cdmlib.git
4 years agoref #8679 Add test for incomplete categorical data
pplitzner [Thu, 5 Dec 2019 07:20:13 +0000 (08:20 +0100)]
ref #8679 Add test for incomplete categorical data

4 years agoFix gcTime calculation
Patrick Plitzner [Wed, 4 Dec 2019 16:58:33 +0000 (17:58 +0100)]
Fix gcTime calculation

4 years agoref #8679 Add cancel points for aggregation progress monitor
Patrick Plitzner [Wed, 4 Dec 2019 16:58:22 +0000 (17:58 +0100)]
ref #8679 Add cancel points for aggregation progress monitor

4 years agoref #8679 Filter out cloned specimen descriptions
Patrick Plitzner [Wed, 4 Dec 2019 16:58:02 +0000 (17:58 +0100)]
ref #8679 Filter out cloned specimen descriptions

4 years ago fix compile error
Andreas Müller [Wed, 4 Dec 2019 13:37:34 +0000 (14:37 +0100)]
 fix compile error

4 years agoref #8679 rename supports fields and make public
Andreas Müller [Wed, 4 Dec 2019 13:07:08 +0000 (14:07 +0100)]
ref #8679 rename supports fields and make public

4 years agomake misappliedName uuid public (needed for PESI)
Andreas Müller [Wed, 4 Dec 2019 13:01:44 +0000 (14:01 +0100)]
make misappliedName uuid public (needed for PESI)

4 years agoref #8679 let AggregationMode and AggregationSourceMode implement IKeyTerm and implem...
Andreas Müller [Wed, 4 Dec 2019 13:01:02 +0000 (14:01 +0100)]
ref #8679 let AggregationMode and AggregationSourceMode implement IKeyTerm and implement some list methods

4 years agoref #8679 move aggregation modes to own class file
Andreas Müller [Wed, 4 Dec 2019 12:19:55 +0000 (13:19 +0100)]
ref #8679 move aggregation modes to own class file

4 years agoref #8677: getNamedAreaDTO
Katja Luther [Wed, 4 Dec 2019 10:48:05 +0000 (11:48 +0100)]
ref #8677: getNamedAreaDTO

4 years agoref #8677: getNamedAreaDTO
Katja Luther [Wed, 4 Dec 2019 10:46:10 +0000 (11:46 +0100)]
ref #8677: getNamedAreaDTO

4 years agoref #8450 Fix quantitative data + add test
Patrick Plitzner [Wed, 4 Dec 2019 10:18:06 +0000 (11:18 +0100)]
ref #8450 Fix quantitative data + add test

4 years agoadd left join for level in ternmDto sql query
Katja Luther [Wed, 4 Dec 2019 08:36:55 +0000 (09:36 +0100)]
add left join for level in ternmDto sql query

4 years agofix cdmlight export test
Katja Luther [Tue, 3 Dec 2019 08:57:39 +0000 (09:57 +0100)]
fix cdmlight export test

4 years agoref #8450 Set max to min if max null and vica versa
Patrick Plitzner [Tue, 3 Dec 2019 16:31:05 +0000 (17:31 +0100)]
ref #8450 Set max to min if max null and vica versa

 - static method

4 years agoref #8450 Set max to min if max null and vica versa
Patrick Plitzner [Tue, 3 Dec 2019 16:28:00 +0000 (17:28 +0100)]
ref #8450 Set max to min if max null and vica versa

4 years agoset monitor methods to protected in DescriptionAggregationBase
Andreas Müller [Tue, 3 Dec 2019 15:33:41 +0000 (16:33 +0100)]
set monitor methods to protected in DescriptionAggregationBase

4 years agoref #8679 Add sources to aggregated description
Patrick Plitzner [Tue, 3 Dec 2019 15:28:56 +0000 (16:28 +0100)]
ref #8679 Add sources to aggregated description

 - within taxon: specimen description
 - parent taxon: aggregated taxon description

4 years agoref #8472 remove final links to old MarkerType.COMPUTED handling
Andreas Müller [Tue, 3 Dec 2019 12:48:54 +0000 (13:48 +0100)]
ref #8472 remove final links to old MarkerType.COMPUTED handling

