cpath-dev Google Group

changing the webservice call in cytoscape plugin to internal instance of cpath

ruth.isser...@utoronto.ca (Ruth Isserlin) — Mon, 23 Nov 2009 19:36:33 UT

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

Re: webservice calls

benjamin.gr...@gmail.com (Benjamin Gross) — Tue, 03 Nov 2009 20:19:06 UT

Hi Pradeep,
These packages get created when you run ant. How are you building the
source ?
I've placed psi-2-biopax.zip onto the web server (pc-dump dir) which
contains the psi to biopax converter. To use the converter, you need
to set an environment variable PATHWAY_TOOLS_ROOT with the paths to

Re: webservice calls

pradeep20...@gmail.com (pradeep kumar s) — Tue, 03 Nov 2009 15:09:55 UT

Dear Benjamin,

Thanks for uploading the latest build. But I get errors when I try to
build the source.
It complains of missing classes:

1)In org.mskcc.pathdb.action.web_ap i.biopax_mode.ExecuteGetParent sXmlResponse
class, org.mskcc.pathdb.schemas.summa ry_response package does not
exist.
2)In org.mskcc.pathdb.action.web_ap i.biopax_mode.ExecuteSearchXml Response

Re: webservice calls

benjamin.gr...@gmail.com (Benjamin Gross) — Mon, 26 Oct 2009 15:03:44 UT

Hi Pradeep,

I've put cpath.zip into the pc-dump directory of the cbio web server I
referred you to last week. That contains the lastest code.

Let me know if you have any problems with it.

Regards,
-Benjamin

Re: webservice calls

pradeep20...@gmail.com (pradeep kumar s) — Mon, 26 Oct 2009 01:14:12 UT

Dear Benjamin,

As suggested by you, I tried to check out the latest CVS build. I am
unsuccessful to do so with anonymous credentials. I have been trying
it for past 2 to 3 days thinking that the server may be down. But this
appears to be persistent. Could you please check if, I am wrong on
this or some problem with server.

Re: webservice calls

benjamin.gr...@gmail.com (Benjamin Gross) — Thu, 22 Oct 2009 02:58:17 UT

You shouldn't have to grab the latest build for web service
functionality, but I would grab it (we just released a new version of
cpath with enhanced searching capabilities). Would you mind
downloading the latest source and creating a new war file ?

Re: webservice calls

pradeep20...@gmail.com (pradeep kumar s) — Thu, 22 Oct 2009 01:10:05 UT

HI Benjamin,

I downloaded the source from the link that is given on cPath download page.
Do I have to download latest build from SVN to avail all the
webservice functionality?

--Pradeep

On Thu, Oct 22, 2009 at 1:30 AM, Benjamin Gross

Re: webservice calls

benjamin.gr...@gmail.com (Benjamin Gross) — Wed, 21 Oct 2009 16:30:34 UT

Hi Pradeep,

You want to use version 2.0 for all webservice calls except
get_neighbors (which is version 3.0). Where did you grab the source
code ?

-B

Re: webservice calls

pradeep20...@gmail.com (pradeep kumar s) — Wed, 21 Oct 2009 15:12:48 UT

Dear Benjamin Gross,

Thanks a lot for answering my question!

These are web service URL I am using:

[link]
or
[link]

I think version=1.0 is right at my data is all version 1.0

Re: webservice calls

benjamin.gr...@gmail.com (Benjamin Gross) — Wed, 21 Oct 2009 14:33:27 UT

Pradeep,

Can you provide me with URL you are constructing to make web service
request ? Also, what response are you getting from server ?

Thx
-Benjamin

webservice calls

pradeep20...@gmail.com (pradeep) — Tue, 20 Oct 2009 08:40:22 UT

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

Where do I set the database download tab url

ruth.isser...@utoronto.ca (Ruth) — Fri, 31 Jul 2009 14:39:41 UT

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

RE: Error on index with latest version of cpath code

ruth.isser...@utoronto.ca (Ruth Isserlin) — Tue, 28 Jul 2009 13:03:09 UT

Hi Ethan,

Thanks for the suggestion. I found the offending record and the XML_BLOB
actually only contained "[PLACE HOLDER]". I removed the record and the
indexing worked.

Thanks.

Ruth

_____

Behalf Of Ethan Cerami
Sent: Monday, July 27, 2009 3:01 PM
To: cpath-dev@googlegroups.com

Re: Error on index with latest version of cpath code

cer...@cbio.mskcc.org (Ethan Cerami) — Mon, 27 Jul 2009 19:01:16 UT

My suggestion would be to modify the indexing code to print out the
cpath ID for each record as it is indexed, so that you can find the
offending record.
Then, look up the XML_BLOB for that offending record, and see which data
source it is. It *might* be possible to update the XML_BLOB directly,

RE: Error on index with latest version of cpath code

ruth.isser...@utoronto.ca (Ruth Isserlin) — Mon, 27 Jul 2009 18:47:21 UT

Mint, Intact, HPRD, Biogrd, Mips (all converted from PSI to Biopax), and
Kegg, Reactome, NCI, Biocarta, Humancyc, Cellmap, Netpath and INOH.
Is there anyway to fix it without re-building?
Ruth

-----Original Message-----
Behalf Of Ethan Cerami
Sent: Monday, July 27, 2009 2:34 PM
To: cpath-dev@googlegroups.com