[InterMine Dev] Fwd: RE: Cytoscape Viewer

Fengyuan Hu fh293 at cam.ac.uk
Wed Mar 2 11:16:40 GMT 2011


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 <avallejos at mcw.edu>
> To: Julie Sullivan <julie at flymine.org>
> CC: <dev at intermine.org>
>
> 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:julie at flymine.org]
> Sent: Tuesday, March 01, 2011 11:31 AM
> To: Vallejos, Andrew
> Cc: dev at intermine.org
> 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: 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
>>
>




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