EDIT

further rename taxonNameEditor -> taxonEditor

ref #10189 split CdmApplicationController into repository and application part in TaxEditor (cont.)

ref #10009 try to remove json-lib-2.4-jdk15

ref #10009 add jcl-over-slf4j and log4j-slf4j-impl as non-ignored libraries

ref 10072 remove log4j12 and apache-log4j-extras from taxeditor and adapt log4j properties

ref #10067, #9359, #10009 adapt dependencies in taxeditor to latest versions in cdmlib and remove all dependencies not needed directly or for export

• this version will not work yet

minor

remove xstream from gitattributes

minor

minor

remove dozer from gitattributes

ref #9359 remove further libraries from lib folder in taxeditor (remaining only tools and swtchart)

removing .classpath file from merge strategy configuration - file is no longer in git

configuring eu.etaxonomy.taxeditor.printpublisher/build.properties with merge=ours

cleanup

ref #9204 remove jaxb1-impl from taxeditor.cdmlib

ref #9204 remove springsource -aopalliance and c-ommons.logging from taxeditor.cdmlib

ref #9207 , ref #9204 upgrade taxeditor.cdmlib to ehcache-2.10.6

ref #9204, ref #9206 cglib from taxeditor.cdmlib, move cglib-nodep to pom

ref #9204 remove avro library from taxeditor.cdmlib

ref #9204 reattache hibernate-envers, upgrade to hibernate 5.1.17 and move hibernate to pom

ref #9204 remove hibernate-envers from taxeditor

ref #9204 remove hibernate-search 4.x libraries from taxeditor

ref #9204 upgrade joda-time and switch to dependency in taxeditor.cdmlib

cleanup

ref #9204 remove batik libraries from taxeditor.cdmlib

cleanup

cleanup and ref #9204 bin.includes for unitils back to 3.4.2 in taxeditor.test

ref #9204 remove xmlunit from taxeditor.cdmlib

ref #9204 remove dbunit from taxeditor.cdmlib and upgrade to 2.7.0 in taxeditor.test

ref #9204 remove ognl from taxeditor

ref #9204 upgrade and remove further libraries in taxeditor (including commons-lang und unitils)

ref #9204 upgrade spring and spring-security and its libraries in taxeditor

ref #9204 upgrade hibernate-validation and libraries in taxeditor

ref #9204 upgrade jackson libraries in taxeditor

Bug fix: CDMSequenceMatrixAdapter now defines valid columns for its character set.
Draft for ExportSingleReadAlignmentWizard added.

Test case for SequenceIDIterator added.

Context menu entry for exporting alignment files added.
ExportSingleReadAlignmentHandler renamed to ExportSequenceToFileHandler.

Exported packages of molecular plugin updated.
Basic export functionality for direct export of consensus sequence alignments implemented (untested).

Initial version of ExportSingleReadAlignmentWizardPage added.

Merge branch 'develop' into LibrAlign

Add missing files to ignore on merge conflict

Add files to ignore on merge conflict if the 'ours' driver is configured

Paste action for AlignmentEditor added.

Cut action for AlignmentEditor implemented.

AbstractFocusedAlignmentAreaHandler added.

AlignmentEditorCopyHandler now sets current action status.

Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/taxeditor into remoting-4.0

Conflicts:
.gitattributes
eu.etaxonomy.taxeditor.cdmlib/.classpath
eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/TaxonEditorInput.java...

• added wizard page listener to react on ENTER key #4853

• added context menu entry for editing classifications
  • used generic extension point for cdmViewer in navigation project (#4865)

• removed empty element from combo dropdown #4448

• refactored naming of modifier section #4448

Merge branch 'move-to-luna' into remoting-4.0

Conflicts:
eu.etaxonomy.taxeditor.cdmlib/.classpath
eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
eu.etaxonomy.taxeditor.cdmlib/build.properties
eu.etaxonomy.taxeditor.cdmlib/pom.xml
eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/etaxonomy/cdm/remotingApplicationContext.xml...

corrected / moved existing tests

bulkeditor: merge of teams and persons and convert team to person and person to team

natural order preferences

add dialog for the natural order preference

#4855 add MoveSynonymToAnotherAcceptedTaxonHandler and some clean up of the plugin.xml especially the delete

• added property tester to check if CdmStore is connected (#4809, #4856)

Partial fix of Ticket #4728

• implemented and added recommended modifier section to Feature DetailView (#4448)

• implemented and added statistical measures section to Feature DetailView (#4448)