4 years agoref #8738 , ref #8702 , ref #8468 last changes for 5.12 update script
Andreas Müller [Tue, 3 Dec 2019 12:06:24 +0000 (13:06 +0100)]
ref #8738 , ref #8702 , ref #8468  last changes for 5.12 update script

4 years agocleanup
Andreas Müller [Mon, 2 Dec 2019 16:32:16 +0000 (17:32 +0100)]
cleanup

4 years agofix potential NPE when retrieving identifiers via type == null
Andreas Müller [Mon, 2 Dec 2019 16:24:32 +0000 (17:24 +0100)]
fix potential NPE when retrieving identifiers via type == null

4 years agocleanup
Andreas Müller [Mon, 2 Dec 2019 15:56:28 +0000 (16:56 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Mon, 2 Dec 2019 15:51:46 +0000 (16:51 +0100)]
cleanup

4 years agoref #8766 Fix potential ArrayIndexOutOfBoundsException
Patrick Plitzner [Mon, 2 Dec 2019 14:54:22 +0000 (15:54 +0100)]
ref #8766 Fix potential ArrayIndexOutOfBoundsException

4 years agoref #8468 replace Inapplicable tables in ClearDB files (remaining)
Andreas Müller [Mon, 2 Dec 2019 14:42:58 +0000 (15:42 +0100)]
ref #8468 replace Inapplicable tables in ClearDB files (remaining)

4 years agoref #8766 remove a.level from TermDto SELECT statement
Patrick Plitzner [Mon, 2 Dec 2019 14:38:50 +0000 (15:38 +0100)]
ref #8766 remove a.level from TermDto SELECT statement

4 years agoref #8468 replace Inapplicable tables in ClearDB files
Andreas Müller [Mon, 2 Dec 2019 14:16:41 +0000 (15:16 +0100)]
ref #8468 replace Inapplicable tables in ClearDB files

4 years agoref #8468 further fix test schema
Andreas Müller [Mon, 2 Dec 2019 14:05:22 +0000 (15:05 +0100)]
ref #8468 further fix test schema

4 years agoref #8468 fix model cache and test sql
Andreas Müller [Mon, 2 Dec 2019 13:18:05 +0000 (14:18 +0100)]
ref #8468 fix model cache and test sql

4 years agoref #8766: add level to TermDto
Katja Luther [Mon, 2 Dec 2019 12:32:41 +0000 (13:32 +0100)]
ref #8766: add level to TermDto

4 years agotypo
Patrick Plitzner [Mon, 2 Dec 2019 12:24:50 +0000 (13:24 +0100)]
typo

4 years agoref #8679 Add initTransaction() super method
Patrick Plitzner [Mon, 2 Dec 2019 12:23:39 +0000 (13:23 +0100)]
ref #8679 Add initTransaction() super method

 - hook for initializing object when a new transaction starts

4 years agominor
Andreas Müller [Mon, 2 Dec 2019 11:54:35 +0000 (12:54 +0100)]
minor

4 years agoref #8468 fix JAXB for removed inapplicableIF
Andreas Müller [Mon, 2 Dec 2019 11:54:10 +0000 (12:54 +0100)]
ref #8468 fix JAXB for removed inapplicableIF

4 years agoref #8468 remove old attributes from TermNode
Andreas Müller [Mon, 2 Dec 2019 11:26:38 +0000 (12:26 +0100)]
ref #8468 remove old attributes from TermNode

4 years agorename TableDroper -> TableDropper
Andreas Müller [Mon, 2 Dec 2019 11:25:54 +0000 (12:25 +0100)]
rename TableDroper -> TableDropper

4 years agofix #8468
Andreas Müller [Mon, 2 Dec 2019 11:23:58 +0000 (12:23 +0100)]
fix #8468

4 years agoref #8738 , ref #8702 add update script to remove null constraints from AUD.uuid...
Andreas Müller [Mon, 2 Dec 2019 11:23:25 +0000 (12:23 +0100)]
ref #8738 , ref #8702 add update script to remove null constraints from AUD.uuid and CdmLing.endPos (II)

4 years agoref #8738 , ref #8702 add update script to remove null constraints from AUD.uuid...
Andreas Müller [Mon, 2 Dec 2019 11:11:53 +0000 (12:11 +0100)]
ref #8738 , ref #8702 add update script to remove null constraints from AUD.uuid and CdmLing.endPos

