taxeditor.git
8 years agoUpdated version in config files to 3.3.3-SNAPSHOT
edit-jenkins [Fri, 11 Apr 2014 15:37:16 +0000 (15:37 +0000)]
Updated version in config files to 3.3.3-SNAPSHOT

8 years agoUpdated version in config files to 3.3.2
edit-jenkins [Fri, 11 Apr 2014 15:30:18 +0000 (15:30 +0000)]
Updated version in config files to 3.3.2

8 years ago - commented "Original Label Data" text field because it is not yet used in trunk
Patric Plitzner [Thu, 10 Apr 2014 06:38:49 +0000 (06:38 +0000)]
 - commented "Original Label Data" text field because it is not yet used in trunk

8 years agoCdmStore : no longer need to set configuration in hibernate classes here
Cherian Mathew [Wed, 9 Apr 2014 14:23:23 +0000 (14:23 +0000)]
CdmStore : no longer need to set configuration in hibernate classes here
CdmStoreConnector : new method to retrieve configuration based on cdm source type

8 years agoCdmPersistentRemoteSource : implemented all source methods including save and delete
Cherian Mathew [Wed, 9 Apr 2014 14:19:16 +0000 (14:19 +0000)]
CdmPersistentRemoteSource : implemented all source methods including save and delete
CdmRemoteSourceException : new exception to deal with cdm source errors
CdmRemoteSourceBase : added default constructor

8 years agoCdmApplicationRemoteController : directly loads CdmApplicationRemoteConfiguration...
Cherian Mathew [Wed, 9 Apr 2014 14:16:59 +0000 (14:16 +0000)]
CdmApplicationRemoteController : directly loads CdmApplicationRemoteConfiguration bean and sets configuration in hibernate classes
CdmApplicationRemoteConfiguration : no longer need the bean name hack due to update in CdmApplicationRemoteController

8 years agoisRemoting is no longer based on a bean in the application context, but
Cherian Mathew [Wed, 9 Apr 2014 14:15:16 +0000 (14:15 +0000)]
isRemoting is no longer based on a bean in the application context, but
the type of cdm source

8 years agoisRemoting is no longer based on a bean in the application context, but
Cherian Mathew [Wed, 9 Apr 2014 14:13:46 +0000 (14:13 +0000)]
isRemoting is no longer based on a bean in the application context, but
the type of cdm source

8 years agocdm.datasources.xml : added test sources settings file
Cherian Mathew [Wed, 9 Apr 2014 14:09:21 +0000 (14:09 +0000)]
cdm.datasources.xml : added test sources settings file
CdmRemoteSourceTest, RemoteLazyLoadingTest : updated tests
HttpInvokerServicesTest, CdmPersistentRemoteSourceTest, CdmApplicationRemoteControllerTest : new test classes for remoting
RemoteApplicationConfigurationTest : no longer a real test, but a super class for remote tests

8 years ago - fixed link to online svn repo
Patric Plitzner [Wed, 9 Apr 2014 08:15:26 +0000 (08:15 +0000)]
 - fixed link to online svn repo

8 years ago - added memento restore mechanism to DerivateView (partially)
Patric Plitzner [Tue, 8 Apr 2014 06:53:41 +0000 (06:53 +0000)]
 - added memento restore mechanism to DerivateView (partially)

8 years ago - set default derivate typ filter to "unknown"
Patric Plitzner [Tue, 8 Apr 2014 06:53:11 +0000 (06:53 +0000)]
 - set default derivate typ filter to "unknown"

8 years ago - javadoc
Patric Plitzner [Tue, 8 Apr 2014 06:52:45 +0000 (06:52 +0000)]
 - javadoc

8 years ago - refresh view instead of setting the editor input
Patric Plitzner [Mon, 7 Apr 2014 11:11:39 +0000 (11:11 +0000)]
 - refresh view instead of setting the editor input

8 years ago - cleaned DerivateView context menu code and classes
Patric Plitzner [Mon, 7 Apr 2014 09:43:10 +0000 (09:43 +0000)]
 - cleaned DerivateView context menu code and classes

