b.stoever [Fri, 13 Jan 2017 14:11:20 +0000 (15:11 +0100)]
Alternative versions for build.properties added. Current state set to "dependencies from JARs". (Can be merged to trunk in this state.)
b.stoever [Fri, 13 Jan 2017 12:33:36 +0000 (13:33 +0100)]
pom.xml and MANIFEST.MF updated in molecular.lib.
b.stoever [Fri, 13 Jan 2017 11:08:26 +0000 (12:08 +0100)]
Adjustments to project structure changes in JPhyloIO.
b.stoever [Sat, 19 Nov 2016 12:29:13 +0000 (13:29 +0100)]
Additional strings externalized in molecular plugin.
Wizard for exporting single read alignments now warns and prompts if files are overwritten.
Bug fix: Changes in the format selection in the wizard now trigger validation again.
ExportSingleReadAlignmentWizardModel uses format list instead of map again.
b.stoever [Fri, 18 Nov 2016 16:01:41 +0000 (17:01 +0100)]
Messages edited.
Support for parameters to export only single reads or only consensus implemented.
JavaDoc extended.
b.stoever [Fri, 18 Nov 2016 14:45:02 +0000 (15:45 +0100)]
Missing files from last commit added.
b.stoever [Fri, 18 Nov 2016 14:43:45 +0000 (15:43 +0100)]
Export single read alignment wizard separated into two pages.
Option to elongate sequences added.
Application information parameters of JPhyloIO set.
b.stoever [Thu, 17 Nov 2016 18:17:38 +0000 (19:17 +0100)]
Exported single read sequences are now filled up with gaps. (Will be dependent on a parameter in the future.)
Texts in ExportSequenceToFileHandler extzernalized and translated.
b.stoever [Thu, 17 Nov 2016 16:22:59 +0000 (17:22 +0100)]
Strings in ExportSingleReadAlignmentWizardPage externalized and translated.
Ben Stöver [Thu, 17 Nov 2016 12:40:59 +0000 (13:40 +0100)]
Fixes in ExportSingleReadAlignmentWizardPage layout.
Default values added to ExportSingleReadAlignmentWizardModel.
Updating values after model binding in ExportSingleReadAlignmentWizardPage implemented.
b.stoever [Wed, 16 Nov 2016 22:18:26 +0000 (23:18 +0100)]
Export single read alignment wizard validation refactored and extended.
Some German translations in molecular plug-in added.
b.stoever [Wed, 16 Nov 2016 20:25:30 +0000 (21:25 +0100)]
Intermediate commit in implementing wizard validation (before moving to MultiValidator).
Plug-in dependencies added to molecular.
b.stoever [Tue, 15 Nov 2016 16:09:30 +0000 (17:09 +0100)]
ExportSingleReadAlignmentWizard now exposes whole format info object.
FileDialog added to ExportSingleReadAlignmentWizardPage.
b.stoever [Mon, 14 Nov 2016 18:34:40 +0000 (19:34 +0100)]
Missing dependency Apache commons.lang added to molecular.lib.
Single read alignment export feature now makes use of wizard. (Selecting which sequences to export is not yet supported.)
b.stoever [Mon, 14 Nov 2016 16:34:28 +0000 (17:34 +0100)]
New JPhyloIO package now exported by molecular.lib.
SingleReadAlignmentPredicates renamed to SingleReadAlignmentRDFXMLConstants.
Pherogram alignment shifts are now written to single read export unsing a custom ObjectTranslator implementation.
Ben Stöver [Sun, 13 Nov 2016 17:24:38 +0000 (18:24 +0100)]
ExportSingleReadAlignmentWizardPage now allows to select output file and
format.
b.stoever [Thu, 27 Oct 2016 17:31:58 +0000 (19:31 +0200)]
CDMSequenceMatrixAdapter now exports sequence metadata.
b.stoever [Thu, 27 Oct 2016 13:55:07 +0000 (15:55 +0200)]
Bug fix: CDMSequenceMatrixAdapter now does not create CharacterSetIntervalEvents if the alignment has no columns.
