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bug #9710

closed

DataIntegrityViolationException after adding a specimen to the matrix

Added by Andreas Müller about 3 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Highest
Assignee:
Katja Luther
Category:
taxeditor
Target version:
Release 5.27
Start date:
Due date:
% Done:

100%

Estimated time:
Severity:
critical
Found in Version:
Tags:
additivity

Description

Murat:

I come across this error message when I add a new specimen to the matrix.
Do I have to reopen the matrix when I make this addition? In this case, the matrix opens very slowly due to the large dataset.

AM:

as far as I understand this error returns repeatedly. Did you recognize any pattern when it does occur? E.g. always when you add a new specimen to the matrix? Or always when working on a new taxon …?

Murat:

I got the following error message several times when I tried to save my recent works.
...
I always reopen the EDIT to fix the problem. However, this is not convenient because it opens too slow. It takes more than two minutes for each samples. 

last remote method : http://api.cybertaxonomy.org:80/flora-greece-bupleurum/remoting/description.service 
last remote request client time : 2021-07-14T11:17:15.244
last remote request response header time : Wed, 14 Jul 2021 09:17:15 GMT
client error time : 2021-07-14T11:17:17.167
login : m.guezel
editor version : 5.24.0
server : api.cybertaxonomy.org (cybertaxonomy.org) / flora-greece-bupleurum
schema version : 5.23.0.0.20210422
os : Windows 7 6.1 amd64
java : 1.8.0_121
org.eclipse.e4.core.di.InjectionException: org.springframework.dao.DataIntegrityViolationException: could not execute statement; SQL [n/a]; constraint [UK_b8inp8cke189cpo47euwn0bgf]; nested exception is org.hibernate.exception.ConstraintViolationException: could not execute statement
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:38)
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:20)
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.dao.DataIntegrityViolationException: could not execute statement; SQL [n/a]; constraint [UK_b8inp8cke189cpo47euwn0bgf]; nested exception is org.hibernate.exception.ConstraintViolationException: could not execute statement
at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:241)
at org.springframework.orm.hibernate5.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:755)
at org.springframework.orm.hibernate5.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:590)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:765)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:734)
at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:522)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:293)
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:213)
at com.sun.proxy.$Proxy1870.mergeDescriptions(Unknown Source)
at sun.reflect.GeneratedMethodAccessor282580.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:333)
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:213)
at com.sun.proxy.$Proxy2206.mergeDescriptions(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:212)
at eu.etaxonomy.cdm.api.remoting.DebuggingRemoteInvocationExecutor.invoke(DebuggingRemoteInvocationExecutor.java:52)
at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78)
at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114)
at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:80)
at org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter.handle(HttpRequestHandlerAdapter.java:51)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder$NotAsyncServlet.service(ServletHolder.java:1395)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:755)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1617)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:317)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:215)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:214)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:177)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1604)
at eu.etaxonomy.cdm.servlet.DateHeaderFilter.doFilter(DateHeaderFilter.java:55)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1604)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1596)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:545)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:590)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1607)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1297)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:485)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1577)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1212)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at eu.etaxonomy.cdm.server.logging.InstanceLogWrapper.handle(InstanceLogWrapper.java:47)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:221)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:500)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:547)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:270)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)
at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:336)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:313)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:171)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:129)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:388)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:806)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:938)
at java.lang.Thread.run(Thread.java:748)
at org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTraceIfPossible(RemoteInvocationUtils.java:45)
at org.springframework.remoting.support.RemoteInvocationResult.recreate(RemoteInvocationResult.java:149)
at org.springframework.remoting.support.RemoteInvocationBasedAccessor.recreateRemoteInvocationResult(RemoteInvocationBasedAccessor.java:85)
at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:158)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy61.mergeDescriptions(Unknown Source)
at eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix.CharacterMatrixPart.save(CharacterMatrixPart.java:221)
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: org.hibernate.exception.ConstraintViolationException: could not execute statement
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:59)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:111)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:97)
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:207)
at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:45)
at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3013)
at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3513)
at org.hibernate.action.internal.EntityInsertAction.execute(EntityInsertAction.java:89)
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:589)
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:463)
at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:337)
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:39)
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1295)
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:468)
at org.hibernate.internal.SessionImpl.flushBeforeTransactionCompletion(SessionImpl.java:3159)
at org.hibernate.internal.SessionImpl.beforeTransactionCompletion(SessionImpl.java:2352)
at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.beforeTransactionCompletion(JdbcCoordinatorImpl.java:491)
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:582)
... 168 more
Caused by: java.sql.SQLIntegrityConstraintViolationException: Duplicate entry 'bfc52e52-bf25-4562-ba01-7344a221a2ce' for key 'UK_b8inp8cke189cpo47euwn0bgf'
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:117)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:97)
at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122)
at com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:953)
at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1092)
at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1040)
at com.mysql.cj.jdbc.ClientPreparedStatement.executeLargeUpdate(ClientPreparedStatement.java:1347)
at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdate(ClientPreparedStatement.java:1025)
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:384)
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:204)
... 186 more

Files

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picture189-1.png (14.3 KB) picture189-1.png Andreas Müller, 09/17/2021 10:49 PM
picture019-1.png (12.7 KB) picture019-1.png Katja Luther, 09/20/2021 10:06 AM

Related issues

Copied to EDIT - bug #9772: Improve DTO usage for character matrixClosedKatja Luther

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 #1

Updated by Katja Luther about 3 years ago

This problem seems to appear when adding a new specimen, save and enter other data to this new description and save again.

