[InterMine Dev] MalariaMine tutorial

Quang Trinh quang.trinh at gmail.com
Wed Oct 19 15:10:04 BST 2011


HI Alex,
  Will do from now on.    Below are the error messages:




I found this error on
http://platinum.res.oicr.on.ca:8080/malariamine/layout.jsp.

---- Error Found ----

java.lang.RuntimeException: Chromosome location information is
missing...at org.intermine.bio.web.logic.GenomicRegionSearchService.setupWebData(GenomicRegionSearchService.java:137)at
org.intermine.bio.web.struts.GenomicRegionSearchOptionsController.execute(GenomicRegionSearchOptionsController.java:62)at
org.apache.struts.tiles.actions.TilesAction.execute(TilesAction.java:76)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:617)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.ApplicationDispatcher.invoke(ApplicationDispatcher.java:646)at
org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:551)at
org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:488)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.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java:991)at
org.apache.jsp.layout_jsp._jspService(layout_jsp.java:217)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
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:646)at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:436)at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:374)at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:302)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:617)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.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.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:619)



On Wed, Oct 19, 2011 at 10:04 AM, Alex Kalderimis <alex at flymine.org> wrote:
> A good thing to do in these cases is to click on the "send us an email"
> link, which will compose an email with the stack trace - you can also
> view the page source to view it. I'll see if I can replicate your error
> and we can compare stack traces!
>
> Alex
>
> On Wed, 2011-10-19 at 09:59 -0400, Quang Trinh wrote:
>> Hi,
>>   I was able to get MalariaMine up and running, however, when clicking
>> on "Region" tab, I get this error message and two menu tabs ( see
>> attached screen shot ).    Is this a bug or something that I did?
>>
>> Thanks,
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> --
> Alex Kalderimis
> Software Developer
> InterMine
> Cambridge Systems Biology Centre
> Tennis Court Road - CB2 1QR
> University of Cambridge
> ajk59 at cam.ac.uk
>
>



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