[InterMine Dev] Webapp does not work (version 0.99)

Daniela Butano db539 at cam.ac.uk
Wed Mar 14 17:36:54 GMT 2012


Have you tried to execute clean-all before release the webapp?
cheers,
daniela
>
> Since switching to 0.99 I have been unable to get to the webapp.  The 
> ant build releases the webapp without error.  The tomcat localhost log 
> file is below...it is the only one with an error that I can see.
>
> Thanks,
>
> Andrew Vallejos
>
> Web Developer
>
> Biotechnology and Bioengineering Center
>
> Human and Molecular Genomics Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> avallejos at mcw.edu
>
> Mar 13, 2012 3:32:42 PM org.apache.catalina.core.ApplicationContext log
>
> SEVERE: action: null
>
> java.lang.NullPointerException
>
>         at 
> org.intermine.web.struts.InitialiserPlugin.loadBagQueries(InitialiserPlugin.java:444)
>
>         at 
> org.intermine.web.struts.InitialiserPlugin.init(InitialiserPlugin.java:172)
>
>         at 
> org.apache.struts.action.ActionServlet.initModulePlugIns(ActionServlet.java:871)
>
>         at 
> org.apache.struts.action.ActionServlet.init(ActionServlet.java:359)
>
>         at javax.servlet.GenericServlet.init(GenericServlet.java:212)
>
>         at 
> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173)
>
>         at 
> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)
>
>         at 
> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
>
>         at 
> org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
>
>         at 
> org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
>
>         at 
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
>
>         at 
> org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
>
>         at 
> org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:943)
>
>         at 
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:563)
>
>         at 
> org.apache.catalina.startup.HostConfig.check(HostConfig.java:1399)
>
>         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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:297)
>
>         at 
> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:857)
>
>         at 
> com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:795)
>
>         at 
> org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1500)
>
>         at 
> org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:670)
>
>         at 
> org.apache.catalina.manager.ManagerServlet.doPut(ManagerServlet.java:435)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:640)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
>
>         at 
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
>
>         at 
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
>
>         at 
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:563)
>
>         at 
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
>
>         at 
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
>
>         at 
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
>
>         at 
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:291)
>
>         at 
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
>
>         at 
> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)
>
>        at 
> org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
>
>         at java.lang.Thread.run(Thread.java:679)
>
> Mar 13, 2012 3:32:42 PM org.apache.catalina.core.ApplicationContext log
>
> INFO: Marking servlet action as unavailable
>
> Mar 13, 2012 3:32:42 PM org.apache.catalina.core.StandardContext 
> loadOnStartup
>
> SEVERE: Servlet /ratmine threw load() exception
>
> javax.servlet.UnavailableException
>
>         at 
> org.apache.struts.action.ActionServlet.initModulePlugIns(ActionServlet.java:880)
>
>         at 
> org.apache.struts.action.ActionServlet.init(ActionServlet.java:359)
>
>         at javax.servlet.GenericServlet.init(GenericServlet.java:212)
>
>         at 
> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173)
>
>         at 
> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)
>
>         at 
> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
>
>         at 
> org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
>
>         at 
> org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
>
>         at 
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
>
>         at 
> org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
>
>        at 
> org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:943)
>
>         at 
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:563)
>
>         at 
> org.apache.catalina.startup.HostConfig.check(HostConfig.java:1399)
>
>         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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:297)
>
>         at 
> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:857)
>
>         at 
> com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:795)
>
>         at 
> org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1500)
>
>         at 
> org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:670)
>
>         at 
> org.apache.catalina.manager.ManagerServlet.doPut(ManagerServlet.java:435)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:640)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
>
>         at 
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
>
>         at 
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
>
>         at 
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:563)
>
>         at 
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
>
>         at 
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
>
>         at 
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
>
>         at 
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:291)
>
>         at 
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
>
>         at 
> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)
>
>         at 
> org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
>
>         at java.lang.Thread.run(Thread.java:679)
>
> Mar 13, 2012 3:33:05 PM org.apache.catalina.session.StandardSession 
> tellNew
>
> SEVERE: Session event listener threw exception
>
> java.lang.NullPointerException
>
>         at 
> org.intermine.web.logic.session.SessionMethods.initSession(SessionMethods.java:461)
>
>         at 
> org.intermine.web.logic.session.SessionListener.sessionCreated(SessionListener.java:31)
>
>         at 
> org.apache.catalina.session.StandardSession.tellNew(StandardSession.java:392)
>
>         at 
> org.apache.catalina.session.StandardSession.setId(StandardSession.java:363)
>
>         at 
> org.apache.catalina.session.StandardSession.setId(StandardSession.java:345)
>
>         at 
> org.apache.catalina.session.ManagerBase.createSession(ManagerBase.java:883)
>
>         at 
> org.apache.catalina.session.StandardManager.createSession(StandardManager.java:291)
>
>         at 
> org.apache.catalina.connector.Request.doGetSession(Request.java:2444)
>
>         at 
> org.apache.catalina.connector.Request.getSession(Request.java:2153)
>
>         at 
> org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:833)
>
>         at 
> org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:844)
>
>         at 
> org.apache.jasper.runtime.PageContextImpl._initialize(PageContextImpl.java:146)
>
>         at 
> org.apache.jasper.runtime.PageContextImpl.initialize(PageContextImpl.java:124)
>
>         at 
> org.apache.jasper.runtime.JspFactoryImpl.internalGetPageContext(JspFactoryImpl.java:107)
>
>         at 
> org.apache.jasper.runtime.JspFactoryImpl.getPageContext(JspFactoryImpl.java:63)
>
>         at org.apache.jsp.index_jsp._jspService(index_jsp.java:44)
>
>         at 
> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>         at 
> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:388)
>
>         at 
> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
>
>         at 
> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
>
>         at 
> com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
>
>         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:235)
>
>         at 
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
>
>         at 
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
>
>         at 
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
>
>         at 
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
>
>         at 
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
>
>         at 
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
>
>         at 
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:291)
>
>         at 
> org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
>
>         at 
> org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)
>
>         at 
> org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:776)
>
>         at 
> org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:705)
>
>         at 
> org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:898)
>
>         at 
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)
>
>         at java.lang.Thread.run(Thread.java:679)
>
> Mar 13, 2012 3:33:05 PM org.apache.catalina.core.StandardWrapperValve 
> invoke
>
> INFO: Servlet action is currently unavailable
>
> Mar 13, 2012 3:33:05 PM org.apache.catalina.core.ApplicationDispatcher 
> invoke
>
> WARNING: Servlet action is currently unavailable
>
> Mar 13, 2012 3:33:33 PM org.apache.catalina.core.StandardWrapperValve 
> invoke
>
> INFO: Servlet action is currently unavailable
>
> Mar 13, 2012 3:33:33 PM org.apache.catalina.core.ApplicationDispatcher 
> invoke
>
> WARNING: Servlet action is currently unavailable
>
> Mar 13, 2012 3:33:35 PM org.apache.catalina.core.StandardWrapperValve 
> invoke
>
> INFO: Servlet action is currently unavailable
>
> Mar 13, 2012 3:33:35 PM org.apache.catalina.core.ApplicationDispatcher 
> invoke
>
> WARNING: Servlet action is currently unavailable
>
> Mar 13, 2012 3:41:11 PM org.apache.catalina.core.StandardWrapperValve 
> invoke
>
> INFO: Servlet action is currently unavailable
>
> Mar 13, 2012 3:41:11 PM org.apache.catalina.core.ApplicationDispatcher 
> invoke
>
> WARNING: Servlet action is currently unavailable
>
>
> _______________________________________________
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> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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