8 years ago - partially added handling of input fields
Patric Plitzner [Mon, 7 Apr 2014 09:42:22 +0000 (09:42 +0000)]
 - partially added handling of input fields

8 years agoadded new remote package
Cherian Mathew [Fri, 4 Apr 2014 16:09:47 +0000 (16:09 +0000)]
added new remote package

8 years agocomments and javadoc
Cherian Mathew [Fri, 4 Apr 2014 15:42:38 +0000 (15:42 +0000)]
comments and javadoc

8 years agoremoved repeated call to get all cdm sources
Cherian Mathew [Fri, 4 Apr 2014 09:42:25 +0000 (09:42 +0000)]
removed repeated call to get all cdm sources

8 years agoupdating to align with refactored cdm source classes / interfaces
Cherian Mathew [Fri, 4 Apr 2014 09:41:10 +0000 (09:41 +0000)]
updating to align with refactored cdm source classes / interfaces

8 years agoAdding CDM Remote Source set of classes to allow editor to connect to a remote cdmserver
Cherian Mathew [Fri, 4 Apr 2014 09:28:07 +0000 (09:28 +0000)]
Adding CDM Remote Source set of classes to allow editor to connect to a remote cdmserver

8 years agoCdmApplicationRemoteConfiguration : removed spring bean name hack, since we now have...
Cherian Mathew [Fri, 4 Apr 2014 09:27:04 +0000 (09:27 +0000)]
CdmApplicationRemoteConfiguration : removed spring bean name hack, since we now have a new controller
CdmApplicationRemoteController : new Controller class to handle remoting
AbstractLazyInitializer / AbstractPersistentCollection : added missing methods to check if proxy object is initialized
CdmRemoteSourceTest : Added new test class to test the CDM Remote Source
httpInvokerServiceClients.xml : added primer service

8 years ago - refactored context menu for DerivateView to be programmatic instead of declarative...
Patric Plitzner [Wed, 2 Apr 2014 14:08:30 +0000 (14:08 +0000)]
 - refactored context menu for DerivateView to be programmatic instead of declarative (using plugin.xml)
 - fixed icon bug for DerivateSearchView

8 years ago - only show Copy/Paste context menu for SingleRead/Sequence
Patric Plitzner [Wed, 2 Apr 2014 11:01:53 +0000 (11:01 +0000)]
 - only show Copy/Paste context menu for SingleRead/Sequence

8 years ago - added update() method to DerivateView
Patric Plitzner [Wed, 2 Apr 2014 09:37:31 +0000 (09:37 +0000)]
 - added update() method to DerivateView
 - display different icon for SingleReads linked to multiple Sequences

8 years ago - added util method to get the TreeNode out of a selection
Patric Plitzner [Wed, 2 Apr 2014 07:55:16 +0000 (07:55 +0000)]
 - added util method to get the TreeNode out of a selection

8 years ago - added Copy/Paste for SingleRead->Sequence to DerivateView
Patric Plitzner [Tue, 1 Apr 2014 15:14:26 +0000 (15:14 +0000)]
 - added Copy/Paste for SingleRead->Sequence to DerivateView
   - copying actually just creates a link

8 years ago - fixed user message
Patric Plitzner [Tue, 1 Apr 2014 08:03:12 +0000 (08:03 +0000)]
 - fixed user message

8 years ago - added gel photo detail element to Amplification wizard
Patric Plitzner [Tue, 1 Apr 2014 07:44:46 +0000 (07:44 +0000)]
 - added gel photo detail element to Amplification wizard

8 years ago - removed Amplification as a TreeNode from the DerivateView
Patric Plitzner [Tue, 1 Apr 2014 06:51:22 +0000 (06:51 +0000)]
 - removed Amplification as a TreeNode from the DerivateView
 - added Amplification to DetailsView of SingleRead as an EntitySelectionElement

8 years ago - fixed javadoc
Patric Plitzner [Tue, 1 Apr 2014 06:49:18 +0000 (06:49 +0000)]
 - fixed javadoc

