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cdmlib / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / specimen / abcd206 @ 4d622b5d

# Date Author Comment
4d622b5d 10/06/2016 05:01 PM Katja Luther

getUuidAndTitleCache of classificationservice does not need the excluded taxa

531fc7bc 05/25/2016 12:11 PM Andreas Müller

Remove generics from Reference in cdmlib (except for cdmlib-model) #5830

0ecfd682 04/28/2016 03:47 PM Andreas Müller

Remove bidirectionality for supplemental data #5743

0db79acb 03/30/2016 11:17 AM Katja Luther

add query to ABCDImportConfigurator

81e42009 02/22/2016 01:58 PM Patrick Plitzner

Fix potential NPE

3e01d1be 11/30/2015 02:48 PM Patrick Plitzner

Show complete stacktrace in import report

b00a67e8 11/30/2015 02:25 PM Patrick Plitzner

Fix counting of specimens created in ABCD import report

44ffca34 11/30/2015 10:23 AM Patrick Plitzner

Parse spatial data for gathering event in ABCD import #5169

bd70ceb2 11/25/2015 11:18 AM Patrick Plitzner

Set Unit/Notes and Gathering/Notes in ABCD import #5168

f16eafb5 11/25/2015 07:44 AM Patrick Plitzner

Import missing parameters for ggbn ABCD import
- some refactoring

eee9b39a 11/16/2015 03:05 PM Patrick Plitzner

Refactored import return type from boolean to ImportResult

1ae59e40 11/16/2015 03:05 PM Patrick Plitzner

Move import report to import state super class

1c7b9181 10/28/2015 03:21 PM Cherian Mathew

#5297 Add cancel and waitForFeedback functionality

Correct work units

3087df1b 10/27/2015 04:24 PM Cherian Mathew

#5297 Refactor ProgressMonitorController, Add Remoting Progress monitor

#5297 Add progress monitor service, Add test services

#5297 Add monit import method

#5297 Update no. of work units

#5297 Add new thread class for remoting monitors

#5297 Add owner field to monitor thread and user checks in service...

eb142a9d 10/26/2015 02:24 PM Patrick Plitzner

Fix NPE in ABCD import collection matching

  • also added for-loop break
216aa231 10/26/2015 02:24 PM Patrick Plitzner

Add stack trace to import report

73bc3754 09/02/2015 11:08 AM Patrick Plitzner

Enhance ABCD import report

94fe584f 09/01/2015 08:24 AM Patrick Plitzner

Refine rank parsing

  • if rank cannot be parsed the taxon will be created as is with a single taxon node without any parent taxon node but the classification itself
  • some code refactoring
  • avoid NPEs
93276717 08/19/2015 08:44 AM Patrick Plitzner

Enhance ignored import due to already existing specimens

8f443c62 08/06/2015 03:57 PM Cherian Mathew

#5130 Extend cdmlib import architecture to allow for remoting and Add import methods to IOService

5aba9cda 07/21/2015 11:26 AM Patrick Plitzner

Add support for ABCD 2.0.6 in UnitAssociationParser

822ae6e6 07/20/2015 05:14 PM Patrick Plitzner

WARNING: head commit changed in the meantime

Log ignored specimens in import report

cc83c990 07/15/2015 09:06 AM Patrick Plitzner

Add two new test files

02668d2d 07/15/2015 09:02 AM Patrick Plitzner

Enhance name parsing
- more logging
- fixed rank assignment

7352c7ff 07/15/2015 07:52 AM Patrick Plitzner

Error logging for name parsing

  • advanced readability
92fac617 07/15/2015 07:49 AM Patrick Plitzner

Enhance name parsing

  • added more error logging
  • avoid creating duplicate taxon names due to parsing problems
ffed529c 07/15/2015 07:48 AM Patrick Plitzner

Remove parseNameAutomatically flag

64b06209 07/14/2015 01:03 PM Patrick Plitzner

Refactor ABCD import

  • use association wrapper to store prefix
  • correctly push and pop import state
  • only delete field unit if it has no other links to objects
3e62e4f0 07/14/2015 09:28 AM Patrick Plitzner

Refactor ABCD import

  • removed "determination on field unit level" flag
  • parse unit associations recursively
  • removed field unit from import state
  • enhanced unit association handling concerning field units and ereivation events
e128b27b 07/13/2015 02:46 PM Patrick Plitzner

