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

2 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

2 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

2 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

2 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

2 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

2 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

2 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.

2 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.)

2 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

2 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

2 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

2 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

2 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

2 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

2 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

2 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

2 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

2 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

2 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

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

2 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

2 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

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

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

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

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

2 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

2 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

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

2 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

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

2 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

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

2 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

2 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

2 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

2 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()

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

2 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

2 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)

2 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...

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

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

2 months agoref #10446 improve Wfo Classification Export and adapt tests (still ignored)
Andreas Müller [Sun, 28 Jan 2024 09:16:54 +0000 (10:16 +0100)]
ref #10446 improve Wfo Classification Export and adapt tests (still ignored)

2 months agoref #10324 update childrenCount correctly in Cdm2CdmImportBase
Andreas Müller [Sun, 28 Jan 2024 09:13:19 +0000 (10:13 +0100)]
ref #10324 update childrenCount correctly in Cdm2CdmImportBase

2 months agofix subgenus abbreviation in test data
Andreas Müller [Fri, 26 Jan 2024 22:53:25 +0000 (23:53 +0100)]
fix subgenus abbreviation in test data

2 months agoref #10446 fix WfoClassificationExport and add test class (still ignored as tests...
Andreas Müller [Fri, 26 Jan 2024 17:15:55 +0000 (18:15 +0100)]
ref #10446 fix WfoClassificationExport and add test class (still ignored as tests need to be adapted) (cont.)

2 months agoref #10446 fix WfoClassificationExport and add test class (still ignored as tests...
Andreas Müller [Fri, 26 Jan 2024 16:25:22 +0000 (17:25 +0100)]
ref #10446 fix WfoClassificationExport and add test class (still ignored as tests need to be adapted)

2 months agoref #10400, ref #10459 adapt binder
Andreas Müller [Fri, 26 Jan 2024 11:44:58 +0000 (12:44 +0100)]
ref #10400, ref #10459 adapt binder

2 months agofix #10451 try to fix test for optional fullname
Andreas Müller [Thu, 25 Jan 2024 22:06:07 +0000 (23:06 +0100)]
fix #10451 try to fix test for optional fullname

2 months agofix #10451 handle optional fullname in ColDpExport
Andreas Müller [Thu, 25 Jan 2024 19:05:42 +0000 (20:05 +0100)]
fix #10451 handle optional fullname in ColDpExport

2 months agocleanup
Andreas Müller [Thu, 25 Jan 2024 18:15:37 +0000 (19:15 +0100)]
cleanup

2 months agoref #10433 add index fungorum urlPattern during term loading
Andreas Müller [Thu, 25 Jan 2024 18:15:25 +0000 (19:15 +0100)]
ref #10433 add index fungorum urlPattern during term loading

2 months agoref #10400 implemented current/preferred determination as additional assoziation...
Andreas Müller [Wed, 24 Jan 2024 13:54:01 +0000 (14:54 +0100)]
ref #10400 implemented current/preferred determination as additional assoziation type

2 months agoref #10453 remove deprecated method in MediaUriTransformationProcessor
Andreas Müller [Wed, 24 Jan 2024 09:56:52 +0000 (10:56 +0100)]
ref #10453 remove deprecated method in MediaUriTransformationProcessor

2 months agoref #10453 add additional null check for missing uri
Andreas Müller [Wed, 24 Jan 2024 09:45:51 +0000 (10:45 +0100)]
ref #10453 add additional null check for missing uri

2 months agoref #10448, #10446 remove doFactualData from WfoExportConfigurator
Andreas Müller [Tue, 23 Jan 2024 22:33:45 +0000 (23:33 +0100)]
ref #10448, #10446 remove doFactualData from WfoExportConfigurator

2 months agocleanup
Andreas Müller [Tue, 23 Jan 2024 22:02:59 +0000 (23:02 +0100)]
cleanup

2 months agofix referencing objects formatter test
Andreas Müller [Tue, 23 Jan 2024 16:59:12 +0000 (17:59 +0100)]
fix referencing objects formatter test

2 months agoref #10434 add referencing objects formatter for Registrations
Andreas Müller [Tue, 23 Jan 2024 16:42:22 +0000 (17:42 +0100)]
ref #10434 add referencing objects formatter for Registrations

