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 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
Andreas Kohlbecker [Wed, 7 Sep 2016 12:56:08 +0000 (14:56 +0200)]
ref #6026 two more date parsing rules
Andreas Kohlbecker [Wed, 7 Sep 2016 10:20:24 +0000 (12:20 +0200)]
ref #6026 type parsing
- parsing of specimen types
Andreas Kohlbecker [Tue, 6 Sep 2016 10:11:58 +0000 (12:11 +0200)]
ref #6026 publication date parsing completed
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)
Andreas Kohlbecker [Tue, 30 Aug 2016 22:25:47 +0000 (00:25 +0200)]
ref #6009 improved plublication date parsing
Andreas Kohlbecker [Tue, 30 Aug 2016 12:07:46 +0000 (14:07 +0200)]
ref #6035 more character replacement rules
Andreas Kohlbecker [Tue, 30 Aug 2016 11:26:35 +0000 (13:26 +0200)]
fix #6035 character replacement rules
Andreas Kohlbecker [Tue, 30 Aug 2016 10:46:02 +0000 (12:46 +0200)]
removing unused code
Andreas Kohlbecker [Tue, 30 Aug 2016 09:46:45 +0000 (11:46 +0200)]
Alternative data files
Andreas Kohlbecker [Thu, 4 Aug 2016 20:16:08 +0000 (22:16 +0200)]
ref #6026 first basic import of types
Andreas Kohlbecker [Wed, 3 Aug 2016 14:09:24 +0000 (16:09 +0200)]
ref #6026 multiple improvements
- better ranks for incertis sedis and old Classes
- Caveats as annotations
Andreas Kohlbecker [Wed, 3 Aug 2016 05:52:38 +0000 (07:52 +0200)]
ref #6026 multiple improvements
- importing notes as annotations
- improved rank guessing
- solving performance problems related to classification root node
- better tilecache and nameCache plausibility checks
Andreas Kohlbecker [Tue, 2 Aug 2016 08:21:59 +0000 (10:21 +0200)]
ref #6026 multiple improvements
- better handling of fossil taxa
- Authors spelling as misspellings
- fix related to publication year
- "Author abbreviation not checked" as annotations
Andreas Kohlbecker [Mon, 1 Aug 2016 13:18:27 +0000 (15:18 +0200)]
#6026 import of taxa and names working
Andreas Kohlbecker [Wed, 27 Jul 2016 15:27:45 +0000 (17:27 +0200)]
Fixing strange dependency problem related to spring-orm version
Andreas Kohlbecker [Wed, 27 Jul 2016 08:49:30 +0000 (10:49 +0200)]
Initial set of classes for the IAPT import
Andreas Kohlbecker [Tue, 26 Jul 2016 15:13:16 +0000 (17:13 +0200)]
removing build.xml
Andreas Kohlbecker [Tue, 26 Jul 2016 15:12:44 +0000 (17:12 +0200)]
gitignore
Andreas Kohlbecker [Tue, 26 Jul 2016 15:09:05 +0000 (17:09 +0200)]
Fixing repository settings and project group id
Patrick Plitzner [Tue, 26 Jul 2016 06:22:52 +0000 (08:22 +0200)]
#5448 Pass rank and nomenclatural code to name parser creation
Patrick Plitzner [Tue, 26 Jul 2016 06:11:43 +0000 (08:11 +0200)]
#5448 Import hybrid with more than 2 parents with protected titlecache
Patrick Plitzner [Tue, 26 Jul 2016 06:07:05 +0000 (08:07 +0200)]
#5448 Add missing ranks to transformer
Patrick Plitzner [Mon, 25 Jul 2016 14:42:57 +0000 (16:42 +0200)]
#5448 Enhance taxon name check
Patrick Plitzner [Mon, 25 Jul 2016 14:42:38 +0000 (16:42 +0200)]