Fix taxon existance check

ab3b8d60 07/13/2015 07:03 AM Patrick Plitzner

Add import report logging to utility methods

9f054d7a 07/08/2015 02:44 PM Patrick Plitzner

Catch exception instead of throwing them

Lets the methods return

a74084cb 07/08/2015 02:24 PM Patrick Plitzner

Error loggind during import

19b24dc9 07/08/2015 09:40 AM Patrick Plitzner

Add exception during import to report

33262f8c 07/08/2015 07:34 AM Patrick Plitzner

Fix classification handling for new and exisiting taxa

50103603 07/07/2015 05:19 PM Patrick Plitzner

Exception handling

  • moved report printing to finally clause to always have a report.
  • fixed possible NPE
1d413cc8 07/07/2015 03:37 PM Patrick Plitzner

Handle default classification in state object

07692ea3 07/07/2015 09:18 AM Patrick Plitzner

Fix classification handling in ABCD import

d823746c 07/06/2015 03:49 PM Patrick Plitzner

Log exceptions during import in the report file

1b4d595b 07/02/2015 09:47 AM Patrick Plitzner

Reset prefix after importing associated units

46713e68 07/02/2015 09:46 AM Patrick Plitzner

Do not close system.out

eeb06b41 07/01/2015 10:55 AM Patrick Plitzner

Soften association type matching.

8d1e4195 07/01/2015 10:55 AM Patrick Plitzner

Map preparation material to derivation event description

2d73d2e2 07/01/2015 10:55 AM Patrick Plitzner

Fix potential NPE

bdc49784 06/30/2015 03:17 PM Patrick Plitzner

Fix potential NPE

18c0b932 06/30/2015 01:21 PM Patrick Plitzner

Evaluate unit association type in ABCD import

  • added test
  • correctly set derivative hierarchy
e0084606 06/30/2015 09:49 AM Patrick Plitzner

Check if primer or amplification already exist

adab4473 06/30/2015 09:49 AM Patrick Plitzner

Evaluate UnitAssociationType during import

Current rule for the relation between the imported unit and its
associated units:
- "same population" => sibling relation
- "same individual" => parent-child

cc19179c 06/30/2015 09:49 AM Patrick Plitzner

Fix potential NPE

e8255db1 06/30/2015 09:49 AM Patrick Plitzner

Parse sample designation in ABCD GGBN import

7920002e 06/30/2015 09:49 AM Patrick Plitzner

Move up name parsing

ed743b53 06/30/2015 09:49 AM Patrick Plitzner

Import associated units

  • Set derivation event correctly
  • adapted test
7b3adf28 06/30/2015 09:49 AM Patrick Plitzner

Import associated units via BioCase query

87460b5e 06/30/2015 09:49 AM Patrick Plitzner

Move prefix parsing to utility method and import state

c95e3daf 06/30/2015 09:49 AM Patrick Plitzner

Move unit parsing to utility class

2574e41b 06/30/2015 09:49 AM Patrick Plitzner

Import associated units in ABCD import

Worked on the order of importing units especially when associated units
are present.
Adapted test.

891ced88 06/30/2015 09:49 AM Patrick Plitzner

??

47f461b2 06/30/2015 09:49 AM Patrick Plitzner

Adapt to method parameter change

631a9c22 06/30/2015 09:49 AM Patrick Plitzner

Import associated units in ABCD import

First changes

64260466 06/30/2015 09:49 AM Patrick Plitzner

Refactor ABCD import

Moved class variables to import state

3f1d496b 06/30/2015 09:49 AM Patrick Plitzner
  • fixed date parsing
    • fixed primer saving
    • added new parameters to test
0fff86a8 06/30/2015 09:49 AM Patrick Plitzner
  • added preservation/preparation parameters
    • fixed parsing of unitID
25cbf231 06/30/2015 09:49 AM Patrick Plitzner
  • correctly connected primer, amplification, single reads and sequences
    • parsed UnitAssociation to correctly set specimen data
    • added UnitAssociationParser
2bc696d1 06/30/2015 09:49 AM Patrick Plitzner
  • refactored dna parsing
    • added utility classes and person parser
    • adapted test
    • added parsing of more molecular parameters
ce7c7aa3 06/23/2015 05:56 PM Andreas Müller