2 months agocleanup
Andreas Müller [Tue, 23 Jan 2024 09:55:21 +0000 (10:55 +0100)]
cleanup

2 months agolog errors
Katja [Tue, 23 Jan 2024 08:12:46 +0000 (09:12 +0100)]
log errors

2 months agoref #10441: some more property path adaptions
Katja [Mon, 22 Jan 2024 13:24:15 +0000 (14:24 +0100)]
ref #10441: some more property path adaptions

2 months agoref #10440: differ between only cdm/server and perfer cdm/server
Katja [Mon, 22 Jan 2024 13:13:08 +0000 (14:13 +0100)]
ref #10440: differ between only cdm/server and perfer cdm/server

2 months agoref #10400 fix FindOccurrencesConfigurator default filter value
Andreas Müller [Sat, 20 Jan 2024 23:54:12 +0000 (00:54 +0100)]
ref #10400 fix FindOccurrencesConfigurator default filter value

2 months agoref #10400 use TaxonOccurrenceRelationType param in webservices
Andreas Müller [Sat, 20 Jan 2024 22:42:15 +0000 (23:42 +0100)]
ref #10400 use TaxonOccurrenceRelationType param in webservices

2 months agocleanup
Andreas Müller [Sat, 20 Jan 2024 22:41:02 +0000 (23:41 +0100)]
cleanup

2 months agoref #10400 minor javadoc
Andreas Müller [Sat, 20 Jan 2024 14:52:51 +0000 (15:52 +0100)]
ref #10400 minor javadoc

2 months agoref #10400 move TaxonOccurrenceRelationType to api
Andreas Müller [Sat, 20 Jan 2024 14:38:50 +0000 (15:38 +0100)]
ref #10400 move TaxonOccurrenceRelationType to api

2 months agoref #10400 refactor occurrenceDao for findByAssociatedTaxon and add association type...
Andreas Müller [Sat, 20 Jan 2024 14:20:05 +0000 (15:20 +0100)]
ref #10400 refactor occurrenceDao for findByAssociatedTaxon and add association type configuration param (cont.)

2 months agoref #10400 fix TypedQuery issue in TaxonNameDaoHibernateImpl.getTypeDesignationQuery()
Andreas Müller [Sat, 20 Jan 2024 10:57:36 +0000 (11:57 +0100)]
ref #10400 fix TypedQuery issue in TaxonNameDaoHibernateImpl.getTypeDesignationQuery()

2 months agoref #10400 refactor occurrenceDao for findByAssociatedTaxon and add association type...
Andreas Müller [Sat, 20 Jan 2024 00:36:16 +0000 (01:36 +0100)]
ref #10400 refactor occurrenceDao for findByAssociatedTaxon and add association type configuration param

2 months agocleanup
Andreas Müller [Fri, 19 Jan 2024 13:59:45 +0000 (14:59 +0100)]
cleanup

2 months agoref #10206 add publish flag to CdmLight and ColDP export in cdmlib
Andreas Müller [Fri, 19 Jan 2024 13:53:31 +0000 (14:53 +0100)]
ref #10206 add publish flag to CdmLight and ColDP export in cdmlib

2 months agoref #10440: save meta data preference as json
Katja [Fri, 19 Jan 2024 13:03:59 +0000 (14:03 +0100)]
ref #10440: save meta data preference as json

2 months agoref #10456: order of occurrences
Katja [Fri, 19 Jan 2024 08:43:25 +0000 (09:43 +0100)]
ref #10456: order of occurrences

2 months agoref #10441: some more propertypath adaptions
Katja [Thu, 18 Jan 2024 21:19:43 +0000 (22:19 +0100)]
ref #10441: some more propertypath adaptions

2 months agofix portal test
Katja [Thu, 18 Jan 2024 19:39:57 +0000 (20:39 +0100)]
fix portal test

2 months agoref #10334 further handle include unpublished in webservices (cont.)
Andreas Müller [Thu, 18 Jan 2024 19:10:11 +0000 (20:10 +0100)]
ref #10334 further handle include unpublished in webservices (cont.)

