javadocs
Andreas Müller [Sat, 6 Feb 2021 20:03:05 +0000 (21:03 +0100)]
ref #9143 rename variable name for preferComputed->preferAggregated and update javadocs

3 years agoref #9143 remove preferComputed rule as default from calling DefilterDistributions...
Andreas Müller [Sat, 6 Feb 2021 19:45:19 +0000 (20:45 +0100)]
ref #9143 remove preferComputed rule as default from calling DefilterDistributions.filterDistributions(...) methods

3 years agouse SetMap in DescriptionUtility
Andreas Müller [Sat, 6 Feb 2021 19:38:44 +0000 (20:38 +0100)]
use SetMap in DescriptionUtility

3 years agoref #5095 fixing variable name for oahServerURI
Andreas Müller [Fri, 5 Feb 2021 17:36:18 +0000 (18:36 +0100)]
ref #5095 fixing variable name for oahServerURI

3 years agofix #6324 fix taxon node dozer mapping for TDWG Ontology (cont.) - add missing mappin...
Andreas Müller [Fri, 5 Feb 2021 16:13:59 +0000 (17:13 +0100)]
fix #6324 fix taxon node dozer mapping for TDWG Ontology (cont.) - add missing mappings-deep.xml changes

3 years agofix #6324 fix taxon node dozer mapping for TDWG Ontology
Andreas Müller [Fri, 5 Feb 2021 15:54:26 +0000 (16:54 +0100)]
fix #6324 fix taxon node dozer mapping for TDWG Ontology

3 years agofix #6324 fix synonym dozer mapping for TDWG Ontology
Andreas Müller [Fri, 5 Feb 2021 12:26:18 +0000 (13:26 +0100)]
fix #6324 fix synonym dozer mapping for TDWG Ontology

3 years agoref #6324 add toString() methods to TDWG classes for debugging
Andreas Müller [Fri, 5 Feb 2021 12:22:39 +0000 (13:22 +0100)]
ref #6324 add toString() methods to TDWG classes for debugging

3 years agocleanup
Andreas Müller [Fri, 5 Feb 2021 12:21:53 +0000 (13:21 +0100)]
cleanup

3 years agoref #6714 remove commented hibernate3-maven-plugin from pom
Andreas Müller [Fri, 5 Feb 2021 08:47:39 +0000 (09:47 +0100)]
ref #6714 remove commented hibernate3-maven-plugin from pom

3 years agoref #9359 remove test scope from objenesis
Andreas Müller [Thu, 4 Feb 2021 22:23:39 +0000 (23:23 +0100)]
ref  #9359 remove test scope from objenesis

3 years agoref #9359, ref #5095 upgrade dozer form 5.5.1 to 6.5.0 and use dozer-spring
Andreas Müller [Thu, 4 Feb 2021 19:51:11 +0000 (20:51 +0100)]
ref #9359, ref #5095 upgrade dozer form 5.5.1 to 6.5.0 and use dozer-spring

3 years agocleanup
Andreas Müller [Thu, 4 Feb 2021 19:02:01 +0000 (20:02 +0100)]
cleanup

3 years agoref #3403 , ref #4716, ref #3332, ref #9359 update dozer to version 5.5.1
Andreas Müller [Thu, 4 Feb 2021 17:38:49 +0000 (18:38 +0100)]
ref #3403 , ref #4716, ref #3332, ref #9359 update dozer to version 5.5.1

3 years agocleanup
Andreas Müller [Thu, 4 Feb 2021 17:29:41 +0000 (18:29 +0100)]
cleanup

3 years agofix #5095 unignore tests (remaining 2 tests in AssemblerTest are caused by changes...
Andreas Müller [Thu, 4 Feb 2021 17:29:06 +0000 (18:29 +0100)]
fix #5095 unignore tests (remaining 2 tests in AssemblerTest are caused by changes in #6324)

