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edit delete draft dataset doesn't work except from draft version #5488

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qqmyers opened this issue Jan 25, 2019 · 6 comments
Closed

edit delete draft dataset doesn't work except from draft version #5488

qqmyers opened this issue Jan 25, 2019 · 6 comments
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@kcondon
Milestone
4.11 - Preservati...

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@qqmyers
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qqmyers commented Jan 25, 2019

The Edit/Delete Draft Dataset button works when used from the draft dataset page but does not work if one is on the page for a published version. The error I see is related to filemetadata so this may be specific to datasets with files. I verified this is an issue on demo.dataverse.org as of v4.10.1. using a test dataset with one file that had been published in the v1.0 version.
FWIW - the DeleteDatasetVersionCommand is called in both cases and it only takes the dataset as a parameter, calling dataset.getLatestVersion(), so it's not clear to me why there's a problem. The error I see occurs in the following line:
DatasetVersion doomedAndMerged = ctxt.em().merge(doomedVersion);

I ran across this in looking at #4760, but am not actively this bug in particular...
@qqmyers
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qqmyers commented Jan 28, 2019

FWIW - I may have at least a work-around for this. In looking at #4760, I found that I needed to do a find(Dataset.class, dataset.getId()) at the start of the DeleteDatasetVersion command to avoid an error about the dataset/it's filemetadatas having been updated previously. I still haven't explored why this might be different depending on the starting page, but I suspect this will fix this issue if the underlying reason is hard to track down.

@djbrooke djbrooke assigned djbrooke and unassigned djbrooke Jan 28, 2019
@pdurbin
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pdurbin commented Feb 12, 2019

We talked about this issue in sprint planning two weeks ago but I don't remember what we decided the approach should be. Are we going to hide the "Delete Draft Dataset" button when you have navigated to a published version?

screen shot 2019-02-12 at 12 44 40 pm

It's easy to replicate this bug. As of 839fb2c in the develop branch on http://phoenix.dataverse.org the UI gives no feedback and here's the stack trace:

[2019-02-12T12:43:59.014-0500] [glassfish 4.1] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [tid: _ThreadID=52 _ThreadName=jk-connector(3)] [timeMillis: 1549993439014] [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]]

[2019-02-12T12:43:59.015-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=52 _ThreadName=jk-connector(3)] [timeMillis: 1549993439015] [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.$Proxy247.submit(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
	at edu.harvard.iq.dataverse.DatasetPage.deleteDatasetVersion(DatasetPage.java:2089)
	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 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: javax.persistence.OptimisticLockException: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=47]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.FileMetadata
	at org.eclipse.persistence.internal.jpa.EntityManagerImpl.mergeInternal(EntityManagerImpl.java:544)
	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.DeleteDatasetVersionCommand.executeImpl(DeleteDatasetVersionCommand.java:64)
	at edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand.execute(AbstractVoidCommand.java:29)
	at edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand.execute(AbstractVoidCommand.java:13)
	at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:232)
	at sun.reflect.GeneratedMethodAccessor156.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:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor99.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.GeneratedMethodAccessor103.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
Caused by: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=47]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.FileMetadata
	at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastMerge(OptimisticLockException.java:152)
	at org.eclipse.persistence.internal.sessions.MergeManager.mergeChangesOfCloneIntoWorkingCopy(MergeManager.java:578)
	at org.eclipse.persistence.internal.sessions.MergeManager.mergeChanges(MergeManager.java:313)
	at org.eclipse.persistence.mappings.CollectionMapping.mergeIntoObject(CollectionMapping.java:1645)
	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)
	... 97 more
]]

