cdmlib-apps.git
7 years agoref #6252 updates for salvador image import
Andreas Müller [Thu, 8 Dec 2016 15:22:18 +0000 (16:22 +0100)]
ref #6252 updates for salvador image import

7 years agoref #2937 start GermanSL import
Andreas Müller [Thu, 8 Dec 2016 15:17:05 +0000 (16:17 +0100)]
ref #2937 start GermanSL import

7 years agoref #3934 Add feature tree to SalvadorActivator
Andreas Müller [Thu, 8 Dec 2016 15:16:10 +0000 (16:16 +0100)]
ref #3934 Add feature tree to SalvadorActivator

7 years agoref #6252 latest Salvador image import changes
Andreas Müller [Wed, 7 Dec 2016 14:03:40 +0000 (15:03 +0100)]
ref #6252 latest Salvador image import changes

7 years agoupdate cdmlib-apps pom version
Andreas Müller [Mon, 5 Dec 2016 10:13:50 +0000 (11:13 +0100)]
update cdmlib-apps pom version

7 years agoref #5448 Import additional information as extension instead of
Patrick Plitzner [Thu, 20 Oct 2016 13:25:19 +0000 (15:25 +0200)]
ref #5448 Import additional information as extension instead of
annotations

7 years agoref #5448 Fix saving of imported families
Patrick Plitzner [Thu, 20 Oct 2016 13:24:52 +0000 (15:24 +0200)]
ref #5448 Fix saving of imported families

7 years agoref #3934 update Salvador import for facts
Andreas Müller [Thu, 24 Nov 2016 09:24:21 +0000 (10:24 +0100)]
ref #3934 update Salvador import for facts

7 years agoref #3934 fix factCategory SQL
Andreas Müller [Sat, 19 Nov 2016 06:59:21 +0000 (07:59 +0100)]
ref #3934 fix factCategory SQL

7 years agoref #3934 update Salvador import for facts
Andreas Müller [Fri, 18 Nov 2016 21:20:10 +0000 (22:20 +0100)]
ref #3934 update Salvador import for facts

7 years agominor compile issues
Andreas Müller [Fri, 18 Nov 2016 15:45:01 +0000 (16:45 +0100)]
minor compile issues

7 years agoref #3934 Latest changes in Salvador import
Andreas Müller [Fri, 18 Nov 2016 15:34:53 +0000 (16:34 +0100)]
ref #3934 Latest changes in Salvador import

7 years agoAdapt BgbmInstancesUpdater to new databases
Andreas Müller [Fri, 18 Nov 2016 15:34:14 +0000 (16:34 +0100)]
Adapt BgbmInstancesUpdater to new databases

7 years agoAdd nom. illeg. superfl. to allowed nom.states. without basionym in BM import
Andreas Müller [Fri, 18 Nov 2016 15:33:34 +0000 (16:33 +0100)]
Add nom. illeg. superfl. to allowed nom.states. without basionym in BM import

7 years agoAdapt BMTaxonRelationExport to new Synonym model
Andreas Müller [Fri, 18 Nov 2016 15:32:39 +0000 (16:32 +0100)]
Adapt BMTaxonRelationExport to new Synonym model

7 years agocleanup
Andreas Müller [Fri, 18 Nov 2016 15:30:52 +0000 (16:30 +0100)]
cleanup

7 years agoMerge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-apps
Andreas Müller [Fri, 18 Nov 2016 15:26:15 +0000 (16:26 +0100)]
Merge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-apps

7 years agominor
Andreas Müller [Fri, 18 Nov 2016 15:26:01 +0000 (16:26 +0100)]
minor

7 years agoMerge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-apps
Andreas Müller [Thu, 10 Nov 2016 12:32:05 +0000 (13:32 +0100)]
Merge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-apps

Conflicts:
app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/SDDExportActivator.java
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/SDDImportActivator.java

7 years agoCleanup and remove deprecated method
Andreas Müller [Thu, 10 Nov 2016 11:54:37 +0000 (12:54 +0100)]
Cleanup and remove deprecated method

7 years agoUpdate Salvador import
Andreas Müller [Thu, 10 Nov 2016 11:53:45 +0000 (12:53 +0100)]
Update Salvador import

7 years agoadapt getDescription() see #5680
Katja Luther [Tue, 8 Nov 2016 08:45:43 +0000 (09:45 +0100)]
adapt getDescription() see #5680