8 years ago - organize imports for new molecular services
Patric Plitzner [Mon, 31 Mar 2014 12:19:33 +0000 (12:19 +0000)]
 - organize imports for new molecular services

8 years ago - fix cdmlib version number in .classpath (why does maven not generate this anymore?)
Patric Plitzner [Mon, 31 Mar 2014 12:19:17 +0000 (12:19 +0000)]
 - fix cdmlib version number in .classpath (why does maven not generate this anymore?)
 - added "molecular" package to exported packages
 - organize imports for new molecular services

8 years ago - used "move derivate" methods of service layer
Patric Plitzner [Mon, 31 Mar 2014 08:10:36 +0000 (08:10 +0000)]
 - used "move derivate" methods of service layer
 - added java doc

8 years agoUpdated version in config files to 3.3.2-SNAPSHOT
edit-jenkins [Fri, 28 Mar 2014 17:01:09 +0000 (17:01 +0000)]
Updated version in config files to 3.3.2-SNAPSHOT

8 years agoUpdated version in config files to 3.3.1
edit-jenkins [Fri, 28 Mar 2014 16:28:13 +0000 (16:28 +0000)]
Updated version in config files to 3.3.1

8 years ago - moved move-logic to occurrence service layer
Patric Plitzner [Wed, 26 Mar 2014 14:37:30 +0000 (14:37 +0000)]
 - moved move-logic to occurrence service layer

8 years ago - reset input fields of DerivateSearchView when context stops
Patric Plitzner [Wed, 26 Mar 2014 12:35:41 +0000 (12:35 +0000)]
 - reset input fields of DerivateSearchView when context stops

8 years ago - added drag'n'drop support for Sequences
Patric Plitzner [Wed, 26 Mar 2014 07:39:46 +0000 (07:39 +0000)]
 - added drag'n'drop support for Sequences
 - added context listener to DerivateSearchView
 - refactored MVC pattern of DerivateSearchView

8 years ago - added support for SingleRead drag'n'drop
Patric Plitzner [Tue, 25 Mar 2014 16:08:44 +0000 (16:08 +0000)]
 - added support for SingleRead drag'n'drop

8 years ago - implemented drag'n'drop support for SpecimenOrObservationBase in Derivate View
Patric Plitzner [Tue, 25 Mar 2014 13:30:25 +0000 (13:30 +0000)]
 - implemented drag'n'drop support for SpecimenOrObservationBase in Derivate View

8 years ago - minor
Patric Plitzner [Tue, 25 Mar 2014 08:35:04 +0000 (08:35 +0000)]
 - minor

8 years ago - minor enhancement
Patric Plitzner [Mon, 24 Mar 2014 15:10:51 +0000 (15:10 +0000)]
 - minor enhancement

8 years ago - added timeout to internet availability check
Patric Plitzner [Mon, 24 Mar 2014 13:24:08 +0000 (13:24 +0000)]
 - added timeout to internet availability check

8 years ago - fixed ClassCastException for FeatureNodeContainers
Patric Plitzner [Mon, 24 Mar 2014 13:23:36 +0000 (13:23 +0000)]
 - fixed ClassCastException for FeatureNodeContainers

8 years ago - added basic drag'n'drop support to DerivateView
Patric Plitzner [Mon, 24 Mar 2014 10:39:36 +0000 (10:39 +0000)]
 - added basic drag'n'drop support to DerivateView

8 years agoadded more tests for both lazy loading entities and collections
Cherian Mathew [Thu, 20 Mar 2014 15:20:24 +0000 (15:20 +0000)]
added more tests for both lazy loading entities and collections

8 years agoadding missing methods
Andreas Kohlbecker [Thu, 20 Mar 2014 15:06:18 +0000 (15:06 +0000)]
adding missing methods

8 years ago#4114 sort order in taxon navigator
Katja Luther [Thu, 20 Mar 2014 12:51:00 +0000 (12:51 +0000)]
#4114 sort order in taxon navigator

