Andreas Müller [Thu, 8 Jan 2015 15:43:18 +0000 (15:43 +0000)]
rename abstract class
Andreas Müller [Thu, 8 Jan 2015 15:40:37 +0000 (15:40 +0000)]
rename abstract class
Andreas Müller [Thu, 8 Jan 2015 15:36:39 +0000 (15:36 +0000)]
merge cdmlib-persistence from validation branch to trunk
Andreas Müller [Thu, 8 Jan 2015 15:34:16 +0000 (15:34 +0000)]
merge cdmlib-service from validation branch to trunk
Andreas Müller [Thu, 8 Jan 2015 15:30:39 +0000 (15:30 +0000)]
merge cdmlib-remote from validation branch to trunk
Andreas Müller [Thu, 8 Jan 2015 15:30:11 +0000 (15:30 +0000)]
merge cdmlib-print from validation branch to trunk
Andreas Müller [Thu, 8 Jan 2015 15:29:28 +0000 (15:29 +0000)]
merge cdmlib-io from validation branch to trunk
Andreas Müller [Thu, 8 Jan 2015 15:28:33 +0000 (15:28 +0000)]
merge cdmlib-ext from validation branch to trunk
Andreas Müller [Thu, 8 Jan 2015 15:27:29 +0000 (15:27 +0000)]
merge cdmlib-commons from validatioin to branch
Andreas Müller [Thu, 8 Jan 2015 15:01:49 +0000 (15:01 +0000)]
remove imports
Andreas Müller [Thu, 8 Jan 2015 14:59:44 +0000 (14:59 +0000)]
correct logger info
Andreas Müller [Thu, 8 Jan 2015 14:30:08 +0000 (14:30 +0000)]
VocEnum
Andreas Müller [Thu, 8 Jan 2015 11:27:09 +0000 (11:27 +0000)]
minor
Andreas Müller [Thu, 8 Jan 2015 10:46:19 +0000 (10:46 +0000)]
first tests for listByIdentifier
Andreas Müller [Wed, 7 Jan 2015 23:21:44 +0000 (23:21 +0000)]
remove imports
Andreas Müller [Wed, 7 Jan 2015 18:45:26 +0000 (18:45 +0000)]
factory method for Identifier Type
Andreas Müller [Wed, 7 Jan 2015 18:44:54 +0000 (18:44 +0000)]
labels for some TermTypes
Andreas Müller [Wed, 7 Jan 2015 18:36:27 +0000 (18:36 +0000)]
first untested version for findByIdentifier #4594
Andreas Müller [Wed, 7 Jan 2015 17:57:49 +0000 (17:57 +0000)]
update javadoc and Override in IdentifiableServiceBase
Katja Luther [Tue, 6 Jan 2015 12:33:37 +0000 (12:33 +0000)]
Andreas Müller [Tue, 6 Jan 2015 12:21:10 +0000 (12:21 +0000)]
avoid NPE in ImageInfo loading #4587
Andreas Müller [Wed, 17 Dec 2014 15:20:19 +0000 (15:20 +0000)]
minor
Andreas Müller [Wed, 17 Dec 2014 12:46:53 +0000 (12:46 +0000)]
add getter and setter for reverse complement
Andreas Müller [Wed, 17 Dec 2014 12:13:04 +0000 (12:13 +0000)]
minor
Andreas Müller [Tue, 16 Dec 2014 20:29:34 +0000 (20:29 +0000)]
add xslx test in io
Andreas Müller [Tue, 16 Dec 2014 20:05:44 +0000 (20:05 +0000)]
minor
Patric Plitzner [Tue, 16 Dec 2014 14:16:58 +0000 (14:16 +0000)]
- added comment
Patric Plitzner [Tue, 16 Dec 2014 14:11:19 +0000 (14:11 +0000)]
- fixed deep delete recursion bug
- fixed tests
Patric Plitzner [Tue, 16 Dec 2014 09:32:37 +0000 (09:32 +0000)]
- extracted deepDelete tests to own java class
- reduced exception logged in DeleteResult
Andreas Kohlbecker [Mon, 15 Dec 2014 21:19:23 +0000 (21:19 +0000)]
disabling dependencyLocationsEnabled option of the maven-project-info-reports-plugin to speed up site building
