Discussions - cpath-dev | Google Groups

	changing the webservice call in cytoscape plugin to internal instance of cpath
	Hi, In my original implementation of my internal cpath I was able to change a cytoscape cpath.url property in my cytoscape properties so that when I created a new network from cpath the cpath plugin pointed to my internal instance of cpath. With my latest build of cpath I was wondering if there... more » By Ruth Isserlin - Nov 23 - 1 new of 1 message

	webservice calls
	I have installed cpath ver0.7 and loaded Reactome data. I am able to get webservice worked to retrieve html content. However when I try following cmd [1] Command: search [2] Command: get_pathways [3] Command: get_neighbors [4] Command: get_parents [5] Command: get_record_by_cpath_id [6] Additional Parameter Details... more » By pradeep - Oct 20 - 10 new of 10 messages

	Where do I set the database download tab url
	Hi, Currently my "Download" tab in my instance of cpath direct to [link] and I would like to change that. I couldn't find a variable in the build.properties. Is there a place where I can set this? Thanks, Ruth By Ruth - Jul 31 - 1 new of 1 message

	Error on index with latest version of cpath code
	Hi, I keep getting the following error when I try and index my instance of cpath. It indexes to 89% and then I get the following error: Fatal Error: org.jdom.input.JDOMParseExcept ion: Error on line 1: Content is not allowed in prolog. There is no stack trace just this line. Thanks, Ruth... more » By Ruth - Jul 27 - 5 new of 5 messages

	Error with latest Reactome and Netpath biopax files
	Hi, I have been re-building my instance of cpath and the reactome and Netpath biopax files keep coming up with the following error: Reading in file: Mus musculus.owl XML Type: BIO_PAX Reading in meta-data from: db.info Data source is: Reactome Reading in file content... Processing file...... more » By Ruth - Jul 3 - 6 new of 6 messages

	Error stack when executing admin.pl
	Hi, When I run admin.pl I get the following stack, it executes fine but I would like to fix the issue if possible. Is there a setting that I need to change to set the pathway commons log file or an environment variable that I am missing? Thanks, Ruth log4j:ERROR setFile(null,true) call failed.... more » By Ruth - Jul 2 - 2 new of 2 messages

	Unable to load entire directory using "admin.pl -f directory import" command
	Hi , I am trying to import an entire directory of biopax files to my instance of cpath using the command "./admin.pl -f directoryName import" and the program tests the validity of all the files in the directory but doesn't actually import any of them The last file it looks at is the db.info to which it says it is not valid RDF but it... more » By Ruth - Jul 2 - 4 new of 4 messages

	Unable to download cpath source from cvs or browse repository
	Hi, I have been trying to get the source from cvs -d :ext:anonym...@cbiocvs2.nci.ni h.gov:/share/content/gforge/cp ath checkout cpath and I keep getting access denied with password anonymouse. The link to browse the repository ([link] cvsweb.php/cpath/?cvsroot=cpat h) is also not working? Is there a tar... more » By Ruth - Jun 4 - 1 new of 1 message

	psi-mi data import error
	Hello: I have this error when attempting to import psi data. Any ideas? ./admin.pl -f ../testData/psi_mi/dip_psi.xml Using CPATH_HOME /home/rewing/lib/java/cpath/ log4j:ERROR setFile(null,true) call failed. java.io.FileNotFoundException: /srv/www/tomcat5/base/logs/pc_ log.txt (No such file or directory)... more » By Rob - Mar 18 - 3 new of 3 messages

cytoscape integration with local cpath install

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... more »

By rex.dw...@syngenta.com - Oct 22 2008 - 6 new of 6 messages