Andreas Müller [Tue, 9 Dec 2014 16:09:06 +0000 (16:09 +0000)]
some adaptations after trunk merge to 3.4.1
Patric Plitzner [Tue, 9 Dec 2014 16:03:13 +0000 (16:03 +0000)]
merge-update from trunk
Andreas Müller [Tue, 9 Dec 2014 15:46:00 +0000 (15:46 +0000)]
dna Quality purification method
Andreas Müller [Tue, 9 Dec 2014 15:45:35 +0000 (15:45 +0000)]
label for PAT voc
Andreas Müller [Tue, 9 Dec 2014 15:44:26 +0000 (15:44 +0000)]
separate Amplification and AmplificationResult.java #4541
Andreas Kohlbecker [Mon, 8 Dec 2014 12:27:35 +0000 (12:27 +0000)]
bug fix
Andreas Kohlbecker [Mon, 8 Dec 2014 12:27:28 +0000 (12:27 +0000)]
CdmUpdater can run on multiple databases supplied as comma separated list
Patric Plitzner [Thu, 4 Dec 2014 15:00:20 +0000 (15:00 +0000)]
- added service method to get descriptions which have a specimen set as describedSpecimen
- added test which fails because the XML is loaded incorrectly
Patric Plitzner [Thu, 4 Dec 2014 14:29:50 +0000 (14:29 +0000)]
- re-added hibernate annotation
Patric Plitzner [Thu, 4 Dec 2014 12:55:56 +0000 (12:55 +0000)]
-removed hibernate search annotation (copy&paste error)
Andreas Müller [Thu, 4 Dec 2014 09:36:27 +0000 (09:36 +0000)]
minor
Andreas Müller [Thu, 4 Dec 2014 09:35:36 +0000 (09:35 +0000)]
use saveOrUpdate in JaxbImport
Patric Plitzner [Thu, 4 Dec 2014 08:52:55 +0000 (08:52 +0000)]
- invoke super method in isDeletable()
Patric Plitzner [Thu, 4 Dec 2014 08:44:34 +0000 (08:44 +0000)]
- changed service method to retrieve the directly related objects
- adapted tests
Patric Plitzner [Thu, 4 Dec 2014 08:43:46 +0000 (08:43 +0000)]
- fixed bidriectionality for DnaSample<->Amplification
Andreas Müller [Wed, 3 Dec 2014 22:55:38 +0000 (22:55 +0000)]
fixing test for SingleReadAlignment and removal of SpecAndObs_Sequence
Andreas Müller [Wed, 3 Dec 2014 21:13:05 +0000 (21:13 +0000)]
implement SingleReadAlignment.java #4529
not yet ready
Andreas Müller [Wed, 3 Dec 2014 21:12:05 +0000 (21:12 +0000)]
minor changes
Andreas Müller [Wed, 3 Dec 2014 21:09:37 +0000 (21:09 +0000)]
remove Specimen_Sequence table from ddl
Andreas Müller [Wed, 3 Dec 2014 21:08:02 +0000 (21:08 +0000)]
add nextUpdater to 331_34 updater
Patric Plitzner [Wed, 3 Dec 2014 16:07:21 +0000 (16:07 +0000)]
- commented unused field from SpecimenDeleteConfigurator
- added TODOs for deletion checking for specimens
- added emtpy isDeletable() method
Patric Plitzner [Wed, 3 Dec 2014 16:05:43 +0000 (16:05 +0000)]
- commented unused fields of DeleteResult
Katja Luther [Wed, 3 Dec 2014 12:49:14 +0000 (12:49 +0000)]
isDeletable returns DeleteResult
Patric Plitzner [Wed, 3 Dec 2014 12:31:03 +0000 (12:31 +0000)]
- implemented bidirectionality for derivation events
Andreas Müller [Wed, 3 Dec 2014 12:29:40 +0000 (12:29 +0000)]
some fixes after trunk integration to 341branch
Patric Plitzner [Wed, 3 Dec 2014 12:22:16 +0000 (12:22 +0000)]
merge-update from trunk
