[InterMine Dev] GeneStructureDisplayer throwing NullPointerException - any ideas?

Sam Hokin shokin at ncgr.org
Wed Apr 27 23:52:12 BST 2016


Hi, devs. I've got two mines that are extremely similar, both pulling genomic data from the same chado database. In both cases the 
objects associated with genes are populated in the same way, namely: transcripts=yes, exons=yes, CDSs=no, introns=no, UTRs=no, 
fivePrimeUTR=no, threePrimeUTR=no. I mention these because they are what GeneStructureDisplayer replaces in the Gene report.

However, one of the mines has no error in GeneStructureDisplayer; it shows the list of transcripts and their exons as it should. In 
the other mine, GeneStructureDisplayer throws a NullPointerException which is, to me, totally uninformative. Since the mines, and 
webconfig-model.xml, are identical in structure, I can't figure out where to start looking.

I've attached the full stack trace when I request a Gene report page. I'd really appreciate any ideas on where to look to get the 
GeneStructureDisplayer to work on this mine!
-------------- next part --------------
 INFO [ajp-apr-8009-exec-4] (ReportController.java:139) - TIME placed inline lists: 0ms
886309 [ajp-apr-8009-exec-4] INFO org.intermine.web.struts.ReportController  - TIME placed inline lists: 0ms
 INFO [ajp-apr-8009-exec-4] (ReportController.java:239) - TIME made list of categories: 74ms
886873 [ajp-apr-8009-exec-4] INFO org.intermine.web.struts.ReportController  - TIME made list of categories: 74ms
 INFO [ajp-apr-8009-exec-4] (ReportObject.java:581) - TIME getHeaderLink creation took: 0ms
886999 [ajp-apr-8009-exec-4] INFO org.intermine.web.logic.results.ReportObject  - TIME getHeaderLink creation took: 0ms
 INFO [ajp-apr-8009-exec-4] (ReportObject.java:287) - TIME objectSummaryFields already set, took: 0ms
887043 [ajp-apr-8009-exec-4] INFO org.intermine.web.logic.results.ReportObject  - TIME objectSummaryFields already set, took: 0ms
 INFO [ajp-apr-8009-exec-4] (ReportObject.java:287) - TIME objectSummaryFields already set, took: 0ms
887621 [ajp-apr-8009-exec-4] INFO org.intermine.web.logic.results.ReportObject  - TIME objectSummaryFields already set, took: 0ms
 INFO [ajp-apr-8009-exec-10] (CommonsLoggingOutput.java:51) - Exec: AjaxServices.getFriendlyMineLinks()
887946 [ajp-apr-8009-exec-10] INFO org.directwebremoting.impl.DefaultRemoter  - Exec: AjaxServices.getFriendlyMineLinks()
 INFO [ajp-apr-8009-exec-5] (CommonsLoggingOutput.java:51) - Exec: AjaxServices.getFriendlyMineLinks()
887965 [ajp-apr-8009-exec-5] INFO org.directwebremoting.impl.DefaultRemoter  - Exec: AjaxServices.getFriendlyMineLinks()
 INFO [ajp-apr-8009-exec-8] (CommonsLoggingOutput.java:51) - Exec: AjaxServices.getFriendlyMineLinks()
887968 [ajp-apr-8009-exec-8] INFO org.directwebremoting.impl.DefaultRemoter  - Exec: AjaxServices.getFriendlyMineLinks()
ERROR [ajp-apr-8009-exec-2] (ReportDisplayer.java:68) - Error rendering report displayer class org.intermine.bio.web.displayer.GeneStructureDisplayer for Gene(4126414): java.lang.NullPointerException: Cannot create a QueryValue with null
	at org.intermine.objectstore.query.QueryValue.<init>(QueryValue.java:41)
	at org.intermine.bio.web.model.GeneModelCache.determineOrganismSettings(GeneModelCache.java:154)
	at org.intermine.bio.web.model.GeneModelCache.getGeneModelOrganismSettings(GeneModelCache.java:135)
	at org.intermine.bio.web.displayer.GeneStructureDisplayer.display(GeneStructureDisplayer.java:57)
	at org.intermine.web.displayer.ReportDisplayer.execute(ReportDisplayer.java:62)
	at org.intermine.web.struts.ReportDisplayerController.execute(ReportDisplayerController.java:43)
	at org.intermine.web.struts.ModifyDetails.ajaxShowDisplayer(ModifyDetails.java:296)
	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:497)
	at org.apache.struts.actions.DispatchAction.dispatchMethod(DispatchAction.java:269)
	at org.apache.struts.actions.DispatchAction.execute(DispatchAction.java:170)
	at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
	at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
	at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
	at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:521)
	at org.apache.coyote.ajp.AbstractAjpProcessor.process(AbstractAjpProcessor.java:850)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:674)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2500)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2489)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)

