cdmlib.git
4 years agoref #8780 test nodes recursive and generic
Andreas Müller [Wed, 18 Dec 2019 11:43:06 +0000 (12:43 +0100)]
ref #8780 test nodes recursive and generic

4 years agocleanup
Andreas Müller [Wed, 18 Dec 2019 11:42:13 +0000 (12:42 +0100)]
cleanup

4 years agofix ConcurrentSessionTest testdata
Andreas Müller [Wed, 18 Dec 2019 11:41:49 +0000 (12:41 +0100)]
fix ConcurrentSessionTest testdata

4 years agocleanup
Andreas Müller [Wed, 18 Dec 2019 11:18:16 +0000 (12:18 +0100)]
cleanup

4 years agoref #8780 reduce test dataset
Andreas Müller [Wed, 18 Dec 2019 11:17:04 +0000 (12:17 +0100)]
ref #8780 reduce test dataset

4 years agoref #8780 add SortIndexUpdaterWrapperTest for term nodes
Andreas Müller [Wed, 18 Dec 2019 10:59:50 +0000 (11:59 +0100)]
ref #8780 add SortIndexUpdaterWrapperTest for term nodes

4 years agoref #8780 cleanup SortIndexUpdaterWrapper
Andreas Müller [Wed, 18 Dec 2019 10:58:56 +0000 (11:58 +0100)]
ref #8780 cleanup SortIndexUpdaterWrapper

4 years agoreplace featureTreeService by termTreeService
Andreas Müller [Wed, 18 Dec 2019 10:58:06 +0000 (11:58 +0100)]
replace featureTreeService by termTreeService

4 years agocleanup
Andreas Müller [Wed, 18 Dec 2019 10:57:07 +0000 (11:57 +0100)]
cleanup

4 years agoref #8780 cleanup
Andreas Müller [Wed, 18 Dec 2019 08:47:40 +0000 (09:47 +0100)]
ref #8780 cleanup

4 years agofix #8780 fix term node sortindex updater (TermNode->TermRelation)
Andreas Müller [Wed, 18 Dec 2019 08:47:16 +0000 (09:47 +0100)]
fix #8780 fix term node sortindex updater (TermNode->TermRelation)

4 years agocleanup
Andreas Müller [Wed, 18 Dec 2019 08:36:45 +0000 (09:36 +0100)]
cleanup

4 years agocleanup
Andreas Müller [Wed, 18 Dec 2019 08:26:38 +0000 (09:26 +0100)]
cleanup

4 years agofix #8770 responding with http code 404 in case name uuid is not found
Andreas Kohlbecker [Mon, 16 Dec 2019 15:32:44 +0000 (16:32 +0100)]
fix #8770 responding with http code 404 in case name uuid is not found

4 years agorename ExternalNameIdentifier to ExternalIdentifier
Katja Luther [Mon, 16 Dec 2019 08:25:37 +0000 (09:25 +0100)]
rename ExternalNameIdentifier to ExternalIdentifier

4 years agoref #8477 Check if duplicates are allowed before adding terms to trees
Patrick Plitzner [Fri, 13 Dec 2019 14:21:56 +0000 (15:21 +0100)]
ref #8477 Check if duplicates are allowed before adding terms to trees

4 years agofixing ClassCastException in CdmLinkSource for taxa
Andreas Kohlbecker [Fri, 13 Dec 2019 11:32:21 +0000 (12:32 +0100)]
fixing ClassCastException in CdmLinkSource for taxa

4 years agoref #8477 Check if duplicates are allowed before adding terms to trees
Patrick Plitzner [Fri, 13 Dec 2019 11:16:43 +0000 (12:16 +0100)]
ref #8477 Check if duplicates are allowed before adding terms to trees

4 years agofix abcd import when gathering date of associated unit is null
Katja Luther [Fri, 13 Dec 2019 11:30:54 +0000 (12:30 +0100)]
fix abcd import when gathering date of associated unit is null

4 years agomake all MAN uuids public
Andreas Müller [Fri, 13 Dec 2019 11:21:48 +0000 (12:21 +0100)]
make all MAN uuids public

