cdmlib.git
4 months agocleanup
Andreas Müller [Fri, 23 Feb 2024 12:15:58 +0000 (13:15 +0100)]
cleanup

4 months agoused defined uuid1
Andreas Müller [Fri, 23 Feb 2024 12:12:23 +0000 (13:12 +0100)]
used defined uuid1

4 months agoremove unused property path
Andreas Müller [Fri, 23 Feb 2024 10:18:40 +0000 (11:18 +0100)]
remove unused property path

4 months ago#7045 move createNodeDtos to result class
Andreas Müller [Fri, 23 Feb 2024 10:13:37 +0000 (11:13 +0100)]
#7045 move createNodeDtos to result class

4 months agoref #10472: add Methods to get accTaxonUuid and nom citation
Katja [Fri, 23 Feb 2024 10:58:07 +0000 (11:58 +0100)]
ref #10472: add Methods to get accTaxonUuid and nom citation

4 months agoref #10322, ref #10474 order derivates on short label
Andreas Müller [Wed, 21 Feb 2024 09:55:42 +0000 (10:55 +0100)]
ref #10322, ref #10474 order derivates on short label

4 months agoextract SpecimenOrObservationBaseComparator
Andreas Müller [Wed, 21 Feb 2024 07:54:55 +0000 (08:54 +0100)]
extract SpecimenOrObservationBaseComparator

4 months agoupdate javadoc for SpecimenTypeDesignationStatus
Andreas Müller [Wed, 21 Feb 2024 07:48:34 +0000 (08:48 +0100)]
update javadoc for SpecimenTypeDesignationStatus

4 months agoref #10322, ref #10474 make SpecimenOrObservationBaseDTO.derivatives ordered
Andreas Müller [Wed, 21 Feb 2024 07:30:28 +0000 (08:30 +0100)]
ref #10322, ref #10474 make SpecimenOrObservationBaseDTO.derivatives ordered

4 months agocleanup
Andreas Müller [Mon, 19 Feb 2024 21:15:29 +0000 (22:15 +0100)]
cleanup

4 months agoremove unused getTaxaByName method from taxonDao
Andreas Müller [Mon, 19 Feb 2024 12:35:06 +0000 (13:35 +0100)]
remove unused getTaxaByName method from taxonDao

4 months agosome javadoc
Andreas Müller [Mon, 19 Feb 2024 12:34:27 +0000 (13:34 +0100)]
some javadoc

4 months agoref #10322, ref #10474 remove not fully implemented specimen implementation from...
Andreas Müller [Mon, 19 Feb 2024 12:33:32 +0000 (13:33 +0100)]
ref #10322, ref #10474 remove not fully implemented specimen implementation from DTO for now

4 months agoref #10322, ref #10474 use timePeriod instead of gatheringStartDate in all occurrence...
Andreas Müller [Sat, 17 Feb 2024 08:58:13 +0000 (09:58 +0100)]
ref #10322, ref #10474 use timePeriod instead of gatheringStartDate in all occurrence context

4 months agoref #10322, ref #10474 fix recordBase handling (cont.)
Andreas Müller [Sat, 17 Feb 2024 07:34:41 +0000 (08:34 +0100)]
ref #10322, ref #10474 fix recordBase handling (cont.)

4 months agoref #10322, ref #10474 fix recordBase handling
Andreas Müller [Sat, 17 Feb 2024 06:57:23 +0000 (07:57 +0100)]
ref #10322, ref #10474 fix recordBase handling

4 months agoref #10322, ref #10474 handle contigFile
Andreas Müller [Sat, 17 Feb 2024 00:27:36 +0000 (01:27 +0100)]
ref #10322, ref #10474 handle contigFile

4 months agoref #10322, ref #10474 add DnaQualityDTO
Andreas Müller [Fri, 16 Feb 2024 23:45:12 +0000 (00:45 +0100)]
ref #10322, ref #10474 add DnaQualityDTO

4 months agoref #10322, ref #10474 add addAmplificationResultDTO, SingleReadDTO and PrimerDTO
Andreas Müller [Fri, 16 Feb 2024 22:45:13 +0000 (23:45 +0100)]
ref #10322, ref #10474 add addAmplificationResultDTO, SingleReadDTO and PrimerDTO

4 months agoref #10322, ref #10474 cleanup fieldunit and improve data handling and comparison...
Andreas Müller [Fri, 16 Feb 2024 20:37:11 +0000 (21:37 +0100)]
ref #10322, ref #10474 cleanup fieldunit and improve data handling and comparison (cont.)