3 years agoref #5095 avoid running dozer tests when dozer.sourceforge.net is not available
Andreas Müller [Thu, 4 Feb 2021 17:26:15 +0000 (18:26 +0100)]
ref #5095 avoid running dozer tests when dozer.sourceforge.net is not available

3 years agofixing incorrect test
Andreas Müller [Thu, 4 Feb 2021 17:22:33 +0000 (18:22 +0100)]
fixing incorrect test

3 years agocleanup
Andreas Müller [Thu, 4 Feb 2021 17:21:49 +0000 (18:21 +0100)]
cleanup

3 years agoref #5095 change dozer mapping from .dtd to .xsd
Andreas Müller [Thu, 4 Feb 2021 16:56:34 +0000 (17:56 +0100)]
ref #5095 change dozer mapping from .dtd to .xsd

3 years agocleanup
Andreas Müller [Thu, 4 Feb 2021 16:30:16 +0000 (17:30 +0100)]
cleanup

3 years agoref #9114 fix dozer mapping by reverting URI mappings to java.net.URI
Andreas Müller [Thu, 4 Feb 2021 15:53:51 +0000 (16:53 +0100)]
ref #9114 fix dozer mapping by reverting URI mappings to java.net.URI

3 years agocleanup
Andreas Müller [Thu, 4 Feb 2021 15:51:33 +0000 (16:51 +0100)]
cleanup

3 years agomissed to add the new enum
Katja Luther [Thu, 4 Feb 2021 09:12:51 +0000 (10:12 +0100)]
missed to add the new enum

3 years agorevert setting publish in clone
Katja Luther [Thu, 4 Feb 2021 08:56:48 +0000 (09:56 +0100)]
revert setting publish in clone

3 years agoadd tests for different sec handling
Katja Luther [Thu, 4 Feb 2021 08:39:04 +0000 (09:39 +0100)]
add tests for different sec handling

3 years agopublish also should be cloned in TaxonBase.clone
Katja Luther [Thu, 4 Feb 2021 08:10:52 +0000 (09:10 +0100)]
publish also should be cloned in TaxonBase.clone

3 years agofix publish handling for synonyms and misapplied names and add sec handling for switc...
Katja Luther [Thu, 4 Feb 2021 07:27:20 +0000 (08:27 +0100)]
fix publish handling for synonyms and misapplied names and add sec handling for switch syn to accepted

3 years agofix #9451 add ClassificationDefaultCacheStrategy
Andreas Müller [Wed, 3 Feb 2021 12:13:37 +0000 (13:13 +0100)]
fix #9451 add ClassificationDefaultCacheStrategy

3 years agoref #9443, ref #5575 tissue sample as DnaSample generation and initialization of...
Andreas Müller [Wed, 3 Feb 2021 12:10:19 +0000 (13:10 +0100)]
ref #9443, ref #5575 tissue sample as DnaSample generation and initialization of DNA sample cache strategies

3 years agoref #5575 refactor initialization of cache strategy (initialize when needed, not...
Andreas Müller [Wed, 3 Feb 2021 12:02:32 +0000 (13:02 +0100)]
ref #5575 refactor initialization of cache strategy (initialize when needed, not in constructor)

3 years agocleanup
Andreas Müller [Wed, 3 Feb 2021 09:54:02 +0000 (10:54 +0100)]
cleanup

3 years agocleanup
Andreas Müller [Tue, 2 Feb 2021 23:36:07 +0000 (00:36 +0100)]
cleanup

3 years agocleanup
Andreas Müller [Tue, 2 Feb 2021 21:05:08 +0000 (22:05 +0100)]
cleanup

3 years agoremove System.exit(-1) from CdmPersistentDataSource
Andreas Müller [Tue, 2 Feb 2021 10:02:14 +0000 (11:02 +0100)]
remove System.exit(-1) from CdmPersistentDataSource

3 years agocleanup
Andreas Müller [Tue, 2 Feb 2021 10:01:23 +0000 (11:01 +0100)]
cleanup