Andreas Müller [Wed, 3 Dec 2014 09:21:29 +0000 (09:21 +0000)]
add first version of BigDecimal (still unclear if we want to keep the UserType) #4499
Andreas Müller [Wed, 3 Dec 2014 09:06:40 +0000 (09:06 +0000)]
minor
Andreas Müller [Wed, 3 Dec 2014 09:03:15 +0000 (09:03 +0000)]
merge PresenceTerm and AbsenceTerm #4521
Patric Plitzner [Wed, 3 Dec 2014 08:36:27 +0000 (08:36 +0000)]
- added isDeleteFromIndividualsAssociation and isDeleteFromTypeDesignation to SpecimenDeleteConfigurator
- implemented deletion for above mentioned flags
- added more information to delete result when deleting specimens
- added tests for above mentioned flags
- extended step by step deletion test
Patric Plitzner [Wed, 3 Dec 2014 08:24:13 +0000 (08:24 +0000)]
- extended toString() method
Andreas Müller [Tue, 2 Dec 2014 11:43:40 +0000 (11:43 +0000)]
remove TODO
Patric Plitzner [Tue, 2 Dec 2014 10:17:10 +0000 (10:17 +0000)]
- added loadStrategy=CleanSweepInsertLoadStrategy.class to tests to fix test failure
Patric Plitzner [Tue, 2 Dec 2014 08:55:16 +0000 (08:55 +0000)]
- added DISTINCT to HQL query for associated taxa
- created and used XML data source in occurrence service test
Patric Plitzner [Mon, 1 Dec 2014 13:48:12 +0000 (13:48 +0000)]
- added xml resources for tests
Patric Plitzner [Mon, 1 Dec 2014 13:47:59 +0000 (13:47 +0000)]
- fixed bidirectional mapping
Patric Plitzner [Mon, 1 Dec 2014 09:24:38 +0000 (09:24 +0000)]
- added occurrence service methods to retrieve all taxa that are associated with a specimen:
- via IndividualsAssociation
- via TypeDesignation
- added test
Andreas Kohlbecker [Thu, 27 Nov 2014 13:15:06 +0000 (13:15 +0000)]
removing old obsolte code
Andreas Müller [Thu, 27 Nov 2014 12:52:36 +0000 (12:52 +0000)]
remove FIMXE on protected constructor
Andreas Müller [Thu, 27 Nov 2014 12:50:12 +0000 (12:50 +0000)]
minor
Patric Plitzner [Wed, 26 Nov 2014 14:31:09 +0000 (14:31 +0000)]
- added TODO comment
Andreas Müller [Wed, 26 Nov 2014 14:04:17 +0000 (14:04 +0000)]
creationi fo PresenceAbsence Terms
Andreas Müller [Wed, 26 Nov 2014 13:30:17 +0000 (13:30 +0000)]
make all defined terms comparable
Patric Plitzner [Wed, 26 Nov 2014 11:47:54 +0000 (11:47 +0000)]
- removed BlankDataSet form test
Patric Plitzner [Wed, 26 Nov 2014 11:06:48 +0000 (11:06 +0000)]
- removed unused code
Patric Plitzner [Wed, 26 Nov 2014 11:06:05 +0000 (11:06 +0000)]
- implemented service method (and test for it) to get all taxa associated with a single specimen
Patric Plitzner [Wed, 26 Nov 2014 08:53:30 +0000 (08:53 +0000)]
- added listAssociatedTaxa() method to occurrence service (non functional)
Cherian Mathew [Mon, 24 Nov 2014 16:32:39 +0000 (16:32 +0000)]
removed unwanted service field
Cherian Mathew [Mon, 24 Nov 2014 16:28:07 +0000 (16:28 +0000)]
Fix (more of a hack) for conversation holder problem, subclassing the current servlet and setting the conversation so that it is bound every time a service call is made.
