Solr document with id of datafile_null, NPE

[eaquigley]

---

Author Name: Philip Durbin (@pdurbin)
Original Redmine Issue: 3809, https://redmine.hmdc.harvard.edu/issues/3809
Original Date: 2014-04-03
Original Assignee: Gustavo Durand

---

dvn-build, jenkins-DVN_4_0-238, e6bce0b

NPE at DataFile dataFile = dataFileService.find(solrSearchResult.getEntityId()); - https://github.com/IQSS/dataverse_temp/blob/e6bce0b93282253bace8f6170fa30c6801a271f8/src/main/java/edu/harvard/iq/dataverse/SearchIncludeFragment.java#L335

I'm not sure how this file ended up not having a database id... rather than "datafile_null" the id in Solr should be datafile_42 or whatever:

[pdurbin@dvn-build ~]$ curl -s 'http://localhost:8983/solr/collection1/select?rows=100&wt=json&indent=true&q=-entityid:*'
{
  "responseHeader":{
    "status":0,
    "QTime":3,
    "params":{
      "indent":"true",
      "q":"-entityid:*",
      "wt":"json",
      "rows":"100"}},
  "response":{"numFound":1,"start":0,"docs":[
      {
        "id":"datafile_null",
        "dvtype":"files",
        "name":"IMG_20140322_144443.jpg",
        "name_sort":"IMG_20140322_144443.jpg",
        "release_or_create_date_dt":"2014-04-01T22:45:30.015Z",
        "perms_ss":["group_public",
          "group_2"],
        "filetypemime_s":"JPEG Image",
        "filetype_s":"image",
        "description":"",
        "hostdataverse_s":"esochld1",
        "parentid":"27",
        "parentname":"other title",
        "_version_":1464375127685726208}]
  }}
[pdurbin@dvn-build ~]$

I'm pretty sure it causes this EJBException (java.lang.IllegalArgumentException: An instance of a null PK has been incorrectly provided for this find operation) when you hit http://dvn-build.hmdc.harvard.edu/?id=&q=&types=dataverses%3Afiles&sort=release_or_create_date_dt&order=desc&page=1

Stacktrace below.

[2014-04-03T11:38:02.136-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539482136] [levelValue: 800] [[
  search called]]

[2014-04-03T11:38:02.140-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539482140] [levelValue: 800] [[
  query from user:   null]]

[2014-04-03T11:38:02.141-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539482141] [levelValue: 800] [[
  queryToPassToSolr: *]]

[2014-04-03T11:38:02.141-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539482141] [levelValue: 800] [[
  sort by: release_or_create_date_dt]]

[2014-04-03T11:38:02.148-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchServiceBean] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539482148] [levelValue: 800] [[
  Solr query:q=*&sort=release_or_create_date_dt+desc&hl=true&hl.snippets=1&hl.fl=description&qt=%2Fspell&facet=true&facet.query=*&fq=dvtype%3A%28dataverses+OR+datasets%29&fq=%7B%21join+from%3Dgroups_s+to%3Dperms_ss%7Did%3Agroup_public&facet.field=hostdataverse_s&facet.field=affiliation_ss&facet.field=releasedate&facet.field=authorName_ss&facet.field=filetype_s&facet.field=dvtype&start=0&rows=10]]

[2014-04-03T11:38:02.173-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchServiceBean] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539482173] [levelValue: 800] [[
  Solr query:q=*&sort=release_or_create_date_dt+desc&hl=true&hl.snippets=1&hl.fl=description&qt=%2Fspell&facet=true&facet.query=*&fq=dvtype%3A%28dataverses+OR+datasets+OR+files%29&fq=%7B%21join+from%3Dgroups_s+to%3Dperms_ss%7Did%3Agroup_public&facet.field=hostdataverse_s&facet.field=affiliation_ss&facet.field=releasedate&facet.field=authorName_ss&facet.field=filetype_s&facet.field=dvtype&start=0&rows=10]]

[2014-04-03T11:38:07.369-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539487369] [levelValue: 800] [[
  search called]]

[2014-04-03T11:38:07.372-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539487372] [levelValue: 800] [[
  query from user:   ]]

[2014-04-03T11:38:07.373-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539487373] [levelValue: 800] [[
  queryToPassToSolr: *]]

[2014-04-03T11:38:07.374-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539487374] [levelValue: 800] [[
  sort by: release_or_create_date_dt]]