7 years agofix #5862 by correctly managing dependencies
Andreas Kohlbecker [Mon, 7 Nov 2016 09:31:14 +0000 (10:31 +0100)]
fix #5862 by correctly managing dependencies

7 years agochange the versions to 4.4
Katja Luther [Fri, 4 Nov 2016 15:19:33 +0000 (16:19 +0100)]
change the versions to 4.4

7 years agofix localH2 username in eFlora
Andreas Müller [Fri, 21 Oct 2016 12:54:42 +0000 (14:54 +0200)]
fix localH2 username in eFlora

7 years agoref #3925 fix excluded flag for Cuba
Andreas Müller [Fri, 21 Oct 2016 12:52:13 +0000 (14:52 +0200)]
ref #3925 fix excluded flag for Cuba

7 years agoCleanup and gitignore in app-import
Andreas Müller [Fri, 21 Oct 2016 12:50:25 +0000 (14:50 +0200)]
Cleanup and gitignore in app-import

7 years agoCleanup app-import test data
Andreas Müller [Fri, 21 Oct 2016 12:48:36 +0000 (14:48 +0200)]
Cleanup app-import test data

7 years agoref #5499 latest changes to Edaphobase import
Andreas Müller [Thu, 13 Oct 2016 11:42:47 +0000 (13:42 +0200)]
ref #5499 latest changes to Edaphobase import

7 years agoref #5974 Remove synonym relationships (not finished yet)
Andreas Müller [Thu, 13 Oct 2016 11:41:46 +0000 (13:41 +0200)]
ref #5974 Remove synonym relationships (not finished yet)

7 years agoref #3658 remove nomenclaturalCode
Andreas Müller [Thu, 13 Oct 2016 11:30:18 +0000 (13:30 +0200)]
ref #3658 remove nomenclaturalCode

7 years agocleanup IAPTImportTest
Andreas Müller [Wed, 28 Sep 2016 12:52:16 +0000 (14:52 +0200)]
cleanup IAPTImportTest

7 years agoref #5448 Remove unnecessary saving
Patrick Plitzner [Wed, 21 Sep 2016 10:00:44 +0000 (12:00 +0200)]
ref #5448 Remove unnecessary saving

7 years agoref #5448 Enhance name checking
Patrick Plitzner [Wed, 21 Sep 2016 10:00:27 +0000 (12:00 +0200)]
ref #5448 Enhance name checking

7 years agofix #6035 one more broken character
Andreas Kohlbecker [Tue, 20 Sep 2016 10:23:00 +0000 (12:23 +0200)]
fix #6035 one more broken character

7 years agofix #6093 including more taxa into algea registry import
Andreas Kohlbecker [Tue, 20 Sep 2016 09:45:25 +0000 (11:45 +0200)]
fix #6093 including more taxa into algea registry import

7 years agoref #6097 filter to include algae only - better match pattern
Andreas Kohlbecker [Mon, 19 Sep 2016 12:14:54 +0000 (14:14 +0200)]
ref #6097 filter to include algae only - better match pattern

7 years ago#6097 filter to include algae only
Andreas Kohlbecker [Mon, 19 Sep 2016 11:33:21 +0000 (13:33 +0200)]
#6097 filter to include algae only

7 years agomoving TestDatabase back to main - a couple of classes had complie errors
Andreas Kohlbecker [Mon, 19 Sep 2016 11:33:13 +0000 (13:33 +0200)]
moving TestDatabase back to main - a couple of classes had complie errors

7 years agoremoving duplicate repository
Andreas Kohlbecker [Mon, 19 Sep 2016 07:29:54 +0000 (09:29 +0200)]
removing duplicate repository

7 years agoMerge branch 'IAPT'
Andreas Kohlbecker [Mon, 19 Sep 2016 06:19:08 +0000 (08:19 +0200)]
Merge branch 'IAPT'

Conflicts:
app-import/.gitignore
app-import/pom.xml

7 years agomove test classes in app-import
Andreas Müller [Thu, 15 Sep 2016 21:13:14 +0000 (23:13 +0200)]
move test classes in app-import

7 years agofix #6095 log duplicate registrations during import IAPT origin/IAPT
Andreas Kohlbecker [Fri, 16 Sep 2016 22:27:53 +0000 (00:27 +0200)]
fix #6095 log duplicate registrations during import

7 years agofix #6094 importing 'registration' data into an Extension object
Andreas Kohlbecker [Fri, 16 Sep 2016 15:20:10 +0000 (17:20 +0200)]
fix #6094 importing 'registration' data into an Extension object