4 months agoref #10322, ref #10474 cleanup fieldunit and improve data handling and comparison
Andreas Müller [Fri, 16 Feb 2024 20:18:34 +0000 (21:18 +0100)]
ref #10322, ref #10474 cleanup fieldunit and improve data handling and comparison

4 months agocleanup
Andreas Müller [Fri, 16 Feb 2024 19:32:35 +0000 (20:32 +0100)]
cleanup

4 months agoref #10322, ref #10472 further remove model objects, use DerivationEvent and some...
Andreas Müller [Fri, 16 Feb 2024 17:46:30 +0000 (18:46 +0100)]
ref #10322, ref #10472 further remove model objects, use DerivationEvent and some cleanup

4 months agoref #10322, ref #10472 remove defiend terms and OccurrenceType from SpecimenOrObserva...
Andreas Müller [Fri, 16 Feb 2024 16:02:00 +0000 (17:02 +0100)]
ref #10322, ref #10472 remove defiend terms and OccurrenceType from SpecimenOrObservationBaseDTO

4 months agoref #10322, ref #10472 remove model objects from specimenDTOs
Andreas Müller [Fri, 16 Feb 2024 15:40:31 +0000 (16:40 +0100)]
ref #10322, ref #10472 remove model objects from specimenDTOs

4 months agoref #10322 clean specimenDTOs and TaggedEntityReference factory method
Andreas Müller [Fri, 16 Feb 2024 15:39:07 +0000 (16:39 +0100)]
ref #10322 clean specimenDTOs and TaggedEntityReference factory method

4 months agoref #10322 split TypedEntityReference in data holder and factory class and remove...
Andreas Müller [Fri, 16 Feb 2024 12:40:06 +0000 (13:40 +0100)]
ref #10322 split TypedEntityReference in data holder and factory class and remove deprecated constructor (cont. ||)

4 months agoref #10322 split TypedEntityReference in data holder and factory class and remove...
Andreas Müller [Fri, 16 Feb 2024 12:31:31 +0000 (13:31 +0100)]
ref #10322 split TypedEntityReference in data holder and factory class and remove deprecated constructor (cont.)

4 months agoref #10322 split TypedEntityReference in data holder and factory class and remove...
Andreas Müller [Fri, 16 Feb 2024 12:30:02 +0000 (13:30 +0100)]
ref #10322 split TypedEntityReference in data holder and factory class and remove deprecated constructor

4 months agocleanup
Andreas Müller [Fri, 16 Feb 2024 10:25:09 +0000 (11:25 +0100)]
cleanup

4 months agoref #10322 fix missing label for CollectionDTO
Andreas Müller [Fri, 16 Feb 2024 10:24:32 +0000 (11:24 +0100)]
ref #10322 fix missing label for CollectionDTO

4 months agoref #10322 cleanup specimen DTOs
Andreas Müller [Fri, 16 Feb 2024 08:37:00 +0000 (09:37 +0100)]
ref #10322 cleanup specimen DTOs

4 months agoref #10322 try to fix derivatives handling
Andreas Müller [Thu, 15 Feb 2024 23:26:33 +0000 (00:26 +0100)]
ref #10322 try to fix derivatives handling

4 months agoCorrect typo in ORCID IdentifierType description
Andreas Müller [Thu, 15 Feb 2024 22:12:35 +0000 (23:12 +0100)]
Correct typo in ORCID IdentifierType description

4 months agoref #10273 add WfoContentExport classes (still dummy, copied from backbone export)
Andreas Müller [Thu, 15 Feb 2024 22:04:34 +0000 (23:04 +0100)]
ref #10273 add WfoContentExport classes (still dummy, copied from backbone export)

4 months agocleanup
Andreas Müller [Thu, 15 Feb 2024 22:02:12 +0000 (23:02 +0100)]
cleanup

4 months agoreduce logging in CdmModelCacher
Andreas Müller [Thu, 15 Feb 2024 20:40:46 +0000 (21:40 +0100)]
reduce logging in CdmModelCacher

4 months agoref #9610: adapted io
Katja [Thu, 15 Feb 2024 16:35:56 +0000 (17:35 +0100)]
ref #9610: adapted io

4 months agoref #9610: adapted tests
Katja [Thu, 15 Feb 2024 15:25:12 +0000 (16:25 +0100)]
ref #9610: adapted tests

