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
Andreas Müller [Mon, 20 Jun 2016 15:18:22 +0000 (17:18 +0200)]
Add id_1 mapping to mexico
Patrick Plitzner [Tue, 21 Jun 2016 11:59:21 +0000 (13:59 +0200)]
Update cdmlib version
Patrick Plitzner [Mon, 20 Jun 2016 15:02:22 +0000 (17:02 +0200)]
Fix ClassCastException, improve taxon name check, fix rank evaluation
#5448
Andreas Müller [Mon, 20 Jun 2016 15:06:18 +0000 (17:06 +0200)]
Update to mexico import #5822 / #5892
Patrick Plitzner [Mon, 20 Jun 2016 06:44:14 +0000 (08:44 +0200)]
Import synonyms of other classifications #5448
Patrick Plitzner [Wed, 15 Jun 2016 16:50:30 +0000 (18:50 +0200)]
Set sec reference for all taxa #5448
Andreas Müller [Fri, 17 Jun 2016 21:46:23 +0000 (23:46 +0200)]
minor
Andreas Müller [Fri, 17 Jun 2016 21:43:48 +0000 (23:43 +0200)]
First version of Mexico import #5822
Katja Luther [Fri, 17 Jun 2016 13:07:29 +0000 (15:07 +0200)]
improve fauna europaea author import
Patrick Plitzner [Thu, 2 Jun 2016 12:19:38 +0000 (14:19 +0200)]
Update version number and add itextpdf due to version depency conflict
Patrick Plitzner [Thu, 2 Jun 2016 12:09:33 +0000 (14:09 +0200)]
Improve name check for unranked taxa #5448
Patrick Plitzner [Thu, 2 Jun 2016 07:28:29 +0000 (09:28 +0200)]
Import unranked taxa #5448
Patrick Plitzner [Thu, 2 Jun 2016 07:06:17 +0000 (09:06 +0200)]
Refactoring/code clean-up #5448
Patrick Plitzner [Thu, 2 Jun 2016 06:53:57 +0000 (08:53 +0200)]
Import common name #5448
Patrick Plitzner [Thu, 2 Jun 2016 06:44:17 +0000 (08:44 +0200)]
Import additional hybrid variants #5448
Patrick Plitzner [Tue, 31 May 2016 09:41:24 +0000 (11:41 +0200)]
Set source ref for taxa #5448
Patrick Plitzner [Wed, 25 May 2016 09:23:19 +0000 (11:23 +0200)]
Improve taxon name check #5448
Andreas Müller [Wed, 25 May 2016 10:24:52 +0000 (12:24 +0200)]
Remove generics from Reference in cdmlib-app #5830
Patrick Plitzner [Wed, 25 May 2016 08:25:06 +0000 (10:25 +0200)]
Improve logging messages #5448
Patrick Plitzner [Wed, 25 May 2016 08:24:35 +0000 (10:24 +0200)]
Add SEQNUM #5448
Patrick Plitzner [Wed, 25 May 2016 08:24:21 +0000 (10:24 +0200)]
Import hybrid formulas #5448
Patrick Plitzner [Tue, 24 May 2016 14:44:52 +0000 (16:44 +0200)]
Add taxa to classifications #5448
Patrick Plitzner [Tue, 24 May 2016 08:28:47 +0000 (10:28 +0200)]
Correctly set relationship direction #5448
Patrick Plitzner [Tue, 24 May 2016 08:28:11 +0000 (10:28 +0200)]
Import concept relations E, W, K, AW, AO, R, O, S #5448
Patrick Plitzner [Mon, 23 May 2016 17:41:49 +0000 (19:41 +0200)]
Refactor names and taxa creation #5448
Patrick Plitzner [Mon, 23 May 2016 17:17:34 +0000 (19:17 +0200)]
Add 8 more classifications #5448
Patrick Plitzner [Mon, 23 May 2016 15:53:47 +0000 (17:53 +0200)]
improve taxon name check #5448
- add new string constants
Patrick Plitzner [Mon, 23 May 2016 14:31:01 +0000 (16:31 +0200)]
Set trinomial hybrids #5448
- improve taxon name check
Patrick Plitzner [Mon, 23 May 2016 13:47:44 +0000 (15:47 +0200)]
Avoid duplicate UUIDs by fixing the order of adding original sources
#5448
Patrick Plitzner [Sun, 22 May 2016 08:24:34 +0000 (10:24 +0200)]
Handle hybrid names (only binomial at the moment)
Patrick Plitzner [Sun, 22 May 2016 08:23:47 +0000 (10:23 +0200)]
Fix typo
Patrick Plitzner [Wed, 18 May 2016 13:13:28 +0000 (15:13 +0200)]
Fix ClassCastException and ordering #5452
Patrick Plitzner [Wed, 18 May 2016 12:56:56 +0000 (14:56 +0200)]
Refactor constants
Patrick Plitzner [Wed, 18 May 2016 07:31:08 +0000 (09:31 +0200)]
Ordering of XML elements and some refactoring #5452
Patrick Plitzner [Wed, 11 May 2016 12:09:29 +0000 (14:09 +0200)]
Export concept realtion type #5452