cdmlib.git
4 years agoref #8651 fix compile error on linux
Andreas Müller [Tue, 5 Nov 2019 15:51:32 +0000 (16:51 +0100)]
ref #8651 fix compile error on linux

4 years agoFix potential NPE
pplitzner [Tue, 5 Nov 2019 15:21:06 +0000 (16:21 +0100)]
Fix potential NPE

4 years agocleanup
Andreas Müller [Tue, 5 Nov 2019 15:09:35 +0000 (16:09 +0100)]
cleanup

4 years agoref #8651 first base classes for unified description aggregation and move SDD aggrega...
Andreas Müller [Tue, 5 Nov 2019 15:08:36 +0000 (16:08 +0100)]
ref #8651 first base classes for unified description aggregation and move SDD aggregation from service to new class

4 years agoFix class cast for streams in aggregation
Patrick Plitzner [Tue, 5 Nov 2019 12:39:32 +0000 (13:39 +0100)]
Fix class cast for streams in aggregation

4 years agocleanup
Andreas Müller [Tue, 5 Nov 2019 09:30:06 +0000 (10:30 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Sun, 3 Nov 2019 12:40:39 +0000 (13:40 +0100)]
cleanup

4 years agobetter exception handling in MethodMapper
Andreas Müller [Sun, 3 Nov 2019 12:23:48 +0000 (13:23 +0100)]
better exception handling in MethodMapper

4 years agorevert changes in abcd import test
Katja Luther [Mon, 4 Nov 2019 13:00:54 +0000 (14:00 +0100)]
revert changes in abcd import test

4 years agoref #8450 Display StateData.count if present
pplitzner [Mon, 4 Nov 2019 12:37:56 +0000 (13:37 +0100)]
ref #8450 Display StateData.count if present

4 years agominor refactoring
pplitzner [Mon, 4 Nov 2019 07:47:47 +0000 (08:47 +0100)]
minor refactoring

4 years agoref #8450 Set "count" when aggregating StateData
Patrick Plitzner [Fri, 1 Nov 2019 16:05:22 +0000 (17:05 +0100)]
ref #8450 Set "count" when aggregating StateData

4 years agoupdate H2 test data and model cache
Andreas Müller [Fri, 1 Nov 2019 13:26:30 +0000 (14:26 +0100)]
update H2 test data and model cache

4 years agocleanup
Andreas Müller [Fri, 1 Nov 2019 13:10:36 +0000 (14:10 +0100)]
cleanup

4 years agoref #8625 add count to StateData to FullCoverageDataGenerator
Andreas Müller [Fri, 1 Nov 2019 13:10:12 +0000 (14:10 +0100)]
ref #8625 add count to StateData to FullCoverageDataGenerator

4 years agofix #8466 remove old FeatureTree tables
Andreas Müller [Fri, 1 Nov 2019 12:28:12 +0000 (13:28 +0100)]
fix #8466 remove old FeatureTree tables

4 years agocleanup
Andreas Müller [Fri, 1 Nov 2019 12:27:25 +0000 (13:27 +0100)]
cleanup

4 years agofix #8625 add count to StateData
Andreas Müller [Fri, 1 Nov 2019 11:33:09 +0000 (12:33 +0100)]
fix #8625 add count to StateData

4 years agomove categorical data up in StateData and cleanup
Andreas Müller [Fri, 1 Nov 2019 11:27:30 +0000 (12:27 +0100)]
move categorical data up in StateData and cleanup

4 years agosome cleanup for TransmissionEngineDistribution
Andreas Müller [Fri, 1 Nov 2019 11:11:17 +0000 (12:11 +0100)]
some cleanup for TransmissionEngineDistribution

4 years agocleanup
Andreas Müller [Fri, 1 Nov 2019 11:10:43 +0000 (12:10 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Thu, 31 Oct 2019 14:58:09 +0000 (15:58 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Thu, 31 Oct 2019 14:09:41 +0000 (15:09 +0100)]
cleanup

