cdmlib.git
4 years agoref #8651, #8467 Use unified aggregation class for matrix aggregation
Patrick Plitzner [Tue, 12 Nov 2019 10:19:02 +0000 (11:19 +0100)]
ref #8651, #8467 Use unified aggregation class for matrix aggregation

 - Link specimen descriptions as sources as direct CDM entities

4 years agoFix potential class cast exception
Patrick Plitzner [Mon, 11 Nov 2019 14:04:51 +0000 (15:04 +0100)]
Fix potential class cast exception

4 years agoref #8628 Improve error messages for ORCID parsing
Andreas Müller [Tue, 12 Nov 2019 08:39:46 +0000 (09:39 +0100)]
ref #8628 Improve error messages for ORCID parsing

4 years agoref #8651 remove MarkerType.Computed where possible
Andreas Müller [Tue, 12 Nov 2019 08:26:37 +0000 (09:26 +0100)]
ref #8651 remove MarkerType.Computed where possible

4 years agocleanup
Andreas Müller [Tue, 12 Nov 2019 08:19:24 +0000 (09:19 +0100)]
cleanup

4 years agoref #8651 fix failing tests due to order of aggregation
Andreas Müller [Tue, 12 Nov 2019 07:34:50 +0000 (08:34 +0100)]
ref #8651 fix failing tests due to order of aggregation

4 years agoref #8651 remove some comments and handle AggregationMode correctly
Andreas Müller [Tue, 12 Nov 2019 00:51:10 +0000 (01:51 +0100)]
ref #8651 remove some comments and handle AggregationMode correctly

4 years agoref #8651 fix failing tests due to use of old description markers
Andreas Müller [Tue, 12 Nov 2019 00:40:01 +0000 (01:40 +0100)]
ref #8651 fix failing tests due to use of old description markers

4 years agoref #8651 merge area and rank aggregation for DistributionAggregation
Andreas Müller [Tue, 12 Nov 2019 00:39:12 +0000 (01:39 +0100)]
ref #8651 merge area and rank aggregation for DistributionAggregation

4 years agofix max rank in DwcaExportController
Andreas Müller [Mon, 11 Nov 2019 23:46:17 +0000 (00:46 +0100)]
fix max rank in DwcaExportController

4 years agoref #5176 add all taxon node filter attributes to distribution aggregation webservice
Andreas Müller [Mon, 11 Nov 2019 23:45:55 +0000 (00:45 +0100)]
ref #5176 add all taxon node filter attributes to distribution aggregation webservice

4 years agoref #8651 more specific description type for DistributionAggregation
Andreas Müller [Mon, 11 Nov 2019 23:44:42 +0000 (00:44 +0100)]
ref #8651 more specific description type for DistributionAggregation

4 years agocleanup
Andreas Müller [Mon, 11 Nov 2019 22:48:41 +0000 (23:48 +0100)]
cleanup

4 years agoref #5176, ref #8651 make DistributionAggregation treeIndex based and use TaxonNodeFilter
Andreas Müller [Mon, 11 Nov 2019 22:35:45 +0000 (23:35 +0100)]
ref #5176, ref #8651 make DistributionAggregation treeIndex based and use TaxonNodeFilter

4 years agoref #8673 Fix NPE for OriginalSourceBase.getCdmSource
Andreas Müller [Mon, 11 Nov 2019 11:12:48 +0000 (12:12 +0100)]
ref #8673 Fix NPE for OriginalSourceBase.getCdmSource

4 years agocleanup
Andreas Müller [Sun, 10 Nov 2019 11:30:55 +0000 (12:30 +0100)]
cleanup

4 years agoref #8673 add Cascade.Delete and orphanRemoval and handle getter/setter on target...
Andreas Müller [Sun, 10 Nov 2019 11:30:42 +0000 (12:30 +0100)]
ref #8673 add Cascade.Delete and orphanRemoval and handle getter/setter on target directly

4 years agoref #8651 remove unnecessary dependency DistributionAggregation in DescriptionElement...
Andreas Müller [Sat, 9 Nov 2019 17:37:51 +0000 (18:37 +0100)]
ref #8651 remove unnecessary dependency DistributionAggregation in DescriptionElementListController

4 years agoref #8651 try to fix failing repository dependency injection in DescriptionListContro...
Andreas Müller [Sat, 9 Nov 2019 17:14:55 +0000 (18:14 +0100)]
ref #8651 try to fix failing repository dependency injection in DescriptionListController (2nd try)

4 years agoref #8651 try to fix failing repository dependency injection in DescriptionListController
Andreas Müller [Sat, 9 Nov 2019 16:52:48 +0000 (17:52 +0100)]
ref #8651 try to fix failing repository dependency injection in DescriptionListController