7 years agoref #6026 SpecimenType = FOSSIL for fossil taxa/names
Andreas Kohlbecker [Fri, 16 Sep 2016 09:13:42 +0000 (11:13 +0200)]
ref #6026 SpecimenType = FOSSIL for fossil taxa/names

7 years agoref #6026 more parser improvements and tests
Andreas Kohlbecker [Fri, 16 Sep 2016 06:19:51 +0000 (08:19 +0200)]
ref #6026 more parser improvements and tests

7 years agomove test classes in app-import
Andreas Müller [Thu, 15 Sep 2016 21:13:14 +0000 (23:13 +0200)]
move test classes in app-import

7 years agoref #6026 more parser improvements and tests
Andreas Kohlbecker [Thu, 15 Sep 2016 20:22:29 +0000 (22:22 +0200)]
ref #6026 more parser improvements and tests

7 years agoref #6026 improving specimenType parsers: better recognition of 'Coll. something...
Andreas Kohlbecker [Thu, 15 Sep 2016 15:51:05 +0000 (17:51 +0200)]
ref #6026 improving specimenType parsers: better recognition of 'Coll. something' types

7 years agoref #6026 solving problems in date and specimenType parsers, also implementing tests
Andreas Kohlbecker [Thu, 15 Sep 2016 15:32:37 +0000 (17:32 +0200)]
ref #6026 solving problems in date and specimenType parsers, also implementing tests

7 years agoref #6035 adding more character fixed and adding source referenence for all names
Andreas Kohlbecker [Thu, 15 Sep 2016 12:04:17 +0000 (14:04 +0200)]
ref #6035 adding more character fixed and adding source referenence for all names

7 years agoref #6026 'Coll. Lange-Bertalot..' as titleCache of Collection
Andreas Kohlbecker [Mon, 12 Sep 2016 22:12:35 +0000 (00:12 +0200)]
ref #6026  'Coll. Lange-Bertalot..' as titleCache of Collection

7 years agoref #6026 using genera as higher taxon for species
Andreas Kohlbecker [Mon, 12 Sep 2016 22:07:51 +0000 (00:07 +0200)]
ref #6026 using genera as higher taxon for species

7 years agofix #6068
Andreas Kohlbecker [Mon, 12 Sep 2016 13:34:14 +0000 (15:34 +0200)]
fix #6068

7 years agoref #6026 3 more character replacement rule
Andreas Kohlbecker [Mon, 12 Sep 2016 13:03:18 +0000 (15:03 +0200)]
ref #6026 3 more character replacement rule

7 years agoref #6026 fixing rank
Andreas Kohlbecker [Mon, 12 Sep 2016 12:36:47 +0000 (14:36 +0200)]
ref #6026 fixing rank

7 years agoref #6026 fixing bug in publication regex pattern
Andreas Kohlbecker [Mon, 12 Sep 2016 10:36:27 +0000 (12:36 +0200)]
ref #6026 fixing bug in publication regex pattern

7 years agoref #6026 speedup of import and fixing a minor bug
Andreas Kohlbecker [Mon, 12 Sep 2016 10:08:54 +0000 (12:08 +0200)]
ref #6026 speedup of import and fixing a minor bug
   - speedup by special handling for hardly to parse reference
   - minor bug during camparison of basionym names

7 years agoref #6026 keepgin deteced ref type in case of 'Vorabdruck'
Andreas Kohlbecker [Mon, 12 Sep 2016 09:33:11 +0000 (11:33 +0200)]
ref #6026 keepgin deteced ref type in case of 'Vorabdruck'

7 years agoref #6026 NameTypes (with minor problems)
Andreas Kohlbecker [Fri, 9 Sep 2016 14:57:05 +0000 (16:57 +0200)]
ref #6026 NameTypes (with minor problems)

7 years agoref #6026 FieldUnit locality working
Andreas Kohlbecker [Fri, 9 Sep 2016 10:21:44 +0000 (12:21 +0200)]
ref #6026 FieldUnit locality working

7 years agoremoving unused repo from the pom.xml (was used for yourkit)
Andreas Kohlbecker [Fri, 9 Sep 2016 09:51:22 +0000 (11:51 +0200)]
removing unused repo from the pom.xml (was used for yourkit)

7 years agominor
Andreas Kohlbecker [Fri, 9 Sep 2016 07:20:42 +0000 (09:20 +0200)]
minor