[2014-04-03T11:38:07.378-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchServiceBean] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539487378] [levelValue: 800] [[
  Solr query:q=*&sort=release_or_create_date_dt+desc&hl=true&hl.snippets=1&hl.fl=description&qt=%2Fspell&facet=true&facet.query=*&fq=dvtype%3A%28dataverses+OR+datasets+OR+files%29&fq=%7B%21join+from%3Dgroups_s+to%3Dperms_ss%7Did%3Agroup_public&facet.field=hostdataverse_s&facet.field=affiliation_ss&facet.field=releasedate&facet.field=authorName_ss&facet.field=filetype_s&facet.field=dvtype&start=0&rows=10]]

[2014-04-03T11:38:07.400-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchServiceBean] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539487400] [levelValue: 800] [[
  Solr query:q=*&sort=release_or_create_date_dt+desc&hl=true&hl.snippets=1&hl.fl=description&qt=%2Fspell&facet=true&facet.query=*&fq=dvtype%3A%28dataverses+OR+datasets+OR+files%29&fq=%7B%21join+from%3Dgroups_s+to%3Dperms_ss%7Did%3Agroup_public&facet.field=hostdataverse_s&facet.field=affiliation_ss&facet.field=releasedate&facet.field=authorName_ss&facet.field=filetype_s&facet.field=dvtype&start=0&rows=10]]

[2014-04-03T11:38:10.093-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490093] [levelValue: 800] [[
  search called]]

[2014-04-03T11:38:10.096-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490096] [levelValue: 800] [[
  query from user:   ]]

[2014-04-03T11:38:10.097-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490097] [levelValue: 800] [[
  queryToPassToSolr: *]]

[2014-04-03T11:38:10.098-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchIncludeFragment] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490098] [levelValue: 800] [[
  sort by: release_or_create_date_dt]]

[2014-04-03T11:38:10.104-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchServiceBean] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490104] [levelValue: 800] [[
  Solr query:q=*&sort=release_or_create_date_dt+desc&hl=true&hl.snippets=1&hl.fl=description&qt=%2Fspell&facet=true&facet.query=*&fq=dvtype%3A%28dataverses+OR+files%29&fq=%7B%21join+from%3Dgroups_s+to%3Dperms_ss%7Did%3Agroup_public&facet.field=hostdataverse_s&facet.field=affiliation_ss&facet.field=releasedate&facet.field=authorName_ss&facet.field=filetype_s&facet.field=dvtype&start=0&rows=10]]

[2014-04-03T11:38:10.129-0400] [glassfish 4.0] [INFO] [] [edu.harvard.iq.dataverse.SearchServiceBean] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490129] [levelValue: 800] [[
  Solr query:q=*&sort=release_or_create_date_dt+desc&hl=true&hl.snippets=1&hl.fl=description&qt=%2Fspell&facet=true&facet.query=*&fq=dvtype%3A%28dataverses+OR+datasets+OR+files%29&fq=%7B%21join+from%3Dgroups_s+to%3Dperms_ss%7Did%3Agroup_public&facet.field=hostdataverse_s&facet.field=affiliation_ss&facet.field=releasedate&facet.field=authorName_ss&facet.field=filetype_s&facet.field=dvtype&start=0&rows=10]]

[2014-04-03T11:38:10.187-0400] [glassfish 4.0] [WARNING] [ejb.system_exception] [javax.enterprise.system.container.ejb.com.sun.ejb.containers] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490187] [levelValue: 900] [[
  EJB5184:A system exception occurred during an invocation on EJB DataFileServiceBean, method: public edu.harvard.iq.dataverse.DataFile edu.harvard.iq.dataverse.DataFileServiceBean.find(java.lang.Object)]]

[2014-04-03T11:38:10.188-0400] [glassfish 4.0] [WARNING] [] [javax.enterprise.system.container.ejb.com.sun.ejb.containers] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490188] [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:4475)
    at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2009)
    at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:1979)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
    at com.sun.proxy.$Proxy394.find(Unknown Source)
    at edu.harvard.iq.dataverse.__EJB31_Generated__DataFileServiceBean__Intf____Bean__.find(Unknown Source)
    at edu.harvard.iq.dataverse.SearchIncludeFragment.search(SearchIncludeFragment.java:335)
    at edu.harvard.iq.dataverse.SearchIncludeFragment$Proxy$_$$_WeldClientProxy.search(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor4000.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at javax.el.ELUtil.invokeMethod(ELUtil.java:326)
    at javax.el.BeanELResolver.invoke(BeanELResolver.java:536)
    at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:256)
    at com.sun.el.parser.AstValue.invoke(AstValue.java:269)
    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.UIViewAction.broadcast(UIViewAction.java:559)
    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.StandardWrapperValve.invoke(StandardWrapperValve.java:318)
    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:354)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
    at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:196)
    at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:173)
    at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
    at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
    at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
    at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
    at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
    at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.IllegalArgumentException: An instance of a null PK has been incorrectly provided for this find operation.
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.findInternal(EntityManagerImpl.java:775)
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.find(EntityManagerImpl.java:719)
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.find(EntityManagerImpl.java:588)
    at com.sun.enterprise.container.common.impl.EntityManagerWrapper.find(EntityManagerWrapper.java:342)
    at edu.harvard.iq.dataverse.DataFileServiceBean.find(DataFileServiceBean.java:38)
    at sun.reflect.GeneratedMethodAccessor3397.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:4695)
    at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:630)
    at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
    at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
    at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
    at sun.reflect.GeneratedMethodAccessor3106.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:582)
    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.GeneratedMethodAccessor3107.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:4667)
    at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4655)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
    ... 54 more
]]