4 months agoref #9610: MediaInfoFileReader should create inputStream only once
Katja [Thu, 15 Feb 2024 13:33:08 +0000 (14:33 +0100)]
ref #9610: MediaInfoFileReader should create inputStream only once

4 months agoref #10271 remove replacing of "wfo-" in WFO Identifiers (according to documentation...
Andreas Müller [Thu, 15 Feb 2024 11:00:24 +0000 (12:00 +0100)]
ref #10271 remove replacing of "wfo-" in WFO Identifiers (according to documentation change)

4 months agoref #10322 add javadoc for RegistrationDTO and RegistrationWrapperDTO
Andreas Müller [Thu, 15 Feb 2024 09:35:39 +0000 (10:35 +0100)]
ref #10322 add javadoc for RegistrationDTO and RegistrationWrapperDTO

4 months agoCleanup
Andreas Müller [Thu, 15 Feb 2024 09:34:01 +0000 (10:34 +0100)]
Cleanup

4 months agoref #10365: code cleaning
Katja Luther [Thu, 15 Feb 2024 08:51:13 +0000 (09:51 +0100)]
ref #10365: code cleaning

4 months agocleanup
Andreas Müller [Wed, 14 Feb 2024 16:18:18 +0000 (17:18 +0100)]
cleanup

4 months agoRemove old FeatureDto_.java
Andreas Müller [Wed, 14 Feb 2024 16:17:33 +0000 (17:17 +0100)]
Remove old FeatureDto_.java

4 months agoref #10322 split service DTOs to api DTOs and Loaders for specimen related DTOs;...
Andreas Müller [Wed, 14 Feb 2024 16:16:43 +0000 (17:16 +0100)]
ref #10322 split service DTOs to api DTOs and Loaders for specimen related DTOs; use SpecimenDTO in TaxonPortalDto

4 months agoref #10271 handle CURI identifiers separately
Andreas Müller [Tue, 13 Feb 2024 12:50:00 +0000 (13:50 +0100)]
ref #10271 handle CURI identifiers separately

4 months agoadd EntityReference for secundum
Katja [Tue, 13 Feb 2024 12:20:18 +0000 (13:20 +0100)]
add EntityReference for secundum

4 months agoref #10271 handle ipni, tropicos and index fungorum identifiers
Andreas Müller [Mon, 12 Feb 2024 22:37:57 +0000 (23:37 +0100)]
ref #10271 handle ipni, tropicos and index fungorum identifiers

4 months agodo not use feature if not contained in feature map
Katja [Mon, 12 Feb 2024 13:45:55 +0000 (14:45 +0100)]
do not use feature if not contained in feature map

5 months agoref #10424 make getDefaultDescription transient
Andreas Müller [Fri, 2 Feb 2024 09:23:02 +0000 (10:23 +0100)]
ref #10424 make getDefaultDescription transient

5 months agoUpdating develop poms back to pre merge state
jenkins [Fri, 2 Feb 2024 00:26:36 +0000 (01:26 +0100)]
Updating develop poms back to pre merge state

5 months agoMerge branch 'master' into develop
jenkins [Fri, 2 Feb 2024 00:26:35 +0000 (01:26 +0100)]
Merge branch 'master' into develop

5 months agoupdating develop poms to master versions to avoid merge conflicts
jenkins [Fri, 2 Feb 2024 00:26:34 +0000 (01:26 +0100)]
updating develop poms to master versions to avoid merge conflicts

5 months agoMerge branch 'release/5.42.0' 5.42.0
jenkins [Fri, 2 Feb 2024 00:26:27 +0000 (01:26 +0100)]
Merge branch 'release/5.42.0'

5 months agoupdating poms for branch'release/5.42.0' with non-snapshot versions
jenkins [Fri, 2 Feb 2024 00:13:36 +0000 (01:13 +0100)]
updating poms for branch'release/5.42.0' with non-snapshot versions

5 months agoupdating poms for 5.43.0-SNAPSHOT development
jenkins [Thu, 1 Feb 2024 23:20:59 +0000 (00:20 +0100)]
updating poms for 5.43.0-SNAPSHOT development

5 months agoref #10271 add IPNI normalizeAuthor to ColDP export origin/release/5.42.0
Andreas Müller [Thu, 1 Feb 2024 22:12:46 +0000 (23:12 +0100)]
ref #10271 add IPNI normalizeAuthor to ColDP export

