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SWORD: "Replacing metadata for a dataset" broken, throws exception #1554

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pdurbin opened this issue Mar 2, 2015 · 7 comments
Closed

SWORD: "Replacing metadata for a dataset" broken, throws exception #1554

pdurbin opened this issue Mar 2, 2015 · 7 comments
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@kcondon
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Type: Bug a defect
Milestone
Beta 14 - Dataver...

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@pdurbin
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pdurbin commented Mar 2, 2015

While working on #1430 I tested the SWORD function "replacing metadata for a dataset" as documented at http://guides.dataverse.org/en/latest/api/sword.html#replacing-metadata-for-a-dataset and it's not working. I throws the OptimisticLockException below.

Here's the curl command I was using to test:

curl --insecure --upload-file scripts/search/tests/data/dataset-trees1-edit.xml -H 'Content-Type: application/atom+xml' https://spruce:spruce@localhost:8181/dvn/api/data-deposit/v1/swordv2/edit/study/doi:10.5072/FK2/OEJKJ2

I don't know how long this has been broken. I don't believe I have a test for this at https://github.com/IQSS/dataverse-apitester

[2015-03-02T15:10:27.757-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=36 _ThreadName=http-listener-2(5)] [timeMillis: 1425327027757] [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.$Proxy919.submit(Unknown Source)
    at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
    at edu.harvard.iq.dataverse.api.datadeposit.ContainerManagerImpl.replaceMetadata(ContainerManagerImpl.java:142)
    at org.swordapp.server.ContainerAPI.put(ContainerAPI.java:222)
    at edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet.doPut(SWORDv2ContainerServlet.java:49)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    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:205)
    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.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
    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:744)
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 [[DatasetVersion id:null]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.DatasetVersion
    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.UpdateDatasetCommand.save(UpdateDatasetCommand.java:111)
    at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.execute(UpdateDatasetCommand.java:59)
    at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.execute(UpdateDatasetCommand.java:33)
    at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:145)
    at sun.reflect.GeneratedMethodAccessor2282.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.GeneratedMethodAccessor95.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.GeneratedMethodAccessor102.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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)
    ... 44 more
Caused by: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:null]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.DatasetVersion
    at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastMerge(OptimisticLockException.java:152)
    at org.eclipse.persistence.internal.sessions.MergeManager.checkNewObjectLockVersion(MergeManager.java:1114)
    at org.eclipse.persistence.internal.sessions.MergeManager.registerObjectForMergeCloneIntoWorkingCopy(MergeManager.java:1086)
    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.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)
    ... 78 more
]]

[2015-03-02T15:10:27.759-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=36 _ThreadName=http-listener-2(5)] [timeMillis: 1425327027759] [levelValue: 900] [[
  StandardWrapperValve[edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet]: Servlet.service() for servlet edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet threw exception
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.$Proxy919.submit(Unknown Source)
    at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
    at edu.harvard.iq.dataverse.api.datadeposit.ContainerManagerImpl.replaceMetadata(ContainerManagerImpl.java:142)
    at org.swordapp.server.ContainerAPI.put(ContainerAPI.java:222)
    at edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet.doPut(SWORDv2ContainerServlet.java:49)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    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:205)
    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.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
    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:744)
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 [[DatasetVersion id:null]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.DatasetVersion
    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.UpdateDatasetCommand.save(UpdateDatasetCommand.java:111)
    at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.execute(UpdateDatasetCommand.java:59)
    at edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand.execute(UpdateDatasetCommand.java:33)
    at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:145)
    at sun.reflect.GeneratedMethodAccessor2282.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.GeneratedMethodAccessor95.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.GeneratedMethodAccessor102.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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)
    ... 44 more
Caused by: Exception [EclipseLink-5010] (Eclipse Persistence Services - 2.5.2.v20140319-9ad6abd): org.eclipse.persistence.exceptions.OptimisticLockException
Exception Description: The object [[DatasetVersion id:null]] cannot be merged because it has changed or been deleted since it was last read. 
Class> edu.harvard.iq.dataverse.DatasetVersion
    at org.eclipse.persistence.exceptions.OptimisticLockException.objectChangedSinceLastMerge(OptimisticLockException.java:152)
    at org.eclipse.persistence.internal.sessions.MergeManager.checkNewObjectLockVersion(MergeManager.java:1114)
    at org.eclipse.persistence.internal.sessions.MergeManager.registerObjectForMergeCloneIntoWorkingCopy(MergeManager.java:1086)
    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.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)
    ... 78 more
]]
@pdurbin pdurbin added this to the In Review - 4.0 milestone Mar 2, 2015
pdurbin added a commit that referenced this issue Mar 2, 2015
@pdurbin
SWORD: only add subject field if missing #1430
1bc8772 
Discovered editing metadata via SWORD isn't working. Opened #1554