888561 [ajp-apr-8009-exec-2] ERROR org.intermine.web.displayer.ReportDisplayer  - Error rendering report displayer class org.intermine.bio.web.displayer.GeneStructureDisplayer for Gene(4126414): java.lang.NullPointerException: Cannot create a QueryValue with null
	at org.intermine.objectstore.query.QueryValue.<init>(QueryValue.java:41)
	at org.intermine.bio.web.model.GeneModelCache.determineOrganismSettings(GeneModelCache.java:154)
	at org.intermine.bio.web.model.GeneModelCache.getGeneModelOrganismSettings(GeneModelCache.java:135)
	at org.intermine.bio.web.displayer.GeneStructureDisplayer.display(GeneStructureDisplayer.java:57)
	at org.intermine.web.displayer.ReportDisplayer.execute(ReportDisplayer.java:62)
	at org.intermine.web.struts.ReportDisplayerController.execute(ReportDisplayerController.java:43)
	at org.intermine.web.struts.ModifyDetails.ajaxShowDisplayer(ModifyDetails.java:296)
	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:497)
	at org.apache.struts.actions.DispatchAction.dispatchMethod(DispatchAction.java:269)
	at org.apache.struts.actions.DispatchAction.execute(DispatchAction.java:170)
	at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
	at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
	at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
	at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:521)
	at org.apache.coyote.ajp.AbstractAjpProcessor.process(AbstractAjpProcessor.java:850)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:674)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2500)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2489)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)

ERROR [ajp-apr-8009-exec-2] (InterMineExceptionHandler.java:74) - java.lang.NullPointerException
	at org.apache.commons.lang.exception.ExceptionUtils.getStackTrace(ExceptionUtils.java:896)
	at org.intermine.web.displayer.ReportDisplayer.execute(ReportDisplayer.java:77)
	at org.intermine.web.struts.ReportDisplayerController.execute(ReportDisplayerController.java:43)
	at org.intermine.web.struts.ModifyDetails.ajaxShowDisplayer(ModifyDetails.java:296)
	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:497)
	at org.apache.struts.actions.DispatchAction.dispatchMethod(DispatchAction.java:269)
	at org.apache.struts.actions.DispatchAction.execute(DispatchAction.java:170)
	at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
	at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
	at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
	at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:521)
	at org.apache.coyote.ajp.AbstractAjpProcessor.process(AbstractAjpProcessor.java:850)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:674)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2500)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2489)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)

888710 [ajp-apr-8009-exec-2] ERROR org.intermine.web.struts.InterMineExceptionHandler  - java.lang.NullPointerException
	at org.apache.commons.lang.exception.ExceptionUtils.getStackTrace(ExceptionUtils.java:896)
	at org.intermine.web.displayer.ReportDisplayer.execute(ReportDisplayer.java:77)
	at org.intermine.web.struts.ReportDisplayerController.execute(ReportDisplayerController.java:43)
	at org.intermine.web.struts.ModifyDetails.ajaxShowDisplayer(ModifyDetails.java:296)
	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:497)
	at org.apache.struts.actions.DispatchAction.dispatchMethod(DispatchAction.java:269)
	at org.apache.struts.actions.DispatchAction.execute(DispatchAction.java:170)
	at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
	at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
	at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
	at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:521)
	at org.apache.coyote.ajp.AbstractAjpProcessor.process(AbstractAjpProcessor.java:850)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:674)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2500)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2489)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)


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