5 months agoref #10271 fix protectd titleCache handling in ColDP Export
Andreas Müller [Thu, 1 Feb 2024 22:11:40 +0000 (23:11 +0100)]
ref #10271 fix protectd titleCache handling in ColDP Export

5 months agoref#10446 normalize to IPNI standard
Andreas Müller [Thu, 1 Feb 2024 21:50:59 +0000 (22:50 +0100)]
ref#10446 normalize to IPNI standard

5 months agoref#10446 fix original spelling handling and add test
Andreas Müller [Thu, 1 Feb 2024 20:27:26 +0000 (21:27 +0100)]
ref#10446 fix original spelling handling and add test

5 months agoref#10446 fix compile error and orth. var. selection
Andreas Müller [Thu, 1 Feb 2024 16:30:57 +0000 (17:30 +0100)]
ref#10446 fix compile error and orth. var. selection

5 months agoref#10446 add warning for missing wfo-id for orth.var. etc.
Andreas Müller [Thu, 1 Feb 2024 16:06:33 +0000 (17:06 +0100)]
ref#10446 add warning for missing wfo-id for orth.var. etc.

5 months agoref#10446 adapt base url handling in tests (cont.)
Andreas Müller [Thu, 1 Feb 2024 13:53:11 +0000 (14:53 +0100)]
ref#10446 adapt base url handling in tests (cont.)

5 months agoref #10440: revert add copyright and copyrightNotice to default values
Katja [Thu, 1 Feb 2024 13:48:05 +0000 (14:48 +0100)]
ref #10440: revert add copyright and copyrightNotice to default values

5 months agoref #10440: handle copyright same as other metadata
Katja [Thu, 1 Feb 2024 13:27:57 +0000 (14:27 +0100)]
ref #10440: handle copyright same as other metadata

5 months agoref#10446 adapt base url handling in tests
Andreas Müller [Thu, 1 Feb 2024 13:14:32 +0000 (14:14 +0100)]
ref#10446 adapt base url handling in tests

5 months agoref #10440: add CopyrightNotice to the default values for metadata
Katja [Thu, 1 Feb 2024 12:05:41 +0000 (13:05 +0100)]
ref #10440: add CopyrightNotice to the default values for metadata

5 months agoref#10446 add names only handling
Andreas Müller [Thu, 1 Feb 2024 10:34:07 +0000 (11:34 +0100)]
ref#10446 add names only handling

5 months agoref#10446 warning for missing base url
Andreas Müller [Thu, 1 Feb 2024 10:09:24 +0000 (11:09 +0100)]
ref#10446 warning for missing base url

5 months agoref#10446 adapt ref uri handling
Andreas Müller [Thu, 1 Feb 2024 09:17:12 +0000 (10:17 +0100)]
ref#10446 adapt ref uri handling

5 months agoref#10446 adapt no-wfoid message
Andreas Müller [Thu, 1 Feb 2024 08:52:12 +0000 (09:52 +0100)]
ref#10446 adapt no-wfoid message

5 months agoref#10446 fix remarks test for taxon notes feature
Andreas Müller [Thu, 1 Feb 2024 07:40:16 +0000 (08:40 +0100)]
ref#10446 fix remarks test for taxon notes feature

5 months agoref#10446 add remarks handling and remove synonyms without wfoId
Andreas Müller [Thu, 1 Feb 2024 07:21:39 +0000 (08:21 +0100)]
ref#10446 add remarks handling and remove synonyms without wfoId

5 months agoref #9500, ref #10330 add term tree based test but still use partOf version to be...
Andreas Müller [Wed, 31 Jan 2024 22:03:53 +0000 (23:03 +0100)]
ref #9500, ref #10330 add term tree based test but still use partOf version to be tested as long as it still exists

5 months agojavadoc and deprecation
Andreas Müller [Wed, 31 Jan 2024 22:02:41 +0000 (23:02 +0100)]
javadoc and deprecation

5 months agoref #9500, ref #10330 add test and handle null parent better
Andreas Müller [Wed, 31 Jan 2024 21:38:04 +0000 (22:38 +0100)]
ref #9500, ref #10330 add test and handle null parent better

5 months agoref #9500, ref #10330 apply subarea preference rule to all ancestors, not only direct...
Andreas Müller [Wed, 31 Jan 2024 20:55:19 +0000 (21:55 +0100)]
ref #9500, ref #10330 apply subarea preference rule to all ancestors, not only direct parents