b.stoever [Wed, 26 Oct 2016 15:31:46 +0000 (17:31 +0200)]
Merge branch 'LibrAlign' of ssh://dev.e-taxonomy.eu/var/git/taxeditor into LibrAlign
b.stoever [Wed, 26 Oct 2016 15:31:21 +0000 (17:31 +0200)]
Merge branch 'LibrAlign' of https://dev.e-taxonomy.eu/git/taxeditor into LibrAlign
# Conflicts:
# eu.etaxonomy.taxeditor.molecular.lib/.classpath
# eu.etaxonomy.taxeditor/rcp.target
Patrick Plitzner [Wed, 26 Oct 2016 08:05:03 +0000 (10:05 +0200)]
Merge branch 'develop' into LibrAlign
Patrick Plitzner [Wed, 26 Oct 2016 08:04:40 +0000 (10:04 +0200)]
Add spring oauth2 dependency
Katja Luther [Tue, 25 Oct 2016 08:42:54 +0000 (10:42 +0200)]
ref #6163: in occurence bulk editor it is possible to add media
Katja Luther [Mon, 24 Oct 2016 12:09:08 +0000 (14:09 +0200)]
ref #5972: the wizard warns the user if the reference is used ssomewhere else
Patrick Plitzner [Mon, 24 Oct 2016 11:47:41 +0000 (13:47 +0200)]
fix #3573 Add non-generic configurator page to ABCD import wizard
Patrick Plitzner [Mon, 24 Oct 2016 11:36:34 +0000 (13:36 +0200)]
#ref #5496 Do not show any terms for preservation method and stage
preferences
Katja Luther [Mon, 24 Oct 2016 11:04:42 +0000 (13:04 +0200)]
ref #6159: minor
Katja Luther [Mon, 24 Oct 2016 09:17:00 +0000 (11:17 +0200)]
ref #6159: fix that some column show no data
Patrick Plitzner [Mon, 24 Oct 2016 10:35:39 +0000 (12:35 +0200)]
Fix potential NPE
Patrick Plitzner [Mon, 24 Oct 2016 07:20:39 +0000 (09:20 +0200)]
Merge branch 'develop' into LibrAlign
# Conflicts:
# eu.etaxonomy.taxeditor.molecular.lib/.classpath
b.stoever [Sat, 22 Oct 2016 12:36:59 +0000 (14:36 +0200)]
Plugin molecular.lib refactored to use direct project dependencies. This should not be merged into trunk, since this is only for development state. (Currently the trunk is anyway already using different Maven dependencies.)
Adjustments to recent changes in JPhyloIO.
Patrick Plitzner [Thu, 20 Oct 2016 15:09:19 +0000 (17:09 +0200)]
ref #6058 store named area filters more individually
Patrick Plitzner [Thu, 20 Oct 2016 13:20:31 +0000 (15:20 +0200)]
Removed p6spy from classpath
Katja Luther [Thu, 20 Oct 2016 13:00:32 +0000 (15:00 +0200)]
minor changes for name details view configuration
Katja Luther [Thu, 20 Oct 2016 12:26:18 +0000 (14:26 +0200)]
add the nameDetails configuration
Katja Luther [Thu, 20 Oct 2016 12:13:31 +0000 (14:13 +0200)]
minor
Katja Luther [Thu, 20 Oct 2016 11:55:27 +0000 (13:55 +0200)]
fix #6050: add the possibility to configure which fields should be displayed in name details view
Katja Luther [Thu, 20 Oct 2016 10:56:11 +0000 (12:56 +0200)]
fix test
Katja Luther [Tue, 18 Oct 2016 09:13:47 +0000 (11:13 +0200)]
ref #6050: test git/redmine and add the pref keys for configurable details view
Katja Luther [Mon, 17 Oct 2016 11:15:46 +0000 (13:15 +0200)]
fix #6129: remove additional authorstring in selection dialog search field
Katja Luther [Mon, 17 Oct 2016 08:12:44 +0000 (10:12 +0200)]
fix #5891: save null instead of empty string for text fields
Katja Luther [Fri, 14 Oct 2016 10:05:22 +0000 (12:05 +0200)]
smaller changes for specimen import and others
Katja Luther [Fri, 14 Oct 2016 09:53:19 +0000 (11:53 +0200)]
minor changes in excel import wizard
Katja Luther [Fri, 14 Oct 2016 09:44:27 +0000 (11:44 +0200)]
minor
Katja Luther [Fri, 14 Oct 2016 09:39:44 +0000 (11:39 +0200)]
delete transient services
Katja Luther [Thu, 13 Oct 2016 12:46:39 +0000 (14:46 +0200)]
minor
Katja Luther [Thu, 13 Oct 2016 12:28:56 +0000 (14:28 +0200)]
remove experimental code
Katja Luther [Thu, 13 Oct 2016 11:15:53 +0000 (13:15 +0200)]
minor
Katja Luther [Thu, 13 Oct 2016 11:14:26 +0000 (13:14 +0200)]
fix #5692: adapt delete algorithm to annotatedLineEditor mechanisms
Andreas Kohlbecker [Wed, 12 Oct 2016 13:11:43 +0000 (15:11 +0200)]
removing p6spy dependencies
Andreas Müller [Wed, 12 Oct 2016 11:35:30 +0000 (13:35 +0200)]
minor
Andreas Kohlbecker [Tue, 11 Oct 2016 16:32:42 +0000 (18:32 +0200)]
removing generated file
Andreas Kohlbecker [Tue, 11 Oct 2016 16:29:48 +0000 (18:29 +0200)]
Revert "ref #6118 catching exception during checkConnection"
This reverts commit
bb7b4f601b49f1ba29f149405246f120b4c46a9a.