4 years agocleanup
Andreas Müller [Sat, 9 Nov 2019 16:51:40 +0000 (17:51 +0100)]
cleanup

4 years agofix #8673 Add CdmLinkSource to OriginalSourceBase
Andreas Müller [Sat, 9 Nov 2019 16:41:44 +0000 (17:41 +0100)]
fix #8673 Add CdmLinkSource to OriginalSourceBase

4 years agoref #8651 try to fix compile error in DescriptionListController
Andreas Müller [Sat, 9 Nov 2019 12:14:30 +0000 (13:14 +0100)]
ref #8651 try to fix compile error in DescriptionListController

4 years agocleanup
Andreas Müller [Sat, 9 Nov 2019 11:42:30 +0000 (12:42 +0100)]
cleanup

4 years agoref #8651 remove @Service annotation from DistributionAggregation and moving some...
Andreas Müller [Sat, 9 Nov 2019 11:41:53 +0000 (12:41 +0100)]
ref #8651 remove @Service annotation from DistributionAggregation and moving some functionality to base class + explicit Configurator for DistributionAggregation

4 years agocleanup
Andreas Müller [Fri, 8 Nov 2019 20:05:42 +0000 (21:05 +0100)]
cleanup

4 years agofix #8628 update cdm.map.ser to Person.orcid
Andreas Müller [Fri, 8 Nov 2019 20:05:20 +0000 (21:05 +0100)]
fix #8628 update cdm.map.ser to Person.orcid

4 years agocleanup
Andreas Müller [Fri, 8 Nov 2019 19:47:36 +0000 (20:47 +0100)]
cleanup

4 years agofix #8628 add ORCID as person identifier
Andreas Müller [Fri, 8 Nov 2019 19:46:55 +0000 (20:46 +0100)]
fix #8628 add ORCID as person identifier

4 years agocleanup
Andreas Müller [Fri, 8 Nov 2019 19:43:23 +0000 (20:43 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Fri, 8 Nov 2019 12:24:40 +0000 (13:24 +0100)]
cleanup

4 years agofix #8253 fix problem with infrageneric autonyms full reference parsing
Andreas Müller [Fri, 8 Nov 2019 12:24:16 +0000 (13:24 +0100)]
fix #8253 fix problem with infrageneric autonyms full reference parsing

4 years agoref #8450 Fix SQLGrammarException when no taxa could be found
Patrick Plitzner [Fri, 8 Nov 2019 09:25:16 +0000 (10:25 +0100)]
ref #8450 Fix SQLGrammarException when no taxa could be found

4 years agocleanup
Andreas Müller [Wed, 6 Nov 2019 21:34:48 +0000 (22:34 +0100)]
cleanup

4 years agofix #8253 correct parsing and formatting for authors of infra generic autonyms
Andreas Müller [Wed, 6 Nov 2019 21:34:04 +0000 (22:34 +0100)]
fix #8253 correct parsing and formatting for authors of infra generic autonyms

4 years agocleanup
Andreas Müller [Wed, 6 Nov 2019 21:09:37 +0000 (22:09 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Wed, 6 Nov 2019 21:06:20 +0000 (22:06 +0100)]
cleanup

4 years agoadding jvmArgs to the maven jetty plugin config to allow for hasslefree mvn jetty...
Andreas Kohlbecker [Wed, 6 Nov 2019 12:26:52 +0000 (13:26 +0100)]
adding jvmArgs to the maven jetty plugin config to allow for hasslefree mvn jetty:run-forked

4 years agoref #8450 Remove description type labels
Patrick Plitzner [Wed, 6 Nov 2019 10:52:58 +0000 (11:52 +0100)]
ref #8450 Remove description type labels

4 years agoref #8651 rename TransmissionEngineDistribution to DistributionAggregation
Andreas Müller [Tue, 5 Nov 2019 16:29:10 +0000 (17:29 +0100)]
ref #8651 rename TransmissionEngineDistribution to DistributionAggregation

4 years agoref #8651 fix compile error on linux (3rd try)
Andreas Müller [Tue, 5 Nov 2019 16:14:59 +0000 (17:14 +0100)]
ref #8651 fix compile error on linux (3rd try)

4 years agoref #8651 minor changes to TransmissionEngineDistribution and moving test
Andreas Müller [Tue, 5 Nov 2019 16:07:18 +0000 (17:07 +0100)]
ref #8651 minor changes to TransmissionEngineDistribution and moving test

4 years agoref #8651 fix compile error on linux (2nd try)
Andreas Müller [Tue, 5 Nov 2019 16:02:16 +0000 (17:02 +0100)]
ref #8651 fix compile error on linux (2nd try)

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