bug #6480: Re-saved by cascade in specimen bulk editor - EDIT - EDIT Project Management

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bug #6480

closed

Re-saved by cascade in specimen bulk editor

Added by Andreas Müller about 6 years ago. Updated over 1 year ago.

Status:

Closed

Priority:

Highest

Assignee:

Katja Luther

Category:

taxeditor

Target version:

Release 4.7

Start date:

Due date:

% Done:

100%

Estimated time:

Severity:

normal

Found in Version:

Description

When trying to delete a specimen that belongs to a field unit and that does have a sibling specimen I get the following exception, if all 3 specimenOrObservations are shown in the bulk editor.

To reproduce you may create in specimen tree editor a field with locality "yyyy" and add 2 child specimen. Go to bulk editor, search for "yyyy". 3 units should show up. Delete one of the 2 derived units, => exception.

login : admin
editor version : 4.6.0.201702272351
server : test.e-taxonomy.eu (edit-test) / cichorieae
schema version : 4.1.0.0.201607300000
os : Windows Server 2012 R2 6.3 amd64
java : 1.8.0_121
org.hibernate.ObjectDeletedException: deleted object would be re-saved by cascade (remove deleted object from associations): [eu.etaxonomy.cdm.model.occurrence.DerivedUnit#5202]
    at org.hibernate.internal.SessionImpl.forceFlush(SessionImpl.java:1301)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:170)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:97)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:73)
    at org.hibernate.internal.SessionImpl.fireSaveOrUpdate(SessionImpl.java:648)
    at org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:640)
    at org.hibernate.engine.spi.CascadingActions$5.cascade(CascadingActions.java:218)
    at org.hibernate.engine.internal.Cascade.cascadeToOne(Cascade.java:398)
    at org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:323)
    at org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:162)
    at org.hibernate.engine.internal.Cascade.cascadeCollectionElements(Cascade.java:431)
    at org.hibernate.engine.internal.Cascade.cascadeCollection(Cascade.java:363)
    at org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:326)
    at org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:162)
    at org.hibernate.engine.internal.Cascade.cascade(Cascade.java:111)
    at org.hibernate.event.internal.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:150)
    at org.hibernate.event.internal.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:141)
    at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:74)
    at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:38)
    at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1282)
    at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:465)
    at org.hibernate.internal.SessionImpl.flushBeforeTransactionCompletion(SessionImpl.java:2963)
    at org.hibernate.internal.SessionImpl.beforeTransactionCompletion(SessionImpl.java:2339)
    at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.beforeTransactionCompletion(JdbcCoordinatorImpl.java:485)
    at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl.beforeCompletionCallback(JdbcResourceLocalTransactionCoordinatorImpl.java:147)
    at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl.access$100(JdbcResourceLocalTransactionCoordinatorImpl.java:38)
    at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.commit(JdbcResourceLocalTransactionCoordinatorImpl.java:231)
    at org.hibernate.engine.transaction.internal.TransactionImpl.commit(TransactionImpl.java:65)
    at org.springframework.orm.hibernate5.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:581)
    at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:761)
    at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:730)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:485)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:291)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy2769.delete(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.remoting.support.RemoteInvocationTraceInterceptor.invoke(RemoteInvocationTraceInterceptor.java:78)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy3045.delete(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:212)
    at org.springframework.remoting.support.DefaultRemoteInvocationExecutor.invoke(DefaultRemoteInvocationExecutor.java:39)
    at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78)
    at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114)
    at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:74)
    at org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter.handle(HttpRequestHandlerAdapter.java:51)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959)
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893)
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:969)
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:871)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:845)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808)
    at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:316)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:122)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:169)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:48)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:213)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:120)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:64)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:53)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:262)
    at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
    at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:121)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
    at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
    at org.eclipse.jetty.server.Server.handle(Server.java:497)
    at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
    at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
    at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555)
    at java.lang.Thread.run(Thread.java:745)
    at org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTraceIfPossible(RemoteInvocationUtils.java:45)
    at org.springframework.remoting.support.RemoteInvocationResult.recreate(RemoteInvocationResult.java:149)
    at org.springframework.remoting.support.RemoteInvocationBasedAccessor.recreateRemoteInvocationResult(RemoteInvocationBasedAccessor.java:85)
    at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:150)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy39.delete(Unknown Source)
    at eu.etaxonomy.taxeditor.bulkeditor.input.OccurrenceEditorInput.delete(OccurrenceEditorInput.java:114)
    at eu.etaxonomy.taxeditor.bulkeditor.input.OccurrenceEditorInput.delete(OccurrenceEditorInput.java:1)
    at eu.etaxonomy.taxeditor.annotatedlineeditor.AnnotatedLineDocumentProvider.doSaveDocument(AnnotatedLineDocumentProvider.java:280)
    at org.eclipse.ui.texteditor.AbstractDocumentProvider$1$SaveOperation.execute(AbstractDocumentProvider.java:610)
    at org.eclipse.ui.texteditor.AbstractDocumentProvider$DocumentProviderOperation.run(AbstractDocumentProvider.java:74)
    at org.eclipse.ui.texteditor.AbstractDocumentProvider.executeOperation(AbstractDocumentProvider.java:553)
    at org.eclipse.ui.texteditor.AbstractDocumentProvider.saveDocument(AbstractDocumentProvider.java:629)
    at org.eclipse.ui.texteditor.AbstractTextEditor.performSave(AbstractTextEditor.java:5048)
    at org.eclipse.ui.texteditor.AbstractTextEditor.doSave(AbstractTextEditor.java:4837)
    at eu.etaxonomy.taxeditor.annotatedlineeditor.AnnotatedLineEditor.doSave(AnnotatedLineEditor.java:250)
    at eu.etaxonomy.taxeditor.bulkeditor.BulkEditor.doSave(BulkEditor.java:263)
    at org.eclipse.ui.texteditor.AbstractTextEditor$TextEditorSavable.doSave(AbstractTextEditor.java:7177)
    at org.eclipse.ui.Saveable.doSave(Saveable.java:214)
    at org.eclipse.ui.internal.SaveableHelper.doSaveModel(SaveableHelper.java:349)
    at org.eclipse.ui.internal.SaveableHelper$3.run(SaveableHelper.java:195)
    at org.eclipse.ui.internal.SaveableHelper$5.run(SaveableHelper.java:277)
    at org.eclipse.jface.operation.ModalContext.runInCurrentThread(ModalContext.java:464)
    at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:372)
    at org.eclipse.jface.window.ApplicationWindow$1.run(ApplicationWindow.java:759)
    at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
    at org.eclipse.jface.window.ApplicationWindow.run(ApplicationWindow.java:756)
    at org.eclipse.ui.internal.WorkbenchWindow.run(WorkbenchWindow.java:2649)
    at org.eclipse.ui.internal.SaveableHelper.runProgressMonitorOperation(SaveableHelper.java:285)
    at org.eclipse.ui.internal.SaveableHelper.runProgressMonitorOperation(SaveableHelper.java:264)
    at org.eclipse.ui.internal.SaveableHelper.saveModels(SaveableHelper.java:207)
    at org.eclipse.ui.internal.SaveableHelper.savePart(SaveableHelper.java:144)
    at org.eclipse.ui.internal.EditorManager.savePart(EditorManager.java:1399)
    at org.eclipse.ui.internal.WorkbenchPage.savePart(WorkbenchPage.java:3416)
    at org.eclipse.ui.internal.WorkbenchPage.saveEditor(WorkbenchPage.java:3429)
    at org.eclipse.ui.internal.handlers.SaveHandler.execute(SaveHandler.java:54)
    at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:293)
    at org.eclipse.core.commands.Command.executeWithChecks(Command.java:476)
    at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508)
    at org.eclipse.ui.internal.handlers.HandlerService.executeCommand(HandlerService.java:169)
    at org.eclipse.ui.internal.handlers.SlaveHandlerService.executeCommand(SlaveHandlerService.java:241)
    at org.eclipse.ui.menus.CommandContributionItem.handleWidgetSelection(CommandContributionItem.java:829)
    at org.eclipse.ui.menus.CommandContributionItem.access$19(CommandContributionItem.java:815)
    at org.eclipse.ui.menus.CommandContributionItem$5.handleEvent(CommandContributionItem.java:805)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4165)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3754)
    at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2701)
    at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2665)
    at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2499)
    at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:679)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:668)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
    at eu.etaxonomy.taxeditor.Application.start(Application.java:24)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1410)