8 years ago - fixed class cast exception resulting from TreeNodes of DerivateView
Patric Plitzner [Wed, 19 Mar 2014 14:53:56 +0000 (14:53 +0000)]
 - fixed class cast exception resulting from TreeNodes of DerivateView

8 years ago - added context menu for TissueSample in DerivateView
Patric Plitzner [Wed, 19 Mar 2014 14:45:36 +0000 (14:45 +0000)]
 - added context menu for TissueSample in DerivateView

8 years agowhile fixing a bug, revert the setting of the comparator.
Katja Luther [Tue, 18 Mar 2014 13:15:06 +0000 (13:15 +0000)]
while fixing a bug, revert the setting of the comparator.

8 years agotaxeditor part of fix for #4121 (Changing password does not work)
Andreas Kohlbecker [Mon, 17 Mar 2014 22:03:05 +0000 (22:03 +0000)]
taxeditor part of fix for #4121 (Changing password does not work)

8 years agoavoiding problems which where due to a fix for ticket #3822
Andreas Kohlbecker [Mon, 17 Mar 2014 22:03:02 +0000 (22:03 +0000)]
avoiding problems which where due to a fix for ticket #3822

8 years agowith the fixed compareTo method the TaxonNodeComparator should work (#4114)
Katja Luther [Mon, 17 Mar 2014 12:50:59 +0000 (12:50 +0000)]
with the fixed compareTo method the TaxonNodeComparator should work (#4114)

8 years ago - added isEnabled() method to IEnableableFormElement
Patric Plitzner [Mon, 17 Mar 2014 09:02:41 +0000 (09:02 +0000)]
 - added isEnabled() method to IEnableableFormElement

8 years ago - added missing interface method
Patric Plitzner [Mon, 17 Mar 2014 08:58:10 +0000 (08:58 +0000)]
 - added missing interface method

8 years ago - removed StoreUtil.getCdmEntity() invocation (#4091)
Patric Plitzner [Mon, 17 Mar 2014 08:43:08 +0000 (08:43 +0000)]
 - removed StoreUtil.getCdmEntity() invocation (#4091)

8 years ago - fixed context menu options
Patric Plitzner [Mon, 17 Mar 2014 07:54:29 +0000 (07:54 +0000)]
 - fixed context menu options

8 years ago - implemented EntitySelectionElement for Primer
Patric Plitzner [Mon, 17 Mar 2014 07:51:57 +0000 (07:51 +0000)]
 - implemented EntitySelectionElement for Primer
 - adapted details views with primer selection element

8 years ago - added missing interface method
Patric Plitzner [Mon, 17 Mar 2014 07:50:39 +0000 (07:50 +0000)]
 - added missing interface method

8 years agoimplementing #4120: User always needs to have the right to change password and hidin...
Andreas Kohlbecker [Fri, 14 Mar 2014 13:52:45 +0000 (13:52 +0000)]
implementing  #4120: User always needs to have the right to change password and hiding all user related menu contributions if no user is logged in

8 years agoRevert "#4114 sort order in taxon navigator " to avoid blocking bug
Andreas Kohlbecker [Fri, 14 Mar 2014 13:52:41 +0000 (13:52 +0000)]
Revert "#4114 sort order in taxon navigator " to avoid blocking bug

This reverts commit 1ef7ab55c5d437aba039bc10ee8d81e12f402309.

8 years agoadding missing manifest file
Cherian Mathew [Thu, 13 Mar 2014 21:24:09 +0000 (21:24 +0000)]
adding missing manifest file

8 years agosetting application configuration and boolean remoting flag (bean) in hibernate proxy...
Cherian Mathew [Thu, 13 Mar 2014 20:23:45 +0000 (20:23 +0000)]
setting application configuration and boolean remoting flag (bean) in hibernate proxy classes to differentiate local and remoting

8 years agoafter review final modification for #4115 ('editor' users cannot create new referenc...
Andreas Kohlbecker [Thu, 13 Mar 2014 15:51:44 +0000 (15:51 +0000)]
after review final modification for  #4115 ('editor' users cannot create new references via the reference select list)