#5448 Fix import of families
Patrick Plitzner [Mon, 18 Jul 2016 15:05:21 +0000 (17:05 +0200)]
#5448 change DB table name
Patrick Plitzner [Mon, 18 Jul 2016 15:05:06 +0000 (17:05 +0200)]
#5448 Fix import of hybrids due to merge conflicts
Patrick Plitzner [Mon, 18 Jul 2016 15:04:28 +0000 (17:04 +0200)]
#5448 Fix potential NPEs
Patrick Plitzner [Mon, 18 Jul 2016 08:40:22 +0000 (10:40 +0200)]
#5448 Fix title cache and LIE issues
Patrick Plitzner [Mon, 18 Jul 2016 08:40:00 +0000 (10:40 +0200)]
#5448 Import cultivar as CultivarPlantName
Patrick Plitzner [Mon, 18 Jul 2016 08:39:18 +0000 (10:39 +0200)]
#5448 Add taxa to their respective families
Patrick Plitzner [Fri, 15 Jul 2016 11:26:57 +0000 (13:26 +0200)]
#5448 Import families
Patrick Plitzner [Fri, 15 Jul 2016 11:17:54 +0000 (13:17 +0200)]
#5448 javadoc
Patrick Plitzner [Fri, 15 Jul 2016 09:52:18 +0000 (11:52 +0200)]
#5448 Fix possible NPE
Patrick Plitzner [Fri, 15 Jul 2016 09:52:05 +0000 (11:52 +0200)]
#5448 Avoid clonig of all taxa for all classifications
Patrick Plitzner [Thu, 14 Jul 2016 13:21:08 +0000 (15:21 +0200)]
#5448 Save concept relations
Patrick Plitzner [Thu, 14 Jul 2016 13:09:24 +0000 (15:09 +0200)]
#5448 typo
Patrick Plitzner [Thu, 14 Jul 2016 12:50:58 +0000 (14:50 +0200)]
#5448 Set species epithet for species groups and aggregates
Patrick Plitzner [Thu, 14 Jul 2016 11:28:14 +0000 (13:28 +0200)]
#5448 Move import of concept relationships to classification import
class
- there we already have the accepted taxa for the synonyms
Patrick Plitzner [Mon, 18 Jul 2016 06:55:21 +0000 (08:55 +0200)]
#5448 Import annotation infos
- hybrid formula
- ehrd, atlas, kart, flor, rl2015, wissk
Patrick Plitzner [Thu, 14 Jul 2016 06:59:19 +0000 (08:59 +0200)]
#5448 Set meaningful reference names
Patrick Plitzner [Thu, 14 Jul 2016 06:42:25 +0000 (08:42 +0200)]
Small additions to import
- import nomenclatural status extra information to ruleConsidered
- refresh title cache of taxa to correctly display sec ref
- advanced title cache consistency check
- import common name with german language
Andreas Müller [Thu, 7 Jul 2016 11:03:49 +0000 (13:03 +0200)]
Adapt cdmlib-app poms to new version
Andreas Müller [Wed, 6 Jul 2016 11:34:04 +0000 (13:34 +0200)]
#5958 fix findByName in pesi
Andreas Müller [Wed, 6 Jul 2016 11:19:12 +0000 (13:19 +0200)]
#5958 fix findByName in pesi
Andreas Müller [Tue, 5 Jul 2016 23:18:36 +0000 (01:18 +0200)]
#5822 / #5892 Mexico rubiaceae import
Andreas Müller [Tue, 5 Jul 2016 23:16:24 +0000 (01:16 +0200)]
Update eflora and pesi to v4.2.0
Andreas Müller [Wed, 29 Jun 2016 11:54:31 +0000 (13:54 +0200)]
#5791 Adapt type of E+M vocabulary.
Patrick Plitzner [Tue, 21 Jun 2016 15:50:19 +0000 (17:50 +0200)]
Add missing nomenclatural status and taxon relations to transformer
#5448
Patrick Plitzner [Tue, 21 Jun 2016 15:49:35 +0000 (17:49 +0200)]
Add missing taxa to related objects #5448
Andreas Müller [Tue, 21 Jun 2016 12:56:14 +0000 (14:56 +0200)]
Cleanup poms in cdmlib-app