[2014-04-03T11:38:10.190-0400] [glassfish 4.0] [WARNING] [] [javax.enterprise.resource.webcontainer.jsf.lifecycle] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490190] [levelValue: 900] [[
  #{SearchIncludeFragment.search()}: javax.ejb.EJBException
javax.faces.FacesException: #{SearchIncludeFragment.search()}: javax.ejb.EJBException
    at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:118)
    at javax.faces.component.UIViewAction.broadcast(UIViewAction.java:559)
    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.StandardWrapperValve.invoke(StandardWrapperValve.java:318)
    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:354)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
    at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:196)
    at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:173)
    at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
    at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
    at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
    at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
    at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
    at java.lang.Thread.run(Thread.java:744)
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)
    ... 36 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:4475)
    at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2009)
    at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:1979)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
    at com.sun.proxy.$Proxy394.find(Unknown Source)
    at edu.harvard.iq.dataverse.__EJB31_Generated__DataFileServiceBean__Intf____Bean__.find(Unknown Source)
    at edu.harvard.iq.dataverse.SearchIncludeFragment.search(SearchIncludeFragment.java:335)
    at edu.harvard.iq.dataverse.SearchIncludeFragment$Proxy$_$$_WeldClientProxy.search(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor4000.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at javax.el.ELUtil.invokeMethod(ELUtil.java:326)
    at javax.el.BeanELResolver.invoke(BeanELResolver.java:536)
    at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:256)
    at com.sun.el.parser.AstValue.invoke(AstValue.java:269)
    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)
    ... 37 more
Caused by: java.lang.IllegalArgumentException: An instance of a null PK has been incorrectly provided for this find operation.
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.findInternal(EntityManagerImpl.java:775)
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.find(EntityManagerImpl.java:719)
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.find(EntityManagerImpl.java:588)
    at com.sun.enterprise.container.common.impl.EntityManagerWrapper.find(EntityManagerWrapper.java:342)
    at edu.harvard.iq.dataverse.DataFileServiceBean.find(DataFileServiceBean.java:38)
    at sun.reflect.GeneratedMethodAccessor3397.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:4695)
    at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:630)
    at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
    at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
    at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
    at sun.reflect.GeneratedMethodAccessor3106.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:582)
    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.GeneratedMethodAccessor3107.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:4667)
    at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4655)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
    ... 54 more
]]

[2014-04-03T11:38:10.195-0400] [glassfish 4.0] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=95 _ThreadName=http-listener-1(3)] [timeMillis: 1396539490195] [levelValue: 900] [[
  StandardWrapperValve[Faces Servlet]: Servlet.service() for servlet Faces Servlet threw exception
java.lang.IllegalArgumentException: An instance of a null PK has been incorrectly provided for this find operation.
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.findInternal(EntityManagerImpl.java:775)
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.find(EntityManagerImpl.java:719)
    at org.eclipse.persistence.internal.jpa.EntityManagerImpl.find(EntityManagerImpl.java:588)
    at com.sun.enterprise.container.common.impl.EntityManagerWrapper.find(EntityManagerWrapper.java:342)
    at edu.harvard.iq.dataverse.DataFileServiceBean.find(DataFileServiceBean.java:38)
    at sun.reflect.GeneratedMethodAccessor3397.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:4695)
    at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:630)
    at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
    at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
    at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
    at sun.reflect.GeneratedMethodAccessor3106.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:582)
    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.GeneratedMethodAccessor3107.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:4667)
    at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4655)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
    at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
    at com.sun.proxy.$Proxy394.find(Unknown Source)
    at edu.harvard.iq.dataverse.__EJB31_Generated__DataFileServiceBean__Intf____Bean__.find(Unknown Source)
    at edu.harvard.iq.dataverse.SearchIncludeFragment.search(SearchIncludeFragment.java:335)
    at edu.harvard.iq.dataverse.SearchIncludeFragment$Proxy$_$$_WeldClientProxy.search(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor4000.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at javax.el.ELUtil.invokeMethod(ELUtil.java:326)
    at javax.el.BeanELResolver.invoke(BeanELResolver.java:536)
    at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:256)
    at com.sun.el.parser.AstValue.invoke(AstValue.java:269)
    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.UIViewAction.broadcast(UIViewAction.java:559)
    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.StandardWrapperValve.invoke(StandardWrapperValve.java:318)
    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:354)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
    at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:196)
    at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:173)
    at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
    at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
    at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
    at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
    at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
    at java.lang.Thread.run(Thread.java:744)
]]

