Dataverse: Can't edit draft datasets on demo.dataverse.org, using the web interface. Native API works.

[markrlondon]

I've just created several datasets today, that I can't edit using the web interface. All the boxes are greyed out. For example, see this link (screenshot attached):

https://demo.dataverse.org/dataset.xhtml?persistentId=doi:10.5072/FK2/JSH8ND&version=DRAFT

But I could delete it, using a Native API command (using curl). Thanks. - Mark

[markrlondon]

The "disabled" class is being added to the buttons. I was able to get rid of the class using the Chrome development tools, and that enabled the Edit button, and I was edit the dataset! Obviously not the correct solution. But it definitely opened my eyes regarding my own web pages, where I disable buttons in the same manner. People can enable them!

[pdurbin]

@markrlondon how easy is it to reproduce the creating of these datasets via API that can't be edited via the GUI? This is a very strange bug. Also, in case this bug isn't examined anytime soon, I'd like to note that the demo site is running 4.7.1 right now.

[markrlondon]

Unfortunately the problem seems to have been transient, as I can't reproduce the problem. All I know is that I created a handful of datasets at the same time, and they all had the same problem. But the problem disappeared later that day. I deleted most of them, but I have left the above dataset alone, in case you tell from it, why I don't have permission to do anything with it. I'll let you know if the problem occurs again. I've been creating a lot of test datasets since then, without a problem.. Go figure!

[pdurbin]

@markrlondon ok, please keep us posted on if you can easily reproduce this in the future or not. Thanks!

[pdurbin]

@markrlondon any more thoughts on this issue? Should we close it? Do you think you can reproduce the bug and give us the steps to do so? Thanks!

[djbrooke]

I'm going to close this one for now. If we (or @markrlondon) can reproduce it, we should reopen.

When this was brought up during backlog grooming today, @mheppler pointed out the potential issue of only having a "disabled" class on the frontend between the user being able to do something and not able to do something. If it's not some completely crazy scenario here, we may need something with more teeth.

[mdmADA]

I just had this happen. DV 4.6.1.

I created a copy tool (coming soon for common use) that uses the APIs to copy a dataset from one dataverse to another by: 1) creating a new dataset in the source dataverse, 2) copying metadata from source ds to destination ds and 3) copying any uploaded files from one to the other.

I created 12 datasets in a row this way. 2 of the Draft datasets are as above - the Publish and Edit buttons are disabled as are the "Upload Files", "Edit Files" and "Download" buttons just above the Files/Metadata/etc tabs:

I thought it might be the final 2 datasets (11th and 12th) created with my tool but it is the 3rd and the 12th. Both had problems with ingest of one or more files but so did the other 10 and those can be edited. I created these datasets yesterday but the uneditable draft problem is still there today (did not resolve on its own).

Additionally, while looking at one of these uneditable draft datasets, just leaving it open in the browser, every 5 seconds or so, the spinner spins for a brief second - not sure why but maybe it is indicative of something going on.

Also, I 'fixed' (?!) it the same way @markrlondon did using Google Chrome developer tools. However, this uneditable issue kept happening in subsequent attempts to copy them. For one of the datasets, I kept deleting it and trying it again until it finally 'worked' after about 4 attempts (worked in that the Edit buttons were not disabled).

The second one with the non-editable issue, I kept deleting it and creating it with my tool but couldn't get it to work - the relevant buttons were disabled each and every time.

I thought it might be a timing issue so I added a 3 second delay between each file API upload and it worked after that - dataset with metadata created, files copied and Draft version editable.

I am not sure if timing is the cause here since the FOOBAR example from @markrlondon only had metadata. But if @markrlondon was creating multiple datasets programatically one after the other in quick succession, perhaps timing IS the issue? Not sure.

[mdmADA]

This is from the log file during one of my attempts to delete-then-create the problematic datasets:

