Andreas Kohlbecker [Thu, 13 Mar 2014 12:22:48 +0000 (12:22 +0000)]
implementing test and fixing bugs 2 regarding #4081 (TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode() requires TAXONNAMEBASE.[UPDATE])
Andreas Kohlbecker [Thu, 13 Mar 2014 12:22:44 +0000 (12:22 +0000)]
implementing test and fixing bugs regarding #4081 (TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode() requires TAXONNAMEBASE.[UPDATE])
Cherian Mathew [Thu, 13 Mar 2014 12:15:48 +0000 (12:15 +0000)]
changed isTopmostNode to check for null parent node taxon
Andreas Kohlbecker [Wed, 12 Mar 2014 13:18:57 +0000 (13:18 +0000)]
implementing exclude map for #4081 (TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode() requires TAXONNAMEBASE.[UPDATE])
Alexander Oppermann [Tue, 11 Mar 2014 15:32:44 +0000 (15:32 +0000)]
redlist WS export added .json and .xml functionality
Andreas Müller [Mon, 10 Mar 2014 15:24:47 +0000 (15:24 +0000)]
improve common name import for markup
Andreas Müller [Mon, 10 Mar 2014 15:09:41 +0000 (15:09 +0000)]
getLangaugeByKey for markup transformer
Patric Plitzner [Mon, 10 Mar 2014 14:59:37 +0000 (14:59 +0000)]
- fixed typo
Andreas Müller [Mon, 10 Mar 2014 14:39:46 +0000 (14:39 +0000)]
rearrange constants
Andreas Müller [Mon, 10 Mar 2014 12:58:36 +0000 (12:58 +0000)]
handle missing name parts for null parent
Andreas Müller [Mon, 10 Mar 2014 12:55:54 +0000 (12:55 +0000)]
improve mods import
Andreas Müller [Sat, 8 Mar 2014 01:48:34 +0000 (01:48 +0000)]
minor
Andreas Müller [Sat, 8 Mar 2014 01:47:56 +0000 (01:47 +0000)]
minor
Andreas Müller [Fri, 7 Mar 2014 19:55:11 +0000 (19:55 +0000)]
Add database index on treeIndex #4105
Andreas Müller [Fri, 7 Mar 2014 17:33:03 +0000 (17:33 +0000)]
minor
Andreas Müller [Fri, 7 Mar 2014 17:30:51 +0000 (17:30 +0000)]
improve TaxonCacheStrategy. Use short form where possible
Andreas Müller [Fri, 7 Mar 2014 17:30:06 +0000 (17:30 +0000)]
fix CacheUpdater
Andreas Kohlbecker [Fri, 7 Mar 2014 16:36:34 +0000 (16:36 +0000)]
making TaxonNodeByNameComparator truely null save - #2912 (NPE in TaxonNodeByNameComparator when Taxon in TaxoNode is null)
Andreas Müller [Fri, 7 Mar 2014 13:31:58 +0000 (13:31 +0000)]
minor
Andreas Müller [Fri, 7 Mar 2014 13:00:30 +0000 (13:00 +0000)]
Cleaning up a bit
Andreas Müller [Fri, 7 Mar 2014 12:42:10 +0000 (12:42 +0000)]
solving some reference cache strategy issues, e.g. #3645
Andreas Müller [Fri, 7 Mar 2014 12:03:24 +0000 (12:03 +0000)]
adding isBlank to StrategyBase
Andreas Müller [Fri, 7 Mar 2014 11:35:35 +0000 (11:35 +0000)]
minor
Andreas Müller [Fri, 7 Mar 2014 11:32:51 +0000 (11:32 +0000)]
Better handling for short citation of references
Andreas Müller [Thu, 6 Mar 2014 00:48:15 +0000 (00:48 +0000)]
minor
Andreas Müller [Thu, 6 Mar 2014 00:46:30 +0000 (00:46 +0000)]
minor and generics
Andreas Kohlbecker [Wed, 5 Mar 2014 16:44:33 +0000 (16:44 +0000)]
fixing broken dependencies by excluding spring-expression
Patric Plitzner [Wed, 5 Mar 2014 14:28:42 +0000 (14:28 +0000)]
- added cascading save to SequenceString of a Sequence
Patric Plitzner [Wed, 5 Mar 2014 12:16:51 +0000 (12:16 +0000)]
- renamed getBaseUnit() to baseUnit()