Andreas Kohlbecker [Tue, 11 Oct 2016 16:13:29 +0000 (18:13 +0200)]
ref #6124 fixing Bundle-Version
Andreas Kohlbecker [Tue, 11 Oct 2016 14:46:16 +0000 (16:46 +0200)]
OOPS!
Andreas Kohlbecker [Tue, 11 Oct 2016 14:44:35 +0000 (16:44 +0200)]
fixing project version in pom.xml which was not updated after the relase
Andreas Kohlbecker [Tue, 11 Oct 2016 14:18:55 +0000 (16:18 +0200)]
ref #6118 catching exception during checkConnection
Katja Luther [Fri, 7 Oct 2016 13:03:37 +0000 (15:03 +0200)]
fix #5888: add the element as argument to postExecute method s
Andreas Müller [Thu, 6 Oct 2016 14:44:40 +0000 (16:44 +0200)]
fix transient services
Andreas Müller [Thu, 6 Oct 2016 10:48:15 +0000 (12:48 +0200)]
fix #6120 Cleanup uuidAndTitleCache methods
Katja Luther [Wed, 5 Oct 2016 12:57:51 +0000 (14:57 +0200)]
minor
Katja Luther [Wed, 5 Oct 2016 12:55:05 +0000 (14:55 +0200)]
ref #6047: add the adapted files
Katja Luther [Wed, 5 Oct 2016 12:52:40 +0000 (14:52 +0200)]
fix #6047: add the possibility to the termComboElement that the idInVoc is used as label
Katja Luther [Tue, 4 Oct 2016 10:19:23 +0000 (12:19 +0200)]
ref #5969: add remark that the nomenclatural code preference is stored in db
Katja Luther [Tue, 4 Oct 2016 10:11:37 +0000 (12:11 +0200)]
ref #5969: check for db connection before ty to read the preferred nomenclatural code
Patrick Plitzner [Mon, 26 Sep 2016 06:52:57 +0000 (08:52 +0200)]
ref #3573 Add streamlined ABCD import configurator page
Patrick Plitzner [Mon, 26 Sep 2016 06:36:20 +0000 (08:36 +0200)]
Fix label for term vocabularies in term editor
Patrick Plitzner [Mon, 26 Sep 2016 04:32:13 +0000 (06:32 +0200)]
Trim code
jenkins [Fri, 23 Sep 2016 14:24:12 +0000 (16:24 +0200)]
Merge branch 'release/4.3.0' into develop
jenkins [Fri, 23 Sep 2016 13:15:14 +0000 (15:15 +0200)]
Updated version in pom / project files to taxeditor version : 4.4.0-SNAPSHOT and cdmlib version : 4.4.0-SNAPSHOT
jenkins [Fri, 23 Sep 2016 13:15:08 +0000 (15:15 +0200)]
Updated version in pom / project files to taxeditor version : 4.3.0 and cdmlib version : 4.3.0
Andreas Müller [Wed, 21 Sep 2016 19:26:18 +0000 (21:26 +0200)]
fix transient services
Andreas Müller [Wed, 21 Sep 2016 09:14:53 +0000 (11:14 +0200)]
fix transient service
Katja Luther [Wed, 21 Sep 2016 07:45:03 +0000 (09:45 +0200)]
also add null check in comparator of nomenclaturalReferenceSelectionDialog
Katja Luther [Wed, 21 Sep 2016 07:35:58 +0000 (09:35 +0200)]
fix #6061: add a null check for abbrevTitleCache and titleCache in comparator
Patrick Plitzner [Tue, 20 Sep 2016 14:59:29 +0000 (16:59 +0200)]
ref #5616 Generalize evaluation of available CdmViewers
Patrick Plitzner [Tue, 20 Sep 2016 13:14:26 +0000 (15:14 +0200)]
Compare taxon editor input based on taxon instead of taxon node (Revert
93c6e0a894d2e4b0c9df6c7c3feff2f20e0b9e38)
Katja Luther [Tue, 20 Sep 2016 12:46:43 +0000 (14:46 +0200)]
fix #6101: add a check for multilanguage preference