Fix Ticket #4729

Fix Ticket #4592

• implemented geo scope detail section (#4592)

• added state vocabulary section to Feature DetailView (#4448)
  • implemented measurement unit section

• added collection section for state vocabularies (#4448)

• imlemente vocabulary combo selection element (#4448)

fix NPE bug and termloading bug for Usage Records #4247

I18n for bulkeditor type #4553

Some changes on TaxEditor i18n: #4553

export of csv files with name informations and for Print output(for caryophyllales)

• i18n language preferences

• added icons for derivates which have character data attached

eu.etaxonomy.taxeditor.product.with.jre : removed since the jre bundling is done on jenkins
ApplicationUtil : added UTC to beta version string
eu.etaxonomy.taxeditor.cdmlib/pom.xml : fixes problem with clean validate - ticket #4733

reverted all changes using maven to setup jre bundle . will do this in a bash script on jenkins instead.

eu.etaxonomy.taxeditor/pom.xml, eu.etaxonomy.taxeditor.product.with.jre/wo.jre : configuration for product bundled with jre
eu.etaxonomy.taxeditor.feature/pom.xml, build.properties.with.jre/wo.jre : configuration for jre dir symlinks and root dir properties...

Added Create Hierarchy Service for Editor as a experimental feature

• added Identifier details section

• added derivate hierarchy section
  • refactored DerivateContentProvider

merge from trunk

• used original label info from facade instead of from the derived unit (fixes #4565)

• implemented framework which links an input element to viewers/editors which are able to display information about the element
  • added ICdmViewer interface
  • added extension point to register ICdmViewer
  • registered EditorCdmViewer for the taxeditor.editor plugin

• added Open in Taxon Editor command to Taxon Bulk Editor (#4536)

• refactored delete configrator dialog
  • added dialog to derivate deletion

ICachedCommonService, CachedCommonServiceImpl : moved class to service package
CdmApplicationRemoteConfiguration, AbstractPersistentCollection, AbstractLazyInitializer : refactored package of CachedCommonService
CdmServiceRequestExecutor : added code for intercepting all services and loading returned objects into current session...

OpenInspectSessionsHandler : handler for opening the inspect session dialog
CacheLoader : moved recursive logic from cdm transient cacher to new class
CdmServiceCacher : now uses CacheLoader to recursively load entities
CdmTransientEntityCacher : moved recursive logic from cdm transient cacher to new class and corrected caching issues...

CdmTransientEntityCacher, EntityCacherDebugResult : moved debug methods to debug result class
ProxyUtils : new class for util methods to do with hibernate proxy objects
ICdmEntitySessionEnabled, CdmEntitySessionInput, PolytomousKeyEditorInput, TaxonNameEditor, PolytomousKeyViewPart, TaxonNavigator, AbstractCdmViewPart, MultiPageTaxonEditor : Added getRootEntities method...

CdmRemoteCacheManager : added cache getter methods
CdmTransientEntityCacher, CdmEntitySession, CdmEntitySessionManager, ICdmEntitySession, ICdmEntitySessionManager, ICdmEntitySessionManagerObserver, MockCdmEntitySession, MockCdmEntitySessionManager , eu.etaxonomy.taxeditor.cdmlib/src/main/resources/cdmlib-ehcache.xml : added statistics config , getter method for live stats and observer to update when sessions are bound and disposed...

• added option to toggle the delete configurator parameters in taxon deletion dialog (#4656)

• added configurator settings to taxon deletion dialog

CdmModelCacher : added recursive search in super classes
CdmTransientEntityCacher : corrected caching
EntityCacherDebugResult : new debug result object
CdmEntitySession, ICdmEntitySession, MockCdmEntitySession : added debug method
CdmEntitySessionInput : new super class for editor input objects...

refactoring and added tests

CdmTransientEntityCacher : comments and cleanup
MockCdmEntitySessionManager, MockCdmEntitySession : implementing new interface methods
renamed ISessionEventListener to ICdmEntitySessionEnabled
ICdmEntitySession, CdmEntitySession : added methods to register session observer and add change events...

reverting incorrect commit

added h2 db to resources and delete test to test class

cleaned up lib dir and updated unitils version
CdmAuthenticatedHttpInvokerRequestExecutor : custom authentication executor (not used for now)
MockCdmEntitySession : mock session for stand-alone editor

merge from trunk

editorApplicationContext : reverted stand-alone app context conf
RemotingLoginDialog : updated dialog with server fetch

updated current tests and added new ones