3 years agofix #9434 add pollen, leaf and trichomes to the PlantKindOfUnit.csv
Andreas Müller [Fri, 29 Jan 2021 23:13:23 +0000 (00:13 +0100)]
fix #9434  add pollen, leaf and trichomes to the PlantKindOfUnit.csv

3 years agoref #9389 removing TODO comment as the situation is clarified now
Andreas Kohlbecker [Fri, 29 Jan 2021 10:21:15 +0000 (11:21 +0100)]
ref #9389 removing TODO comment as the situation is clarified now

3 years agoref #9253 removing useless init strategy from within @Transactional method
Andreas Kohlbecker [Fri, 29 Jan 2021 10:05:20 +0000 (11:05 +0100)]
ref #9253 removing useless init strategy from within @Transactional method

3 years agofix #9429 fix duplicated sec-detail in taxon cachestrategy
Andreas Müller [Thu, 28 Jan 2021 22:33:55 +0000 (23:33 +0100)]
fix #9429 fix duplicated sec-detail in taxon cachestrategy

3 years agocleanup
Andreas Müller [Thu, 28 Jan 2021 22:33:14 +0000 (23:33 +0100)]
cleanup

3 years agoUpdating develop poms back to pre merge state
jenkins [Thu, 28 Jan 2021 12:43:22 +0000 (13:43 +0100)]
Updating develop poms back to pre merge state

3 years agoMerge branch 'master' into develop
jenkins [Thu, 28 Jan 2021 12:43:21 +0000 (13:43 +0100)]
Merge branch 'master' into develop

3 years agoupdating develop poms to master versions to avoid merge conflicts
jenkins [Thu, 28 Jan 2021 12:43:20 +0000 (13:43 +0100)]
updating develop poms to master versions to avoid merge conflicts

3 years agoMerge branch 'release/5.19.0' 5.19.0
jenkins [Thu, 28 Jan 2021 12:43:15 +0000 (13:43 +0100)]
Merge branch 'release/5.19.0'

3 years agoupdating poms for branch'release/5.19.0' with non-snapshot versions
jenkins [Thu, 28 Jan 2021 12:22:23 +0000 (13:22 +0100)]
updating poms for branch'release/5.19.0' with non-snapshot versions

3 years agoupdating poms for 5.20.0-SNAPSHOT development
jenkins [Thu, 28 Jan 2021 11:59:57 +0000 (12:59 +0100)]
updating poms for 5.20.0-SNAPSHOT development

3 years agoref #9395 solving problem in derivation-dto-graph assembly (replaced field units) origin/release/5.19.0
Andreas Kohlbecker [Wed, 27 Jan 2021 12:02:04 +0000 (13:02 +0100)]
ref #9395 solving problem in derivation-dto-graph assembly (replaced field units)

3 years agoref #7599 ref #9395 documenting requirements
Andreas Kohlbecker [Wed, 27 Jan 2021 10:20:45 +0000 (11:20 +0100)]
ref #7599 ref #9395 documenting requirements

3 years agoref #9301 static helper method to find the nom. act of a registration
Andreas Kohlbecker [Tue, 26 Jan 2021 13:15:36 +0000 (14:15 +0100)]
ref #9301 static helper method to find the nom. act of a registration

3 years agoref #9395 simplifying findByGeneticAccessionNumber() as extra code has no imact on...
Andreas Kohlbecker [Tue, 26 Jan 2021 11:38:40 +0000 (12:38 +0100)]
ref #9395 simplifying findByGeneticAccessionNumber() as extra code has no imact on performance

3 years agoref #9395 findByAccessionNumber() -> findByGeneticAccessionNumber(), preserving old...
Andreas Kohlbecker [Tue, 26 Jan 2021 11:34:06 +0000 (12:34 +0100)]
ref #9395 findByAccessionNumber() -> findByGeneticAccessionNumber(), preserving old method as deprecated