---

Related issue(s): #287
Redmine related issue(s): 3701

---

[eaquigley]

---

Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-04-03T17:11:19Z

---

I put some bad data in my local Solr with...

murphy:dataverse_temp pdurbin$ curl http://localhost:8983/solr/update/json?commit=true -H 'Content-type:application/json' --data-binary @/tmp/bad
{"responseHeader":{"status":0,"QTime":10}}
murphy:dataverse_temp pdurbin$ 
murphy:dataverse_temp pdurbin$ cat /tmp/bad
[     
 {
        "id":"datafile_null",
        "dvtype":"files",
        "name":"image.png",
        "name_sort":"image.png",
        "release_or_create_date_dt":"2014-04-03T12:51:42.749Z",
        "perms_ss":["group_public",
          "group_2"],
        "filetypemime_s":"PNG Image",
        "filetype_s":"image",
        "description":"",
        "subtree_ss":["/birds"],
        "hostdataverse_s":"Birds",
        "parentid":"16",
        "parentname":"bird1"
  }
]
murphy:dataverse_temp pdurbin$

(

good data would look more like this:

        "id":"datafile_17",
        "entityid":17,

)

... to reproduce the problem. Then I added a

                if (solrSearchResult.getEntityId() == null) {
                    // avoiding EJBException a la https://redmine.hmdc.harvard.edu/issues/3809
                    logger.warning(SearchFields.ENTITY_ID + " was null for Solr document id:" + solrSearchResult.getId() + ", skipping. Bad Solr data?");
                    break;
                }

in this commit:

dcb5e2c null check of solr entityid to avoid EJBException (null PK in find) #3809

That should should avoid the EJBException and instead print this to server.log:

WARNING: entityid was null for Solr document id:datafile_null, skipping. Bad Solr data?

Elda seems pretty sure she can reproduce the bad data getting into Solr in the first place with some file upload trickery so she wants this ticket next. Passing to her.

[eaquigley]

---

Original Redmine Comment
Author Name: Elda Sotiri (@esotiri)
Original Date: 2014-04-08T13:38:35Z

---

can't seem to be able to reproduce this. I will keep an eye..

[eaquigley]

---

Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-04-08T14:02:49Z

---

Elda Sotiri wrote:

can't seem to be able to reproduce this. I will keep an eye..

I'm not sure if this is why but I add to add an @em.flush()@ here or else I was getting stuff like "group_usernull" instead of "group_user6"...

 public DataverseUser save(DataverseUser dataverseUser) {

•     return em.merge(dataverseUser);
  

•    DataverseUser savedUser = em.merge(dataverseUser);
  

•    em.flush();
  

•    String indexingResult = indexService.indexUser(savedUser);
  

•    logger.info("during user save, indexing results was: " + indexingResult);
  

•    return savedUser;
  

  }

... in 136da87 index user on create, index groups with root dataverse #3800

Maybe an @em.flush()@ should be added to where file id's are persisted if it isn't there already. The problem is similar: "datafile_null" because datafile.getId() was null.

[eaquigley]

---

Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-04-08T14:04:41Z

---

Leonid, can you please check out my last comment about em.flush? Do we need an equivalent for files? datafile.getId() is sometimes null.

[eaquigley]

---

Original Redmine Comment
Author Name: Gustavo Durand (@scolapasta)
Original Date: 2014-04-23T16:48:27Z

---

Let's review if anything needs to be done for beta.

[eaquigley]

---

Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-05-07T20:12:57Z

---

I can no longer replicate this problem reliably. I even removed the reminder to run "index all" from my integration test:

d10add4#diff-aa699baedd36d74b1409985a5435fc64L34

[eaquigley]

@pdurbin & @scolapasta can this ticket be closed?

[pdurbin]

I'm fine with it being closed. As I said here, I haven't been able to reproduce it for over a month: #394 (comment)