Patrick Plitzner [Wed, 21 Dec 2016 08:14:30 +0000 (02:14 -0600)]
Merge branch 'master' into noChecklistClone
Andreas Kohlbecker [Tue, 20 Dec 2016 10:52:53 +0000 (11:52 +0100)]
ref #6190 removing svn property place holder in first line of code
Andreas Müller [Fri, 9 Dec 2016 10:22:42 +0000 (11:22 +0100)]
ref #6252 and ref #3934 Improve image import, fix distribution import and add area level / type
Andreas Müller [Thu, 8 Dec 2016 20:23:14 +0000 (21:23 +0100)]
ref #6252 improve salvador image import
Andreas Müller [Thu, 8 Dec 2016 20:21:49 +0000 (21:21 +0100)]
ref #3937 Remove marker from salvador import
Andreas Müller [Thu, 8 Dec 2016 15:22:18 +0000 (16:22 +0100)]
ref #6252 updates for salvador image import
Andreas Müller [Thu, 8 Dec 2016 15:17:05 +0000 (16:17 +0100)]
ref #2937 start GermanSL import
Andreas Müller [Thu, 8 Dec 2016 15:16:10 +0000 (16:16 +0100)]
ref #3934 Add feature tree to SalvadorActivator
Andreas Müller [Wed, 7 Dec 2016 14:03:40 +0000 (15:03 +0100)]
ref #6252 latest Salvador image import changes
Andreas Müller [Mon, 5 Dec 2016 10:13:50 +0000 (11:13 +0100)]
update cdmlib-apps pom version
Patrick Plitzner [Thu, 1 Dec 2016 08:29:37 +0000 (09:29 +0100)]
Merge branch 'master' into noChecklistClone
# Conflicts:
# app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportFamily.java
# app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java
Patrick Plitzner [Thu, 1 Dec 2016 08:09:58 +0000 (09:09 +0100)]
ref #5448 Correctly set sec reference on synonyms and avoid for
misapplied names
Patrick Plitzner [Thu, 20 Oct 2016 13:25:19 +0000 (15:25 +0200)]
ref #5448 Import additional information as extension instead of
annotations
Patrick Plitzner [Thu, 20 Oct 2016 13:24:52 +0000 (15:24 +0200)]
ref #5448 Fix saving of imported families
Patrick Plitzner [Tue, 29 Nov 2016 16:42:09 +0000 (17:42 +0100)]
Avoid cloning taxa for checklist classification
Andreas Müller [Thu, 24 Nov 2016 09:24:21 +0000 (10:24 +0100)]
ref #3934 update Salvador import for facts
Andreas Müller [Sat, 19 Nov 2016 06:59:21 +0000 (07:59 +0100)]
ref #3934 fix factCategory SQL
Andreas Müller [Fri, 18 Nov 2016 21:20:10 +0000 (22:20 +0100)]
ref #3934 update Salvador import for facts
Andreas Müller [Fri, 18 Nov 2016 15:45:01 +0000 (16:45 +0100)]
minor compile issues
Andreas Müller [Fri, 18 Nov 2016 15:34:53 +0000 (16:34 +0100)]
ref #3934 Latest changes in Salvador import
Andreas Müller [Fri, 18 Nov 2016 15:34:14 +0000 (16:34 +0100)]
Adapt BgbmInstancesUpdater to new databases
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
Andreas Müller [Fri, 18 Nov 2016 15:32:39 +0000 (16:32 +0100)]
Adapt BMTaxonRelationExport to new Synonym model
Andreas Müller [Fri, 18 Nov 2016 15:30:52 +0000 (16:30 +0100)]
cleanup
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
Andreas Müller [Fri, 18 Nov 2016 15:26:01 +0000 (16:26 +0100)]
minor
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
Andreas Müller [Thu, 10 Nov 2016 11:54:37 +0000 (12:54 +0100)]
Cleanup and remove deprecated method
Andreas Müller [Thu, 10 Nov 2016 11:53:45 +0000 (12:53 +0100)]
Update Salvador import
Katja Luther [Tue, 8 Nov 2016 08:45:43 +0000 (09:45 +0100)]
adapt getDescription() see #5680
Andreas Kohlbecker [Mon, 7 Nov 2016 09:31:14 +0000 (10:31 +0100)]
fix #5862 by correctly managing dependencies
Katja Luther [Fri, 4 Nov 2016 15:19:33 +0000 (16:19 +0100)]