5 months agocleanup
Andreas Müller [Wed, 31 Jan 2024 20:45:42 +0000 (21:45 +0100)]
cleanup

5 months agocleanup
Andreas Müller [Wed, 31 Jan 2024 17:10:54 +0000 (18:10 +0100)]
cleanup

5 months agoavoid LIE
Katja [Wed, 31 Jan 2024 12:38:08 +0000 (13:38 +0100)]
avoid LIE

5 months agoref #10446 fix fullSampleDataTest
Andreas Müller [Wed, 31 Jan 2024 10:16:47 +0000 (11:16 +0100)]
ref #10446 fix fullSampleDataTest

5 months agoref #10446 improve logging for missing wfo-ids and others
Andreas Müller [Wed, 31 Jan 2024 09:49:41 +0000 (10:49 +0100)]
ref #10446 improve logging for missing wfo-ids and others

5 months agoref #10446 remove duplicated missing wfo-id warning
Andreas Müller [Wed, 31 Jan 2024 09:20:20 +0000 (10:20 +0100)]
ref #10446 remove duplicated missing wfo-id warning

5 months agoref #10446 improve report formatting
Andreas Müller [Wed, 31 Jan 2024 09:18:40 +0000 (10:18 +0100)]
ref #10446 improve report formatting

5 months agoref #10446 fix statusNote i18n handling
Andreas Müller [Wed, 31 Jan 2024 01:14:29 +0000 (02:14 +0100)]
ref #10446 fix statusNote i18n handling

5 months agoref #10446 cleanup doc
Andreas Müller [Wed, 31 Jan 2024 00:40:03 +0000 (01:40 +0100)]
ref #10446 cleanup doc

5 months agoref #10446 handle excluded for WFO export and others
Andreas Müller [Wed, 31 Jan 2024 00:36:24 +0000 (01:36 +0100)]
ref #10446 handle excluded for WFO export and others

5 months agoref #10446 fix synonym handling
Andreas Müller [Tue, 30 Jan 2024 22:54:27 +0000 (23:54 +0100)]
ref #10446 fix synonym handling

5 months agoref #10446 fix test and add sourceLinkBaseUrl handling
Andreas Müller [Tue, 30 Jan 2024 18:12:45 +0000 (19:12 +0100)]
ref #10446 fix test and add sourceLinkBaseUrl handling

5 months agoref #10446 update javadoc for source link base url
Andreas Müller [Tue, 30 Jan 2024 17:38:41 +0000 (18:38 +0100)]
ref #10446 update javadoc for source link base url

5 months agoref #10446 override testFullSampleData as fullSampleData test must throw a warning
Andreas Müller [Tue, 30 Jan 2024 17:33:56 +0000 (18:33 +0100)]
ref #10446 override testFullSampleData as fullSampleData test must throw a warning

5 months agoref #10446 add source link export and move created, modified source link and excluded...
Andreas Müller [Tue, 30 Jan 2024 17:32:48 +0000 (18:32 +0100)]
ref #10446 add source link export and move created, modified source link and excluded info to handleTaxon()

5 months agoref #10446 javadoc ticket backlink
Andreas Müller [Tue, 30 Jan 2024 17:13:58 +0000 (18:13 +0100)]
ref #10446 javadoc ticket backlink

5 months agoref #10446 fix WFO Backbone export and tests
Andreas Müller [Tue, 30 Jan 2024 17:08:55 +0000 (18:08 +0100)]
ref #10446 fix WFO Backbone export and tests

5 months agoref #10446 rename WfoClassification/Export... to WfoBackbone... (javadoc)
Andreas Müller [Mon, 29 Jan 2024 23:12:17 +0000 (00:12 +0100)]
ref #10446 rename WfoClassification/Export... to WfoBackbone... (javadoc)

5 months agoref #10446 rename WfoClassification/Export... to WfoBackbone...
Andreas Müller [Mon, 29 Jan 2024 21:40:53 +0000 (22:40 +0100)]
ref #10446 rename WfoClassification/Export... to WfoBackbone...

5 months agoavoid NPE in RowWrapperDto - continue
Katja [Mon, 29 Jan 2024 14:20:33 +0000 (15:20 +0100)]
avoid NPE in RowWrapperDto - continue

5 months agoavoid NPE in RowWrapperDto
Katja [Mon, 29 Jan 2024 14:18:10 +0000 (15:18 +0100)]
avoid NPE in RowWrapperDto