Delete Files: Cannot delete shape files from dataset

[kcondon]

When attempting to delete all files from dataset with 184, mostly Stata tabular files, in production on S3 (RT 260944) got unable to delete message in UI and this in server.log. It turns out this is from trying to delete one of the 18 unmapped shape files in the dataset:

[2018-04-17T12:32:22.575-0400] [glassfish 4.1] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [tid: _ThreadID=2529 _ThreadName=jk-connector(22)] [timeMillis: 1523982742575] [levelValue: 900] [[
A system exception occurred during an invocation on EJB EjbDataverseEngine, method: public java.lang.Object edu.harvard.iq.dataverse.EjbDataverseEngine.submit(edu.harvard.iq.dataverse.engine.command.Command) throws edu.harvard.iq.dataverse.engine.command.exception.CommandException]]

[2018-04-17T12:32:22.575-0400] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=2529 _ThreadName=jk-connector(22)] [timeMillis: 1523982742575] [levelValue: 900] [[

javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:748)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:698)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
at com.sun.proxy.$Proxy245.submit(Unknown Source)
at edu.harvard.iq.dataverse.EJB31_Generated__EjbDataverseEngine__Intf____Bean.submit(Unknown Source)
at edu.harvard.iq.dataverse.DatasetPage.save(DatasetPage.java:2490)
at edu.harvard.iq.dataverse.DatasetPage.deleteFilesAndSave(DatasetPage.java:2410)
at sun.reflect.GeneratedMethodAccessor1956.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at javax.el.ELUtil.invokeMethod(ELUtil.java:332)
at javax.el.BeanELResolver.invoke(BeanELResolver.java:537)
at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:256)
at com.sun.el.parser.AstValue.invoke(AstValue.java:283)
at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:304)
at org.jboss.weld.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40)
at org.jboss.weld.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:105)
at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:87)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102)
at javax.faces.component.UICommand.broadcast(UICommand.java:315)
at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:790)
at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1282)
at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:81)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:198)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:646)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:295)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:412)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalArgumentException: Cannot merge an entity that has been removed: edu.harvard.iq.dvn.core.study.FileMetadata[id=2403977]
at org.eclipse.persistence.internal.sessions.MergeManager.registerObjectForMergeCloneIntoWorkingCopy(MergeManager.java:1063)
at org.eclipse.persistence.internal.sessions.MergeManager.mergeChangesOfCloneIntoWorkingCopy(MergeManager.java:557)
at org.eclipse.persistence.internal.sessions.MergeManager.mergeChanges(MergeManager.java:313)
at org.eclipse.persistence.mappings.CollectionMapping.mergeIntoObject(CollectionMapping.java:1638)
at org.eclipse.persistence.internal.descriptors.ObjectBuilder.mergeIntoObject(ObjectBuilder.java:4132)
at org.eclipse.persistence.internal.sessions.MergeManager.mergeChangesOfCloneIntoWorkingCopy(MergeManager.java:594)
at org.eclipse.persistence.internal.sessions.MergeManager.mergeChanges(MergeManager.java:313)
at org.eclipse.persistence.mappings.CollectionMapping.mergeIntoObject(CollectionMapping.java:1638)
at org.eclipse.persistence.internal.descriptors.ObjectBuilder.mergeIntoObject(ObjectBuilder.java:4132)
at org.eclipse.persistence.internal.sessions.MergeManager.mergeChangesOfCloneIntoWorkingCopy(MergeManager.java:594)
at org.eclipse.persistence.internal.sessions.MergeManager.mergeChanges(MergeManager.java:313)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.mergeCloneWithReferences(UnitOfWorkImpl.java:3521)
at org.eclipse.persistence.internal.sessions.RepeatableWriteUnitOfWork.mergeCloneWithReferences(RepeatableWriteUnitOfWork.java:384)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.mergeCloneWithReferences(UnitOfWorkImpl.java:3481)
at org.eclipse.persistence.internal.jpa.EntityManagerImpl.mergeInternal(EntityManagerImpl.java:542)
at org.eclipse.persistence.internal.jpa.EntityManagerImpl.merge(EntityManagerImpl.java:519)
at com.sun.enterprise.container.common.impl.EntityManagerWrapper.merge(EntityManagerWrapper.java:305)
at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.save(UpdateDatasetCommand.java:245)
at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.execute(UpdateDatasetCommand.java:108)
at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.execute(UpdateDatasetCommand.java:33)
at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:214)
at sun.reflect.GeneratedMethodAccessor823.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:64)
at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at sun.reflect.GeneratedMethodAccessor105.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at sun.reflect.GeneratedMethodAccessor107.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 63 more
]]

[mheppler]

Related to all the efforts made in Destroy Dataset: Cannot destroy a dataset that has a mapped shape file #4093.

[cmbz]

To focus on the most important features and bugs, we are closing issues created before 2020 (version 5.0) that are not new feature requests with the label 'Type: Feature'.

If you created this issue and you feel the team should revisit this decision, please reopen the issue and leave a comment.