webservice calls

[pradeep]

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
[7] Error Codes

it does not work.

How can I get to work the above command from by local installation.

Thank you,
--pradeep

[Benjamin Gross]

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

[pradeep kumar s]

Dear Benjamin Gross,

Thanks a lot for answering my question!

These are web service URL I am using:

1.

http://localhost/cpath/webservice.do?version=2.0&q=BRCA2&format=xml&cmd=search
or
http://localhost/cpath/webservice.do?version=1.0&q=BRCA2&format=xml&cmd=search

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

but both of them give the error:

<error>
<error_code>450</error_code>
<error_msg>Bad Command (command not recognized)</error_msg>
-
<error_details>
Command: 'search' is not recognized. Please try again.
</error_details>
</error>


2.

http://localhost/cpath/webservice.do?version=2.0&cmd=get_pathways&q=O14763

Get this error:

An Error Has Occurred
Command: 'get_pathways' is not recognized. Please try again.

3.

http://localhost/cpath/webservice.do?cmd=get_pathways&version=2.0&q=O14763&input_id_type=UNIPROT

An Error Has Occurred
Command: 'get_pathways' is not recognized. Please try again.

4.
http://localhost/cpath/webservice.do?version=3.0&cmd=get_neighbors&q=9854


An Error Has Occurred
Command: 'get_neighbors' is not recognized. Please try again.


I am trying to get result in some xml format so that I can parse and
use for some other purpose.

Thank you very much.

Sincerely,
--Pradeep

[Benjamin Gross]

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

[pradeep kumar s]

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

[Benjamin Gross]

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 ?

[pradeep kumar s]

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.

This is what I used:

For anonoymous CVS access:
export CVS_RSH=ssh
cvs -d :ext:anon...@cbiocvs2.nci.nih.gov:/share/content/gforge/cpath
checkout cpath
When prompted, enter password: anonymous.

Attached is the pic of tortoiseCVS:
I faced similar problems from command line.

Thank you for the attention and help.

Regards,
--Pradeep
P.S: I have also applied for an account, yet to receive email from the admin.





On Thu, Oct 22, 2009 at 11:58 AM, Benjamin Gross

[Benjamin Gross]

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

> <cvs.png>

[pradeep kumar s]

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_api.biopax_mode.ExecuteGetParentsXmlResponse
class, org.mskcc.pathdb.schemas.summary_response package does not
exist.
2)In org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteSearchXmlResponse
class, org.mskcc.pathdb.schemas.search_response package does not
exist.
Please do the needful.

Question2:

Documentation of cpath mentions about Biogrid(PSI format) to biopax
converters. where can I find the scripts to convert in cpath src
directory?

Thank you,

Sincerely,
--Pradeep







On Tue, Oct 27, 2009 at 12:03 AM, Benjamin Gross

[Benjamin Gross]

Hi Pradeep,

It complains of missing classes:

1)In org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteGetParentsXmlResponse
class, org.mskcc.pathdb.schemas.summary_response package does not
exist.
2)In org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteSearchXmlResponse
class, org.mskcc.pathdb.schemas.search_response package does not
exist.
Please do the needful.

These packages get created when you run ant.  How are you building the source ?

Question2:

Documentation of cpath mentions about  Biogrid(PSI format) to biopax
converters. where can I find the scripts to convert in cpath src
directory?

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 the jars in this zip.  You can process an entire directory using psi-mi-batch-converter.py or a single file using psi-mi-converter.sh.

Let me know if you have any questions,

-Benjamin