Re: Fwd: RE: Cytoscape Viewer

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Re: Fwd: RE: Cytoscape Viewer

Fengyuan Hu
Hi Andrew,

I am the developer for the Network Viewer.

First of all, you are not suppose to have an "internal error" thrown
from the plugin, it's an old behavior in intermine 0.95 and earlier
releases.

Very recently, I had done some code refactoring on the network related
Java classes and jsp (all new features have been included in 0.96), all
network class names should start with "CytoscapeNetwork" + sth, except a
class called "CytoscapeInteractionExtentionAction" which has been
obsolete and will be removed in the next release.

I'm wondering if it's possible you've mixed 0.95 and 0.96 somehow? Could
you please verify that?

Quick ways to check:

1. for 0.96, under "/bio/webapp/resources/webapp/model/cytoscape" dir,
you should see a javascript file "displaynetwork.js"
(http://intermine.org/browser/branches/intermine_0_96/bio/webapp/resources/webapp/model/cytoscape),
it didn't exist in 0.95.

2. Do you have a Java class called "CytoscapeNetworkAjaxAction.java
<http://intermine.org/browser/branches/intermine_0_96/bio/webapp/src/org/intermine/bio/web/struts/CytoscapeNetworkAjaxAction.java>"
in your code base?

Thanks
Fengyuan

> -------- Original Message --------
> Subject: RE: [InterMine Dev] Cytoscape Viewer
> Date: Tue, 1 Mar 2011 12:27:48 -0600
> From: Vallejos, Andrew <[hidden email]>
> To: Julie Sullivan <[hidden email]>
> CC: <[hidden email]>
>
> 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
>>
>


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