4 years agocleanup
Andreas Müller [Mon, 2 Dec 2019 11:04:36 +0000 (12:04 +0100)]
cleanup

4 years agorename SchemaUpdater v5.x packages
Andreas Müller [Mon, 2 Dec 2019 11:01:56 +0000 (12:01 +0100)]
rename SchemaUpdater v5.x packages

4 years agoref #8679 Set batchMinFreeHeap in test setup
Patrick Plitzner [Mon, 2 Dec 2019 06:40:11 +0000 (07:40 +0100)]
ref #8679 Set batchMinFreeHeap in test setup

4 years agoref #8679 Replace existing description elements in re-aggregation
Patrick Plitzner [Fri, 29 Nov 2019 12:48:16 +0000 (13:48 +0100)]
ref #8679 Replace existing description elements in re-aggregation

 -add test for re-aggregation

4 years agoref #8679 Load dataset in each session
Patrick Plitzner [Fri, 29 Nov 2019 11:58:03 +0000 (12:58 +0100)]
ref #8679 Load dataset in each session

4 years agofix test
Katja Luther [Fri, 29 Nov 2019 00:07:45 +0000 (01:07 +0100)]
fix test

4 years agoadd check for taxon and name in test
Katja Luther [Thu, 28 Nov 2019 23:11:20 +0000 (00:11 +0100)]
add check for taxon and name in test

4 years agofix delete problems of taxa used in multiple classifications
Katja Luther [Thu, 28 Nov 2019 23:02:35 +0000 (00:02 +0100)]
fix delete problems of taxa used in multiple classifications

4 years agoref #8679 Add checks and repairs for valid quantitative data
Patrick Plitzner [Thu, 28 Nov 2019 14:31:10 +0000 (15:31 +0100)]
ref #8679 Add checks and repairs for valid quantitative data

4 years agoEnhance toString()
Patrick Plitzner [Thu, 28 Nov 2019 14:24:17 +0000 (15:24 +0100)]
Enhance toString()

4 years agoref #8679 Remove usage of apache commons math
Patrick Plitzner [Thu, 28 Nov 2019 12:27:06 +0000 (13:27 +0100)]
ref #8679 Remove usage of apache commons math

4 years agominor
Andreas Müller [Thu, 28 Nov 2019 11:30:06 +0000 (12:30 +0100)]
minor

4 years agoref #8679 PropertyPath and code cleanup
Patrick Plitzner [Thu, 28 Nov 2019 11:17:44 +0000 (12:17 +0100)]
ref #8679 PropertyPath and code cleanup

4 years agoref #8679 Convert to base class aggregation architecture
Patrick Plitzner [Thu, 28 Nov 2019 09:12:20 +0000 (10:12 +0100)]
ref #8679 Convert to base class aggregation architecture

 - convert aggregation of quantitative data to parent
 - convert aggregation of categorical data to parent

4 years agoEnhance toString()
Patrick Plitzner [Thu, 28 Nov 2019 06:54:20 +0000 (07:54 +0100)]
Enhance toString()

4 years agoref #8679 Convert to base class aggregation architecture
Patrick Plitzner [Thu, 28 Nov 2019 06:20:14 +0000 (07:20 +0100)]
ref #8679 Convert to base class aggregation architecture

 - init dataset in preAccumulate
 - filter SpecimenDescriptions by data set

4 years agoref #8679 Convert to base class aggregation architecture
Patrick Plitzner [Thu, 28 Nov 2019 06:10:33 +0000 (07:10 +0100)]
ref #8679 Convert to base class aggregation architecture

 - convert aggregation of quantitative data within taxon

4 years agoref #8679 Add apache commons math to pom
Patrick Plitzner [Thu, 28 Nov 2019 06:07:50 +0000 (07:07 +0100)]
ref #8679 Add apache commons math to pom

4 years agoadd toString()
Patrick Plitzner [Thu, 28 Nov 2019 06:07:03 +0000 (07:07 +0100)]
add toString()

4 years agoref #8679 Convert to base class aggregation architecture
Patrick Plitzner [Wed, 27 Nov 2019 16:40:57 +0000 (17:40 +0100)]
ref #8679 Convert to base class aggregation architecture