8 years agoimplementing #4123 (add idInVocabulary to term labels in editor)
Andreas Kohlbecker [Thu, 13 Mar 2014 15:09:15 +0000 (15:09 +0000)]
implementing #4123 (add idInVocabulary to term labels in editor)

8 years agoremoving unavailable extension eu.etaxonomy.cdm.remote.controller.csv
Andreas Kohlbecker [Thu, 13 Mar 2014 15:09:11 +0000 (15:09 +0000)]
removing unavailable extension eu.etaxonomy.cdm.remote.controller.csv

8 years agoadded remote collection method checks in addition to local for lists and sets
Cherian Mathew [Thu, 13 Mar 2014 15:00:56 +0000 (15:00 +0000)]
added remote collection method checks in addition to local for lists and sets

8 years ago#4114 sort order in taxon navigator
Katja Luther [Thu, 13 Mar 2014 13:24:08 +0000 (13:24 +0000)]
#4114 sort order in taxon navigator

8 years agocatching PermissionDeniedExceptions when only doing a check, so these exceptions...
Andreas Kohlbecker [Thu, 13 Mar 2014 12:39:49 +0000 (12:39 +0000)]
catching PermissionDeniedExceptions when only doing a check, so these exceptions no longer pollute the log

8 years agoavoiding NPE
Andreas Kohlbecker [Thu, 13 Mar 2014 12:39:45 +0000 (12:39 +0000)]
avoiding NPE

8 years agoadded test class for persistent collections and also a base class for configuringsett...
Cherian Mathew [Thu, 13 Mar 2014 09:00:53 +0000 (09:00 +0000)]
added test class for persistent collections and also a base class for configuringsetting up remote configuration.

8 years agoadded call to remoting with correct check
Cherian Mathew [Wed, 12 Mar 2014 14:24:37 +0000 (14:24 +0000)]
added call to remoting with correct check

8 years agofixing #4115 ('editor' users cannot create new references via the reference select...
Andreas Kohlbecker [Tue, 11 Mar 2014 17:47:18 +0000 (17:47 +0000)]
fixing #4115 ('editor' users cannot create new references via the reference select list)

8 years agofixing #4116 (ClassCastException when selecting Euro+Med top level area in Distributi...
Andreas Kohlbecker [Tue, 11 Mar 2014 17:10:09 +0000 (17:10 +0000)]
fixing #4116 (ClassCastException when selecting Euro+Med top level area in DistributionElement details view)

8 years agofixing problem of publish checkbox disabled state being overwritten
Andreas Kohlbecker [Tue, 11 Mar 2014 16:38:15 +0000 (16:38 +0000)]
fixing problem of publish checkbox disabled state being overwritten

8 years ago - refactored selection of DerivateView to be TreeNode
Patric Plitzner [Tue, 11 Mar 2014 07:38:55 +0000 (07:38 +0000)]
 - refactored selection of DerivateView to be TreeNode
 - adapted selection handling
 - restructured derivate hierarchy
  - Amplifications are now a direct child of Sequences
  - the can only be created when having a SingleRead
  - this representation does not affect the cdm structure

8 years ago - fixed refresh problem
Patric Plitzner [Tue, 11 Mar 2014 07:34:50 +0000 (07:34 +0000)]
 - fixed refresh problem

8 years ago - clean code
Patric Plitzner [Mon, 10 Mar 2014 15:01:56 +0000 (15:01 +0000)]
 - clean code

8 years agofixing: #4110 (imlement nicer warning dialogue in Taxon Editor for permission denied...
Andreas Kohlbecker [Mon, 10 Mar 2014 11:43:47 +0000 (11:43 +0000)]
fixing: #4110 (imlement nicer warning dialogue in Taxon Editor for permission denied exception)

8 years agomore details in exception message of StoreUtil.getCdmEntity()
Andreas Kohlbecker [Thu, 6 Mar 2014 17:09:03 +0000 (17:09 +0000)]
more details in exception message of StoreUtil.getCdmEntity()

