Compare proteins error: /home/Support/Inactive Forums/CPAS Forum (Inactive)

Compare proteins error

CPAS Forum (Inactive)

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Compare proteins error

mmetod

2006-05-19 04:48

Status: Closed

Compare proteins gives an error. This is the message I am getting:
500: Unexpected server error

[Show more details]
java.lang.NullPointerException
       at org.fhcrc.cpas.view.HomeTemplate.initDefaultMenu(HomeTemplate.java:103)
       at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:68)
       at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:61)
       at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:49)
       at MS2.MS2Controller._renderInTemplate(MS2Controller.java:240)
       at MS2.MS2Controller.compareRuns(MS2Controller.java:2975)
       at MS2.MS2Controller.showCompare(MS2Controller.java:2895)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:585)
       at org.apache.beehive.netui.pageflow.FlowController.invokeActionMethod(FlowController.java:824)
       at org.apache.beehive.netui.pageflow.FlowController.getActionMethodForward(FlowController.java:754)
       at org.apache.beehive.netui.pageflow.FlowController.internalExecute(FlowController.java:428)
       at org.apache.beehive.netui.pageflow.PageFlowController.internalExecute(PageFlowController.java:285)
       at org.apache.beehive.netui.pageflow.FlowController.execute(FlowController.java:308)
       at org.apache.beehive.netui.pageflow.internal.FlowControllerAction.execute(FlowControllerAction.java:48)
       at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.access$201(PageFlowRequestProcessor.java:106)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor$ActionRunner.execute(PageFlowRequestProcessor.java:2049)
       at org.apache.beehive.netui.pageflow.interceptor.action.internal.ActionInterceptors.wrapAction(ActionInterceptors.java:90)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processActionPerform(PageFlowRequestProcessor.java:2120)
       at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processInternal(PageFlowRequestProcessor.java:601)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.process(PageFlowRequestProcessor.java:887)
       at org.apache.beehive.netui.pageflow.AutoRegisterActionServlet.process(AutoRegisterActionServlet.java:611)
       at org.apache.beehive.netui.pageflow.PageFlowActionServlet.process(PageFlowActionServlet.java:157)
       at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:432)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
       at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463)
       at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
       at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
       at org.fhcrc.cpas.view.ViewServlet.service(ViewServlet.java:120)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
       at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463)
       at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
       at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
       at org.apache.beehive.netui.pageflow.internal.DefaultForwardRedirectHandler.forward(DefaultForwardRedirectHandler.java:127)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.doForward(PageFlowRequestProcessor.java:1825)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processForwardConfig(PageFlowRequestProcessor.java:1699)
       at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:229)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processInternal(PageFlowRequestProcessor.java:601)
       at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.process(PageFlowRequestProcessor.java:887)
       at org.apache.beehive.netui.pageflow.AutoRegisterActionServlet.process(AutoRegisterActionServlet.java:611)
       at org.apache.beehive.netui.pageflow.PageFlowActionServlet.process(PageFlowActionServlet.java:157)
       at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:432)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
       at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463)
       at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
       at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
       at org.fhcrc.cpas.view.ViewServlet.service(ViewServlet.java:120)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.fhcrc.cpas.data.TransactionFilter.doFilter(TransactionFilter.java:36)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.fhcrc.cpas.security.AuthFilter.doFilter(AuthFilter.java:78)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.fhcrc.cpas.module.ModuleLoader.doFilter(ModuleLoader.java:235)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
       at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856)
       at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
       at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
       at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
       at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
       at java.lang.Thread.run(Thread.java:595)

request attributes
javax.servlet.forward.request_uri = /cpas/MS2/applyView.do
javax.servlet.forward.context_path = /cpas
javax.servlet.forward.servlet_path = /MS2/applyView.do
javax.servlet.forward.query_string = .select=16&.select=17&column=Protein&action=showCompare
mS2ViewForm = MS2.MS2Controller$MS2ViewForm@99860f
_netui:sharedFlow:global.Global = global.Global@6a00ca
_netui:fwdModule = /MS2
_netui:_actionURI = /cpas/MS2/showCompare.do
org.apache.struts.action.ERROR = {java.lang.Throwable=[java.lang.Throwable[null]]}
org.apache.struts.action.EXCEPTION = java.lang.NullPointerException
sharedFlow = {}
_netui:changedAttrs = [_netui:facesBacking]
url_rewriters = [org.apache.beehive.netui.pageflow.internal.DefaultURLRewriter@0]
_defaultMsgs = org.apache.beehive.netui.pageflow.internal.ExpressionAwareMessageResources@1304e60
_netui:failoverAttrs = {_netui:curPageFlow=MS2.MS2Controller@b34bf3}
globalApp = global.Global@6a00ca
pageInput = {}
org.apache.struts.action.mapping.instance = ActionConfig[path=/showCompare,parameter=MS2.MS2Controller,scope=request,type=org.apache.beehive.netui.pageflow.internal.FlowControllerAction
bundle = {_defaultMsgs=StrutsBundleNode messageResource: org.apache.struts.util.PropertyMessageResources@13e86ec locale: en_GB}
pageFlow = MS2.MS2Controller@b34bf3
_netui:curPageFlow = MS2.MS2Controller@b34bf3
org.apache.beehive.controls.runtime.servlet.ServletBeanContext = org.apache.beehive.netui.pageflow.internal.PageFlowBeanContext@c199f
_netui:servletContext = org.apache.catalina.core.ApplicationContextFacade@6646fc
org.apache.struts.action.MODULE = org.apache.struts.config.impl.ModuleConfigImpl@be6858

core schema database configuration
Server URL jdbc:postgresql://localhost/cpas
Product Name PostgreSQL
Product Version 8.0.6
Driver Name PostgreSQL Native Driver
Driver Version PostgreSQL 8.1 JDBC3 with SSL (build 404)

Did anyone encounter the same problem.
Regards,

Metodi

mmetod responded:	2006-05-19 04:55
The same happens with compare peptides. This time it gives java.lang.NullPointerException. Metodi

mmetod responded:	2006-05-20 03:51
I cleaned the pipeline and reloaded the raw datafiles. Now it works fine. Not clear whar caused the problem though.

Matthew Bellew responded:	2006-05-22 09:34
We recently fixed a bug that caused this error only in folders with spaces (or other special characters). If this matches your problem, it will be fixed in the 1.4 drop.

mmetod responded:	2006-05-25 05:48
Many thanks Matthew. Metodi

adam responded:	2007-01-03 15:47

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Compare proteins error

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