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

Vallejos, Andrew avallejos at mcw.edu
Tue Mar 13 20:54:35 GMT 2012


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(InitialiserPlu
gin.java:444)

        at
org.intermine.web.struts.InitialiserPlugin.init(InitialiserPlugin.java:1
72)

        at
org.apache.struts.action.ActionServlet.initModulePlugIns(ActionServlet.j
ava: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.jav
a:1173)

        at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)

        at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.j
ava:4421)

        at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4734
)

        at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.ja
va: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.jav
a:57)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.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(DefaultMBea
nServerInterceptor.java:857)

        at
com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:795)

        at
org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:150
0)

        at
org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:67
0)

        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(Applica
tionFilterChain.java:290)

        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:206)

        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:233)

        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:191)

        at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(Authenticator
Base.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:2
91)

        at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:85
9)

        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.j
ava: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.jav
a:1173)

        at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)

        at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.j
ava:4421)

        at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4734
)

        at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.ja
va: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.jav
a:57)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.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(DefaultMBea
nServerInterceptor.java:857)

        at
com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:795)

        at
org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:150
0)

        at
org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:67
0)

        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(Applica
tionFilterChain.java:290)

        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:206)

        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:233)

        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:191)

        at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(Authenticator
Base.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:2
91)

        at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:85
9)

        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(SessionMethod
s.java:461)

        at
org.intermine.web.logic.session.SessionListener.sessionCreated(SessionLi
stener.java:31)

        at
org.apache.catalina.session.StandardSession.tellNew(StandardSession.java
:392)

        at
org.apache.catalina.session.StandardSession.setId(StandardSession.java:3
63)

        at
org.apache.catalina.session.StandardSession.setId(StandardSession.java:3
45)

        at
org.apache.catalina.session.ManagerBase.createSession(ManagerBase.java:8
83)

        at
org.apache.catalina.session.StandardManager.createSession(StandardManage
r.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.jav
a:833)

        at
org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.jav
a:844)

        at
org.apache.jasper.runtime.PageContextImpl._initialize(PageContextImpl.ja
va:146)

        at
org.apache.jasper.runtime.PageContextImpl.initialize(PageContextImpl.jav
a:124)

        at
org.apache.jasper.runtime.JspFactoryImpl.internalGetPageContext(JspFacto
ryImpl.java:107)

        at
org.apache.jasper.runtime.JspFactoryImpl.getPageContext(JspFactoryImpl.j
ava: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.ja
va: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(Applica
tionFilterChain.java:290)

        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:206)

        at
com.planetj.servlet.filter.compression.CompressingFilter.doFilter(Compre
ssingFilter.java:270)

        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:235)

        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:206)

        at
org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharact
erEncodingFilter.java:139)

        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:235)

        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:206)

        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:233)

        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.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:2
91)

        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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