Delete works in the specimen tree editor.

Files

NLS_error.png (14.7 KB) NLS_error.png

Andreas Müller, 06/15/2017 02:40 PM

Related issues

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Updated by Katja Luther about 6 years ago

I don't get an exception, but I have to close the Specimen Editor to see the result.

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Updated by Katja Luther about 6 years ago

Status changed from New to In Progress

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Updated by Katja Luther about 6 years ago

Status changed from In Progress to Resolved
% Done changed from 0 to 50

Applied in changeset cdmlib|09a260bbd5261aa3635a12edfb0cb1d9fb76424a.

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Updated by Katja Luther about 6 years ago

Assignee changed from Katja Luther to Andreas Müller
% Done changed from 50 to 80

please review

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Updated by Andreas Müller about 6 years ago

Status changed from Resolved to Feedback
Assignee changed from Andreas Müller to Katja Luther

I still get the exception. Here is what I do in a bit more detail:

Open Specimen-Editor
Create FieldUnit with locality "xyza"
Save
Add PreservedSpecimen for the above FieldUnit with Accession Number "2222"
Save
Add PreservedSpecimen for the above FieldUnit with Accession Number "3333"
Save
Goto Specimen Bulk Editor
Search for "xyza" => should return 3 entries
Delete Preserved Specimen entry labeled "3333"
Save => exception

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Updated by Katja Luther about 6 years ago

Status changed from Feedback to Resolved
% Done changed from 80 to 50

Applied in changeset cdmlib|07dbf1bcf8687df44cd3e5fcb90acedb4a6a71f6.

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Updated by Katja Luther about 6 years ago

Status changed from Resolved to Feedback
% Done changed from 50 to 80

sorry, did not see that the problem was in bulkeditor. now I added the delete configurator to the bulk editor delete and removed the gathering event from field unit before deletion.

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Updated by Katja Luther about 6 years ago

Status changed from Feedback to Resolved
Assignee changed from Katja Luther to Andreas Müller

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Updated by Andreas Müller almost 6 years ago

File NLS_error.png NLS_error.png added
Status changed from Resolved to Feedback
Assignee changed from Andreas Müller to Katja Luther

There is a problem with the message displayed in Confirm Deletion dialog. Looks like i18n does not work correctly. See attachement.

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#10

Updated by Andreas Müller almost 6 years ago

Labels:

"Delete Children" => "Delete children", to be consistent
Delete from "Described specimen" => ... "described specimen"

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#11

Updated by Andreas Müller almost 6 years ago

I wonder if "Delete children" makes sense in bulk editor. This is a flat view. Users may not know what a "child" is. Either we completely remove it or we adjust it to "Delete all derived units". This is different in the Specimen-Editor where the tree is visible and therefore it might be clearer what is meant by "child".

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#12