cdmlib.git
5 years agoavoiding NPE
Andreas Kohlbecker [Thu, 11 Jul 2019 16:00:56 +0000 (18:00 +0200)]
avoiding NPE

5 years agoref #8283 Add media uuids to term dto
Patrick Plitzner [Thu, 11 Jul 2019 06:09:09 +0000 (08:09 +0200)]
ref #8283 Add media uuids to term dto

 - fix HQL response handling for left outer joins

5 years agominor in cdm light export
Katja Luther [Fri, 5 Jul 2019 21:04:50 +0000 (23:04 +0200)]
minor in cdm light export

5 years agorevert condensed distribution string and some performance issues in cdm light
Katja Luther [Fri, 5 Jul 2019 20:14:17 +0000 (22:14 +0200)]
revert condensed distribution string and some performance issues in cdm light

5 years agoadd condensed distribution string to cdm light export
Katja Luther [Fri, 5 Jul 2019 11:23:47 +0000 (13:23 +0200)]
add condensed distribution string to cdm light export

5 years agoMerge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Katja Luther [Fri, 5 Jul 2019 12:06:19 +0000 (14:06 +0200)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop

5 years agosmaller changes in abcd import
Katja Luther [Fri, 5 Jul 2019 12:05:45 +0000 (14:05 +0200)]
smaller changes in abcd import

5 years agoref #8248, #6774 Add top level term evaluation to test
Patrick Plitzner [Fri, 5 Jul 2019 09:09:08 +0000 (11:09 +0200)]
ref #8248, #6774 Add top level term evaluation to test

5 years agofix dummy line in cdmlight export simple facts table
Katja Luther [Fri, 5 Jul 2019 07:13:42 +0000 (09:13 +0200)]
fix dummy line in cdmlight export simple facts table

5 years agoaddinional RegistrationService test and a bit of cleaning up
Andreas Kohlbecker [Thu, 4 Jul 2019 22:24:55 +0000 (00:24 +0200)]
addinional RegistrationService test and a bit of cleaning up

5 years agoref #8352 controller and service to find registrations by name
Andreas Kohlbecker [Thu, 4 Jul 2019 20:38:21 +0000 (22:38 +0200)]
ref #8352 controller and service to find registrations by name

5 years agoref #8354 implenting registration serch by taxonUUIDs which also covers typedesignations
Andreas Kohlbecker [Thu, 4 Jul 2019 19:50:22 +0000 (21:50 +0200)]
ref #8354 implenting registration serch by taxonUUIDs which also covers typedesignations

5 years agoRestrictionConverter converts uuid strings to UUID objetcs which have beed passed...
Andreas Kohlbecker [Thu, 4 Jul 2019 18:39:15 +0000 (20:39 +0200)]
RestrictionConverter converts uuid strings to UUID objetcs which have beed passed as json value

5 years agocleaning up controller code
Andreas Kohlbecker [Thu, 4 Jul 2019 17:08:26 +0000 (19:08 +0200)]
cleaning up controller code

5 years agoref #8248, #6774 Adapt tests
Patrick Plitzner [Thu, 4 Jul 2019 15:40:10 +0000 (17:40 +0200)]
ref #8248, #6774 Adapt tests

5 years agoref #6774 Export reference uuid
Patrick Plitzner [Thu, 4 Jul 2019 15:39:56 +0000 (17:39 +0200)]
ref #6774 Export reference uuid

5 years agoref #8248 Check for existing media and references
Patrick Plitzner [Thu, 4 Jul 2019 12:18:30 +0000 (14:18 +0200)]
ref #8248 Check for existing media and references

5 years agoref #8248, #6774 Fix order of term import
Patrick Plitzner [Thu, 4 Jul 2019 11:29:31 +0000 (13:29 +0200)]
ref #8248, #6774 Fix order of term import

 - add top level term property to import/export

5 years agoref #8248 Fix possible NPE
Patrick Plitzner [Wed, 3 Jul 2019 13:44:22 +0000 (15:44 +0200)]
ref #8248 Fix possible NPE

5 years agoref #6774 Move recursive model export to util class
Patrick Plitzner [Wed, 3 Jul 2019 13:44:04 +0000 (15:44 +0200)]
ref #6774 Move recursive model export to util class

5 years agoadding AnnotationType to getEmptyDefinedTermBase()
Andreas Kohlbecker [Thu, 4 Jul 2019 11:27:25 +0000 (13:27 +0200)]
adding AnnotationType to getEmptyDefinedTermBase()

