[InterMine Dev] Cytoscape Viewer

Vallejos, Andrew avallejos at mcw.edu
Tue Mar 1 15:13:54 GMT 2011


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

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