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:
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.
rex.dw...@syngenta.com wrote: > 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:
> 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./
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: cpath-dev@googlegroups.com [mailto:cpath-dev@googlegroups.com] On
Behalf Of Ethan Cerami
Sent: Wednesday, October 22, 2008 1:44 PM
To: cytoscape-helpdesk@googlegroups.com
Cc: cpath-dev@googlegroups.com
Subject: Re: [cytoscape-helpdesk] cytoscape integration with local cpath
install
Hi Rex,
The cpath beta_07 tar file probably doesn't have the latest code that is
required for the "new" cpath plugin.
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:
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.
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.
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.
rex.dw...@syngenta.com wrote: > 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:* cpath-dev@googlegroups.com [mailto:cpath-dev@googlegroups.com] > *On Behalf Of *Ethan Cerami > *Sent:* Wednesday, October 22, 2008 1:44 PM > *To:* cytoscape-helpdesk@googlegroups.com > *Cc:* cpath-dev@googlegroups.com > *Subject:* Re: [cytoscape-helpdesk] cytoscape integration with local > cpath install
> Hi Rex,
> The cpath beta_07 tar file probably doesn't have the latest code that > is required for the "new" cpath plugin.
> After building from this, try the cpath2 plugin again.
> If you have other issues, feel free to email me.
> Ethan
> rex.dw...@syngenta.com wrote: >> 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:
>> 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./
> /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./
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: cpath-dev@googlegroups.com [mailto:cpath-dev@googlegroups.com] On
Behalf Of Ethan Cerami
Sent: Wednesday, October 22, 2008 2:41 PM
To: cpath-dev@googlegroups.com
Subject: Re: [cytoscape-helpdesk] cytoscape integration with local cpath
install
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.
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: cpath-dev@googlegroups.com
[mailto:cpath-dev@googlegroups.com] On Behalf Of Ethan Cerami
Sent: Wednesday, October 22, 2008 1:44 PM
To: cytoscape-helpdesk@googlegroups.com
Cc: cpath-dev@googlegroups.com
Subject: Re: [cytoscape-helpdesk] cytoscape integration with
local cpath install
Hi Rex,
The cpath beta_07 tar file probably doesn't have the latest code
that is required for the "new" cpath plugin.
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:
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.
________________________________
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.
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.
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.
rex.dw...@syngenta.com wrote: > 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:* cpath-dev@googlegroups.com [mailto:cpath-dev@googlegroups.com] > *On Behalf Of *Ethan Cerami > *Sent:* Wednesday, October 22, 2008 2:41 PM > *To:* cpath-dev@googlegroups.com > *Subject:* Re: [cytoscape-helpdesk] cytoscape integration with local > cpath install
> 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.dw...@syngenta.com wrote: >> 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:* cpath-dev@googlegroups.com >> [mailto:cpath-dev@googlegroups.com] *On Behalf Of *Ethan Cerami >> *Sent:* Wednesday, October 22, 2008 1:44 PM >> *To:* cytoscape-helpdesk@googlegroups.com >> *Cc:* cpath-dev@googlegroups.com >> *Subject:* Re: [cytoscape-helpdesk] cytoscape integration with local >> cpath install
>> Hi Rex,
>> The cpath beta_07 tar file probably doesn't have the latest code that >> is required for the "new" cpath plugin.
>> After building from this, try the cpath2 plugin again.
>> If you have other issues, feel free to email me.
>> Ethan
>> rex.dw...@syngenta.com wrote: >>> 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:
>>> 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./
>> /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./
> /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./
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