4 years agoadd dummy file to cdmlib-cache/src/test/java to make the folder exist in git-repo
Andreas Müller [Thu, 31 Oct 2019 13:29:03 +0000 (14:29 +0100)]
add dummy file to cdmlib-cache/src/test/java to make the folder exist in git-repo

4 years agoref #8450 Fix potential NPE
Patrick Plitzner [Wed, 30 Oct 2019 15:33:55 +0000 (16:33 +0100)]
ref #8450 Fix potential NPE

4 years agoref #8450 Recurse through parent taxon nodes for default description
Patrick Plitzner [Wed, 30 Oct 2019 15:30:20 +0000 (16:30 +0100)]
ref #8450 Recurse through parent taxon nodes for default description

4 years agoremove whitespace after title for default references with only title and year
Andreas Müller [Wed, 30 Oct 2019 13:47:47 +0000 (14:47 +0100)]
remove whitespace after title for default references with only title and year

4 years agofix test because dna provider is not set as default anymore
Katja Luther [Wed, 30 Oct 2019 13:18:52 +0000 (14:18 +0100)]
fix test because dna provider is not set as default anymore

4 years agocleanup
Andreas Müller [Wed, 30 Oct 2019 12:59:39 +0000 (13:59 +0100)]
cleanup

4 years agoref #8612 use better generics for findByExample
Andreas Müller [Wed, 30 Oct 2019 12:59:19 +0000 (13:59 +0100)]
ref #8612 use better generics for findByExample

4 years agoadd test file
Katja Luther [Wed, 30 Oct 2019 12:49:20 +0000 (13:49 +0100)]
add test file

4 years agoadd test for import abcd with search for available dna
Katja Luther [Wed, 30 Oct 2019 12:07:58 +0000 (13:07 +0100)]
add test for import abcd with search for available dna

4 years agoremove default dna source
Katja Luther [Wed, 30 Oct 2019 12:07:02 +0000 (13:07 +0100)]
remove default dna source

4 years agochange biocase provider to herbar to fix test
Katja Luther [Wed, 30 Oct 2019 12:05:45 +0000 (13:05 +0100)]
change biocase provider to herbar to fix test

4 years agoref #8631: fix errors in abcd import
Katja Luther [Wed, 30 Oct 2019 08:53:06 +0000 (09:53 +0100)]
ref #8631: fix errors in abcd import

4 years agoDo not show empty brackets if no identifier is present for specimen
Patrick Plitzner [Mon, 28 Oct 2019 10:21:32 +0000 (11:21 +0100)]
Do not show empty brackets if no identifier is present for specimen

4 years agocleanup
Andreas Müller [Sat, 26 Oct 2019 06:52:02 +0000 (08:52 +0200)]
cleanup

4 years agonormalize getAllXXX methods in ReferenceService
Andreas Müller [Sat, 26 Oct 2019 06:51:48 +0000 (08:51 +0200)]
normalize getAllXXX methods in ReferenceService

4 years agocleanup
Andreas Müller [Sat, 26 Oct 2019 06:11:27 +0000 (08:11 +0200)]
cleanup

4 years agoref #8612 add marker type for epublished references
Andreas Müller [Sat, 26 Oct 2019 06:10:51 +0000 (08:10 +0200)]
ref #8612 add marker type for epublished references

4 years agoref #8612 add Now to VerbatimTimePeriod factory methods
Andreas Müller [Sat, 26 Oct 2019 06:10:15 +0000 (08:10 +0200)]
ref #8612 add Now to VerbatimTimePeriod factory methods

4 years agoref #8612 add addOriginalSpelling to TaxonName
Andreas Müller [Sat, 26 Oct 2019 06:09:26 +0000 (08:09 +0200)]
ref #8612 add addOriginalSpelling to TaxonName

4 years agocleanup
Andreas Müller [Tue, 22 Oct 2019 11:25:41 +0000 (13:25 +0200)]
cleanup

4 years agorename isLectotype to hasDesignationSource
Andreas Müller [Tue, 22 Oct 2019 11:25:24 +0000 (13:25 +0200)]
rename isLectotype to hasDesignationSource