 - convert aggregation of categorical data within taxon

4 years agoAdd count to toString()
Patrick Plitzner [Wed, 27 Nov 2019 16:34:55 +0000 (17:34 +0100)]
Add count to toString()

4 years agoref #8724 fix JAXB for CdmLink
Andreas Müller [Thu, 28 Nov 2019 10:03:15 +0000 (11:03 +0100)]
ref #8724 fix JAXB for CdmLink

4 years agoref #7623: fix NPE
Katja Luther [Thu, 28 Nov 2019 09:03:41 +0000 (10:03 +0100)]
ref #7623: fix NPE

4 years agoFix potential NPE
Patrick Plitzner [Wed, 27 Nov 2019 13:55:29 +0000 (14:55 +0100)]
Fix potential NPE

4 years agoref #8724 handle taxon in CdmLinkSource
Andreas Müller [Wed, 27 Nov 2019 13:58:04 +0000 (14:58 +0100)]
ref #8724 handle taxon in CdmLinkSource

4 years agoref #8724 add Taxon to ICdmTarget
Andreas Müller [Wed, 27 Nov 2019 13:26:31 +0000 (14:26 +0100)]
ref #8724 add Taxon to ICdmTarget

4 years agominor
Andreas Müller [Wed, 27 Nov 2019 13:08:39 +0000 (14:08 +0100)]
minor

4 years agoref #7623: improve gathering agent parsing and query generation
Katja Luther [Wed, 27 Nov 2019 13:28:57 +0000 (14:28 +0100)]
ref #7623: improve gathering agent parsing and query generation

4 years agoref #8679 Test leaf color
Patrick Plitzner [Wed, 27 Nov 2019 08:18:39 +0000 (09:18 +0100)]
ref #8679 Test leaf color

4 years agofix NPE in media rights part of biocase import
Katja Luther [Tue, 26 Nov 2019 16:18:33 +0000 (17:18 +0100)]
fix NPE in media rights part of biocase import

4 years agoref #8679 Add leaf color
pplitzner [Wed, 27 Nov 2019 06:31:28 +0000 (07:31 +0100)]
ref #8679 Add leaf color

4 years agoref #8679 Refactoring
pplitzner [Tue, 26 Nov 2019 17:41:16 +0000 (18:41 +0100)]
ref #8679 Refactoring

4 years agoref #8679 Add specimen to sibling taxon
pplitzner [Tue, 26 Nov 2019 17:16:43 +0000 (18:16 +0100)]
ref #8679 Add specimen to sibling taxon

4 years agoAvoid empty description elements
Patrick Plitzner [Tue, 26 Nov 2019 15:39:52 +0000 (16:39 +0100)]
Avoid empty description elements

4 years agoadapt TestAggregations to areaUuidList (2)
Andreas Müller [Tue, 26 Nov 2019 16:01:23 +0000 (17:01 +0100)]
adapt TestAggregations to areaUuidList (2)

4 years agoadapt TestAggregations to areaUuidList
Andreas Müller [Tue, 26 Nov 2019 15:45:38 +0000 (16:45 +0100)]
adapt TestAggregations to areaUuidList

4 years agoupdate TestAggregations
Andreas Müller [Tue, 26 Nov 2019 15:42:35 +0000 (16:42 +0100)]
update TestAggregations

4 years agocleanup
Andreas Müller [Tue, 26 Nov 2019 15:32:13 +0000 (16:32 +0100)]
cleanup

4 years agoref #8679 add tests to StructuredDescriptionAggregation and fix toGrandParent issue...
Andreas Müller [Tue, 26 Nov 2019 15:30:52 +0000 (16:30 +0100)]
ref #8679 add tests to StructuredDescriptionAggregation and fix toGrandParent issue and allow Feature

4 years agoimplement another possibility of gathering agent text in abcd (agentText)
Katja Luther [Tue, 26 Nov 2019 14:01:52 +0000 (15:01 +0100)]
implement another possibility of gathering agent text in abcd (agentText)

4 years agoref #8677: revert a change of last commit
Katja Luther [Tue, 26 Nov 2019 12:39:36 +0000 (13:39 +0100)]
ref #8677: revert a change of last commit