5 years agocode cleaning
Katja Luther [Wed, 3 Jul 2019 10:48:04 +0000 (12:48 +0200)]
code cleaning

5 years agousing CleanSweepInsertLoadStrategy in SecurityTest
Andreas Kohlbecker [Tue, 2 Jul 2019 14:51:53 +0000 (16:51 +0200)]
using CleanSweepInsertLoadStrategy in SecurityTest

5 years agoadding missing REGISTRATION* tables to the ClearDBDataSet.xml
Andreas Kohlbecker [Tue, 2 Jul 2019 14:42:15 +0000 (16:42 +0200)]
adding missing REGISTRATION* tables to the ClearDBDataSet.xml

5 years agousing CleanSweepInsertLoadStrategy in DerivedUnitConverterIntegrationTest
Andreas Kohlbecker [Tue, 2 Jul 2019 14:17:36 +0000 (16:17 +0200)]
using CleanSweepInsertLoadStrategy in DerivedUnitConverterIntegrationTest

5 years agofix #8287 implementing support for null type status as filter value in Registration...
Andreas Kohlbecker [Tue, 2 Jul 2019 13:10:44 +0000 (15:10 +0200)]
fix #8287 implementing support for null type status as filter value in Registration service

5 years agoRevert "adding missing MatchMode in createRestriction()"
Andreas Kohlbecker [Tue, 2 Jul 2019 12:31:33 +0000 (14:31 +0200)]
Revert "adding missing MatchMode in createRestriction()"

This reverts commit 1eca13fafa584494a9300c1a6844d435ca5ae897.

5 years agoref #8248 Add character to export (partially)
Patrick Plitzner [Tue, 2 Jul 2019 12:06:59 +0000 (14:06 +0200)]
ref #8248 Add character to export (partially)

5 years agoignoring RedmineRegistrationMessageServiceTest since RedmineRegistrationMessageServic...
Andreas Kohlbecker [Tue, 2 Jul 2019 11:37:18 +0000 (13:37 +0200)]
ignoring RedmineRegistrationMessageServiceTest since RedmineRegistrationMessageService is going to be removed

5 years agoadding missing MatchMode in createRestriction()
Andreas Kohlbecker [Tue, 2 Jul 2019 11:33:58 +0000 (13:33 +0200)]
adding missing MatchMode in createRestriction()

5 years agofix failing test (add anywher to createRestrictions)
Katja Luther [Tue, 2 Jul 2019 08:41:23 +0000 (10:41 +0200)]
fix failing test (add anywher to createRestrictions)

5 years agoref #8330 removing unused and obsolete service methods which are replaces by the...
Andreas Kohlbecker [Mon, 1 Jul 2019 16:52:32 +0000 (18:52 +0200)]
ref #8330 removing unused and obsolete service methods which are replaces by the new one

5 years agoref #7620 rest service /registrationDTO/find with filter string for references
Andreas Kohlbecker [Mon, 1 Jul 2019 16:34:48 +0000 (18:34 +0200)]
ref #7620 rest service /registrationDTO/find with filter string for references

5 years agoref #7620 filtered registration search implemented with filter string for references
Andreas Kohlbecker [Mon, 1 Jul 2019 16:32:58 +0000 (18:32 +0200)]
ref #7620 filtered registration search implemented with filter string for references

5 years agoref #8330 ref #7885 removing confusing typo in test data
Andreas Kohlbecker [Mon, 1 Jul 2019 15:07:25 +0000 (17:07 +0200)]
ref #8330 ref #7885 removing confusing typo in test data

5 years agoref #7885 tests for registration search by typified name and implementing order by
Andreas Kohlbecker [Mon, 1 Jul 2019 14:31:43 +0000 (16:31 +0200)]
ref #7885 tests for registration search by typified name and implementing order by

5 years agoref #8330 dao method for filtered registration search implemented: reprocduces existi...
Andreas Kohlbecker [Mon, 1 Jul 2019 13:28:00 +0000 (15:28 +0200)]
ref #8330 dao method for filtered registration search implemented: reprocduces existing functionality plus extended name search ref #7885

5 years agoref #8330 completing documentation regarding wildcards and fixing bug with MatchMode...
Andreas Kohlbecker [Sun, 30 Jun 2019 15:35:37 +0000 (17:35 +0200)]
ref #8330 completing documentation regarding wildcards and fixing bug with MatchMode LIKE when using Restrictions