3 years agocleanup
Andreas Müller [Tue, 26 Jan 2021 11:32:48 +0000 (12:32 +0100)]
cleanup

3 years agoref #9395 fully implementing maxDepth for derivative assembly and fixing OccurrenceSe...
Andreas Kohlbecker [Tue, 26 Jan 2021 11:16:53 +0000 (12:16 +0100)]
ref #9395 fully implementing maxDepth for derivative assembly and fixing OccurrenceServiceImpl._findRootUnitDTO()

3 years agocleanup
Andreas Müller [Tue, 26 Jan 2021 10:43:10 +0000 (11:43 +0100)]
cleanup

3 years agoref #9360 preliminary exception for debugging NPE
Andreas Müller [Tue, 26 Jan 2021 08:59:29 +0000 (09:59 +0100)]
ref #9360 preliminary exception for debugging NPE

3 years agoref #9389 ref #9415 improving information assembly in derivation bouquet by recursion...
Andreas Kohlbecker [Mon, 25 Jan 2021 18:49:59 +0000 (19:49 +0100)]
ref #9389 ref #9415 improving information assembly in derivation bouquet by recursion - adapting test

3 years agoref #9389 ref #9415 improving information assembly in derivation bouquet by recursion...
Andreas Kohlbecker [Mon, 25 Jan 2021 18:12:17 +0000 (19:12 +0100)]
ref #9389 ref #9415 improving information assembly in derivation bouquet by recursion, fixing multiple problems

3 years agoavoid NotSerializableException for SourceDto
Katja Luther [Mon, 25 Jan 2021 10:26:30 +0000 (11:26 +0100)]
avoid NotSerializableException for SourceDto

3 years agocleanup
Andreas Müller [Fri, 22 Jan 2021 15:32:23 +0000 (16:32 +0100)]
cleanup

3 years agoref #9365 update code for reuse taxon (change order for check name and check taxon...
Andreas Müller [Fri, 22 Jan 2021 15:32:07 +0000 (16:32 +0100)]
ref #9365 update code for reuse taxon (change order for check name and check taxon and throw exceptions if not exists)

3 years agocleanup
Andreas Müller [Fri, 22 Jan 2021 15:08:13 +0000 (16:08 +0100)]
cleanup

3 years agomake comparators of TaxonNodeXxxSortMode singletons
Andreas Müller [Fri, 22 Jan 2021 13:53:49 +0000 (14:53 +0100)]
make comparators of TaxonNodeXxxSortMode singletons

3 years agocleanup
Andreas Müller [Fri, 22 Jan 2021 13:47:45 +0000 (14:47 +0100)]
cleanup

3 years agoref #9354 unify TaxonNodeDao.listChildrenOf(...) methods (fix test)
Andreas Müller [Fri, 22 Jan 2021 12:52:54 +0000 (13:52 +0100)]
ref #9354 unify TaxonNodeDao.listChildrenOf(...) methods (fix test)

3 years agoref #9354 unify TaxonNodeDao.listChildrenOf(...) methods
Andreas Müller [Fri, 22 Jan 2021 12:26:17 +0000 (13:26 +0100)]
ref #9354 unify TaxonNodeDao.listChildrenOf(...) methods

3 years agomove TaxonNodeSortMode to model.compare
Andreas Müller [Fri, 22 Jan 2021 12:24:22 +0000 (13:24 +0100)]
move TaxonNodeSortMode to model.compare

3 years agocleanup
Andreas Müller [Fri, 22 Jan 2021 12:23:16 +0000 (13:23 +0100)]
cleanup

3 years agoref #9276 renaming DerivationTreeSummaryDTO fields in SpecimenOrObservationBaseDTO
Andreas Kohlbecker [Fri, 22 Jan 2021 10:34:47 +0000 (11:34 +0100)]
ref #9276 renaming DerivationTreeSummaryDTO fields in SpecimenOrObservationBaseDTO

3 years agoref #9276 documenting DerivateDataDTO and renaming to DerivationTreeSummaryDTO
Andreas Kohlbecker [Fri, 22 Jan 2021 10:32:44 +0000 (11:32 +0100)]
ref #9276 documenting DerivateDataDTO and renaming to DerivationTreeSummaryDTO

3 years agotry to fix TaxoNodeByNameComparator issue in application context files.
Andreas Müller [Fri, 22 Jan 2021 10:33:42 +0000 (11:33 +0100)]
try to fix TaxoNodeByNameComparator issue in application context files.

