Mine Pathways Displayer not working - help needed with understanding whats wrong

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Mine Pathways Displayer not working - help needed with understanding whats wrong

Jayaraman, Pushkala

Hello,

I tried to implement the “pathways from other mines” section that you see in Flymine and yeastmine pages..

It used to work until a couple days ago but now it suddenly stopped working and im not sure whats wrong..

I also get this error.. is this related to the “mine pathways displayer”?

 

104659 [TP-Processor6] ERROR org.intermine.webservice.server.core.TableRowIterator  - Couldn't find any paths for org.intermine.model.bio.Homologue from amongst [Gene.homologues.gene.primaryIdentifier, Gene.homologues.gene.symbol, Gene.homologues.gene.organism.name, Gene.homologues.homologue.primaryIdentifier, Gene.homologues.homologue.symbol, Gene.homologues.homologue.organism.name]

 

 

 

Pushkala Jayaraman

Programmer/Analyst - Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

414-955-2229

http://rgd.mcw.edu

 


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Re: Mine Pathways Displayer not working - help needed with understanding whats wrong

Jayaraman, Pushkala

In my error logs I also found this. would the following error be the real cause..? I didnt change anything in my end..

I wonder how they suddenly change in type GeneShadow. How do I fix this?:

 

SEVERE: Servlet.service() for servlet jsp threw exception

javax.el.PropertyNotFoundException: Property 'pathways' not found on type org.intermine.model.bio.GeneShadow

        at javax.el.BeanELResolver$BeanProperties.get(BeanELResolver.java:214)

        at javax.el.BeanELResolver$BeanProperties.access$400(BeanELResolver.java:191)

        at javax.el.BeanELResolver.property(BeanELResolver.java:300)

        at javax.el.BeanELResolver.getValue(BeanELResolver.java:81)

        at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:54)

        at org.apache.el.parser.AstValue.getValue(AstValue.java:123)

        at org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)

        at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:938)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspx_meth_c_005fforEach_005f2(minePathwaysDisplayer_jsp.java:436)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspx_meth_c_005fwhen_005f0(minePathwaysDisplayer_jsp.java:279)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspx_meth_c_005fchoose_005f0(minePathwaysDisplayer_jsp.java:114)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspService(minePathwaysDisplayer_jsp.java:87)

        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.doInclude(ApplicationDispatcher.java:551)

        at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:488)

        at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:968)

        at org.apache.jsp.reportDisplayer_jsp._jspService(reportDisplayer_jsp.java:67)

        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.action.RequestProcessor.processForwardConfig(RequestProcessor.java:396)

        at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:347)

        at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)

        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)

        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.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:662)

Sep 5, 2013 9:54:13 AM org.apache.catalina.core.StandardWrapperValve invoke

SEVERE: Servlet.service() for servlet action threw exception

javax.el.PropertyNotFoundException: Property 'pathways' not found on type org.intermine.model.bio.GeneShadow

        at javax.el.BeanELResolver$BeanProperties.get(BeanELResolver.java:214)

       at javax.el.BeanELResolver$BeanProperties.access$400(BeanELResolver.java:191)

        at javax.el.BeanELResolver.property(BeanELResolver.java:300)

        at javax.el.BeanELResolver.getValue(BeanELResolver.java:81)

        at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:54)

        at org.apache.el.parser.AstValue.getValue(AstValue.java:123)

        at org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)

        at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:938)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspx_meth_c_005fforEach_005f2(minePathwaysDisplayer_jsp.java:436)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspx_meth_c_005fwhen_005f0(minePathwaysDisplayer_jsp.java:279)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspx_meth_c_005fchoose_005f0(minePathwaysDisplayer_jsp.java:114)

        at org.apache.jsp.model.minePathwaysDisplayer_jsp._jspService(minePathwaysDisplayer_jsp.java:87)

        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.doInclude(ApplicationDispatcher.java:551)

        at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:488)

        at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:968)

        at org.apache.jsp.reportDisplayer_jsp._jspService(reportDisplayer_jsp.java:67)

        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.action.RequestProcessor.processForwardConfig(RequestProcessor.java:396)

        at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:347)

        at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)

        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)

        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.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:662)

 

 

 

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jayaraman, Pushkala
Sent: Thursday, September 05, 2013 9:48 AM
To: [hidden email]
Subject: [InterMine Dev] Mine Pathways Displayer not working - help needed with understanding whats wrong

 

Hello,

I tried to implement the “pathways from other mines” section that you see in Flymine and yeastmine pages..

It used to work until a couple days ago but now it suddenly stopped working and im not sure whats wrong..

I also get this error.. is this related to the “mine pathways displayer”?

 

104659 [TP-Processor6] ERROR org.intermine.webservice.server.core.TableRowIterator  - Couldn't find any paths for org.intermine.model.bio.Homologue from amongst [Gene.homologues.gene.primaryIdentifier, Gene.homologues.gene.symbol, Gene.homologues.gene.organism.name, Gene.homologues.homologue.primaryIdentifier, Gene.homologues.homologue.symbol, Gene.homologues.homologue.organism.name]

 

 

 

Pushkala Jayaraman

Programmer/Analyst - Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

414-955-2229

http://rgd.mcw.edu

 


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Re: Mine Pathways Displayer not working - help needed with understanding whats wrong

Alex Kalderimis-2
In reply to this post by Jayaraman, Pushkala
Hi there Pushkala,

it looks like a model problem - do you recall what changed in you mine
in between now and the last time the displayer was seen to be working?