4 years agoref #8458: revert removing of fieldUnitDto list as parameter
Katja Luther [Mon, 21 Oct 2019 08:50:10 +0000 (10:50 +0200)]
ref #8458: revert removing of fieldUnitDto list as parameter

4 years agoref #1445: code cleaning - continue
Katja Luther [Thu, 17 Oct 2019 12:40:23 +0000 (14:40 +0200)]
ref #1445: code cleaning - continue

4 years agoref #1445: code cleaning
Katja Luther [Thu, 17 Oct 2019 12:38:03 +0000 (14:38 +0200)]
ref #1445: code cleaning

4 years agoref #1445: improve search for identical names
Katja Luther [Thu, 17 Oct 2019 12:01:23 +0000 (14:01 +0200)]
ref #1445: improve search for identical names

4 years agoadapt defaultApplicationContext to moved longRunningService
Katja Luther [Thu, 17 Oct 2019 10:17:00 +0000 (12:17 +0200)]
adapt defaultApplicationContext to moved longRunningService

4 years agomove longrunningService to service
Katja Luther [Thu, 17 Oct 2019 10:09:14 +0000 (12:09 +0200)]
move longrunningService to service

4 years agoMerge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Katja Luther [Thu, 17 Oct 2019 08:04:42 +0000 (10:04 +0200)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop

4 years agofix app-import cache updater
Katja Luther [Thu, 17 Oct 2019 08:04:07 +0000 (10:04 +0200)]
fix app-import cache updater

4 years agoref #8595 Add sources to description init strategy
Patrick Plitzner [Wed, 16 Oct 2019 15:45:09 +0000 (17:45 +0200)]
ref #8595 Add sources to description init strategy

4 years agoref #8450 Add service method to find default description
Patrick Plitzner [Wed, 16 Oct 2019 06:47:14 +0000 (08:47 +0200)]
ref #8450 Add service method to find default description

4 years agoref #8450 Store default description wrapper in specimen wrapper
pplitzner [Mon, 14 Oct 2019 08:28:19 +0000 (10:28 +0200)]
ref #8450 Store default description wrapper in specimen wrapper

4 years agoref #7957 Add (web) service for filtering descriptions by type
Patrick Plitzner [Fri, 11 Oct 2019 13:13:38 +0000 (15:13 +0200)]
ref #7957 Add (web) service for filtering descriptions by type

4 years agoremove old CommonService.getSourcedObjectSByIdInSource
Andreas Müller [Sat, 12 Oct 2019 22:51:08 +0000 (00:51 +0200)]
remove old CommonService.getSourcedObjectSByIdInSource

4 years agoadd additional method for more specific return type of CommonService.getSourcedObject...
Andreas Müller [Sat, 12 Oct 2019 21:46:11 +0000 (23:46 +0200)]
add additional method for more specific return type of CommonService.getSourcedObjectSByIdInSource

4 years agoadd more specific return type to CommonService.getSourcedObjectByIdInSource
Andreas Müller [Sat, 12 Oct 2019 21:04:32 +0000 (23:04 +0200)]
add more specific return type to CommonService.getSourcedObjectByIdInSource

4 years agocleanup
Andreas Müller [Sat, 12 Oct 2019 15:26:10 +0000 (17:26 +0200)]
cleanup

4 years agoref #8509, ref #8508 some fixes to E+M PESI export and validation
Andreas Müller [Sat, 12 Oct 2019 10:07:34 +0000 (12:07 +0200)]
ref #8509, ref #8508  some fixes to E+M PESI export and validation

4 years agoref #2717 improve SimpleFilterMapper to use allowed and not allowed values
Andreas Müller [Fri, 11 Oct 2019 11:48:20 +0000 (13:48 +0200)]
ref #2717 improve SimpleFilterMapper to use allowed and not allowed values

4 years agoref #2717 fix notNull handling in ObjectMapper
Andreas Müller [Fri, 11 Oct 2019 11:46:12 +0000 (13:46 +0200)]
ref #2717 fix notNull handling in ObjectMapper

4 years agoref #2717 improve ExportIgnore and NotYetImplemented and NullMapper
Andreas Müller [Fri, 11 Oct 2019 11:45:32 +0000 (13:45 +0200)]
ref #2717 improve ExportIgnore and NotYetImplemented and NullMapper

4 years agofix annotation mapper includedTypes handling
Andreas Müller [Fri, 11 Oct 2019 11:44:31 +0000 (13:44 +0200)]
fix annotation mapper includedTypes handling

4 years agocleanup
Andreas Müller [Fri, 11 Oct 2019 11:44:04 +0000 (13:44 +0200)]
cleanup

4 years agofix incorrect obligatory handling in DoiMapper and TimePeriodMapper
Andreas Müller [Thu, 10 Oct 2019 10:01:03 +0000 (12:01 +0200)]
fix incorrect obligatory handling in DoiMapper and TimePeriodMapper

4 years agoref #2717 allow notNull for SingleAttribute mappers (needed for required fields in...
Andreas Müller [Thu, 10 Oct 2019 10:00:18 +0000 (12:00 +0200)]
ref #2717 allow notNull for SingleAttribute mappers (needed for required fields in PESI)

4 years agoref #2717 fix incorrect error handling in CollectionExportMapping, only throw excepti...
Andreas Müller [Thu, 10 Oct 2019 09:58:30 +0000 (11:58 +0200)]
ref #2717 fix incorrect error handling in CollectionExportMapping, only throw exception for single record, not all records

4 years agofix incorrect defaultValue handling in BooleanMapper factory method
Andreas Müller [Thu, 10 Oct 2019 09:56:41 +0000 (11:56 +0200)]
fix incorrect defaultValue handling in BooleanMapper factory method

4 years agocleanup
Andreas Müller [Thu, 10 Oct 2019 09:55:44 +0000 (11:55 +0200)]
cleanup

4 years agocleanup
Andreas Müller [Wed, 9 Oct 2019 19:01:11 +0000 (21:01 +0200)]
cleanup

4 years agoref #2717 add EM common name area UUIDs to BerlinModelTransformer
Andreas Müller [Wed, 9 Oct 2019 19:00:57 +0000 (21:00 +0200)]
ref #2717 add EM common name area UUIDs to BerlinModelTransformer

4 years agocleanup
Andreas Müller [Wed, 9 Oct 2019 11:08:17 +0000 (13:08 +0200)]
cleanup

4 years ago#8577 fix handling of long values in getUniqueInteger
Andreas Müller [Wed, 9 Oct 2019 09:04:06 +0000 (11:04 +0200)]
#8577 fix handling of long values in getUniqueInteger

4 years agocleanup
Andreas Müller [Wed, 9 Oct 2019 09:00:47 +0000 (11:00 +0200)]
cleanup

4 years agoref #1445: fix helper methods for pesi merging
Katja Luther [Wed, 9 Oct 2019 08:40:50 +0000 (10:40 +0200)]
ref #1445: fix helper methods for pesi merging

4 years agofix default schema validation for ImportConfiguratorBase
Andreas Müller [Tue, 8 Oct 2019 20:53:47 +0000 (22:53 +0200)]
fix default schema validation for ImportConfiguratorBase

4 years agocleanup
Andreas Müller [Tue, 8 Oct 2019 20:53:03 +0000 (22:53 +0200)]
cleanup

4 years agoref #1444 add diffIndex method to CdmUtils
Andreas Müller [Mon, 7 Oct 2019 18:45:08 +0000 (20:45 +0200)]
ref #1444 add diffIndex method to CdmUtils

4 years agosmaller changes in CdmLightExport (syn sec and fullAuthor in references)
Katja Luther [Tue, 8 Oct 2019 10:23:42 +0000 (12:23 +0200)]
smaller changes in CdmLightExport (syn sec and fullAuthor in references)

4 years agoref #1444, ref #8509 adapt IncludedInMapper and TaxonRelationshipType uuid access...
Andreas Müller [Sun, 6 Oct 2019 22:51:47 +0000 (00:51 +0200)]
ref #1444, ref #8509 adapt IncludedInMapper and TaxonRelationshipType uuid access to ERMS needs