4 years agoremove unneccary instanceof
Andreas Müller [Fri, 13 Dec 2019 11:21:21 +0000 (12:21 +0100)]
remove unneccary instanceof

4 years agofix abcd import when gathering date of associated unit is null
Katja Luther [Fri, 13 Dec 2019 10:37:25 +0000 (11:37 +0100)]
fix abcd import when gathering date of associated unit is null

4 years agoref #8313 Return a collection of strings for display value
Patrick Plitzner [Thu, 12 Dec 2019 13:45:06 +0000 (14:45 +0100)]
ref #8313 Return a collection of strings for display value

4 years agoref #8736 minor performance improvement when adding specimens to matrix
Patrick Plitzner [Wed, 11 Dec 2019 17:46:53 +0000 (18:46 +0100)]
ref #8736 minor performance improvement when adding specimens to matrix

4 years agofix #8736 Fix LIE when adding specimens to matrix
Patrick Plitzner [Wed, 11 Dec 2019 17:19:34 +0000 (18:19 +0100)]
fix #8736 Fix LIE when adding specimens to matrix

4 years agoref #8679 handle null values in missing values correctly
Andreas Müller [Mon, 9 Dec 2019 23:13:11 +0000 (00:13 +0100)]
ref #8679 handle null values in missing values correctly

4 years agocleanup
Andreas Müller [Mon, 9 Dec 2019 21:43:41 +0000 (22:43 +0100)]
cleanup

4 years agoref #8679 fix structured desc aggregation for missing values and min/max only values
Andreas Müller [Mon, 9 Dec 2019 20:55:57 +0000 (21:55 +0100)]
ref #8679 fix structured desc aggregation for missing values and min/max only values

4 years agocleanup
Andreas Müller [Mon, 9 Dec 2019 17:13:23 +0000 (18:13 +0100)]
cleanup

4 years agoadd comment that volumes with dot are maybe handled incorrectly
Andreas Müller [Mon, 9 Dec 2019 16:02:53 +0000 (17:02 +0100)]
add comment that volumes with dot are maybe handled incorrectly

4 years agocleanup
Andreas Müller [Mon, 9 Dec 2019 16:01:50 +0000 (17:01 +0100)]
cleanup

4 years agoadd Ko and Se to BerlinModelTransformer for PESI
Andreas Müller [Mon, 9 Dec 2019 16:01:11 +0000 (17:01 +0100)]
add Ko and Se to BerlinModelTransformer for PESI

4 years agoremove duplicated call of getTitleWithoutYearAndAuthorGeneric
Andreas Müller [Mon, 9 Dec 2019 15:20:15 +0000 (16:20 +0100)]
remove duplicated call of getTitleWithoutYearAndAuthorGeneric

4 years agocleanup
Andreas Müller [Mon, 9 Dec 2019 15:13:33 +0000 (16:13 +0100)]
cleanup

4 years agoref #8679 add done() to monitoring if unexpected exception occurred.
Andreas Müller [Sat, 7 Dec 2019 08:57:21 +0000 (09:57 +0100)]
ref #8679 add done() to monitoring if unexpected exception occurred.

4 years agoadd getNameCache(name, tagRules) to INameCacheStrategy
Andreas Müller [Sat, 7 Dec 2019 08:56:06 +0000 (09:56 +0100)]
add getNameCache(name, tagRules) to INameCacheStrategy

4 years agofix missing type designations of synonyms on specimen page
Katja Luther [Thu, 5 Dec 2019 14:36:59 +0000 (15:36 +0100)]
fix missing type designations of synonyms on specimen page

4 years agoref #8679 top level error handling and renaming aggregation methods
Andreas Müller [Thu, 5 Dec 2019 13:57:50 +0000 (14:57 +0100)]
ref #8679 top level error handling and renaming aggregation methods

4 years agoref #8679 try to fix progress tasks and percentage not showing up
Andreas Müller [Thu, 5 Dec 2019 13:36:35 +0000 (14:36 +0100)]
ref #8679 try to fix progress tasks and percentage not showing up

4 years agocleanup
Andreas Müller [Thu, 5 Dec 2019 13:35:42 +0000 (14:35 +0100)]
cleanup

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