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 #2

Updated by Katja Luther about 3 years ago

  • Status changed from New to In Progress
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 #3

Updated by Andreas Müller almost 3 years ago

  • Status changed from In Progress to Resolved
  • % Done changed from 0 to 30

I put this to resolved as it is easier to find during review this way. We may split the ticket after release if not fully ready until then.

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 #4

Updated by Andreas Müller almost 3 years ago

  • Assignee changed from Katja Luther to Andreas Müller
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 #5

Updated by Andreas Müller almost 3 years ago

Loading seems to be much faster now. Very good!

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 #6

Updated by Andreas Müller almost 3 years ago

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

Playing around I got 

last remote method : http://test.e-taxonomy.eu:80/cdmserver/rem_conf_am/remoting/taxonnode.service
last remote request client time : 2021-09-17T22:21:13.761
last remote request response header time : Fri, 17 Sep 2021 20:21:14 GMT
client error time : 2021-09-17T22:21:44.808
login : admin
editor version : 5.27.0.202109161022
server : test.e-taxonomy.eu (edit-test) / rem_conf_am
schema version : 5.27.0.0.20210913
os : Windows Server 2012 R2 6.3 amd64
java : 1.8.0_131
java.lang.NullPointerException
    at eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix.CharacterMatrixConfigLabelAccumulator.hasDefaultValue(CharacterMatrixConfigLabelAccumulator.java:173)
    at eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix.CharacterMatrixConfigLabelAccumulator.hasDefaultValue(CharacterMatrixConfigLabelAccumulator.java:154)
    at eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix.CharacterMatrixConfigLabelAccumulator.accumulateConfigLabels(CharacterMatrixConfigLabelAccumulator.java:113)
    at org.eclipse.nebula.widgets.nattable.layer.AbstractLayer.getConfigLabelsByPosition(AbstractLayer.java:110)
    at org.eclipse.nebula.widgets.nattable.layer.AbstractLayerTransform.getConfigLabelsByPosition(AbstractLayerTransform.java:335)
    at org.eclipse.nebula.widgets.nattable.layer.AbstractLayerTransform.getConfigLabelsByPosition(AbstractLayerTransform.java:335)

Probably DescriptionBaseDto.getElements() should never return null but empty List instead. This should be verified in the constructor already (similar to model objects). Then you can also remove the "elements = new ArrayList<>();" in addElement() in case elements is null.

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 #7

Updated by Andreas Müller almost 3 years ago

I get the strange behavior that the matrix only shows the most left factual data column correctly. All other columns are grey though they contain data. When I scroll to the right and a new column is the most left column this column shows the data, etc.

Looks like this:

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 #9

Updated by Andreas Müller almost 3 years ago

Also I get (during save I think, but not sure)

last remote method : http://test.e-taxonomy.eu:80/cdmserver/rem_conf_am/remoting/common.service
last remote request client time : 2021-09-17T22:32:33.565
last remote request response header time : Fri, 17 Sep 2021 20:32:33 GMT
client error time : 2021-09-17T22:32:33.596
login : admin
editor version : 5.27.0.202109161022
server : test.e-taxonomy.eu (edit-test) / rem_conf_am
schema version : 5.27.0.0.20210913
os : Windows Server 2012 R2 6.3 amd64
java : 1.8.0_131
org.eclipse.e4.core.di.InjectionException: java.lang.NullPointerException
    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:38)
    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:20)
    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: java.lang.NullPointerException
    at eu.etaxonomy.cdm.persistence.dto.TermDto.fromTerm(TermDto.java:85)
    at eu.etaxonomy.cdm.persistence.dto.TermDto.fromTerm(TermDto.java:73)
    at eu.etaxonomy.cdm.api.service.dto.StatisticalMeasurementValueDto.fromStatisticalMeasurementValue(StatisticalMeasurementValueDto.java:34)
    at eu.etaxonomy.cdm.api.service.dto.QuantitativeDataDto.fromQuantitativeData(QuantitativeDataDto.java:46)
    at eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto.fromDescription(DescriptionBaseDto.java:249)
    at eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix.CharacterMatrixPart.save(CharacterMatrixPart.java:249)
    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

This looks like dirty data but I updated all data before to not have null value for StatisticalMeasurement.type .
After this that database was again filled with statistcalMeasurment data having no type (new records as far as I can see).

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 #10

Updated by Andreas Müller almost 3 years ago

I worked with 5.27.0.202109161022 beta as there is no newer version for nightly (build does not work). Also the current local version does not work against the test server.

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 #11

Updated by Katja Luther almost 3 years ago

Andreas Müller wrote:

I get the strange behavior that the matrix only shows the most left factual data column correctly. All other columns are grey though they contain data. When I scroll to the right and a new column is the most left column this column shows the data, etc.

Looks like this:

Strange, locally this behaviour does not appear, need to check whether I have missed to check in some files.

I also checked the actual nightly build and your test DB and all values are shown.

Now I could reproduce this behaviour, if a second exact value with min/max is added, the type is set to null...

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 #12

Updated by Andreas Müller almost 3 years ago

  • Copied to bug #9772: Improve DTO usage for character matrix added
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 #13

Updated by Andreas Müller almost 3 years ago

  • Status changed from Feedback to Closed
  • % Done changed from 30 to 100

further discussions on DTO handling were moved to #9772.

This ticket can be closed as it originally handles only the exception.

Please reopen if you think something is still missing.

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 #14

Updated by Andreas Müller almost 3 years ago

  • Target version changed from Release 5.51 to Release 5.27
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