Andreas Kohlbecker [Wed, 5 Mar 2014 10:48:11 +0000 (10:48 +0000)]
setting correct port number for remote integration tests
Patric Plitzner [Wed, 5 Mar 2014 07:43:08 +0000 (07:43 +0000)]
- added util method to get for getting a CDM entity (used in authenication/permission framework)
- made use of this method where the type of the parameter was too general (like object)
- made getBaseUnit() of DerivedUnitFacade public
Andreas Müller [Tue, 4 Mar 2014 18:10:49 +0000 (18:10 +0000)]
minor
Andreas Müller [Tue, 4 Mar 2014 18:09:28 +0000 (18:09 +0000)]
minor
Patric Plitzner [Tue, 4 Mar 2014 16:17:33 +0000 (16:17 +0000)]
- refactored to use "base" unit wherever possible (base unit is derivedUnit or fieldUnit)
Andreas Kohlbecker [Tue, 4 Mar 2014 15:30:20 +0000 (15:30 +0000)]
changing ports in config to avoid conflics
Andreas Kohlbecker [Tue, 4 Mar 2014 14:45:00 +0000 (14:45 +0000)]
automatically testing of cdmlib-remote-webapp during the maven lifecycle - #4094: automatically test cdmlib-remote-webapp
Patric Plitzner [Tue, 4 Mar 2014 08:20:31 +0000 (08:20 +0000)]
- added cascading save for contig file of Sequence
Andreas Müller [Mon, 3 Mar 2014 14:14:14 +0000 (14:14 +0000)]
handle setType in DerivedUnitFacade better
Patric Plitzner [Mon, 3 Mar 2014 08:48:20 +0000 (08:48 +0000)]
- added cascading save to pherogram (Media) of SingleRead
- added media section to DetailsViews for Amplification (gel photo) and SingelRead (pherogram)
Andreas Müller [Fri, 28 Feb 2014 13:24:08 +0000 (13:24 +0000)]
some minor changing for handling getType()
Andreas Kohlbecker [Fri, 28 Feb 2014 10:45:51 +0000 (10:45 +0000)]
implementing #4082 (implement default permission groups)
Andreas Kohlbecker [Fri, 28 Feb 2014 08:26:04 +0000 (08:26 +0000)]
fixing problem with deleting groups see #4054 (Taxeditor, Group Bulkeditor cannot delete Group)
Alexander Oppermann [Thu, 27 Feb 2014 13:58:33 +0000 (13:58 +0000)]
Spring Security configuration added for remote and web app
Alexander Oppermann [Thu, 27 Feb 2014 13:58:01 +0000 (13:58 +0000)]
Spring Security configuration added for remote and web app
Katja Luther [Thu, 27 Feb 2014 08:41:34 +0000 (08:41 +0000)]
fix problem with changeSynonymToAcceptedTaxon of a synonym being part of an homotypical group
Andreas Müller [Wed, 26 Feb 2014 20:22:49 +0000 (20:22 +0000)]
improve author parsing
Andreas Müller [Wed, 26 Feb 2014 15:26:44 +0000 (15:26 +0000)]
minor
Andreas Müller [Wed, 26 Feb 2014 14:57:39 +0000 (14:57 +0000)]
Change signature for IPartionedIO.setRelatedObjects
Andreas Kohlbecker [Wed, 26 Feb 2014 11:21:59 +0000 (11:21 +0000)]
adding TeamOrPersonBaseVoter
Andreas Kohlbecker [Wed, 26 Feb 2014 11:18:28 +0000 (11:18 +0000)]
adding permission class for Teams and Persons wich according validator
Andreas Kohlbecker [Wed, 26 Feb 2014 09:45:13 +0000 (09:45 +0000)]
CdmPermissionClasses for names and references, tests implemented, bug in CdmPermissionClass.from() fixed - #4055 (action enablement adapts to the users granted authorities)
Patric Plitzner [Wed, 26 Feb 2014 08:32:09 +0000 (08:32 +0000)]
- fixed possible NPE when DerivedUnitFacade is used with only a FieldUnit and no DerivedUnit
