cytoscape integration with local cpath install

[rex....@syngenta.com]

I am trying to integrate cytoscape with a local mirror of pathway commons behind our company firewall.  I am running cytoscape 2.6.1 and trying to use the "new" cpath interface  File->Import->Network from web services... instead of the old one that appears to be deprecated. 

So I've successfully downloaded the source to the cpath2 plugin, and rebuilt it with the URL of our local tomcat server in place of pathway commons.  I can see from the tomcat logs that cytoscape is sending the right queries to the cpath application.

My issue now seems to be with cpath.  I've installed from cpath_beta_07_rc2.tar.gz.

cytoscape sends cpath queries with "cmd=search", and cpath doesn't recognize that command.  As I understand the cpath administrator guide (1/22/08) there are two modes, biopax and psi_mi, which I choose by setting web.skin in build.properties.  Poking around, there seem to be 4-5 cosmetic "skins" defined but only the two modes.  I've tried all the available skins, but none solves the problem -- pasting the query from cytoscape directly into the browser:

 

http://cpathhost.syngenta.org:8080/cpath/webservice.do?cmd=search&q=TP53&output=xml&version=2.0&maxHits=10&startIndex=0 always fails with the message

An Error Has Occurred

Command: 'search' is not recognized. Please try again.

whereas http://www.pathwaycommons.org/pc/webservice.do?cmd=search&q=TP53&output=xml&version=2.0&maxHits=10&startIndex=0  works just fine.

 

Can anyone help me get cpath configured correctly?  (or the cytoscape plug-in, if that's the problem.

 

Rex

---

This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

[Ethan Cerami]

Hi Rex,

The cpath beta_07 tar file probably doesn't have the latest code that is required for the "new" cpath plugin.

You are best off downloading the source from the NCI CVS Server.  Instructions are here:  http://cbio.mskcc.org/software/cpath/source.html

After building from this, try the cpath2 plugin again.

If you have other issues, feel free to email me.

Ethan

[rex....@syngenta.com]

Hi Ethan,

Thanks.  I requested the account per instructions on the page.

I am a little confused about the connection between the cpath database and the cpath webapp.  Does the database have two schemata dep. on whether the mode is biopax or psi-mi? or is it just a matter of how the webapp delivers the results?  More to the point, will I have to reload the database?

Thanks again.

Rex

P.S.: I've been assuming there are no licenses for this s.w. or the databases even for commericial users.  If that's not right, please let me know how to straighten that out.

 

---

From: cpat...@googlegroups.com [mailto:cpat...@googlegroups.com] On Behalf Of Ethan Cerami
Sent: Wednesday, October 22, 2008 1:44 PM
To: cytoscape...@googlegroups.com
Cc: cpat...@googlegroups.com
Subject: Re: [cytoscape-helpdesk] cytoscape integration with local cpath install

[Ethan Cerami]

Rex,

You should be able to check out the code anonymously, w/o having to wait for an account approval.

The db schema is the same for both biopax and psi-mi modes.  But, you probably will need to reload the database, as the schema may have changed since release 7.

Also, there are no usage restrictions for commercial users.

Ethan

[rex....@syngenta.com]

Hi again Ethan,

I'm making some good progress here, but always more trouble...

 

We generally use proxy auto-config with a long script written by someone in Basel.   There are a bunch of different proxies, but only one is relevant for this story.  The problem is that a proxy is required for any link-outs from cytoscape, but the proxy will not respond to internal requests.  As you know cytoscape allows one to specify a proxy, but then it is used for every request.  So I get to choose between internal and external connectivity...

 

Java now provides a class called ProxySelector, and there is a default system ProxySelector.  You pass it a uri and it returns appropriate proxy information.

If you are running an applet or doing a web start, the proxyselector can be configured on the java control panel to use the browser defaults, which means: obey the pac script.  However, a free-standing application evidently does not do this, and the default selector always returns "no proxy".  The configuration script is in javascript, not java, and there doesn't seem to be an easy way to load it up into a java application (although some hard ways are proposed on various web pages.)  In either case, you can write your own implementation of the ProxySelector class and register it as the default. 

 

So anyway, I will have to code up my own proxy handler for my internal version of cpath, and it looks like ProxySelector is the way I will go.  Is there any interest in replacing the current proxy mechanism in cytoscape with ProxySelector and, if so, does it make sense for me to attack the problem more generally rather than just writing what I need to get things going here at Syngenta?

 

Rex

 

 

 

 

 

 

---

From: cpat...@googlegroups.com [mailto:cpat...@googlegroups.com] On Behalf Of Ethan Cerami

Sent: Wednesday, October 22, 2008 2:41 PM
To: cpat...@googlegroups.com

[Ethan Cerami]

Rex,

If you are interested in writing a more generic / better proxy handler for Cytoscape, that would be great.  To get started, first touch base with one of the Cytoscape core developers.  For example, Mike Smoot <msm...@ucsd.edu> is the chief architect for Cytoscape, and tries to coordinate all the core development work.

Good luck,

Ethan