5 years agoref #8330 documentation for RegistrationService.page and RegistrationWorkingsetServic...
Andreas Kohlbecker [Sun, 30 Jun 2019 14:22:42 +0000 (16:22 +0200)]
ref #8330 documentation for RegistrationService.page and RegistrationWorkingsetService.pageDTO

5 years agoref #8330 implementing tests for RegsitrationService.page and RegistrationWorkingsetS...
Andreas Kohlbecker [Sun, 30 Jun 2019 14:10:09 +0000 (16:10 +0200)]
ref #8330 implementing tests for RegsitrationService.page and RegistrationWorkingsetService.pageDTO

5 years agoref #8344: add dummy line in empty simple facts table
Katja Luther [Mon, 1 Jul 2019 11:43:14 +0000 (13:43 +0200)]
ref #8344: add dummy line in empty simple facts table

5 years agoref #7296 removing all config files related to the RemineMessagingService since this...
Andreas Kohlbecker [Thu, 27 Jun 2019 12:25:53 +0000 (14:25 +0200)]
ref #7296 removing all config files related to the RemineMessagingService since this has been dropped completely

5 years agoref #8321 cleaning up cotroller code
Andreas Kohlbecker [Thu, 6 Jun 2019 11:08:44 +0000 (13:08 +0200)]
ref #8321 cleaning up cotroller code

5 years agosmaller changes in ABCD import - continue
Katja Luther [Thu, 27 Jun 2019 12:11:38 +0000 (14:11 +0200)]
smaller changes in ABCD import - continue

5 years agoMerge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Katja Luther [Thu, 27 Jun 2019 12:10:29 +0000 (14:10 +0200)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop

5 years agosmaller changes in ABCD import
Katja Luther [Thu, 27 Jun 2019 12:09:49 +0000 (14:09 +0200)]
smaller changes in ABCD import

5 years agoref #8182: minor
Katja Luther [Thu, 27 Jun 2019 07:08:24 +0000 (09:08 +0200)]
ref #8182: minor

5 years agoref #8182: accession number is required in webservice
Katja Luther [Wed, 26 Jun 2019 12:13:32 +0000 (14:13 +0200)]
ref #8182: accession number is required in webservice

5 years agoref #8182: add header to failed response
Katja Luther [Wed, 26 Jun 2019 11:56:23 +0000 (13:56 +0200)]
ref #8182: add header to failed response

5 years agoref #8182: handle not existing dna for accession number
Katja Luther [Wed, 26 Jun 2019 08:05:09 +0000 (10:05 +0200)]
ref #8182: handle not existing dna for accession number

5 years agocdmlight: change area category to the area level
Katja Luther [Tue, 25 Jun 2019 12:33:46 +0000 (14:33 +0200)]
cdmlight: change area category to the area level

5 years agoref #8248 Add feature to export (partially)
Patrick Plitzner [Tue, 25 Jun 2019 11:39:37 +0000 (13:39 +0200)]
ref #8248 Add feature to export (partially)

5 years agoref #8248, #6774 Add character to export
Patrick Plitzner [Tue, 25 Jun 2019 08:24:43 +0000 (10:24 +0200)]
ref #8248, #6774 Add character to export

 - adapt test

5 years agoref #8248, #6774 Add sources to import/export
Patrick Plitzner [Fri, 21 Jun 2019 15:59:05 +0000 (17:59 +0200)]
ref #8248, #6774 Add sources to import/export

5 years agoref #8248, #6774 Improve import/export performance
Patrick Plitzner [Fri, 21 Jun 2019 12:18:35 +0000 (14:18 +0200)]
ref #8248, #6774 Improve import/export performance

5 years agoref #8335 Add character matrix table state DB preference
Patrick Plitzner [Wed, 19 Jun 2019 15:04:01 +0000 (17:04 +0200)]
ref #8335 Add character matrix table state DB preference

5 years agoadd hybrid name save to import base class
Andreas Müller [Mon, 17 Jun 2019 10:08:02 +0000 (12:08 +0200)]
add hybrid name save to import base class

5 years agoadd E+M rank uuids to rank class
Andreas Müller [Mon, 17 Jun 2019 10:07:19 +0000 (12:07 +0200)]
add E+M rank uuids to rank class

5 years agoMerge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop
Katja Luther [Mon, 17 Jun 2019 09:48:07 +0000 (11:48 +0200)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into develop

5 years agoset dnaSource to null in test
Katja Luther [Mon, 17 Jun 2019 09:47:40 +0000 (11:47 +0200)]
set dnaSource to null in test

