[InterMine Dev] debugging error on Lists tab

Sibyl Gao sibyl at wormbase.org
Mon Aug 31 21:10:50 BST 2015


Hi,

After checking the stack trace, it seems that the problem is caused by defaultValues in org.intermine.api.mines.LocalMine being empty. I think it’s a property to be set in the mine.properties file, but I’m not sure what value should it be set to. I’m attaching the stack trace below. 

Thank you very much!

Sibyl

Stack trace:

      java.util.NoSuchElementException
	at java.util.LinkedHashMap$LinkedHashIterator.nextEntry(LinkedHashMap.java:396)
	at java.util.LinkedHashMap$KeyIterator.next(LinkedHashMap.java:405)
	at org.intermine.api.mines.LocalMine.getDefaultValue(LocalMine.java:133)
	at org.intermine.web.struts.BagBuildController.getDefaultValue(BagBuildController.java:214)
	at org.intermine.web.struts.BagBuildController.execute(BagBuildController.java:142)
	at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
	at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
	at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
	at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
	at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:604)
	at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:543)
	at org.apache.struts.tiles.UrlController.execute(UrlController.java:92)
	at org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:879)
	at org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
	at org.apache.jsp.bag_jsp._jspx_meth_tiles_005finsert_005f0(bag_jsp.java:203)
	at org.apache.jsp.bag_jsp._jspx_meth_c_005fwhen_005f0(bag_jsp.java:175)
	at org.apache.jsp.bag_jsp._jspx_meth_c_005fchoose_005f0(bag_jsp.java:143)
	at org.apache.jsp.bag_jsp._jspService(bag_jsp.java:92)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
	at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:604)
	at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:543)
	at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:954)
	at org.apache.jasper.runtime.PageContextImpl.doInclude(PageContextImpl.java:688)
	at org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:682)
	at sun.reflect.GeneratedMethodAccessor1663.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:129)
	at org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:152)
	at org.apache.struts.tiles.taglib.InsertTag.doInclude(InsertTag.java:764)
	at org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:896)
	at org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
	at org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java:1067)
	at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:227)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
	at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
	at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
	at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
	at org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForward(TilesRequestProcessor.java:370)
	at org.apache.struts.action.RequestProcessor.processForward(RequestProcessor.java:566)
	at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:212)
	at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
	at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
	at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
	at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
	at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)
> On Aug 31, 2015, at 1:50 PM, Sibyl Gao <sibyl at wormbase.org> wrote:
> 
> Hi InterMine Staff,
> 
> I ran into a puzzling issue on the Lists tab. Some error must have occurred and an error page is injected into the Lists tab, right above the create list form. The create list form itself seems to work fine. Do you have any suggestions on how to debug this?
> 
> Thank you very much.
> 
> Sibyl
> 
> 
> <Screen Shot 2015-08-31 at 12.42.49 PM.png>




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