change the versions to 4.4
Andreas Müller [Fri, 21 Oct 2016 12:54:42 +0000 (14:54 +0200)]
fix localH2 username in eFlora
Andreas Müller [Fri, 21 Oct 2016 12:52:13 +0000 (14:52 +0200)]
ref #3925 fix excluded flag for Cuba
Andreas Müller [Fri, 21 Oct 2016 12:50:25 +0000 (14:50 +0200)]
Cleanup and gitignore in app-import
Andreas Müller [Fri, 21 Oct 2016 12:48:36 +0000 (14:48 +0200)]
Cleanup app-import test data
Andreas Müller [Thu, 13 Oct 2016 11:42:47 +0000 (13:42 +0200)]
ref #5499 latest changes to Edaphobase import
Andreas Müller [Thu, 13 Oct 2016 11:41:46 +0000 (13:41 +0200)]
ref #5974 Remove synonym relationships (not finished yet)
Andreas Müller [Thu, 13 Oct 2016 11:30:18 +0000 (13:30 +0200)]
ref #3658 remove nomenclaturalCode
Andreas Müller [Wed, 28 Sep 2016 12:52:16 +0000 (14:52 +0200)]
cleanup IAPTImportTest
Patrick Plitzner [Wed, 21 Sep 2016 10:00:44 +0000 (12:00 +0200)]
ref #5448 Remove unnecessary saving
Patrick Plitzner [Wed, 21 Sep 2016 10:00:27 +0000 (12:00 +0200)]
ref #5448 Enhance name checking
Andreas Kohlbecker [Tue, 20 Sep 2016 10:23:00 +0000 (12:23 +0200)]
fix #6035 one more broken character
Andreas Kohlbecker [Tue, 20 Sep 2016 09:45:25 +0000 (11:45 +0200)]
fix #6093 including more taxa into algea registry import
Andreas Kohlbecker [Mon, 19 Sep 2016 12:14:54 +0000 (14:14 +0200)]
ref #6097 filter to include algae only - better match pattern
Andreas Kohlbecker [Mon, 19 Sep 2016 11:33:21 +0000 (13:33 +0200)]
#6097 filter to include algae only
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
Andreas Kohlbecker [Mon, 19 Sep 2016 07:29:54 +0000 (09:29 +0200)]
removing duplicate repository
Andreas Kohlbecker [Mon, 19 Sep 2016 06:19:08 +0000 (08:19 +0200)]
Merge branch 'IAPT'
Conflicts:
app-import/.gitignore
app-import/pom.xml
Andreas Müller [Thu, 15 Sep 2016 21:13:14 +0000 (23:13 +0200)]
move test classes in app-import
Andreas Kohlbecker [Fri, 16 Sep 2016 22:27:53 +0000 (00:27 +0200)]
fix #6095 log duplicate registrations during import
Andreas Kohlbecker [Fri, 16 Sep 2016 15:20:10 +0000 (17:20 +0200)]
fix #6094 importing 'registration' data into an Extension object
Andreas Kohlbecker [Fri, 16 Sep 2016 09:13:42 +0000 (11:13 +0200)]
ref #6026 SpecimenType = FOSSIL for fossil taxa/names
Andreas Kohlbecker [Fri, 16 Sep 2016 06:19:51 +0000 (08:19 +0200)]
ref #6026 more parser improvements and tests
Andreas Müller [Thu, 15 Sep 2016 21:13:14 +0000 (23:13 +0200)]
move test classes in app-import
Andreas Kohlbecker [Thu, 15 Sep 2016 20:22:29 +0000 (22:22 +0200)]
ref #6026 more parser improvements and tests
Andreas Kohlbecker [Thu, 15 Sep 2016 15:51:05 +0000 (17:51 +0200)]
ref #6026 improving specimenType parsers: better recognition of 'Coll. something' types
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
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
Andreas Kohlbecker [Mon, 12 Sep 2016 22:12:35 +0000 (00:12 +0200)]
ref #6026 'Coll. Lange-Bertalot..' as titleCache of Collection
Andreas Kohlbecker [Mon, 12 Sep 2016 22:07:51 +0000 (00:07 +0200)]
ref #6026 using genera as higher taxon for species
Andreas Kohlbecker [Mon, 12 Sep 2016 13:34:14 +0000 (15:34 +0200)]
fix #6068
Andreas Kohlbecker [Mon, 12 Sep 2016 13:03:18 +0000 (15:03 +0200)]
ref #6026 3 more character replacement rule
Andreas Kohlbecker [Mon, 12 Sep 2016 12:36:47 +0000 (14:36 +0200)]
