cdmlib.git
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.*

3 years agomerge the two create taxon methods
Katja Luther [Thu, 21 Jan 2021 13:40:44 +0000 (14:40 +0100)]
merge the two create taxon methods

3 years agofix isDeletable for taxon with name used only once
Katja Luther [Thu, 21 Jan 2021 13:39:27 +0000 (14:39 +0100)]
fix isDeletable for taxon with name used only once

3 years agoref 6308: result should be ok, if taxon can be deleted but not the name
Katja Luther [Wed, 20 Jan 2021 15:24:21 +0000 (16:24 +0100)]
ref 6308: result should be ok, if taxon can be deleted but not the name

3 years agoref #7223 proper definition of IPersonalCommunication in ReferencePropertyDefinitions
Andreas Kohlbecker [Wed, 20 Jan 2021 14:12:51 +0000 (15:12 +0100)]
ref #7223 proper definition of IPersonalCommunication in ReferencePropertyDefinitions

3 years agoref #9290 castTo method for TypedEntityReference
Andreas Kohlbecker [Wed, 20 Jan 2021 13:08:52 +0000 (14:08 +0100)]
ref #9290 castTo method for TypedEntityReference

3 years agofix #9391: fix test
Katja Luther [Wed, 20 Jan 2021 11:43:12 +0000 (12:43 +0100)]
fix #9391: fix test

3 years agoref 6308: check for namedeletion in taxonbase isDeletable and add warning if not...
Katja Luther [Wed, 20 Jan 2021 10:55:10 +0000 (11:55 +0100)]
ref 6308: check for namedeletion in taxonbase isDeletable and add warning if not deletable

3 years agofix #9391: fix test
Katja Luther [Wed, 20 Jan 2021 10:03:57 +0000 (11:03 +0100)]
fix #9391: fix test

3 years agofix #9391: if no level exist remove class name in label with level in namedArea
Katja Luther [Wed, 20 Jan 2021 08:38:48 +0000 (09:38 +0100)]
fix #9391: if no level exist remove class name in label with level in namedArea

3 years agoref #8889: sort taxonnodes for distribution editor on server side
Katja Luther [Tue, 19 Jan 2021 13:41:46 +0000 (14:41 +0100)]
ref #8889: sort taxonnodes for distribution editor on server side

3 years agoref #9354: add nodeDto to TaxonDistributionDTO
Katja Luther [Mon, 18 Jan 2021 16:21:19 +0000 (17:21 +0100)]
ref #9354: add nodeDto to TaxonDistributionDTO

3 years agofix #9395 DerivedUnit.collectFieldUnits() as DerivedUnit.collectRootUnits() to return...
Andreas Kohlbecker [Mon, 18 Jan 2021 13:05:46 +0000 (14:05 +0100)]
fix #9395 DerivedUnit.collectFieldUnits() as DerivedUnit.collectRootUnits() to return all types of root units - removig debug code

3 years agocleanup
Andreas Müller [Wed, 13 Jan 2021 22:01:13 +0000 (23:01 +0100)]
cleanup

3 years agofix #9395 DerivedUnit.collectFieldUnits() as DerivedUnit.collectRootUnits() to return...
Andreas Kohlbecker [Mon, 18 Jan 2021 11:17:49 +0000 (12:17 +0100)]
fix #9395 DerivedUnit.collectFieldUnits() as DerivedUnit.collectRootUnits() to return all types of root units

3 years agoref #9356: adapt TypeDesignationComparator
Katja Luther [Fri, 15 Jan 2021 08:58:50 +0000 (09:58 +0100)]
ref #9356: adapt TypeDesignationComparator

3 years agoref #9332 re-organizing source(es) in TypeDesignation init-strategy
Andreas Kohlbecker [Thu, 14 Jan 2021 14:14:03 +0000 (15:14 +0100)]
ref #9332 re-organizing source(es) in TypeDesignation init-strategy

3 years agoref #7711: delete last media in galery should not delete description
Katja Luther [Thu, 14 Jan 2021 09:10:04 +0000 (10:10 +0100)]
ref #7711: delete last media in galery should not delete description

3 years agofix #9387 extending init strategy
Andreas Kohlbecker [Thu, 14 Jan 2021 07:49:39 +0000 (08:49 +0100)]
fix #9387 extending init strategy

3 years agoadd javadoc comment
Andreas Müller [Wed, 13 Jan 2021 15:20:09 +0000 (16:20 +0100)]
add javadoc comment

3 years agofix #9384, ref #9279 fixed incorrect implementation of createShortCitation and added...
Andreas Müller [Wed, 13 Jan 2021 15:14:09 +0000 (16:14 +0100)]
fix #9384, ref #9279 fixed incorrect implementation of createShortCitation and added tests