4 years agoref #8677: use changes DistributionAggregationConfig in controller
Katja Luther [Tue, 26 Nov 2019 11:58:50 +0000 (12:58 +0100)]
ref #8677: use changes DistributionAggregationConfig in controller

4 years agoref #8677: use uuid list instead of namedArea list in DistributionAggregationConfig
Katja Luther [Tue, 26 Nov 2019 11:08:30 +0000 (12:08 +0100)]
ref #8677: use uuid list instead of namedArea list in DistributionAggregationConfig

4 years agoref #8469 avoid merge to singular branches
Andreas Müller [Mon, 25 Nov 2019 23:01:11 +0000 (00:01 +0100)]
ref #8469 avoid merge to singular branches

4 years agocleanup
Andreas Müller [Mon, 25 Nov 2019 21:54:26 +0000 (22:54 +0100)]
cleanup

4 years agoref #8469 fix min max issue
Andreas Müller [Mon, 25 Nov 2019 21:53:28 +0000 (22:53 +0100)]
ref #8469 fix min max issue

4 years agoref #8469 handle all sub-branch taxa on the level they belong to
Andreas Müller [Mon, 25 Nov 2019 18:32:57 +0000 (19:32 +0100)]
ref #8469 handle all sub-branch taxa on the level they belong to

4 years agoref #8469 first handling of taxa covering all subbranches, but probably wrong approach
Andreas Müller [Mon, 25 Nov 2019 11:14:05 +0000 (12:14 +0100)]
ref #8469 first handling of taxa covering all subbranches, but probably wrong approach

4 years agoref #8469 fix no feature left, prepare taxon covering all subbranches, cleanup
Andreas Müller [Sun, 24 Nov 2019 03:20:35 +0000 (04:20 +0100)]
ref #8469 fix no feature left, prepare taxon covering all subbranches, cleanup

4 years agocleanup
Andreas Müller [Sat, 23 Nov 2019 21:38:13 +0000 (22:38 +0100)]
cleanup

4 years agoref #8713 Only add aggregated cat. data if states are present
pplitzner [Mon, 25 Nov 2019 08:00:51 +0000 (09:00 +0100)]
ref #8713 Only add aggregated cat. data if states are present

4 years agoref #8450 Only add aggregated quant. data if data present
pplitzner [Mon, 25 Nov 2019 07:52:41 +0000 (08:52 +0100)]
ref #8450 Only add aggregated quant. data if data present

4 years agoref #8469 fix reuse of reature states filter
Andreas Müller [Sat, 23 Nov 2019 20:45:25 +0000 (21:45 +0100)]
ref #8469 fix reuse of reature states filter

4 years agocleanup
Andreas Müller [Fri, 22 Nov 2019 21:06:46 +0000 (22:06 +0100)]
cleanup

4 years agoref #8679 preliminary fix failing test for rank aggregation with absent status
Andreas Müller [Fri, 22 Nov 2019 21:06:09 +0000 (22:06 +0100)]
ref #8679 preliminary fix failing test for rank aggregation with absent status

4 years agoref #8679 remove old COMPUTE marker and move ignore lists to configurator and some...
Andreas Müller [Fri, 22 Nov 2019 20:18:00 +0000 (21:18 +0100)]
ref #8679 remove old COMPUTE marker and move ignore lists to configurator and some cleanup

4 years agoref #8469 introduce KeyTaxon to allow multiple data and multiple descriptions per...
Andreas Müller [Thu, 21 Nov 2019 22:45:18 +0000 (23:45 +0100)]
ref #8469 introduce KeyTaxon to allow multiple data and multiple descriptions per taxon

4 years agoref #8469 fix multiple dependencies for 1 parent feature issue
Andreas Müller [Thu, 21 Nov 2019 13:59:03 +0000 (14:59 +0100)]
ref #8469 fix multiple dependencies for 1 parent feature issue

4 years agocleanup
Andreas Müller [Thu, 21 Nov 2019 13:57:49 +0000 (14:57 +0100)]
cleanup

4 years agoref #8469 use FeatureState in PolytomousKeyGenerator
Andreas Müller [Thu, 21 Nov 2019 13:07:30 +0000 (14:07 +0100)]
ref #8469 use FeatureState in PolytomousKeyGenerator