bug #8315
closedParsing existing references with inReferences changes the inReference
100%
Description
mail Mareike Liese:
Hallo,
leider kann ich in der Datenbank nichts speichern.
Ich hab über die Art auf Enter geklickt, und anschließend aus einer Excel Tabelle das Synonym kopiert und eingefügt. Beim speichern kommt dann diese Meldung.
Freundliche Grüße
Mareike Liese
login : m.liese editor version : 5.7.1 server : api.cybertaxonomy.org (cybertaxonomy.org) / caryophyllales_spp schema version : 5.5.0.0.20190221 os : Windows 7 6.1 amd64 java : 1.8.0_121 org.eclipse.e4.core.di.InjectionException: org.springframework.orm.hibernate5.HibernateSystemException: [UPDATE] not permitted for 'm.liese' on Reference[uuid:47edf58d-cb47-4c61-b2f6-2a779ca842d5', toString:'Reference [type=Article, id= 26293, uuid=47edf58d-cb47-4c61-b2f6-2a779ca842d5]']; nested exception is eu.etaxonomy.cdm.database.PermissionDeniedException: [UPDATE] not permitted for 'm.liese' on Reference[uuid:47edf58d-cb47-4c61-b2f6-2a779ca842d5', toString:'Reference [type=Article, id= 26293, uuid=47edf58d-cb47-4c61-b2f6-2a779ca842d5]'] at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:65) at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:282) at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:247) at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:90) at org.eclipse.e4.ui.internal.workbench.PartServiceSaveHandler.save(PartServiceSaveHandler.java:57) at org.eclipse.ui.internal.WorkbenchWindow$7.save(WorkbenchWindow.java:594) at org.eclipse.e4.ui.internal.workbench.PartServiceImpl.savePart(PartServiceImpl.java:1390) at eu.etaxonomy.taxeditor.workbench.SaveHandler.execute(SaveHandler.java:36) 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.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55) at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:282) at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:264) at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:132) at org.eclipse.e4.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:152) at org.eclipse.core.commands.Command.executeWithChecks(Command.java:494) at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:488) at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210) at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:433) at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.handleWidgetSelection(AbstractContributionItem.java:454) at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem$3.handleEvent(AbstractContributionItem.java:482) at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84) at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4418) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1079) at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4236) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3824) at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$4.run(PartRenderingEngine.java:1121) at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336) at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1022) at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:150) at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:693) at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336) at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:610) at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148) 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:134) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243) 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:673) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:610) at org.eclipse.equinox.launcher.Main.run(Main.java:1519) Caused by: org.springframework.orm.hibernate5.HibernateSystemException: [UPDATE] not permitted for 'm.liese' on Reference[uuid:47edf58d-cb47-4c61-b2f6-2a779ca842d5', toString:'Reference [type=Article, id= 26293, uuid=47edf58d-cb47-4c61-b2f6-2a779ca842d5]']; nested exception is eu.etaxonomy.cdm.database.PermissionDeniedException: [UPDATE] not permitted for 'm.liese' on Reference[uuid:47edf58d-cb47-4c61-b2f6-2a779ca842d5', toString:'Reference [type=Article, id= 26293, uuid=47edf58d-cb47-4c61-b2f6-2a779ca842d5]'] at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:219) at org.springframework.orm.hibernate5.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:741) at org.springframework.orm.hibernate5.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:589) 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.$Proxy1750.merge(Unknown Source) at sun.reflect.GeneratedMethodAccessor20159.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) 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.$Proxy1849.merge(Unknown Source) at sun.reflect.GeneratedMethodAccessor41454.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:212) at org.springframework.remoting.support.DefaultRemoteInvocationExecutor.invoke(DefaultRemoteInvocationExecutor.java:39) at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78) at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114) at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:74) at org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter.handle(HttpRequestHandlerAdapter.java:51) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:969) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:871) at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:845) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808) at org.eclipse.jetty.servlet.ServletHandler$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$3.run(QueuedThreadPool.java:555) at java.lang.Thread.run(Thread.java:745) at org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTraceIfPossible(RemoteInvocationUtils.java:45) at org.springframework.remoting.support.RemoteInvocationResult.recreate(RemoteInvocationResult.java:149) at org.springframework.remoting.support.RemoteInvocationBasedAccessor.recreateRemoteInvocationResult(RemoteInvocationBasedAccessor.java:85) at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:150) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208) at com.sun.proxy.$Proxy48.merge(Unknown Source) at eu.etaxonomy.taxeditor.editor.e4.TaxonEditorInputE4.merge(TaxonEditorInputE4.java:428) at eu.etaxonomy.taxeditor.editor.name.e4.TaxonNameEditorE4.save(TaxonNameEditorE4.java:409) 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.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55) ... 48 more Caused by: eu.etaxonomy.cdm.database.PermissionDeniedException: [UPDATE] not permitted for 'm.liese' on Reference[uuid:47edf58d-cb47-4c61-b2f6-2a779ca842d5', toString:'Reference [type=Article, id= 26293, uuid=47edf58d-cb47-4c61-b2f6-2a779ca842d5]'] at eu.etaxonomy.cdm.persistence.hibernate.CdmSecurityHibernateInterceptor.checkPermissions(CdmSecurityHibernateInterceptor.java:207) at eu.etaxonomy.cdm.persistence.hibernate.CdmSecurityHibernateInterceptor.onFlushDirty(CdmSecurityHibernateInterceptor.java:129) at org.hibernate.event.internal.DefaultFlushEntityEventListener.invokeInterceptor(DefaultFlushEntityEventListener.java:348) at org.hibernate.event.internal.DefaultFlushEntityEventListener.handleInterception(DefaultFlushEntityEventListener.java:325) at org.hibernate.event.internal.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:276) at org.hibernate.event.internal.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:143) at org.hibernate.event.internal.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:216) at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:85) 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) ... 149 more
Updated by Katja Luther almost 5 years ago
This problem appears because the parser checks whether the inreference already exists in DB and when one or more references with the same titleCache exist the inReference is set with this reference. But if there are more than one matching references for the inReference the reference is changed, but the user does not have the rights to change references.
The solution is to skip the inReference check because if the reference already exist, the inReference exists as well.
Updated by Katja Luther almost 5 years ago
- Status changed from New to Resolved
- % Done changed from 0 to 50
Applied in changeset taxeditor|c9d22df2150151a1181ff5c8b8167e1ff5896a73.
Updated by Andreas Müller almost 5 years ago
- Assignee changed from Katja Luther to Andreas Müller
Should I review?
Updated by Andreas Müller almost 5 years ago
Think about including into HFX for 5.7
Updated by Andreas Müller almost 5 years ago
- Status changed from Resolved to Feedback
- Assignee changed from Andreas Müller to Katja Luther
Hmm, difficult to test, some first tests worked fine. I think we can close it and cherry pick + change version.
Updated by Katja Luther almost 5 years ago
- Status changed from Feedback to Resolved
Applied in changeset taxeditor|34965c7d9a020910d8a3e36ed3299fb05936f47b.
nach hotfix/5.7.3 gecherry-picked
Updated by Katja Luther almost 5 years ago
- Target version changed from Release 5.8 to Release 5.7
Updated by Andreas Müller almost 5 years ago
- Status changed from Resolved to Closed
- Target version changed from Release 5.7 to Release 5.8
- % Done changed from 50 to 100
Updated by Andreas Müller almost 5 years ago
- Target version changed from Release 5.8 to Release 5.7
moved accidentaly back to 5.8