Andreas Kohlbecker [Mon, 24 Nov 2014 10:50:36 +0000 (10:50 +0000)]
setting java source compliance to version 1.7
Patric Plitzner [Mon, 24 Nov 2014 09:12:50 +0000 (09:12 +0000)]
- converted dnaQuality from DefinedTerm to OrderedTerm (#4434)
Andreas Kohlbecker [Fri, 21 Nov 2014 14:36:47 +0000 (14:36 +0000)]
whitespace
Andreas Kohlbecker [Fri, 21 Nov 2014 14:36:46 +0000 (14:36 +0000)]
ignoring VAADIN compilation artefacts
Andreas Kohlbecker [Fri, 21 Nov 2014 14:36:46 +0000 (14:36 +0000)]
adding documentation URL to commentn
Andreas Kohlbecker [Fri, 21 Nov 2014 14:36:43 +0000 (14:36 +0000)]
adding missing log4j.properties to artifact (fixes excessive loggin on DEBUG level)
Andreas Müller [Fri, 21 Nov 2014 13:21:54 +0000 (13:21 +0000)]
Add institution to DerivationEvent and Amplification
Andreas Müller [Fri, 21 Nov 2014 12:55:03 +0000 (12:55 +0000)]
add DnaMarker to Primer #4470
Andreas Müller [Fri, 21 Nov 2014 09:38:47 +0000 (09:38 +0000)]
fix bug, add OrederedTerm to hibernate cfg
Andreas Müller [Fri, 21 Nov 2014 09:24:11 +0000 (09:24 +0000)]
Andreas Müller [Fri, 21 Nov 2014 09:16:18 +0000 (09:16 +0000)]
add DNA Quality Type vocabulary
Cherian Mathew [Thu, 20 Nov 2014 15:20:08 +0000 (15:20 +0000)]
added test for saveOrUpdate within conversation sessions
Andreas Müller [Wed, 19 Nov 2014 16:44:45 +0000 (16:44 +0000)]
Branch for model 3.4.1
Andreas Müller [Wed, 19 Nov 2014 16:44:23 +0000 (16:44 +0000)]
Add DnaQuality.csv (not fully ready)
Andreas Kohlbecker [Wed, 19 Nov 2014 16:31:58 +0000 (16:31 +0000)]
fixing component scan in jars
Patric Plitzner [Tue, 18 Nov 2014 13:44:04 +0000 (13:44 +0000)]
- when moving derivate also set "derivedFrom" to the new DerivationEvent
Cherian Mathew [Tue, 18 Nov 2014 08:52:14 +0000 (08:52 +0000)]
ICdmCacher, DefaultTermInitializer : added comments
CdmCacher : added code to disallow null values in cache and moved term initialisation code to specific subclass
CdmDaoCacher : replaced with specialised CdmTermCacher
defaultApplicationContext : removed remoting exception
Andreas Müller [Mon, 17 Nov 2014 17:31:36 +0000 (17:31 +0000)]
cleanup javadoc
Andreas Müller [Mon, 17 Nov 2014 16:50:51 +0000 (16:50 +0000)]
update JaxbImportActivator
Alexander Oppermann [Fri, 14 Nov 2014 16:31:43 +0000 (16:31 +0000)]
made changes to be compliant with TaxonomicEditor Export
Andreas Kohlbecker [Fri, 14 Nov 2014 15:10:36 +0000 (15:10 +0000)]
reverting eclipse launcher
Andreas Müller [Thu, 13 Nov 2014 15:23:32 +0000 (15:23 +0000)]
minor
Andreas Müller [Thu, 13 Nov 2014 15:17:57 +0000 (15:17 +0000)]
improve cache update algorithm
Patric Plitzner [Wed, 12 Nov 2014 14:41:55 +0000 (14:41 +0000)]
- fixed possible NPE
Patric Plitzner [Wed, 12 Nov 2014 14:31:52 +0000 (14:31 +0000)]
- fixed typo with semantic meaning
Patric Plitzner [Wed, 12 Nov 2014 10:28:23 +0000 (10:28 +0000)]