7 years agofix #5893: fauna europaea reference import with more atomized data
Katja Luther [Fri, 2 Sep 2016 09:54:48 +0000 (11:54 +0200)]
fix #5893: fauna europaea reference import with more atomized data

7 years ago#5448 Imporve name check for multiple ex authors
Patrick Plitzner [Thu, 1 Sep 2016 14:59:46 +0000 (16:59 +0200)]
#5448 Imporve name check for multiple ex authors

7 years ago#5448 Improve import of families
Patrick Plitzner [Thu, 1 Sep 2016 14:59:30 +0000 (16:59 +0200)]
#5448 Improve import of families
 - clone families for checklist
 - load in related objects method

7 years ago#5448 Change abbrev label of unranked infraspecfic rank before importing
Patrick Plitzner [Thu, 1 Sep 2016 11:27:40 +0000 (13:27 +0200)]
#5448 Change abbrev label of unranked infraspecfic rank before importing

7 years agoref #5448 Reduce multiple ex authors to only two
Patrick Plitzner [Wed, 31 Aug 2016 10:27:39 +0000 (12:27 +0200)]
ref #5448 Reduce multiple ex authors to only two

7 years agoref #5448 Reduce multiple ex authors to only two
Patrick Plitzner [Tue, 30 Aug 2016 14:23:00 +0000 (16:23 +0200)]
ref #5448 Reduce multiple ex authors to only two

7 years agoadaption to specimen import changes
Katja Luther [Mon, 22 Aug 2016 11:21:36 +0000 (11:21 +0000)]
adaption to specimen import changes

7 years ago#5448 Fix import of hybrid formula
Patrick Plitzner [Wed, 3 Aug 2016 13:18:28 +0000 (15:18 +0200)]
#5448 Fix import of hybrid formula

7 years agoref #5448 code cleanup
Patrick Plitzner [Wed, 3 Aug 2016 12:20:31 +0000 (14:20 +0200)]
ref #5448 code cleanup

7 years ago#5448 Refactor hybrid name import/check
Patrick Plitzner [Wed, 3 Aug 2016 09:58:39 +0000 (11:58 +0200)]
#5448 Refactor hybrid name import/check

7 years ago#5448 Use SEQNUM as id column
Patrick Plitzner [Wed, 3 Aug 2016 08:38:34 +0000 (10:38 +0200)]
#5448 Use SEQNUM as id column
 - enhance hybrid name check

7 years ago#5448 Import genus hybrid formulas
Patrick Plitzner [Tue, 2 Aug 2016 09:45:14 +0000 (11:45 +0200)]
#5448 Import genus hybrid formulas

7 years ago#5448 Support corner cases
Patrick Plitzner [Mon, 1 Aug 2016 12:51:09 +0000 (14:51 +0200)]
#5448 Support corner cases
 - SPI and KMB as ranks
 - nomenclatural status type
 - HYB name checking

7 years ago#5448 Handle rank "SPI"
Patrick Plitzner [Mon, 1 Aug 2016 10:21:41 +0000 (12:21 +0200)]
#5448 Handle rank "SPI"

7 years ago#5448 Import non-CDM ranks
Patrick Plitzner [Mon, 1 Aug 2016 10:16:36 +0000 (12:16 +0200)]
#5448 Import non-CDM ranks

7 years ago#5448 Remove non-exisiting hybrid category
Patrick Plitzner [Thu, 28 Jul 2016 09:12:26 +0000 (11:12 +0200)]
#5448 Remove non-exisiting hybrid category

7 years ago#5448 Import HYB 'nf'
Patrick Plitzner [Wed, 27 Jul 2016 13:34:19 +0000 (15:34 +0200)]
#5448 Import HYB 'nf'

7 years ago#5448 Import rank "SAM"
Patrick Plitzner [Wed, 27 Jul 2016 13:34:03 +0000 (15:34 +0200)]
#5448 Import rank "SAM"

7 years ago#6000 Use new CASUAL Method instead of deprecated INTRODUCED_ADVENTITIOUS
Andreas Müller [Thu, 28 Jul 2016 10:55:04 +0000 (12:55 +0200)]
#6000 Use new CASUAL Method instead of deprecated INTRODUCED_ADVENTITIOUS

7 years ago#5448 Add "distinct" to SQL query as family table contains duplicate
Patrick Plitzner [Tue, 26 Jul 2016 15:27:20 +0000 (17:27 +0200)]
#5448 Add "distinct" to SQL query as family table contains duplicate
rows