Alex

On Thu, Sep 05, 2013 at 02:47:50PM +0000, Jayaraman, Pushkala wrote:

> Hello,
> I tried to implement the "pathways from other mines" section that you see in Flymine and yeastmine pages..
> It used to work until a couple days ago but now it suddenly stopped working and im not sure whats wrong..
> I also get this error.. is this related to the "mine pathways displayer"?
>
> 104659 [TP-Processor6] ERROR org.intermine.webservice.server.core.TableRowIterator  - Couldn't find any paths for org.intermine.model.bio.Homologue from amongst [Gene.homologues.gene.primaryIdentifier, Gene.homologues.gene.symbol, Gene.homologues.gene.organism.name, Gene.homologues.homologue.primaryIdentifier, Gene.homologues.homologue.symbol, Gene.homologues.homologue.organism.name]
>
>
>
> Pushkala Jayaraman
> Programmer/Analyst - Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> 414-955-2229
> http://rgd.mcw.edu
>

> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


--
----------
Alex Kalderimis
Software Developer
InterMine
Dept. of Genetics
University of Cambridge
[hidden email]

_______________________________________________
dev mailing list
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Re: Mine Pathways Displayer not working - help needed with understanding whats wrong

Jayaraman, Pushkala
Nothing changed!
I just commented out stuff to check if the other datasources were working..
So its saying it cant find any paths for Homologue?

-----Original Message-----
From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex Kalderimis
Sent: Friday, September 06, 2013 10:05 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [InterMine Dev] Mine Pathways Displayer not working - help needed with understanding whats wrong

Hi there Pushkala,

it looks like a model problem - do you recall what changed in you mine in between now and the last time the displayer was seen to be working?

Alex

On Thu, Sep 05, 2013 at 02:47:50PM +0000, Jayaraman, Pushkala wrote:

> Hello,
> I tried to implement the "pathways from other mines" section that you see in Flymine and yeastmine pages..
> It used to work until a couple days ago but now it suddenly stopped working and im not sure whats wrong..
> I also get this error.. is this related to the "mine pathways displayer"?
>
> 104659 [TP-Processor6] ERROR
> org.intermine.webservice.server.core.TableRowIterator  - Couldn't find
> any paths for org.intermine.model.bio.Homologue from amongst
> [Gene.homologues.gene.primaryIdentifier, Gene.homologues.gene.symbol,
> Gene.homologues.gene.organism.name,
> Gene.homologues.homologue.primaryIdentifier,
> Gene.homologues.homologue.symbol,
> Gene.homologues.homologue.organism.name]
>
>
>
> Pushkala Jayaraman
> Programmer/Analyst - Rat Genome Database Human and Molecular Genetics
> Center Medical College of Wisconsin
> 414-955-2229
> http://rgd.mcw.edu
>

> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


--
----------
Alex Kalderimis
Software Developer
InterMine
Dept. of Genetics
University of Cambridge
[hidden email]

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Re: Mine Pathways Displayer not working - help needed with understanding whats wrong

Alex Kalderimis-2
Looking at the java source, this looks like this might be a bug in the
webservice code. Could you forward on the parameters for the
webservice request that generates this error message?

Alex

On Fri, Sep 06, 2013 at 03:06:52PM +0000, Jayaraman, Pushkala wrote:

> Nothing changed!
> I just commented out stuff to check if the other datasources were working..
> So its saying it cant find any paths for Homologue?
>
> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex Kalderimis
> Sent: Friday, September 06, 2013 10:05 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Mine Pathways Displayer not working - help needed with understanding whats wrong
>
> Hi there Pushkala,
>
> it looks like a model problem - do you recall what changed in you mine in between now and the last time the displayer was seen to be working?
>
> Alex
>
> On Thu, Sep 05, 2013 at 02:47:50PM +0000, Jayaraman, Pushkala wrote:
> > Hello,
> > I tried to implement the "pathways from other mines" section that you see in Flymine and yeastmine pages..
> > It used to work until a couple days ago but now it suddenly stopped working and im not sure whats wrong..
> > I also get this error.. is this related to the "mine pathways displayer"?
> >
> > 104659 [TP-Processor6] ERROR
> > org.intermine.webservice.server.core.TableRowIterator  - Couldn't find
> > any paths for org.intermine.model.bio.Homologue from amongst
> > [Gene.homologues.gene.primaryIdentifier, Gene.homologues.gene.symbol,
> > Gene.homologues.gene.organism.name,
> > Gene.homologues.homologue.primaryIdentifier,
> > Gene.homologues.homologue.symbol,
> > Gene.homologues.homologue.organism.name]
> >
> >
> >
> > Pushkala Jayaraman
> > Programmer/Analyst - Rat Genome Database Human and Molecular Genetics
> > Center Medical College of Wisconsin
> > 414-955-2229
> > http://rgd.mcw.edu
> >
>
> > _______________________________________________
> > dev mailing list
> > [hidden email]
> > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
> --
> ----------
> Alex Kalderimis
> Software Developer
> InterMine
> Dept. of Genetics
> University of Cambridge
> [hidden email]

--
----------
Alex Kalderimis
Software Developer
InterMine
Dept. of Genetics
University of Cambridge
[hidden email]

_______________________________________________
dev mailing list
[hidden email]
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