3 years agocleanup
Andreas Müller [Wed, 13 Jan 2021 15:12:08 +0000 (16:12 +0100)]
cleanup

3 years agoTypedEntityReference: factory method with option to supress the label & using this...
Andreas Kohlbecker [Tue, 12 Jan 2021 15:57:35 +0000 (16:57 +0100)]
TypedEntityReference: factory method with option to supress the label & using this in TypeDesignationSetFormatter

3 years agofixing inappropriate use of TypedEntityReference for creating tagged text in TypeDesi...
Andreas Kohlbecker [Tue, 12 Jan 2021 15:50:11 +0000 (16:50 +0100)]
fixing inappropriate use of TypedEntityReference for creating tagged text in TypeDesignationSetFormatter

3 years agofixing NPE in RegistrationDTOController when identifier is not found
Andreas Kohlbecker [Tue, 12 Jan 2021 15:32:45 +0000 (16:32 +0100)]
fixing NPE in RegistrationDTOController when identifier is not found

3 years agofix #9384 fixing author team truncation
Andreas Kohlbecker [Tue, 12 Jan 2021 15:32:16 +0000 (16:32 +0100)]
fix #9384 fixing author team truncation

3 years agoref #6591 adapt PESI import to new original spellings handling
Andreas Müller [Sun, 10 Jan 2021 09:56:48 +0000 (10:56 +0100)]
ref #6591  adapt PESI import to new original spellings handling

3 years agocleanup
Andreas Müller [Sun, 10 Jan 2021 09:54:29 +0000 (10:54 +0100)]
cleanup

3 years agocleanup
Andreas Müller [Sat, 9 Jan 2021 15:11:36 +0000 (16:11 +0100)]
cleanup

3 years agoref #5573, ref #7612 adapt MediaSpecimenDefaultCacheStrategy to OccurrenceCacheStrate...
Andreas Müller [Sat, 9 Jan 2021 10:22:27 +0000 (11:22 +0100)]
ref #5573, ref #7612 adapt MediaSpecimenDefaultCacheStrategy to OccurrenceCacheStrategyBase

3 years agoref #5575 add first version of DnaSample cache strategy
Andreas Müller [Sat, 9 Jan 2021 10:21:16 +0000 (11:21 +0100)]
ref #5575 add first version of DnaSample cache strategy

3 years agoref #7612 a first (preliminary) version of MediaSpecimenDefaultCacheStrategy
Andreas Müller [Sat, 9 Jan 2021 00:30:30 +0000 (01:30 +0100)]
ref #7612 a first (preliminary) version of MediaSpecimenDefaultCacheStrategy

3 years agocleanup and use TermTestBase for model tests
Andreas Müller [Sat, 9 Jan 2021 00:03:07 +0000 (01:03 +0100)]
cleanup and use TermTestBase for model tests

3 years agocleanup
Andreas Müller [Fri, 8 Jan 2021 21:30:14 +0000 (22:30 +0100)]
cleanup

3 years agouncomment RdfViewTest.testNameInformationRdf as it seems to work currently
Andreas Müller [Wed, 6 Jan 2021 12:07:21 +0000 (13:07 +0100)]
uncomment RdfViewTest.testNameInformationRdf as it seems to work currently

3 years agocleanup
Andreas Müller [Wed, 6 Jan 2021 12:01:18 +0000 (13:01 +0100)]
cleanup

3 years agoref #9114 fix RdfViewTest
Andreas Müller [Wed, 6 Jan 2021 12:00:03 +0000 (13:00 +0100)]
ref #9114 fix RdfViewTest

3 years agocleanup
Andreas Müller [Wed, 6 Jan 2021 10:00:18 +0000 (11:00 +0100)]
cleanup

3 years agoref #9114 further adapt jsonConfigurations and add new constructor to URI wrapper
Andreas Müller [Wed, 6 Jan 2021 10:00:01 +0000 (11:00 +0100)]
ref #9114 further adapt jsonConfigurations and add new constructor to URI wrapper

3 years agoref #9114 adapt json mapping to new URI wrapper
Andreas Müller [Wed, 6 Jan 2021 09:18:13 +0000 (10:18 +0100)]
ref #9114  adapt json mapping to new URI wrapper

3 years agoref #9114 adapt javadoc for new URI wrapper user type
Andreas Müller [Wed, 6 Jan 2021 09:17:49 +0000 (10:17 +0100)]
ref #9114  adapt javadoc for new URI wrapper user type

3 years agocleanup
Andreas Müller [Wed, 6 Jan 2021 08:02:35 +0000 (09:02 +0100)]
cleanup