3 years agofix compile error and rename TaxonNodeNaturalComparator
Andreas Müller [Fri, 22 Jan 2021 10:16:54 +0000 (11:16 +0100)]
fix compile error and rename TaxonNodeNaturalComparator

3 years agomoving further Comparators to model.compare
Andreas Müller [Fri, 22 Jan 2021 10:07:21 +0000 (11:07 +0100)]
moving further Comparators to model.compare

3 years agocleanup
Andreas Müller [Fri, 22 Jan 2021 09:43:39 +0000 (10:43 +0100)]
cleanup

3 years agoref #9354 fix NPE in TaxonNodeByRankAndNameComparator
Andreas Müller [Fri, 22 Jan 2021 09:43:19 +0000 (10:43 +0100)]
ref #9354 fix NPE in TaxonNodeByRankAndNameComparator

3 years agoref #9395 adapting services and web-services to return all root units
Andreas Kohlbecker [Fri, 22 Jan 2021 09:47:46 +0000 (10:47 +0100)]
ref #9395 adapting services and web-services to return all root units

3 years agomove some comparators to model.compare package, add subpackages to model.compare...
Andreas Müller [Fri, 22 Jan 2021 09:02:18 +0000 (10:02 +0100)]
move some comparators to model.compare package, add subpackages to model.compare and  some cleanup

3 years agoimplement Comparator contract for TypedEntityComparator.java correctly
Andreas Müller [Fri, 22 Jan 2021 07:39:31 +0000 (08:39 +0100)]
implement Comparator contract for TypedEntityComparator.java correctly

3 years agofix compile error
Andreas Müller [Thu, 21 Jan 2021 18:41:32 +0000 (19:41 +0100)]
fix compile error

3 years agoimprove generics for AgentService.getUuidAndAbbrevTitleCache
Andreas Müller [Thu, 21 Jan 2021 18:26:06 +0000 (19:26 +0100)]
improve generics for AgentService.getUuidAndAbbrevTitleCache

3 years agocleanup
Andreas Müller [Thu, 21 Jan 2021 18:25:25 +0000 (19:25 +0100)]
cleanup

3 years agoref #9356 adapt TypeDesignationComparator to fix case when both type status are null...
Andreas Müller [Thu, 21 Jan 2021 18:23:26 +0000 (19:23 +0100)]
ref #9356 adapt TypeDesignationComparator to fix case when both type status are null ; and cleanup null compare part above

3 years agocleanup and improve generics
Andreas Müller [Thu, 21 Jan 2021 16:40:09 +0000 (17:40 +0100)]
cleanup and improve generics

3 years agofix delete taxon/name and merge createTaxon methods - continue
Katja Luther [Thu, 21 Jan 2021 16:29:49 +0000 (17:29 +0100)]
fix delete taxon/name and merge createTaxon methods - continue

3 years agocleanup
Andreas Müller [Thu, 21 Jan 2021 15:12:39 +0000 (16:12 +0100)]
cleanup

3 years agoref #9142 code simplification
Andreas Müller [Thu, 21 Jan 2021 15:12:23 +0000 (16:12 +0100)]
ref #9142 code simplification

3 years agoref #9301 extending init-strategy to include typeDesignation.source.*
Andreas Kohlbecker [Thu, 21 Jan 2021 14:31:16 +0000 (15:31 +0100)]
ref  #9301 extending init-strategy to include typeDesignation.source.*