- used blank data set for test
Patric Plitzner [Wed, 12 Nov 2014 08:51:52 +0000 (08:51 +0000)]
- used ImageFile instead of more generic MediaRepresentationPart when creating the Media (fixes #4402)
- fixed a typo
Patric Plitzner [Tue, 11 Nov 2014 08:33:10 +0000 (08:33 +0000)]
- added delete configurator to occurence service
Patric Plitzner [Tue, 11 Nov 2014 08:18:04 +0000 (08:18 +0000)]
- fixed typo
Katja Luther [Mon, 10 Nov 2014 08:49:18 +0000 (08:49 +0000)]
changes in service layer for fixes in bulg editor and search for misapplied names and common names in editor
Andreas Müller [Thu, 6 Nov 2014 11:54:12 +0000 (11:54 +0000)]
minor
Patric Plitzner [Tue, 4 Nov 2014 13:58:37 +0000 (13:58 +0000)]
- provide contig and read information in portal and webservice
Patric Plitzner [Mon, 3 Nov 2014 09:29:02 +0000 (09:29 +0000)]
- extende DerivateHierarchyDTO to also show contig and primer info
Patric Plitzner [Wed, 29 Oct 2014 14:10:58 +0000 (14:10 +0000)]
- removed comma in specimen citation
Katja Luther [Wed, 29 Oct 2014 12:17:29 +0000 (12:17 +0000)]
Patric Plitzner [Wed, 29 Oct 2014 10:39:34 +0000 (10:39 +0000)]
- added exception throwing to URI assembly in Sequence class
- handled exception in editor details view
Patric Plitzner [Tue, 28 Oct 2014 18:24:53 +0000 (18:24 +0000)]
- adapted derivate hierarchy assembly to cdmlib3.4 changes (TissueSample, DnaSample as one class)
Patric Plitzner [Tue, 28 Oct 2014 18:20:15 +0000 (18:20 +0000)]
- extended init test
Patric Plitzner [Tue, 28 Oct 2014 14:27:22 +0000 (14:27 +0000)]
- made constructor protected to avoid JavaAssistEnhancementException
Katja Luther [Tue, 28 Oct 2014 13:09:11 +0000 (13:09 +0000)]
fix #4450
Alexander Oppermann [Tue, 28 Oct 2014 13:07:14 +0000 (13:07 +0000)]
Changes for production mode for vaadin
Alexander Oppermann [Mon, 27 Oct 2014 15:37:56 +0000 (15:37 +0000)]
changed startup parameter for vaadin. Only for testing.
Alexander Oppermann [Mon, 27 Oct 2014 10:38:08 +0000 (10:38 +0000)]
latest changes for Vaadin Editor
* added in Web.XML production mode
Katja Luther [Mon, 27 Oct 2014 10:21:22 +0000 (10:21 +0000)]
Katja Luther [Mon, 27 Oct 2014 10:20:34 +0000 (10:20 +0000)]
Patric Plitzner [Mon, 27 Oct 2014 08:09:41 +0000 (08:09 +0000)]
- added service method deleteDerivateHierarchy()
Andreas Müller [Thu, 23 Oct 2014 11:44:17 +0000 (11:44 +0000)]
remove NOT NULL on OriginalSourceType_AUD.sourceType on existing data #4445
Andreas Müller [Thu, 23 Oct 2014 07:20:18 +0000 (07:20 +0000)]
revert contact URLs #3920, #4444
Andreas Müller [Wed, 22 Oct 2014 20:57:50 +0000 (20:57 +0000)]
workaround for Contact.urls to solve #4444 preliminary
Andreas Müller [Wed, 22 Oct 2014 16:54:40 +0000 (16:54 +0000)]
last update to schema updater 34.
Alexander Oppermann [Wed, 22 Oct 2014 16:01:47 +0000 (16:01 +0000)]
removed useless widgetset