5 years agoref #8248, #6774 Add progress monitor to import/export
Patrick Plitzner [Mon, 17 Jun 2019 09:47:13 +0000 (11:47 +0200)]
ref #8248, #6774 Add progress monitor to import/export

5 years agosmaller changes in abcd import and cdm light export
Katja Luther [Mon, 17 Jun 2019 07:57:31 +0000 (09:57 +0200)]
smaller changes in abcd import and cdm light export

5 years agoref #6774 Add progress monitor to owl export
Patrick Plitzner [Mon, 17 Jun 2019 08:35:24 +0000 (10:35 +0200)]
ref #6774 Add progress monitor to owl export

5 years agoref #8248, #6774 Add media to import/export
Patrick Plitzner [Fri, 14 Jun 2019 11:51:36 +0000 (13:51 +0200)]
ref #8248, #6774 Add media to import/export

5 years agoref #8248 Only add term to vocabulary if term is newly created
Patrick Plitzner [Fri, 14 Jun 2019 09:58:35 +0000 (11:58 +0200)]
ref #8248 Only add term to vocabulary if term is newly created

5 years agoref #8248 Only add term to vocabulary if term is newly created
Patrick Plitzner [Fri, 14 Jun 2019 09:53:59 +0000 (11:53 +0200)]
ref #8248 Only add term to vocabulary if term is newly created

5 years agoref #8248, #6774 Add plural to import/export
Patrick Plitzner [Thu, 13 Jun 2019 11:15:30 +0000 (13:15 +0200)]
ref #8248, #6774 Add plural to import/export

 - add test for plural and abbrevLabel

5 years agoref #8248, #6774 Add symbol, symbol2 and idInVocabulary to import/export
Patrick Plitzner [Thu, 13 Jun 2019 07:48:24 +0000 (09:48 +0200)]
ref #8248, #6774 Add symbol, symbol2 and idInVocabulary to import/export

 - change rdf identifier to lowercase

5 years agofix #8257 remove remaining deprecated FeatureNode.NewInstance method
Andreas Müller [Wed, 5 Jun 2019 11:17:03 +0000 (13:17 +0200)]
fix #8257 remove remaining deprecated FeatureNode.NewInstance method

5 years agooverwrite equals for taxonnodeDto
Katja Luther [Wed, 5 Jun 2019 07:34:09 +0000 (09:34 +0200)]
overwrite equals for taxonnodeDto

5 years agoref #8047: configurable display of status in drop down, new enum and predicate
Katja Luther [Tue, 4 Jun 2019 20:21:01 +0000 (22:21 +0200)]
ref #8047: configurable display of status in drop down, new enum and predicate

5 years agoref #8321 implementing page by restriction method to allow for flexible web service...
Andreas Kohlbecker [Tue, 4 Jun 2019 10:39:13 +0000 (12:39 +0200)]
ref #8321 implementing page by restriction method to allow for flexible web service queries, also protecting unpublished taxa and names ref #3560

5 years agoadd rollback check in ExcelImportBase
Andreas Müller [Tue, 4 Jun 2019 08:14:11 +0000 (10:14 +0200)]
add rollback check in ExcelImportBase

5 years agofix compilation error in BaseListController
Andreas Müller [Tue, 4 Jun 2019 08:10:49 +0000 (10:10 +0200)]
fix compilation error in BaseListController

5 years agofix test as cdm light creates all tables now
Katja Luther [Tue, 4 Jun 2019 06:58:09 +0000 (08:58 +0200)]
fix test as cdm light creates all tables now

5 years agogeneric webservice method for all cdm entitiy list controllers to search by Restriction
Andreas Kohlbecker [Mon, 3 Jun 2019 15:25:17 +0000 (17:25 +0200)]
generic webservice method for all cdm entitiy list controllers to search by Restriction

5 years agoref #8322: adapt TaxonNodeDtoComparator to compare the names by taggedTitle
Katja Luther [Mon, 3 Jun 2019 11:01:18 +0000 (13:01 +0200)]
ref #8322: adapt TaxonNodeDtoComparator to compare the names by taggedTitle

5 years agoref #5857, ref #8319 adding TypedEntityRefernces to nom status TaggedText and fixing...
Andreas Kohlbecker [Fri, 31 May 2019 07:22:48 +0000 (09:22 +0200)]
ref #5857, ref #8319 adding TypedEntityRefernces to nom status TaggedText and fixing json serialization for EntitiyReferences in taxon.taggedTitle processing