Andreas Müller [Tue, 25 Feb 2014 22:30:38 +0000 (22:30 +0000)]
add NO_REAK_SPACE to UTF-8
Katja Luther [Tue, 25 Feb 2014 08:34:18 +0000 (08:34 +0000)]
fix NPE in onFlushDirty
Andreas Müller [Fri, 21 Feb 2014 21:33:34 +0000 (21:33 +0000)]
toString for Reference
Andreas Müller [Fri, 21 Feb 2014 21:32:27 +0000 (21:32 +0000)]
minor
Cherian Mathew [Thu, 20 Feb 2014 16:50:28 +0000 (16:50 +0000)]
CdmApplicationDefaultConfiguration : refactoring autowiring for datasource to allow for remoting
Alexander Oppermann [Thu, 20 Feb 2014 10:08:03 +0000 (10:08 +0000)]
Set vaadin generated folders to svn:ignore
Katja Luther [Thu, 20 Feb 2014 09:09:03 +0000 (09:09 +0000)]
add deletegroup
Katja Luther [Thu, 20 Feb 2014 08:48:29 +0000 (08:48 +0000)]
save(Collection<User> users ) uses createUser to encrypt the pwd
Andreas Kohlbecker [Wed, 19 Feb 2014 14:45:06 +0000 (14:45 +0000)]
additional functionality for #4055 (action enablement adapts to the users granted authorities)
Patric Plitzner [Wed, 19 Feb 2014 14:33:27 +0000 (14:33 +0000)]
- changed hard-coded limit to 100
Patric Plitzner [Wed, 19 Feb 2014 14:33:13 +0000 (14:33 +0000)]
- replaced saveOrUpdate() with "bundle" method save()
p.kelbert [Wed, 19 Feb 2014 09:05:25 +0000 (09:05 +0000)]
commit changes TaxonX import
Andreas Müller [Tue, 18 Feb 2014 12:10:33 +0000 (12:10 +0000)]
throw exceptions in Source
Alexander Oppermann [Mon, 17 Feb 2014 15:39:21 +0000 (15:39 +0000)]
Replaced getTitleCache with getNameCache on request
Cherian Mathew [Fri, 14 Feb 2014 16:49:30 +0000 (16:49 +0000)]
switching off remoting
Cherian Mathew [Fri, 14 Feb 2014 16:47:29 +0000 (16:47 +0000)]
CdmApplicationDefaultConfiguration : moved autowiring for sessionFactory and transactionManager from members to set functions
to allow for remoting
CdmApplicationController : catching UnsupportedOperationException for database service call to allow for remoting
defaultApplicationContext : added CdmApplicationRemoteConfiguration exclude to application component scan
httpInvokerServices.xml : corrected bean names
cdmlib-remote-servlet : removed http invoker services config to separate xml file for ease to switch to remoting
Andreas Müller [Fri, 14 Feb 2014 16:47:08 +0000 (16:47 +0000)]
minor
Andreas Müller [Fri, 14 Feb 2014 16:46:36 +0000 (16:46 +0000)]
correct generics for classification
Andreas Müller [Fri, 14 Feb 2014 16:37:54 +0000 (16:37 +0000)]
make description.setTaxon protected and cleanup cyprus altitudes and destinations
Andreas Müller [Fri, 14 Feb 2014 16:33:05 +0000 (16:33 +0000)]
minor
Cherian Mathew [Fri, 14 Feb 2014 11:16:27 +0000 (11:16 +0000)]
refactoring http invoker section to a separate config file to make it easy to test / switch to / from remoting
Andreas Müller [Fri, 14 Feb 2014 10:45:17 +0000 (10:45 +0000)]
fix setting of DerivedUnitFacade.type #4057 and some cleaning up
Cherian Mathew [Thu, 13 Feb 2014 11:25:48 +0000 (11:25 +0000)]
reverting back the cdm application configuration refatoring
Cherian Mathew [Wed, 12 Feb 2014 14:10:21 +0000 (14:10 +0000)]
renaming ICdmApplicationConfiguration to ICdmApplicationDefaultConfiguration
