Cytoscape integration

[iaink]

I have posed a query on the cytoscape-discuss forum and thought I
should post it here as well.
http://groups.google.com/group/cytoscape-discuss/browse_frm/thread/3660d7d7d40daea9

I have Cytoscape running successfully through webstart, on my local
disk. However when I run it from a webserver, I seem unable to get
Cytoscape to find the properties file. I can get cytoscape to load the
cpath plugin directly, but then I don't know how to pass the cpath
property "dataservice.cpath_read_location", to cpath.

Any advice on either getting cytoscape to find the properties file, or
on how to pass the property in a different way?

Many thanks

Iain K

[Gary Bader]

Hi Iain,
Sorry - we're in a grant crunch right now. We don't have a lot of
webstart experience here - but it is a big issue for other Cytoscape
users. I will track this down and get back to you.

Best,
Gary

[Gary Bader]

Hi Iain,
Sorry for the delay - we're still in a massive grant crunch until the
end of the month. Melissa Cline from the Pasteur looked into it for you
- response below. It looks like this is another unfriendly bit of
Cytoscape for webstarts. You might want to hack your copy of Cytoscape
to read the cytosape.props file from a jar until this part of Cytoscape
is generalized/fixed.

Hope that helps,
Gary

-------

Hi Gary,

I spent a few minutes digging into this today.

1. The cmdline switch for cytoprops doesn't currently support reading
from jar files - as with vizmap.props. Iliana says that putting in this
functionality shouldn't be hard, so when we do one, we might want to do
the other too.
2. There isn't really a local directory with webstart, so no
cytoscape.props is read from the local directory.
3. If there's a cytoscape.props in the user's local .cytoscape
directory, it will be used.
4. If the properties are changed during execution of a webstart bundle,
they'll be written out to .cytoscape/cytoscape.props. This might not be
desirable behavior...

Melissa