[2019-02-12T12:43:59.017-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.resource.webcontainer.jsf.lifecycle] [tid: _ThreadID=52 _ThreadName=jk-connector(3)] [timeMillis: 1549993439017] [levelValue: 900] [[
  #{DatasetPage.deleteDatasetVersion()}: javax.ejb.EJBException
javax.faces.FacesException: #{DatasetPage.deleteDatasetVersion()}: javax.ejb.EJBException
	at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:118)
	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: javax.faces.el.EvaluationException: javax.ejb.EJBException
	at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:101)
	at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102)
	... 45 more
Caused by: 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.$Proxy247.submit(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
	at edu.harvard.iq.dataverse.DatasetPage.deleteDatasetVersion(DatasetPage.java:2089)
	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 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)
	... 46 more
Caused by: javax.persistence.OptimisticLockException: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=47]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.FileMetadata
	at org.eclipse.persistence.internal.jpa.EntityManagerImpl.mergeInternal(EntityManagerImpl.java:544)
	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.DeleteDatasetVersionCommand.executeImpl(DeleteDatasetVersionCommand.java:64)
	at edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand.execute(AbstractVoidCommand.java:29)
	at edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand.execute(AbstractVoidCommand.java:13)
	at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:232)
	at sun.reflect.GeneratedMethodAccessor156.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:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor99.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.GeneratedMethodAccessor103.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
Caused by: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=47]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.FileMetadata
	at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastMerge(OptimisticLockException.java:152)
	at org.eclipse.persistence.internal.sessions.MergeManager.mergeChangesOfCloneIntoWorkingCopy(MergeManager.java:578)
	at org.eclipse.persistence.internal.sessions.MergeManager.mergeChanges(MergeManager.java:313)
	at org.eclipse.persistence.mappings.CollectionMapping.mergeIntoObject(CollectionMapping.java:1645)
	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)
	... 97 more
]]

[2019-02-12T12:43:59.021-0500] [glassfish 4.1] [SEVERE] [] [javax.enterprise.resource.webcontainer.jsf.context] [tid: _ThreadID=52 _ThreadName=jk-connector(3)] [timeMillis: 1549993439021] [levelValue: 1000] [[
  javax.faces.el.EvaluationException: javax.ejb.EJBException
	at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:101)
	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: 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.$Proxy247.submit(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
	at edu.harvard.iq.dataverse.DatasetPage.deleteDatasetVersion(DatasetPage.java:2089)
	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 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)
	... 46 more
Caused by: javax.persistence.OptimisticLockException: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=47]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.FileMetadata
	at org.eclipse.persistence.internal.jpa.EntityManagerImpl.mergeInternal(EntityManagerImpl.java:544)
	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.DeleteDatasetVersionCommand.executeImpl(DeleteDatasetVersionCommand.java:64)
	at edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand.execute(AbstractVoidCommand.java:29)
	at edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand.execute(AbstractVoidCommand.java:13)
	at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:232)
	at sun.reflect.GeneratedMethodAccessor156.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:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor99.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.GeneratedMethodAccessor103.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
Caused by: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [edu.harvard.iq.dvn.core.study.FileMetadata[id=47]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.FileMetadata
	at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastMerge(OptimisticLockException.java:152)
	at org.eclipse.persistence.internal.sessions.MergeManager.mergeChangesOfCloneIntoWorkingCopy(MergeManager.java:578)
	at org.eclipse.persistence.internal.sessions.MergeManager.mergeChanges(MergeManager.java:313)
	at org.eclipse.persistence.mappings.CollectionMapping.mergeIntoObject(CollectionMapping.java:1645)
	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)
	... 97 more
]]

[2019-02-12T12:44:18.106-0500] [glassfish 4.1] [INFO] [] [org.primefaces.component.outputpanel.OutputPanelRenderer] [tid: _ThreadID=50 _ThreadName=jk-connector(1)] [timeMillis: 1549993458106] [levelValue: 800] [[
  autoUpdate attribute is deprecated and will be removed in a future version, use p:autoUpdate component instead.]]

[2019-02-12T12:44:18.555-0500] [glassfish 4.1] [INFO] [] [org.primefaces.component.outputpanel.OutputPanelRenderer] [tid: _ThreadID=53 _ThreadName=jk-connector(4)] [timeMillis: 1549993458555] [levelValue: 800] [[
  autoUpdate attribute is deprecated and will be removed in a future version, use p:autoUpdate component instead.]]

@djbrooke
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We should show this option in the drop down and it should work.

@qqmyers
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qqmyers commented Feb 13, 2019

I can confirm that the change I suggested above works. I've made that change as part of an implementation of #4760 for which I'm putting together a PR. You can pick it up that way or I can separate out. If there's a better solution, let me know and I can test whether it also helps in my #4760 approach...

@djbrooke
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Thanks @qqmyers, we'll hold off on working on this right now.

@qqmyers qqmyers mentioned this issue Feb 14, 2019
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@djbrooke
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Thanks @qqmyers for the PR!

@kcondon kcondon self-assigned this Feb 14, 2019
@kcondon kcondon closed this as completed Feb 14, 2019
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@kcondon kcondon

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4.11 - Preservation Integrations
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@pdurbin @kcondon @qqmyers @djbrooke