5 years agofix #8319 NomenclaturalStatus webservice and according service methods implemented
Andreas Kohlbecker [Fri, 31 May 2019 07:15:52 +0000 (09:15 +0200)]
fix #8319 NomenclaturalStatus webservice and according service methods implemented

5 years agofix #8314 implementing taxonname.taggedFullTitle for model class and in web service...
Andreas Kohlbecker [Wed, 29 May 2019 17:47:56 +0000 (19:47 +0200)]
fix #8314 implementing taxonname.taggedFullTitle for model class and in web service controller

5 years agoref #8273: check for DNA data for provided biocase provider
Katja Luther [Wed, 29 May 2019 11:04:08 +0000 (13:04 +0200)]
ref #8273: check for DNA data for provided biocase provider

5 years agominor
Katja Luther [Wed, 29 May 2019 11:00:33 +0000 (13:00 +0200)]
minor

5 years agoref #8182: adapt occurrence DTOs to use them in details page of blast result
Katja Luther [Wed, 29 May 2019 10:59:54 +0000 (12:59 +0200)]
ref #8182: adapt occurrence DTOs to use them in details page of blast result

5 years agoref #8045: add toString() to the preference enums
Katja Luther [Wed, 29 May 2019 10:52:08 +0000 (12:52 +0200)]
ref #8045: add toString() to the preference enums

5 years agoref #8248 Add term vocbulary import test + code cleanup
Patrick Plitzner [Wed, 29 May 2019 09:51:00 +0000 (11:51 +0200)]
ref #8248 Add term vocbulary import test + code cleanup

5 years agoref #8248 Fix property string access
Patrick Plitzner [Wed, 29 May 2019 08:37:55 +0000 (10:37 +0200)]
ref #8248 Fix property string access

5 years agoref #6774 Init export configurator
Patrick Plitzner [Wed, 29 May 2019 07:41:35 +0000 (09:41 +0200)]
ref #6774 Init export configurator

5 years agoref #8248 Adapt test to import
Patrick Plitzner [Tue, 28 May 2019 15:51:08 +0000 (17:51 +0200)]
ref #8248 Adapt test to import

5 years agoref #8248 Set UUID during import
Patrick Plitzner [Tue, 28 May 2019 15:50:35 +0000 (17:50 +0200)]
ref #8248 Set UUID during import

5 years agoref #6774 Adapt test to export format
Patrick Plitzner [Tue, 28 May 2019 13:02:24 +0000 (15:02 +0200)]
ref #6774 Adapt test to export format

5 years agofix tests for cdmlight
Katja Luther [Mon, 27 May 2019 12:56:04 +0000 (14:56 +0200)]
fix tests for cdmlight

5 years agofix preference service
Katja Luther [Mon, 27 May 2019 12:13:39 +0000 (14:13 +0200)]
fix preference service

5 years agoref #8248, #6774 Fix bean names
Patrick Plitzner [Mon, 27 May 2019 12:00:43 +0000 (14:00 +0200)]
ref #8248, #6774 Fix bean names

5 years agoref #8045: add remove to preference service and dao
Katja Luther [Mon, 27 May 2019 10:48:41 +0000 (12:48 +0200)]
ref #8045: add remove to preference service and dao

5 years agoref #8248 Implement termvocabulary import
Patrick Plitzner [Mon, 27 May 2019 07:58:17 +0000 (09:58 +0200)]
ref #8248 Implement termvocabulary import

5 years agoref #6774 Set vocabulary for partOf and kindOf terms in export
Patrick Plitzner [Mon, 27 May 2019 07:39:17 +0000 (09:39 +0200)]
ref #6774 Set vocabulary for partOf and kindOf terms in export

5 years agoref #6774 Fix node hierarchy in export
Patrick Plitzner [Mon, 27 May 2019 07:15:33 +0000 (09:15 +0200)]
ref #6774 Fix node hierarchy in export

5 years agoref #8248 Extract CDM entity creation to util
Patrick Plitzner [Mon, 27 May 2019 07:11:06 +0000 (09:11 +0200)]
ref #8248 Extract CDM entity creation to util

5 years agoref #8248, #6774 Extract model creation form import and export to util
Patrick Plitzner [Sun, 26 May 2019 13:48:31 +0000 (15:48 +0200)]
ref #8248, #6774 Extract model creation form import and export to util

5 years agoref #8248 Move rdf model to import state
Patrick Plitzner [Sun, 26 May 2019 13:30:48 +0000 (15:30 +0200)]
ref #8248 Move rdf model to import state