Local Exception Stack:
Exception [EclipseLink-5006] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:815]] cannot be updated because it has changed or been deleted since it was last read.
Class> edu.harvard.iq.dataverse.DatasetVersion Primary Key> 815
at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastReadWhenUpdating(OptimisticLockException.java:144)
at org.eclipse.persistence.descriptors.VersionLockingPolicy.validateUpdate(VersionLockingPolicy.java:790)
at org.eclipse.persistence.internal.queries.DatabaseQueryMechanism.updateObjectForWriteWithChangeSet(DatabaseQueryMechanism.java:1087)
at org.eclipse.persistence.queries.UpdateObjectQuery.executeCommitWithChangeSet(UpdateObjectQuery.java:84)
at org.eclipse.persistence.internal.queries.DatabaseQueryMechanism.executeWriteWithChangeSet(DatabaseQueryMechanism.java:301)
at org.eclipse.persistence.queries.WriteObjectQuery.executeDatabaseQuery(WriteObjectQuery.java:58)
at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:899)
at org.eclipse.persistence.queries.DatabaseQuery.executeInUnitOfWork(DatabaseQuery.java:798)
at org.eclipse.persistence.queries.ObjectLevelModifyQuery.executeInUnitOfWorkObjectLevelModifyQuery(ObjectLevelModifyQuery.java:108)
at org.eclipse.persistence.queries.ObjectLevelModifyQuery.executeInUnitOfWork(ObjectLevelModifyQuery.java:85)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:2896)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1804)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1786)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1737)
at org.eclipse.persistence.internal.sessions.CommitManager.commitChangedObjectsForClassWithChangeSet(CommitManager.java:267)
at org.eclipse.persistence.internal.sessions.CommitManager.commitAllObjectsForClassWithChangeSet(CommitManager.java:192)
at org.eclipse.persistence.internal.sessions.CommitManager.commitAllObjectsWithChangeSet(CommitManager.java:138)
at org.eclipse.persistence.internal.sessions.AbstractSession.writeAllObjectsWithChangeSet(AbstractSession.java:4207)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.commitToDatabase(UnitOfWorkImpl.java:1441)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.commitToDatabaseWithChangeSet(UnitOfWorkImpl.java:1531)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.issueSQLbeforeCompletion(UnitOfWorkImpl.java:3168)
at org.eclipse.persistence.internal.sessions.RepeatableWriteUnitOfWork.issueSQLbeforeCompletion(RepeatableWriteUnitOfWork.java:352)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:158)
at org.eclipse.persistence.transaction.JTASynchronizationListener.beforeCompletion(JTASynchronizationListener.java:68)
at com.sun.enterprise.transaction.JavaEETransactionImpl.commit(JavaEETransactionImpl.java:452)
at com.sun.enterprise.transaction.JavaEETransactionManagerSimplified.commit(JavaEETransactionManagerSimplified.java:854)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:719)
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.$Proxy321.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.__EJB31_Generated__IngestServiceBean__Intf____Bean__.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.IngestMessageBean.onMessage(IngestMessageBean.java:86)
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.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:73)
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.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 org.glassfish.ejb.mdb.MessageBeanContainer.deliverMessage(MessageBeanContainer.java:1219)
at org.glassfish.ejb.mdb.MessageBeanListenerImpl.deliverMessage(MessageBeanListenerImpl.java:81)
at com.sun.enterprise.connectors.inbound.MessageEndpointInvocationHandler.invoke(MessageEndpointInvocationHandler.java:171)
at com.sun.proxy.$Proxy456.onMessage(Unknown Source)
at com.sun.messaging.jms.ra.OnMessageRunner.run(OnMessageRunner.java:283)
at com.sun.enterprise.connectors.work.OneWork.doWork(OneWork.java:107)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
]]

[2018-11-23T11:20:08.193+1100] [glassfish 4.1] [WARNING] [enterprise_distributedtx.before_completion_excep] [javax.enterprise.resource.jta.com.sun.enterprise.transaction] [tid: _ThreadID=67 _ThreadName=p: thread-pool-1; w: 5] [timeMillis: 1542932408193] [levelValue: 900] [[
DTX5014: Caught exception in beforeCompletion() callback:
javax.persistence.OptimisticLockException: Exception [EclipseLink-5006] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:815]] cannot be updated because it has changed or been deleted since it was last read.
Class> edu.harvard.iq.dataverse.DatasetVersion Primary Key> 815
at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl$1.handleException(EntityManagerSetupImpl.java:694)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.handleException(AbstractSynchronizationListener.java:275)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:170)
at org.eclipse.persistence.transaction.JTASynchronizationListener.beforeCompletion(JTASynchronizationListener.java:68)
at com.sun.enterprise.transaction.JavaEETransactionImpl.commit(JavaEETransactionImpl.java:452)
at com.sun.enterprise.transaction.JavaEETransactionManagerSimplified.commit(JavaEETransactionManagerSimplified.java:854)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:719)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
at com.sun.proxy.$Proxy321.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.__EJB31_Generated__IngestServiceBean__Intf____Bean__.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.IngestMessageBean.onMessage(IngestMessageBean.java:86)
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.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:73)
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.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 org.glassfish.ejb.mdb.MessageBeanContainer.deliverMessage(MessageBeanContainer.java:1219)
at org.glassfish.ejb.mdb.MessageBeanListenerImpl.deliverMessage(MessageBeanListenerImpl.java:81)
at com.sun.enterprise.connectors.inbound.MessageEndpointInvocationHandler.invoke(MessageEndpointInvocationHandler.java:171)
at com.sun.proxy.$Proxy456.onMessage(Unknown Source)
at com.sun.messaging.jms.ra.OnMessageRunner.run(OnMessageRunner.java:283)
at com.sun.enterprise.connectors.work.OneWork.doWork(OneWork.java:107)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
Caused by: Exception [EclipseLink-5006] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:815]] cannot be updated because it has changed or been deleted since it was last read.
Class> edu.harvard.iq.dataverse.DatasetVersion Primary Key> 815
at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastReadWhenUpdating(OptimisticLockException.java:144)
at org.eclipse.persistence.descriptors.VersionLockingPolicy.validateUpdate(VersionLockingPolicy.java:790)
at org.eclipse.persistence.internal.queries.DatabaseQueryMechanism.updateObjectForWriteWithChangeSet(DatabaseQueryMechanism.java:1087)
at org.eclipse.persistence.queries.UpdateObjectQuery.executeCommitWithChangeSet(UpdateObjectQuery.java:84)
at org.eclipse.persistence.internal.queries.DatabaseQueryMechanism.executeWriteWithChangeSet(DatabaseQueryMechanism.java:301)
at org.eclipse.persistence.queries.WriteObjectQuery.executeDatabaseQuery(WriteObjectQuery.java:58)
at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:899)
at org.eclipse.persistence.queries.DatabaseQuery.executeInUnitOfWork(DatabaseQuery.java:798)
at org.eclipse.persistence.queries.ObjectLevelModifyQuery.executeInUnitOfWorkObjectLevelModifyQuery(ObjectLevelModifyQuery.java:108)
at org.eclipse.persistence.queries.ObjectLevelModifyQuery.executeInUnitOfWork(ObjectLevelModifyQuery.java:85)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:2896)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1804)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1786)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1737)
at org.eclipse.persistence.internal.sessions.CommitManager.commitChangedObjectsForClassWithChangeSet(CommitManager.java:267)
at org.eclipse.persistence.internal.sessions.CommitManager.commitAllObjectsForClassWithChangeSet(CommitManager.java:192)
at org.eclipse.persistence.internal.sessions.CommitManager.commitAllObjectsWithChangeSet(CommitManager.java:138)
at org.eclipse.persistence.internal.sessions.AbstractSession.writeAllObjectsWithChangeSet(AbstractSession.java:4207)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.commitToDatabase(UnitOfWorkImpl.java:1441)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.commitToDatabaseWithChangeSet(UnitOfWorkImpl.java:1531)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.issueSQLbeforeCompletion(UnitOfWorkImpl.java:3168)
at org.eclipse.persistence.internal.sessions.RepeatableWriteUnitOfWork.issueSQLbeforeCompletion(RepeatableWriteUnitOfWork.java:352)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:158)
... 41 more
]]

eMillis: 1542932408194] [levelValue: 900] [[
A system exception occurred during an invocation on EJB IngestServiceBean, method: public boolean edu.harvard.iq.dataverse.ingest.IngestServiceBean.ingestAsTabula
r(java.lang.Long)]]

[2018-11-23T11:20:08.194+1100] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=67 _ThreadName=p: thread-pool-1; w: 5] [timeMillis: 154
2932408194] [levelValue: 900] [[