The new behavior for subject/keyword is not documented. Opened #1553
This was referenced Mar 2, 2015
Closed
Closed
@pdurbin pdurbin mentioned this issue Mar 3, 2015
Closed
pdurbin added a commit to IQSS/dataverse-apitester that referenced this issue Mar 3, 2015
@pdurbin
SWORD: add test for edit dataset
8928ae3 
disabled until there is a fix for IQSS/dataverse#1554
@pdurbin
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pdurbin commented Mar 3, 2015

As I noted at #973 (comment) from what I can tell the ability to edit dataset metadata via SWORD broke with the switch from the importXML method on foreignMetadataImportService to importGenericService in ContainerManagerImpl.java. If I use the old method, the test (disabled for now) I just wrote at IQSS/dataverse-apitester@8928ae3 passes.

Understandably, @scolapasta doesn't was us to simply revert to the importXML method on foreignMetadataImportService because there's logic in importGenericService that we want. He said to pass this ticket to him.

@pdurbin pdurbin assigned scolapasta and unassigned pdurbin Mar 3, 2015
@pdurbin pdurbin added the Type: Bug a defect label Mar 4, 2015
@pdurbin
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pdurbin commented Mar 5, 2015

@scolapasta found where the new importXML calls this method and sets the id to null. Commenting it out allows the dataset to be edited via SWORD but we want to check with @michbarsinai and @ekraffmiller and @rtreacy about why the id is set to null here.

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
index 49525c7..f7d0abe 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
@@ -172,7 +172,7 @@ public class JsonParser {
             dsv.setDeaccessionLink(obj.getString("deaccessionLink", null));
             dsv.setVersionNumber((long) obj.getInt("versionNumber", -1));
             dsv.setMinorVersionNumber(parseLong(obj.getString("minorVersionNumber", null)));
-            dsv.setId(parseLong(obj.getString("id", null)));
+//            dsv.setId(parseLong(obj.getString("id", null)));

             String versionStateStr = obj.getString("versionState", null);
             if (versionStateStr != null) {

@scolapasta
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Wondering if the logic should be to check if the id already exists, if so then if not the same throw an exception. Otherwise proceed.

@ekraffmiller
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Yes, Gustavo's suggestion seems right to me

@scolapasta scolapasta assigned ekraffmiller and unassigned scolapasta Mar 5, 2015
ekraffmiller added a commit that referenced this issue Mar 5, 2015
@ekraffmiller
check for existing datasetversion id when updating with parsed json (#…
9c25094 
…1554)
@ekraffmiller ekraffmiller assigned kcondon and unassigned ekraffmiller Mar 5, 2015
pdurbin added a commit to IQSS/dataverse-apitester that referenced this issue Mar 6, 2015
@pdurbin
edit metadata via SWORD test now passes, enable it
24c3138 
See also IQSS/dataverse#1554
and IQSS/dataverse@9c25094
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pdurbin commented Mar 6, 2015

I enabled the test at IQSS/dataverse-apitester@24c3138 and ran a build on apitest. It passed: https://build.hmdc.harvard.edu:8443/job/apitest.dataverse.org-apitester/org.dataverse$apitester/19/testReport/org.dataverse.apitester.sword/SwordTest/

@kcondon kcondon assigned posixeleni and unassigned kcondon Mar 18, 2015
@posixeleni posixeleni assigned kcondon and unassigned posixeleni Mar 18, 2015
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Will need @kcondon to QA this one

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pdurbin commented Jan 6, 2016

I added an API test to replace metadata via SWORD in eb3d08d and it works fine:

INFO: Title updated from "My Working Title" to "My Awesome Dataset" -- https://build.hmdc.harvard.edu:8443/job/phoenix.dataverse.org-apitest-4.2.3/18/console

I don't if that's enough to close this issue, but I'm satisfied.

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