4 years agoref #1444 make getTaxonRelationshipType public in importers to make it usable in...
Andreas Müller [Sun, 6 Oct 2019 07:36:35 +0000 (09:36 +0200)]
ref #1444 make getTaxonRelationshipType public in importers to make it usable in mappers

4 years agoref #1444 handle no language as unknown language for imported new nomenclatural status
Andreas Müller [Sun, 6 Oct 2019 07:34:55 +0000 (09:34 +0200)]
ref #1444 handle no language as unknown language for imported new nomenclatural status

4 years agoref #1444, ref #8509 move ERMS synonym taxon relationship uuids to TaxonRelationship...
Andreas Müller [Sun, 6 Oct 2019 07:32:34 +0000 (09:32 +0200)]
ref #1444, ref #8509 move ERMS synonym taxon relationship uuids to TaxonRelationship class

4 years agoref #1444 adapt DbImportSynonymMapper to ERMS requirements
Andreas Müller [Sun, 6 Oct 2019 07:28:09 +0000 (09:28 +0200)]
ref #1444 adapt DbImportSynonymMapper to ERMS requirements

4 years agoref #1444 add getSynonymRelationTypesByKey to IInputTransformer
Andreas Müller [Sun, 6 Oct 2019 07:26:02 +0000 (09:26 +0200)]
ref #1444 add getSynonymRelationTypesByKey to IInputTransformer

4 years agoref #8509 fix NPE in getAnnotations(by type-uuid)
Andreas Müller [Sun, 6 Oct 2019 07:24:17 +0000 (09:24 +0200)]
ref #8509 fix NPE in getAnnotations(by type-uuid)

4 years agoreduce log level for non latin nom status representations
Andreas Müller [Sun, 6 Oct 2019 07:23:13 +0000 (09:23 +0200)]
reduce log level for non latin nom status representations

4 years agocleanup
Andreas Müller [Sun, 6 Oct 2019 07:20:20 +0000 (09:20 +0200)]
cleanup

4 years agoref #5873: check for general description editing right
Katja Luther [Tue, 1 Oct 2019 13:03:55 +0000 (15:03 +0200)]
ref #5873: check for general description editing right

4 years agorevert some changes
Katja Luther [Tue, 1 Oct 2019 11:38:42 +0000 (13:38 +0200)]
revert some changes

4 years agoref #5873: filter nodes without permission
Katja Luther [Tue, 1 Oct 2019 11:26:56 +0000 (13:26 +0200)]
ref #5873: filter nodes without permission

4 years agoref #1444 allow to create new NomenclaturalStatusTypes during import
Andreas Müller [Mon, 30 Sep 2019 08:16:27 +0000 (10:16 +0200)]
ref #1444 allow to create new NomenclaturalStatusTypes during import

4 years agocleanup
Andreas Müller [Mon, 30 Sep 2019 08:15:43 +0000 (10:15 +0200)]
cleanup

4 years agocleanup
Andreas Müller [Sun, 29 Sep 2019 20:23:04 +0000 (22:23 +0200)]
cleanup

4 years agoref #1444 add resetTitleCache method
Andreas Müller [Sun, 29 Sep 2019 20:22:49 +0000 (22:22 +0200)]
ref #1444 add resetTitleCache method

4 years agoref #1444 adapt DbImportMethodMapper for ERMS titleCache testing
Andreas Müller [Sun, 29 Sep 2019 19:54:56 +0000 (21:54 +0200)]
ref #1444 adapt DbImportMethodMapper for ERMS titleCache testing

4 years agocleanup
Andreas Müller [Sun, 29 Sep 2019 19:52:16 +0000 (21:52 +0200)]
cleanup

4 years agoref #8509 handle non-default language textdata correctly in DbTextDataMapper
Andreas Müller [Sun, 29 Sep 2019 18:18:28 +0000 (20:18 +0200)]
ref #8509 handle non-default language textdata correctly in DbTextDataMapper