[Treebase-guts] [ treebase-Bugs-2903251 ] Exception when uploading nexus to a new submission

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Bugs item #2903251, was opened at 2009-11-24 17:34
Message generated for change (Comment added) made by rvos
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Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Rutger Vos (rvos)
Summary: Exception when uploading nexus to a new submission

Initial Comment:
When I log in as a normal user (user: pieltest, password: pieltest) and I try to upload a nexus file to a new submission, I get the following error.

bp

Uncaught Exception Encountered
java.lang.ExceptionInInitializerError at mesquite.Mesquite.main(Mesquite.java:2261) at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232) at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657) at 

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>Comment By: Rutger Vos (rvos)
Date: 2009-12-10 16:26

Message:
ALERT: (Mesquite): Please find the Mesquite manual file named
"manual.html", which should be in the "docs/mesquite" directory.
java.lang.NullPointerException
        at
mesquite.lib.MesquiteFileDialog.<init>(MesquiteFileDialog.java:31)
        at
mesquite.lib.MesquiteFile.checkFilePath(MesquiteFile.java:2015)
        at mesquite.Mesquite.findMesquiteDirectory(Mesquite.java:583)
        at
mesquite.Mesquite.processSingleXMLPreference(Mesquite.java:802)
        at
mesquite.lib.MesquiteModule.processPreferencesFromXML(MesquiteModule.java:745)
        at
mesquite.lib.MesquiteModule.loadPreferences(MesquiteModule.java:704)
        at mesquite.Mesquite.init(Mesquite.java:184)
        at mesquite.Mesquite.<init>(Mesquite.java:2033)
        at mesquite.Mesquite.main(Mesquite.java:2088)
        at
org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232)
        at
org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121)
        at
org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657)
        at
org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:581)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
        at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
        at $Proxy80.addNexusFilesJDBC(Unknown Source)
        at
org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:196)
        at
org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267)
        at
org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140)
        at
org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265)
        at
org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
        at
org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
        at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858)
        at
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
        at
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
        at
org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at
org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at
org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
        at
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at
com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
        at
com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at
org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
        at
org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
        at
org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
        at
org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
        at
org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
        at
org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
        at
org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
        at
org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
        at
org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
        at
org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
        at
org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191)
        at
org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
        at
org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
        at
org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
        at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873)
        at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
        at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
        at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
        at java.lang.Thread.run(Thread.java:636)

Exception caught in Mesquite: null
ALERT: (Mesquite): Mesquite cannot function: no file coordinator
available
(Following stack trace from object of class: class
mesquite.lib.ProjectRead)
java.lang.NullPointerException
        at mesquite.lib.ProjectRead.run(ProjectRead.java:212)
        at java.lang.Thread.run(Thread.java:636)
        at mesquite.lib.MesquiteThread.run(MesquiteThread.java:63)
        at mesquite.lib.ProjectReadThread.run(ProjectReadThread.java:55)

ALERT: (Mesquite): File reading could not be completed because an
exception or error occurred (i.e. a crash; class
java.lang.NullPointerExcepti
on). If you save any files, you might best use Save As... in case data
were lost or file saving doesn't work properly.  To report this as a bug
, PLEASE send along the Mesquite_Log file from Mesquite_Support_Files.
-

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-12-10 16:00

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

You can respond by visiting: 
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