Patrick Plitzner [Tue, 20 Sep 2016 11:44:28 +0000 (13:44 +0200)]
ref #5616 Fix class check for bulk editor porperty tester
- handle UuidAndTitleClache
Andreas Müller [Mon, 19 Sep 2016 19:50:47 +0000 (21:50 +0200)]
ref #6082 try to fix dependency issues in managed TaxEditor
Andreas Kohlbecker [Mon, 19 Sep 2016 13:45:21 +0000 (15:45 +0200)]
fix #6082 fixing incomplete entries in the eu.etaxonomy.taxeditor.webapp/build.properties
Patrick Plitzner [Mon, 19 Sep 2016 12:38:43 +0000 (14:38 +0200)]
i18n for view titles
Patrick Plitzner [Mon, 19 Sep 2016 10:37:44 +0000 (12:37 +0200)]
Generalize title creation for cdm view parts
Patrick Plitzner [Mon, 19 Sep 2016 10:12:56 +0000 (12:12 +0200)]
Compare taxon editor input based on taxon node instead of taxon
Katja Luther [Mon, 19 Sep 2016 11:45:17 +0000 (13:45 +0200)]
fix #5607: add sec reference to property path solves the problem of not reload the right sec reference
Katja Luther [Mon, 19 Sep 2016 11:22:44 +0000 (13:22 +0200)]
remove System.out.println...
Katja Luther [Mon, 19 Sep 2016 11:07:56 +0000 (13:07 +0200)]
fix #6056: when creating checklisteditorInput don't init session at the beginning, but at the end of constructor
Andreas Müller [Fri, 16 Sep 2016 19:11:57 +0000 (21:11 +0200)]
fix transientServices (2)
Andreas Müller [Fri, 16 Sep 2016 18:41:59 +0000 (20:41 +0200)]
fix transientService
Andreas Müller [Thu, 15 Sep 2016 22:43:26 +0000 (00:43 +0200)]
ref #6089 Fix not compiling operation
Andreas Müller [Thu, 15 Sep 2016 22:35:15 +0000 (00:35 +0200)]
ref #6089 Fix failing test and transient service after taxonomicChildrenCount and taxonomicParentCache removal
Andreas Müller [Thu, 15 Sep 2016 22:26:37 +0000 (00:26 +0200)]
Rename Checklist-Editor -> Distribution-Editor
Katja Luther [Thu, 15 Sep 2016 12:23:27 +0000 (14:23 +0200)]
fix #5702: filter for current name in name details view if select new name
Katja Luther [Thu, 15 Sep 2016 11:54:13 +0000 (13:54 +0200)]
ref #5837: if nomenclatural titleCache and titleCache are equal only one is shown in selection dialog
Katja Luther [Thu, 15 Sep 2016 11:22:59 +0000 (13:22 +0200)]
ref 6061: using * at the beginning of search pattern triggers a search on abbrevTitleCache and titleCache
Katja Luther [Thu, 15 Sep 2016 11:18:42 +0000 (13:18 +0200)]
ref #5969: check if there is a NC preference in db if not use the local NC preference
Katja Luther [Thu, 15 Sep 2016 09:50:27 +0000 (11:50 +0200)]
fix #5874: display of infrageneric epithet are different for zoological and botanical names
Katja Luther [Thu, 15 Sep 2016 08:40:05 +0000 (10:40 +0200)]
ref #6061: remove the current selection as filter in nomenclatural author selection dialog
Katja Luther [Wed, 14 Sep 2016 12:45:40 +0000 (14:45 +0200)]
ref #6041: revert the changes and wait for the decision of the user meeting
Andreas Müller [Wed, 14 Sep 2016 13:42:46 +0000 (15:42 +0200)]
Minor language correction