ref #6026 fixing rank
Andreas Kohlbecker [Mon, 12 Sep 2016 10:36:27 +0000 (12:36 +0200)]
ref #6026 fixing bug in publication regex pattern
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
Andreas Kohlbecker [Mon, 12 Sep 2016 09:33:11 +0000 (11:33 +0200)]
ref #6026 keepgin deteced ref type in case of 'Vorabdruck'
Andreas Kohlbecker [Fri, 9 Sep 2016 14:57:05 +0000 (16:57 +0200)]
ref #6026 NameTypes (with minor problems)
Andreas Kohlbecker [Fri, 9 Sep 2016 10:21:44 +0000 (12:21 +0200)]
ref #6026 FieldUnit locality working
Andreas Kohlbecker [Fri, 9 Sep 2016 09:51:22 +0000 (11:51 +0200)]
removing unused repo from the pom.xml (was used for yourkit)
Andreas Kohlbecker [Fri, 9 Sep 2016 07:20:42 +0000 (09:20 +0200)]
minor
Katja Luther [Fri, 2 Sep 2016 09:54:48 +0000 (11:54 +0200)]
fix #5893: fauna europaea reference import with more atomized data
Patrick Plitzner [Thu, 1 Sep 2016 14:59:46 +0000 (16:59 +0200)]
#5448 Imporve name check for multiple ex authors
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
Patrick Plitzner [Thu, 1 Sep 2016 11:27:40 +0000 (13:27 +0200)]
#5448 Change abbrev label of unranked infraspecfic rank before importing
Patrick Plitzner [Wed, 31 Aug 2016 10:27:39 +0000 (12:27 +0200)]
ref #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
Katja Luther [Mon, 22 Aug 2016 11:21:36 +0000 (11:21 +0000)]
adaption to specimen import changes
Patrick Plitzner [Wed, 3 Aug 2016 13:18:28 +0000 (15:18 +0200)]
#5448 Fix import of hybrid formula
Patrick Plitzner [Wed, 3 Aug 2016 12:20:31 +0000 (14:20 +0200)]
ref #5448 code cleanup
Patrick Plitzner [Wed, 3 Aug 2016 09:58:39 +0000 (11:58 +0200)]
#5448 Refactor hybrid name import/check
Patrick Plitzner [Wed, 3 Aug 2016 08:38:34 +0000 (10:38 +0200)]
#5448 Use SEQNUM as id column
- enhance hybrid name check
Patrick Plitzner [Tue, 2 Aug 2016 09:45:14 +0000 (11:45 +0200)]
#5448 Import genus hybrid formulas
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
Patrick Plitzner [Mon, 1 Aug 2016 10:21:41 +0000 (12:21 +0200)]
#5448 Handle rank "SPI"
Patrick Plitzner [Mon, 1 Aug 2016 10:16:36 +0000 (12:16 +0200)]
#5448 Import non-CDM ranks
Patrick Plitzner [Thu, 28 Jul 2016 09:12:26 +0000 (11:12 +0200)]
#5448 Remove non-exisiting hybrid category
Patrick Plitzner [Wed, 27 Jul 2016 13:34:19 +0000 (15:34 +0200)]
#5448 Import HYB 'nf'
Patrick Plitzner [Wed, 27 Jul 2016 13:34:03 +0000 (15:34 +0200)]
#5448 Import rank "SAM"
Andreas Müller [Thu, 28 Jul 2016 10:55:04 +0000 (12:55 +0200)]
#6000 Use new CASUAL Method instead of deprecated INTRODUCED_ADVENTITIOUS
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
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
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
Patrick Plitzner [Tue, 26 Jul 2016 09:09:41 +0000 (11:09 +0200)]
#5448 Add family rank
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
Andreas Kohlbecker [Fri, 9 Sep 2016 06:59:11 +0000 (08:59 +0200)]
ref #6026 handling 'Vorabdrucke' as Book Volume/Issue
Andreas Kohlbecker [Fri, 9 Sep 2016 05:36:31 +0000 (07:36 +0200)]
ref #6026 support for making statistics on parsed type data - typo
Andreas Kohlbecker [Thu, 8 Sep 2016 13:40:38 +0000 (15:40 +0200)]
ref #6026 importing Basionyms
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)
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