javax.ejb.EJBException: Transaction aborted
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:725)
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.$Proxy321.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.__EJB31_Generated__IngestServiceBean__Intf____Bean__.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.IngestMessageBean.onMessage(IngestMessageBean.java:86)
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.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:73)
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.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 org.glassfish.ejb.mdb.MessageBeanContainer.deliverMessage(MessageBeanContainer.java:1219)
at org.glassfish.ejb.mdb.MessageBeanListenerImpl.deliverMessage(MessageBeanListenerImpl.java:81)
at com.sun.enterprise.connectors.inbound.MessageEndpointInvocationHandler.invoke(MessageEndpointInvocationHandler.java:171)
at com.sun.proxy.$Proxy456.onMessage(Unknown Source)
at com.sun.messaging.jms.ra.OnMessageRunner.run(OnMessageRunner.java:283)
at com.sun.enterprise.connectors.work.OneWork.doWork(OneWork.java:107)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
Caused by: javax.transaction.RollbackException: Transaction marked for rollback.
at com.sun.enterprise.transaction.JavaEETransactionImpl.commit(JavaEETransactionImpl.java:490)
at com.sun.enterprise.transaction.JavaEETransactionManagerSimplified.commit(JavaEETransactionManagerSimplified.java:854)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:719)
... 37 more
Caused by: javax.persistence.OptimisticLockException: Exception [EclipseLink-5006] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:815]] cannot be updated because it has changed or been deleted since it was last read.
Class> edu.harvard.iq.dataverse.DatasetVersion Primary Key> 815
at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl$1.handleException(EntityManagerSetupImpl.java:694)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.handleException(AbstractSynchronizationListener.java:275)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:170)
at org.eclipse.persistence.transaction.JTASynchronizationListener.beforeCompletion(JTASynchronizationListener.java:68)
at com.sun.enterprise.transaction.JavaEETransactionImpl.commit(JavaEETransactionImpl.java:452)
... 39 more
Caused by: Exception [EclipseLink-5006] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:815]] cannot be updated because it has changed or been deleted since it was last read.
Class> edu.harvard.iq.dataverse.DatasetVersion Primary Key> 815
at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastReadWhenUpdating(OptimisticLockException.java:144)
at org.eclipse.persistence.descriptors.VersionLockingPolicy.validateUpdate(VersionLockingPolicy.java:790)
at org.eclipse.persistence.internal.queries.DatabaseQueryMechanism.updateObjectForWriteWithChangeSet(DatabaseQueryMechanism.java:1087)
at org.eclipse.persistence.queries.UpdateObjectQuery.executeCommitWithChangeSet(UpdateObjectQuery.java:84)
at org.eclipse.persistence.internal.queries.DatabaseQueryMechanism.executeWriteWithChangeSet(DatabaseQueryMechanism.java:301)
at org.eclipse.persistence.queries.WriteObjectQuery.executeDatabaseQuery(WriteObjectQuery.java:58)
at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:899)
at org.eclipse.persistence.queries.DatabaseQuery.executeInUnitOfWork(DatabaseQuery.java:798)
at org.eclipse.persistence.queries.ObjectLevelModifyQuery.executeInUnitOfWorkObjectLevelModifyQuery(ObjectLevelModifyQuery.java:108)
at org.eclipse.persistence.queries.ObjectLevelModifyQuery.executeInUnitOfWork(ObjectLevelModifyQuery.java:85)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:2896)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1804)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1786)
at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1737)
at org.eclipse.persistence.internal.sessions.CommitManager.commitChangedObjectsForClassWithChangeSet(CommitManager.java:267)
at org.eclipse.persistence.internal.sessions.CommitManager.commitAllObjectsForClassWithChangeSet(CommitManager.java:192)
at org.eclipse.persistence.internal.sessions.CommitManager.commitAllObjectsWithChangeSet(CommitManager.java:138)
at org.eclipse.persistence.internal.sessions.AbstractSession.writeAllObjectsWithChangeSet(AbstractSession.java:4207)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.commitToDatabase(UnitOfWorkImpl.java:1441)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.commitToDatabaseWithChangeSet(UnitOfWorkImpl.java:1531)
at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.issueSQLbeforeCompletion(UnitOfWorkImpl.java:3168)
at org.eclipse.persistence.internal.sessions.RepeatableWriteUnitOfWork.issueSQLbeforeCompletion(RepeatableWriteUnitOfWork.java:352)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:158)
... 41 more
]]

[mdmADA]

And I totally agree with needing something "with more teeth" between the user and being able to do something...

[pdurbin]

@mdmADA I don't want to lose track of your comments on a close issue so I'm reopening it, assigning it to you, and moving it to the "Community Dev" column at https://waffle.io/IQSS/dataverse so we remember to touch base with you about what a good fix might be. Thanks.

[pdurbin]

I guess the only thing I'll add is that an OptimisticLockException is never a good thing. Any more leads on a fix, @mdmADA ? Or steps to reproduce the bug, especially on the "develop" branch?

[mdmADA]

Hi @pdurbin. An OptimisticLockException is definitely not a good thing.

I have a number of things on the go at the moment but will add 'attempt to reproduce bug #4045" to my TO-DO list.

As for a possible fix, I haven't have had time to think about that either. My instinct tells me the failed data file ingest caused the OptimisticLockException issue somewhere down the line and adding in a pause between each file upload gave the system time to recover from that Exception (if that's possible and/or makes sense). I am not sure how one would go about adding in a pause when something has "gummed up" the system and it needs time to recover... will add that to my TO-DO list too.

Thanks!

[pdurbin]

@mdmADA hi! This issue is still assigned to you but please let us know if we should throw it back in the inbox instead. No pressure either way! Thanks.

[mdmADA]

Yeah, as much as I would like to look at this, I won't have time so you should probably throw it back into the inbox. 📥

[pdurbin]

@mdmADA thanks. Done. I'm not sure if we'll still call it the inbox once we migrate off Waffle (#5651) but I unassigned you at least. Thanks for the feedback on this issue.