Cytoscape Viewer

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

Cytoscape Viewer

Vallejos, Andrew

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(CytoscapeNetworkNodeData.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.prepareNetworkData(CytoscapeInteractionsController.java:249)

                at org.intermine.bio.web.struts.CytoscapeInteractionsController.execute(CytoscapeInteractionsController.java:165)

                at org.apache.struts.tiles.actions.TilesAction.execute(TilesAction.java:75)

                at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.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(ApplicationFilterChain.java:290)

                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

                at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630)

                at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:535)

                at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:472)

                at org.apache.struts.tiles.UrlController.execute(UrlController.java:91)

                at org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTag.java:873)

                at org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)

                at org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_tiles_005finsert_005f0(objectDetailsDisplayers_jsp.java:521)

                at org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fif_005f2(objectDetailsDisplayers_jsp.java:419)

                at org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fforEach_005f1(objectDetailsDisplayers_jsp.java:368)

                at org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fif_005f0(objectDetailsDisplayers_jsp.java:292)

                at org.apache.jsp.objectDetailsDisplayers_jsp._jspx_meth_c_005fforEach_005f0(objectDetailsDisplayers_jsp.java:251)

                at org.apache.jsp.objectDetailsDisplayers_jsp._jspService(objectDetailsDisplayers_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.java: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(ApplicationFilterChain.java:290)

                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

                at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630)

                at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:535)

                at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:472)

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

                at org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:611)

                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(InsertTag.java:890)

                at org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)

                at org.apache.jsp.objectDetails_jsp._jspx_meth_tiles_005finsert_005f4(objectDetails_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.java: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(ApplicationFilterChain.java:290)

                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

                at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630)

                at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:535)

                at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:472)

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

                at org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:611)

                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(InsertTag.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.java: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(ApplicationFilterChain.java:290)

                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

                at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630)

                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:1056)

                at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:261)

                at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:237)

                at org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForward(TilesRequestProcessor.java:339)

                at org.apache.struts.action.RequestProcessor.processForward(RequestProcessor.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(ApplicationFilterChain.java:290)

                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: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:286)

                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

[hidden email]


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Cytoscape Viewer

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

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Cytoscape Viewer

Vallejos, Andrew
I am on branch 0.96.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Julie Sullivan
Sent: Tuesday, March 01, 2011 5:06 AM
To: [hidden email]
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
>
> [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Cytoscape Viewer

Julie Sullivan
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: [hidden email] [mailto:[hidden email]] On
> Behalf Of Julie Sullivan
> Sent: Tuesday, March 01, 2011 5:06 AM
> To: [hidden email]
> 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
>>
>> [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Cytoscape Viewer

Vallejos, Andrew
I renamed "CytoscapeInteractionsController" to
"CytoscapeNetworkController" in my struts-config-model.xml file (not
sure how I messed that one up).

Now I can getting an Internal error thrown by the Cytoscape Web plugin,
but nothing is showing up in the log files.

-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Tuesday, March 01, 2011 11:31 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Cytoscape Viewer

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: [hidden email] [mailto:[hidden email]] On
> Behalf Of Julie Sullivan
> Sent: Tuesday, March 01, 2011 5:06 AM
> To: [hidden email]
> 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
>>
>> [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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