Andreas Müller [Mon, 15 Dec 2014 17:25:26 +0000 (17:25 +0000)]
refactor validation classes
Andreas Müller [Mon, 15 Dec 2014 16:58:22 +0000 (16:58 +0000)]
minor
Andreas Kohlbecker [Mon, 15 Dec 2014 14:46:42 +0000 (14:46 +0000)]
site-delpoy chmod = false
Andreas Müller [Mon, 15 Dec 2014 12:52:10 +0000 (12:52 +0000)]
add original label info to specimen facade #4218, #4565
edit-jenkins [Mon, 15 Dec 2014 12:46:14 +0000 (12:46 +0000)]
[maven-release-plugin] prepare for next development iteration
edit-jenkins [Mon, 15 Dec 2014 12:46:09 +0000 (12:46 +0000)]
[maven-release-plugin] prepare release cdmlib-parent-3.4.0
Patric Plitzner [Mon, 15 Dec 2014 12:00:37 +0000 (12:00 +0000)]
- fully implemented deep delete (child derivates)
- added tests
Andreas Müller [Mon, 15 Dec 2014 11:46:09 +0000 (11:46 +0000)]
minor
Andreas Müller [Mon, 15 Dec 2014 11:29:32 +0000 (11:29 +0000)]
add username, groupname and GrantedAuthority deduplication #4102
Andreas Kohlbecker [Mon, 15 Dec 2014 10:26:07 +0000 (10:26 +0000)]
turning java code level back to 1.6 to investigate existing problems
Andreas Kohlbecker [Mon, 15 Dec 2014 10:22:05 +0000 (10:22 +0000)]
more logging output
Andreas Kohlbecker [Mon, 15 Dec 2014 10:21:57 +0000 (10:21 +0000)]
typo
Andreas Müller [Fri, 12 Dec 2014 16:47:09 +0000 (16:47 +0000)]
add poi-ooxml and upgrade to 3.10-FINAL
Andreas Müller [Fri, 12 Dec 2014 15:50:45 +0000 (15:50 +0000)]
minor
Andreas Müller [Fri, 12 Dec 2014 15:25:16 +0000 (15:25 +0000)]
javadoc for Amplification and AmplificationResult
Andreas Müller [Fri, 12 Dec 2014 14:59:26 +0000 (14:59 +0000)]
minor
Andreas Müller [Fri, 12 Dec 2014 13:17:42 +0000 (13:17 +0000)]
added unit test for derived unit facade with parent but no field unit #4532
Patric Plitzner [Fri, 12 Dec 2014 08:41:39 +0000 (08:41 +0000)]
- implemented isDeletable() and delete()
- fixed test XML files and tests
Andreas Müller [Thu, 11 Dec 2014 23:50:24 +0000 (23:50 +0000)]
fix Occurrence test
Patric Plitzner [Thu, 11 Dec 2014 20:35:55 +0000 (20:35 +0000)]
- added isDeleteMolecularData flag to configurator
Patric Plitzner [Thu, 11 Dec 2014 20:35:04 +0000 (20:35 +0000)]
- use labelCache instead of description for amplification labeling
Patric Plitzner [Thu, 11 Dec 2014 20:34:10 +0000 (20:34 +0000)]
- change visibility of createTestDataSet to public
Patric Plitzner [Thu, 11 Dec 2014 20:32:35 +0000 (20:32 +0000)]
- change visibility of createTestDataSet to public
Andreas Müller [Thu, 11 Dec 2014 15:29:15 +0000 (15:29 +0000)]
test for Amplification labelCache
Patric Plitzner [Thu, 11 Dec 2014 15:07:52 +0000 (15:07 +0000)]
- organized imports
Andreas Müller [Thu, 11 Dec 2014 15:02:30 +0000 (15:02 +0000)]
implement Amplification.labelCache generation
Patric Plitzner [Thu, 11 Dec 2014 14:51:04 +0000 (14:51 +0000)]
- added cascade saving for amplification result
- made constructor protected to avoid JavaAssistEnhancementException