Rename NonViralName.xxxAuthorTeam to xxxAuthorship #4968

beba0b4b 06/15/2015 09:05 AM Patrick Plitzner
  • text formatting
45b5cb33 06/15/2015 09:04 AM Patrick Plitzner
  • re-enabled dna quality parsing
db49def5 06/09/2015 09:40 AM Patrick Plitzner
  • added more ggbn ABCD parameters to import and test
f407988d 06/08/2015 10:28 AM Patrick Plitzner
  • added more parameters to GGBN parser and test
d26d6619 05/26/2015 01:40 PM Andreas Müller

moving UuidAndTitleCache from model to persistence. #4799

207d5d50 05/20/2015 02:03 PM Patrick Plitzner
  • implemented importing of DNA ABCD units
    • DNA sampled will be attached to already existing specimens
    • re-enabled tests
0200c616 05/18/2015 04:35 PM Patrick Plitzner
  • added null check
06ca4e16 05/18/2015 04:09 PM Patrick Plitzner
  • improved name matching for NamedAreas (continents) in ABCD import (#4910)
    • added null check
    • fixed ggbn extension check
742aad84 05/12/2015 10:47 AM Patrick Plitzner
  • added config option to ignore already existing specimens during import
    • for ggbn import already existing specimens are searched and attached if associated to the dna unit
    • refactored AbcdReport to also display the unitId
ccd80f9f 03/18/2015 09:35 AM Patrick Plitzner
  • added option to cancel import
75efb034 03/17/2015 06:07 PM Patrick Plitzner
  • avoid duplicate taxon nodes in default classification
888abfcf 03/17/2015 02:26 PM Patrick Plitzner
  • refactored code
ae058fd5 03/17/2015 02:19 PM Patrick Plitzner
  • enhanced progress monitor
e2e537ff 03/17/2015 02:07 PM Patrick Plitzner
  • enhanced progress monitor
    • fixed multiple default classification creation
4fb0c1bd 03/17/2015 01:36 PM Patrick Plitzner
  • fixed potential NPE
22926545 03/17/2015 12:46 PM Patrick Plitzner
  • fixed taxon node matching for default classification
5e0e1b40 03/17/2015 11:03 AM Patrick Plitzner
  • fixed potential NPE
71662a8c 03/16/2015 09:10 PM Patrick Plitzner
  • fixed potential NPE when adding taxon nodes for infra species
a8931728 03/16/2015 04:49 PM Patrick Plitzner
  • some code speed up
    • better default classification handling
96a6c6d2 03/16/2015 03:26 PM Patrick Plitzner
  • fixed adding to default classification
cab1ae9e 03/16/2015 02:50 PM Patrick Plitzner
  • implemented new config option "Move new taxa to default classification"
8d425e15 03/16/2015 02:18 PM Patrick Plitzner
  • added new config option "Move new taxa to default classification"
    • do not add associations for identifications with preferredFlag=false
18f98b68 03/16/2015 10:10 AM Patrick Plitzner
  • enhanced report
89b754ae 03/16/2015 09:58 AM Patrick Plitzner
  • enhanced ggbn parsing
    • enhanced report
93186c1a 03/12/2015 07:20 PM Patrick Plitzner
  • fixed rank parsing
    • added deprecate annotation to config option
f5e6b489 03/12/2015 04:07 PM Patrick Plitzner
  • temp changes for name matching
f2137d95 03/11/2015 04:17 PM Patrick Plitzner
  • some name matching enhancements
ef183cff 03/11/2015 10:50 AM Patrick Plitzner
  • added info messages to report
    • enhanced taxon name matching
c96e9783 03/05/2015 02:05 PM Patrick Plitzner
  • fixed name matching when ignoring authorship
609a2f23 03/04/2015 05:06 PM Patrick Plitzner
  • fixed getTaxonForName()
927fd98d 03/04/2015 04:35 PM Patrick Plitzner
  • added removeCountryFromLocalityText option to configurator (basically implementing the hack #4677)
27205004 03/04/2015 02:51 PM Patrick Plitzner
  • shortened regex
341a29eb 03/04/2015 02:34 PM Patrick Plitzner
  • fixed temporary geolocation hack
2396aeef 03/04/2015 12:30 PM Patrick Plitzner
  • fixed name matching when ignoring author
9fc0c8e4 03/04/2015 11:36 AM Patrick Plitzner
  • re-added temporary hack
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