2 months agoref #10334 further handle include unpublished in webservices
Andreas Müller [Thu, 18 Jan 2024 19:06:56 +0000 (20:06 +0100)]
ref #10334 further handle include unpublished in webservices

2 months agocleanup OccurrenceService
Andreas Müller [Thu, 18 Jan 2024 17:38:30 +0000 (18:38 +0100)]
cleanup OccurrenceService

2 months agoref #10334 add getDistributionServiceRequestParameterString(taxonDescriptions, ...)
Andreas Müller [Thu, 18 Jan 2024 17:38:01 +0000 (18:38 +0100)]
ref #10334 add getDistributionServiceRequestParameterString(taxonDescriptions, ...)

2 months agoref #10334 remove further unused methods
Andreas Müller [Thu, 18 Jan 2024 16:41:40 +0000 (17:41 +0100)]
ref #10334 remove further unused methods

2 months agoadd typedesignations of synonyms to list of specimen dtos
Katja [Thu, 18 Jan 2024 14:28:36 +0000 (15:28 +0100)]
add typedesignations of synonyms to list of specimen dtos

2 months agoref #10334 further cleanup
Andreas Müller [Thu, 18 Jan 2024 14:01:31 +0000 (15:01 +0100)]
ref #10334 further cleanup

2 months agoref #10334 fix test
Andreas Müller [Thu, 18 Jan 2024 14:00:45 +0000 (15:00 +0100)]
ref #10334 fix test

2 months agoref #10334 remove unused description related methods and add some more includePublish...
Andreas Müller [Thu, 18 Jan 2024 13:50:17 +0000 (14:50 +0100)]
ref #10334 remove unused description related methods and add some more includePublished handling

3 months agocleanup
Andreas Müller [Thu, 18 Jan 2024 00:02:31 +0000 (01:02 +0100)]
cleanup

3 months agoref #10334 evaluate descriptionBase.publish in webservices (cont. II)
Andreas Müller [Thu, 18 Jan 2024 00:02:02 +0000 (01:02 +0100)]
ref #10334 evaluate descriptionBase.publish in webservices (cont. II)

3 months agoref #10334 evaluate descriptionBase.publish in webservices (cont.)
Andreas Müller [Wed, 17 Jan 2024 21:39:22 +0000 (22:39 +0100)]
ref #10334 evaluate descriptionBase.publish in webservices (cont.)

3 months agocleanup
Andreas Müller [Wed, 17 Jan 2024 21:39:07 +0000 (22:39 +0100)]
cleanup

3 months agoref #10334 evaluate descriptionBase.publish in webservices
Andreas Müller [Wed, 17 Jan 2024 21:36:15 +0000 (22:36 +0100)]
ref #10334 evaluate descriptionBase.publish in webservices

3 months agoref #7443 add parser for fungi and zoological names with in-authors
Andreas Müller [Wed, 17 Jan 2024 19:10:11 +0000 (20:10 +0100)]
ref #7443 add parser for fungi and zoological names with in-authors

3 months agocleanup
Andreas Müller [Wed, 17 Jan 2024 16:53:57 +0000 (17:53 +0100)]
cleanup

3 months agoref #7413 fully move in-authors to INonViralName
Andreas Müller [Wed, 17 Jan 2024 12:20:25 +0000 (13:20 +0100)]
ref #7413 fully move in-authors to INonViralName

3 months agoref #7413: move in-author methods to INonViralName
Katja Luther [Wed, 17 Jan 2024 12:03:34 +0000 (13:03 +0100)]
ref #7413: move in-author methods to INonViralName

3 months agoref #10454, ref #7781 add separator for nameUsedInSource
Andreas Müller [Wed, 17 Jan 2024 10:13:09 +0000 (11:13 +0100)]
ref #10454, ref #7781 add separator for nameUsedInSource

3 months agoref #10453: catch/log the error if makeNewMediaRepresentationsFor fails
Katja [Wed, 17 Jan 2024 10:09:17 +0000 (11:09 +0100)]
ref #10453: catch/log the error if makeNewMediaRepresentationsFor fails

3 months agoref #9500 remove ignoreDistributionStatusUndefined from DistributionInfoConfiguration...
Andreas Müller [Tue, 16 Jan 2024 23:54:17 +0000 (00:54 +0100)]
ref #9500 remove ignoreDistributionStatusUndefined from DistributionInfoConfiguration (cont.)