8 years agodnd support in taxon navigator for Taxonnodes protected regarding user permissions...
Andreas Kohlbecker [Thu, 6 Mar 2014 16:59:40 +0000 (16:59 +0000)]
dnd support in taxon navigator for Taxonnodes protected regarding user permissions - #4055 (action enablement adapts to the users granted authorities)

8 years agoavoiding NPE and other exceptions
Andreas Kohlbecker [Wed, 5 Mar 2014 17:18:31 +0000 (17:18 +0000)]
avoiding NPE and other exceptions

8 years agoupdating project url in pom.xml
Andreas Kohlbecker [Wed, 5 Mar 2014 17:18:26 +0000 (17:18 +0000)]
updating project url in pom.xml

8 years agono longer using a conversation for the login dialog and thus fixing problems after...
Andreas Kohlbecker [Wed, 5 Mar 2014 17:18:25 +0000 (17:18 +0000)]
no longer using a conversation for the login dialog and thus fixing problems after putting wrong credentials

8 years agofixing setEnabled method
Andreas Kohlbecker [Wed, 5 Mar 2014 17:15:22 +0000 (17:15 +0000)]
fixing setEnabled method

8 years ago - removed dummy data from SpecimenImport
Patric Plitzner [Wed, 5 Mar 2014 14:33:12 +0000 (14:33 +0000)]
 - removed dummy data from SpecimenImport

8 years ago - fixed event handling by creating and linking the missing elements
Patric Plitzner [Wed, 5 Mar 2014 14:28:32 +0000 (14:28 +0000)]
 - fixed event handling by creating and linking the missing elements

8 years ago - added missing DNA Quality section
Patric Plitzner [Wed, 5 Mar 2014 12:24:41 +0000 (12:24 +0000)]
 - added missing DNA Quality section

8 years ago - adpated DNA DetailsViews according to current development
Patric Plitzner [Wed, 5 Mar 2014 12:18:55 +0000 (12:18 +0000)]
 - adpated DNA DetailsViews according to current development

8 years ago - renamed getBaseUnit() to baseUnit()
Patric Plitzner [Wed, 5 Mar 2014 12:16:51 +0000 (12:16 +0000)]
 - renamed getBaseUnit() to baseUnit()

8 years ago - added transparency to icons
Patric Plitzner [Wed, 5 Mar 2014 12:16:11 +0000 (12:16 +0000)]
 - added transparency to icons

8 years ago - added util method to get for getting a CDM entity (used in authenication/permissio...
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

8 years ago - added icons for Amplification, Sequence and SingleRead
Patric Plitzner [Tue, 4 Mar 2014 16:18:28 +0000 (16:18 +0000)]
 - added icons for Amplification, Sequence and SingleRead

8 years ago - added code to show icon for Amplification, Sequence and SingleRead (image files...
Patric Plitzner [Tue, 4 Mar 2014 08:25:39 +0000 (08:25 +0000)]
 - added code to show icon for Amplification, Sequence and SingleRead (image files still missing)
 - removed text fields for media file in dna DetailsViews
 - added contig file in Sequence DetailsView

8 years ago - added cascading save to pherogram (Media) of SingleRead
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)

8 years agofixing missing text of Group members (User) in details section
Andreas Kohlbecker [Fri, 28 Feb 2014 11:17:31 +0000 (11:17 +0000)]
fixing missing text of Group members (User) in details section

8 years agofix problem with changeSynonymToAcceptedTaxon of a synonym being part of an homotypic...
Katja Luther [Thu, 27 Feb 2014 08:42:33 +0000 (08:42 +0000)]
fix problem with changeSynonymToAcceptedTaxon of a synonym being part of an homotypical group

8 years agoprotecting editing capabilities of names references and authors - #4055 (action...
Andreas Kohlbecker [Wed, 26 Feb 2014 16:25:40 +0000 (16:25 +0000)]
protecting editing capabilities of names references and authors -  #4055 (action enablement adapts to the users granted authorities)