[InterMine Dev] Cytoscape Viewer

Julie Sullivan julie at flymine.org
Tue Mar 1 17:30:30 GMT 2011


The class mentioned in your error message (CytoscapeInteractionsController) was 
renamed to be "CytoscapeNetworkController" in 0.96, see:

http://intermine.org/browser/branches/intermine_0_96/bio/webapp/src/org/intermine/bio/web/struts

Is this an old error message?  Can you verify which branch you are on?  We need 
to be sure which set of files you are working with.

On 03/01/2011 03:13 PM, Vallejos, Andrew wrote:
> I am on branch 0.96.
>
> -----Original Message-----
> From: dev-bounces at intermine.org [mailto:dev-bounces at intermine.org] On
> Behalf Of Julie Sullivan
> Sent: Tuesday, March 01, 2011 5:06 AM
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] Cytoscape Viewer
>
> Hi Andrew,
>
> We've made lots of improvements to the Cytoscape viewer in 0.96.  Is
> that which
> branch you are on?  If not, could it be?
>
> On 02/24/2011 10:00 PM, Vallejos, Andrew wrote:
>> I just added cytoscape to DevRatMine. And it threw an error.  I only
>> have BioGrid loaded, do I also need IntAct data as well?
>>
>>
>>
>> -Andrew
>>
>>
>>
>>         java.lang.NullPointerException
>>
>>                   at
>>
> org.intermine.bio.web.model.CytoscapeNetworkNodeData.hashCode(CytoscapeN
>> etworkNodeData.java:148)
>>
>>                   at java.util.HashMap.put(HashMap.java:389)
>>
>>                   at java.util.HashSet.add(HashSet.java:217)
>>
>>                   at
>>
> org.intermine.bio.web.struts.CytoscapeInteractionsController.prepareNetw
>> orkData(CytoscapeInteractionsController.java:249)
>>
>>                   at
>>
> org.intermine.bio.web.struts.CytoscapeInteractionsController.execute(Cyt
>> oscapeInteractionsController.java:165)
>>
>>                   at
>>
> org.apache.struts.tiles.actions.TilesAction.execute(TilesAction.java:75)
>>
>>                   at
>>
> org.apache.struts.action.RequestProcessor.processActionPerform(RequestPr
>> ocessor.java:421)
>>
>>                   at
>>
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
>> 226)
>>
>>                   at
>>
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1164)
>>
>>                   at
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:397)
>>
>>                   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(Applica
>> tionFilterChain.java:290)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
>> erChain.java:206)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
>> her.java:630)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDisp
>> atcher.java:535)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispat
>> cher.java:472)
>>
>>                   at
>> org.apache.struts.tiles.UrlController.execute(UrlController.java:91)
>>
>>                   at
>>
> org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTa
>> g.java:873)
>>
>>                   at
>> org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)
>>
>>                   at
>>
> org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_tiles_005finsert_0
>> 05f0(objectDetailsDisplayers_jsp.java:521)
>>
>>                   at
>>
> org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fif_005f2(obj
>> ectDetailsDisplayers_jsp.java:419)
>>
>>                   at
>>
> org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fforEach_005f
>> 1(objectDetailsDisplayers_jsp.java:368)
>>
>>                   at
>>
> org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fif_005f0(obj
>> ectDetailsDisplayers_jsp.java:292)
>>
>>                   at
>>
> org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fforEach_005f
>> 0(objectDetailsDisplayers_jsp.java:251)
>>
>>                   at
>>
> org.apache.jsp.objectDetailsDisplayers_jsp._jspService(objectDetailsDisp
>> layers_jsp.java:117)
>>
>>                   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:374)
>>
>>                   at
>>
> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
>>
>>                   at
>> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
>>
>>                   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.ApplicationDispatcher.invoke(ApplicationDispatc
>> her.java:630)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDisp
>> atcher.java:535)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispat
>> cher.java:472)
>>
>>                   at
>>
> org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.ja
>> va:968)
>>
>>                   at
>>
> org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:6
>> 11)
>>
>>                   at
>>
> org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:101)
>>
>>                   at
>> org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:137)
>>
>>                   at
>> org.apache.struts.taglib.tiles.InsertTag.doInclude(InsertTag.java:758)
>>
>>                   at
>>
> org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTa
>> g.java:890)
>>
>>                   at
>> org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)
>>
>>                   at
>>
> org.apache.jsp.objectDetails_jsp._jspx_meth_tiles_005finsert_005f4(objec
>> tDetails_jsp.java:1558)
>>
>>                   at
>>
> org.apache.jsp.objectDetails_jsp._jspx_meth_c_005fif_005f1(objectDetails
>> _jsp.java:399)
>>
>>                   at
>>
> org.apache.jsp.objectDetails_jsp._jspService(objectDetails_jsp.java:169)
>>
>>                   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:374)
>>
>>                   at
>>
> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
>>
>>                   at
>> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
>>
>>                   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.ApplicationDispatcher.invoke(ApplicationDispatc
>> her.java:630)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDisp
>> atcher.java:535)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispat
>> cher.java:472)
>>
>>                   at
>>
> org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.ja
>> va:968)
>>
>>                   at
>>
> org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:6
>> 11)
>>
>>                   at
>>
> org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:101)
>>
>>                   at
>> org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:137)
>>
>>                   at
>> org.apache.struts.taglib.tiles.InsertTag.doInclude(InsertTag.java:758)
>>
>>                   at
>>
> org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTa
>> g.java:890)
>>
>>                   at
>> org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)
>>
>>                   at
>>
> org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java
>> :1398)
>>
>>                   at
>> org.apache.jsp.layout_jsp._jspService(layout_jsp.java:306)
>>
>>                   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:374)
>>
>>                   at
>>
> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
>>
>>                   at
>> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
>>
>>                   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.ApplicationDispatcher.invoke(ApplicationDispatc
>> her.java:630)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
>> nDispatcher.java:436)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
>> atcher.java:374)
>>
>>                   at
>>
> org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
>> cher.java:302)
>>
>>                   at
>>
> org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.jav
>> a:1056)
>>
>>                   at
>>
> org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProc
>> essor.java:261)
>>
>>                   at
>>
> org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(Til
>> esRequestProcessor.java:237)
>>
>>                   at
>>
> org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForw
>> ard(TilesRequestProcessor.java:339)
>>
>>                   at
>>
> org.apache.struts.action.RequestProcessor.processForward(RequestProcesso
>> r.java:553)
>>
>>                   at
>>
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
>> 211)
>>
>>                   at
>>
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1164)
>>
>>                   at
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:397)
>>
>>                   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(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.core.StandardHostValve.invoke(StandardHostValve.java
>> :128)
>>
>>                   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
>> 86)
>>
>>                   at
>> org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
>>
>>                   at
>> org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
>>
>>                   at
>> org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
>>
>>                   at
>>
> org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
>> 697)
>>
>>                   at
>>
> org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
>> java:889)
>>
>>                   at
>>
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
>> .java:690)
>>
>>                   at java.lang.Thread.run(Thread.java:636)
>>
>>
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> avallejos at mcw.edu
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



More information about the dev mailing list