Cherian Mathew [Wed, 12 Feb 2014 13:15:06 +0000 (13:15 +0000)]
renaming CdmApplicationController to CdmApplicationDefaultController
Cherian Mathew [Wed, 12 Feb 2014 13:13:32 +0000 (13:13 +0000)]
refactoring cdm application configuration / controller to allow for remoting
Cherian Mathew [Wed, 12 Feb 2014 13:10:56 +0000 (13:10 +0000)]
httpInvokerServices : remoting services spring config file
ConversationHolder : constructor made protected for ConversationHolderMock
ConversationHolderMock : empty conversation holder for remoting
cdmlib-remote-servlet.xml : added http invoker service configuration (currently commented)
Katja Luther [Wed, 12 Feb 2014 12:27:48 +0000 (12:27 +0000)]
move business logic from change concept to synonym to the service layer
Katja Luther [Wed, 12 Feb 2014 10:14:54 +0000 (10:14 +0000)]
cdmlib fix for deleting groups in bulkeditor #4054
Cherian Mathew [Tue, 11 Feb 2014 17:40:46 +0000 (17:40 +0000)]
added initializeCollection method to initialize a lazy loaded collection
Andreas Kohlbecker [Tue, 11 Feb 2014 16:17:46 +0000 (16:17 +0000)]
A utils class which helps finding security related exceptions in Throwables
Andreas Kohlbecker [Tue, 11 Feb 2014 16:17:40 +0000 (16:17 +0000)]
A utils class which helps finding security related exceptions in Throwables
Katja Luther [Tue, 11 Feb 2014 09:26:39 +0000 (09:26 +0000)]
move taxon to homotypical synonym fixed
Patric Plitzner [Tue, 11 Feb 2014 09:10:52 +0000 (09:10 +0000)]
- added generated vaadin file and folders to svn:ignore
Andreas Kohlbecker [Mon, 10 Feb 2014 18:21:28 +0000 (18:21 +0000)]
User.getAuthorities() made public as preliminary solution to #4053 (Transient field User.authorities not refreshed on reloading entity)
Katja Luther [Mon, 10 Feb 2014 13:26:08 +0000 (13:26 +0000)]
Katja Luther [Mon, 10 Feb 2014 12:11:36 +0000 (12:11 +0000)]
Katja Luther [Mon, 10 Feb 2014 11:26:19 +0000 (11:26 +0000)]
fix changeTaxonToSynonym with homotypic Synonyms
Alexander Oppermann [Mon, 10 Feb 2014 09:36:35 +0000 (09:36 +0000)]
cleaned unused imports
Alexander Oppermann [Mon, 10 Feb 2014 09:25:40 +0000 (09:25 +0000)]
removed not used functionality see Ticket #3520
Alexander Oppermann [Fri, 7 Feb 2014 14:24:30 +0000 (14:24 +0000)]
WS CSV for redlist project
Alexander Oppermann [Fri, 7 Feb 2014 14:24:12 +0000 (14:24 +0000)]
WS CSV for redlist project
Andreas Kohlbecker [Thu, 6 Feb 2014 14:59:05 +0000 (14:59 +0000)]
removing @Override
Andreas Kohlbecker [Thu, 6 Feb 2014 14:21:17 +0000 (14:21 +0000)]
part 1 of fixing #2414 (Group updating doesn't work) by using CascaseType.REFRESH and test method extended
Andreas Kohlbecker [Thu, 6 Feb 2014 14:21:14 +0000 (14:21 +0000)]
more log output to debug CdmDataSourceBase.testConnection()
Andreas Kohlbecker [Thu, 6 Feb 2014 14:21:11 +0000 (14:21 +0000)]
fixing and implementing test for #3782 (Security Context is not updated after editing GrantedAuthorities of a Group)
Andreas Kohlbecker [Thu, 6 Feb 2014 14:21:06 +0000 (14:21 +0000)]
removing old TODO
Andreas Kohlbecker [Thu, 6 Feb 2014 14:21:03 +0000 (14:21 +0000)]
adding method checkServiceAvailable to UriUtils