Andreas Müller [Thu, 11 Dec 2014 14:30:45 +0000 (14:30 +0000)]
doc
Andreas Müller [Thu, 11 Dec 2014 14:29:11 +0000 (14:29 +0000)]
handle duplicates in identifier list
Andreas Müller [Thu, 11 Dec 2014 12:44:01 +0000 (12:44 +0000)]
minor
Andreas Müller [Thu, 11 Dec 2014 12:39:59 +0000 (12:39 +0000)]
updated webapp h2 test database
Andreas Müller [Wed, 10 Dec 2014 23:11:31 +0000 (23:11 +0000)]
minor
Andreas Müller [Wed, 10 Dec 2014 23:07:30 +0000 (23:07 +0000)]
solve identifier conflict
Andreas Müller [Wed, 10 Dec 2014 23:02:58 +0000 (23:02 +0000)]
merge 3.4.1 into trunk
Andreas Müller [Wed, 10 Dec 2014 22:23:10 +0000 (22:23 +0000)]
Bidirectional identifier handling
Andreas Müller [Wed, 10 Dec 2014 22:22:35 +0000 (22:22 +0000)]
latest changes to AmplificationResult and DnaQuality
Andreas Müller [Wed, 10 Dec 2014 21:40:32 +0000 (21:40 +0000)]
updating DnaQuality with typedPurificationMethod to allow both #4434 , #4552
Andreas Müller [Wed, 10 Dec 2014 20:46:19 +0000 (20:46 +0000)]
conflict fiexes after merging trunk
Patric Plitzner [Wed, 10 Dec 2014 15:28:01 +0000 (15:28 +0000)]
merge-update from trunk
Patric Plitzner [Wed, 10 Dec 2014 15:27:32 +0000 (15:27 +0000)]
-fixed possible NPE (fixes #4532)
Patric Plitzner [Wed, 10 Dec 2014 15:25:08 +0000 (15:25 +0000)]
merge-update from trunk
Andreas Müller [Wed, 10 Dec 2014 14:47:31 +0000 (14:47 +0000)]
update scripts for splitting Amplification and adding labelCache and reversecomplement
Patric Plitzner [Wed, 10 Dec 2014 14:27:35 +0000 (14:27 +0000)]
- added abstract method createTestData() to CdmIntegrationalTest
- method should be used for generatin test XML data sets
- making it abstract and enforcing implementation in sub classes ensures that the same structure is used thus making it easier for the developer to find similar examples.
- added empty method implementation in sub classes
Patric Plitzner [Wed, 10 Dec 2014 10:49:58 +0000 (10:49 +0000)]
- fixed testLoadData()
- the field unit element in the XML needed to have the derivedFrom parameter
Patric Plitzner [Wed, 10 Dec 2014 09:36:10 +0000 (09:36 +0000)]
- added isPublish() method to facade
Andreas Müller [Tue, 9 Dec 2014 22:29:33 +0000 (22:29 +0000)]
JAXB annotations for amplification results
Andreas Müller [Tue, 9 Dec 2014 21:56:35 +0000 (21:56 +0000)]
preliminary set OccurrenceServie.loadData test to ignore, as data is not loading correctly
Andreas Müller [Tue, 9 Dec 2014 21:55:33 +0000 (21:55 +0000)]
preliminary set OccurrenceServie.loadData test to ignore, as data is not loading correctly
Andreas Müller [Tue, 9 Dec 2014 21:26:59 +0000 (21:26 +0000)]
latest changes for AmplificationResult
Andreas Müller [Tue, 9 Dec 2014 16:34:38 +0000 (16:34 +0000)]
add labelCache to Amplification #4542
Andreas Müller [Tue, 9 Dec 2014 16:33:35 +0000 (16:33 +0000)]
some bugfixes to new Amplification modelling #4541
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