7 years ago#5488 Improve import of family taxa
Patrick Plitzner [Tue, 26 Jul 2016 13:30:01 +0000 (15:30 +0200)]
#5488 Improve import of family taxa
 - Load families in related object methods

7 years ago#5448 Fix hybrid import where specific epithets are not from same genus
Patrick Plitzner [Tue, 26 Jul 2016 09:10:24 +0000 (11:10 +0200)]
#5448 Fix hybrid import where specific epithets are not from same genus

7 years ago#5448 Add family rank
Patrick Plitzner [Tue, 26 Jul 2016 09:09:41 +0000 (11:09 +0200)]
#5448 Add family rank

7 years ago#5448 Fix hybrid import where specific epithets are not from same genus
Patrick Plitzner [Tue, 26 Jul 2016 07:09:28 +0000 (09:09 +0200)]
#5448 Fix hybrid import where specific epithets are not from same genus

7 years agoref #6026 handling 'Vorabdrucke' as Book Volume/Issue
Andreas Kohlbecker [Fri, 9 Sep 2016 06:59:11 +0000 (08:59 +0200)]
ref #6026 handling 'Vorabdrucke' as Book Volume/Issue

7 years agoref #6026 support for making statistics on parsed type data - typo
Andreas Kohlbecker [Fri, 9 Sep 2016 05:36:31 +0000 (07:36 +0200)]
ref #6026 support for making statistics on parsed type data - typo

7 years agoref #6026 importing Basionyms
Andreas Kohlbecker [Thu, 8 Sep 2016 13:40:38 +0000 (15:40 +0200)]
ref #6026 importing Basionyms

7 years agoref #6026 support for making statistics on parsed type data:
Andreas Kohlbecker [Thu, 8 Sep 2016 12:47:42 +0000 (14:47 +0200)]
ref #6026 support for making statistics on parsed type data:
Type parsing statistics:
 - Type: field 'Type' can not be parsed (parse problem of whole typeString)
 - Type: fielUnitStr can not be parsed (parse problem of fielUnitStr)
 - Type: Could not parse specimen (parse problems in holotype, isotype)

7 years agoref #6026 better type parsing
Andreas Kohlbecker [Thu, 8 Sep 2016 12:38:32 +0000 (14:38 +0200)]
ref #6026 better type parsing
  - FieldUnit: collector, fieldnumber, date
  - Specimen: Collection, Subcollection, accession number
Does not work in all cases

7 years agoref #6026 two more date parsing rules
Andreas Kohlbecker [Wed, 7 Sep 2016 12:56:08 +0000 (14:56 +0200)]
ref #6026 two more date parsing rules

7 years agoref #6026 type parsing
Andreas Kohlbecker [Wed, 7 Sep 2016 10:20:24 +0000 (12:20 +0200)]
ref #6026 type parsing
   - parsing of specimen types

7 years agoref #6026 publication date parsing completed root/branches/cdmlib-apps/IAPT
Andreas Kohlbecker [Tue, 6 Sep 2016 10:11:58 +0000 (12:11 +0200)]
ref #6026 publication date parsing completed

7 years agoref #6009 improved plublication date parsing
Andreas Kohlbecker [Tue, 6 Sep 2016 06:58:50 +0000 (08:58 +0200)]
ref #6009 improved plublication date parsing
   - all dates recognized
   - all months recognized
   - special time spans not implemented (Winter, Fall, April-June, etc)

7 years agoref #6009 improved plublication date parsing
Andreas Kohlbecker [Tue, 30 Aug 2016 22:25:47 +0000 (00:25 +0200)]
ref #6009 improved plublication date parsing

7 years agofix #5893: fauna europaea reference import with more atomized data root/trunk/cdmlib-apps
Katja Luther [Fri, 2 Sep 2016 09:54:48 +0000 (11:54 +0200)]
fix #5893: fauna europaea reference import with more atomized data

7 years ago#5448 Imporve name check for multiple ex authors
Patrick Plitzner [Thu, 1 Sep 2016 14:59:46 +0000 (16:59 +0200)]
#5448 Imporve name check for multiple ex authors

7 years ago#5448 Improve import of families
Patrick Plitzner [Thu, 1 Sep 2016 14:59:30 +0000 (16:59 +0200)]
#5448 Improve import of families
 - clone families for checklist
 - load in related objects method