#147 critical bug- propagate to genes function

closed-fixed
Bugs (45)
9
2005-11-07
2005-11-07
No

When searching for genes to use for propogating
annotations an SQL error is returned after clicking
'search'. See earlier email for error message contents.

Discussion

  • Leonore Reiser

    Leonore Reiser - 2005-11-07

    Logged In: YES
    user_id=1008942

    here is the error message:
    HTTP Status 500 -

    type Exception report

    message

    description The server encountered an internal error () that
    prevented it from fulfilling this request.

    exception

    java.lang.NullPointerException
    at pub.search.SqlSearcher.doSearch(SqlSearcher.java:71)
    at pub.search.Genes.makeGeneNameConstraint(Genes.java:138)
    at pub.search.Genes.addGeneNameConstraint(Genes.java:125)
    at
    pub.servlets.update.propagate_annotation.GeneSearcher.search(GeneSearcher.java:74)
    at
    pub.servlets.update.propagate_annotation.PropagateAnnotation.doGeneSearch(PropagateAnnotation.java:176)
    at
    pub.servlets.update.propagate_annotation.PropagateAnnotation.handleGeneSearchRequest(PropagateAnnotation.java:121)
    at
    pub.servlets.update.propagate_annotation.PropagateAnnotation.handleRequest(PropagateAnnotation.java:76)
    at pub.servlets.update.Update.doService(Update.java:54)
    at pub.servlets.PubServlet.doIt(PubServlet.java:88)
    at pub.servlets.PubServlet.doPost(PubServlet.java:280)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:760)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)
    at
    org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247)
    at
    org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193)
    at
    org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:256)
    at
    org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)
    at
    org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)
    at
    org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)
    at
    org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at
    org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)
    at
    org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)
    at
    org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)
    at
    org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2416)
    at
    org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180)
    at
    org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)
    at
    org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:171)
    at
    org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641)
    at
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:172)
    at
    org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641)
    at
    org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)
    at
    org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)
    at
    org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:174)
    at
    org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)
    at
    org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)
    at
    org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)
    at
    org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java:223)
    at
    org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:601)
    at
    org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:392)
    at
    org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:565)
    at
    org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:619)
    at java.lang.Thread.run(Thread.java:536)

    Apache Tomcat/4.1.27

     
  • Danny Yoo

    Danny Yoo - 2005-11-07
    • labels: --> Bugs
     
  • Danny Yoo

    Danny Yoo - 2005-11-07

    Logged In: YES
    user_id=49843

    Changing category so I can find this bug again.

     
  • Danny Yoo

    Danny Yoo - 2005-11-07
    • status: open --> open-fixed
     
  • Danny Yoo

    Danny Yoo - 2005-11-07
    • priority: 5 --> 9
    • assigned_to: nobody --> dyoo
     
  • Leonore Reiser

    Leonore Reiser - 2005-11-07

    Logged In: YES
    user_id=1008942

    Looks great- thanks for fixing this.

     
  • Danny Yoo

    Danny Yoo - 2005-11-07

    Logged In: YES
    user_id=49843

    Closing bug.

     
  • Danny Yoo

    Danny Yoo - 2005-11-07
    • status: open-fixed --> closed-fixed
     

Log in to post a comment.

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks