cbio-cancer-genomics-portal - Mandrian

[kmezhoud]

Dear all,
There are two modules in the maven project in this link
http://code.google.com/p/cbio-cancer-genomics-portal/wiki/Cytoscap3MondrianApp
:

1 - cbioportal-client: This is a Java API for the cBio portal web services
2- mondrian-cy3-app: This is the Mondian app, which is dependent on
cbioportal-client

From the source code that I can download as zip file from this link
http://code.google.com/p/cbio-cancer-genomics-portal/source/browse?repo=mondrian,

How can I built the apps (jar) using eclipse or shell.

Thanks!
kmezhoud

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[Igor Rodchenkov]

I do not see the app available from the Cy3 Apps Store; so looks you are to build it from sources.

Normally, one would not have to build the cbioportal-client though (if it's probably available in a public Maven repository).

If not, build it first (see below; but in my case, mvn install fails due to a junit test fails).

I'd recommend to checkout the sources as described at https://code.google.com/p/cbio-cancer-genomics-portal/source/checkout?repo=mondrian 

(you need a Mercurial client installed or e.g., SourceTree application. You also need Maven 3.0.x installed and JDK6) but downloading the sources archive might work as well.

Switch to the directory where the sources were placed, and execute:

cd cbioportal-client

mvn clean install

Then, switch to the mondrian-cy3-app in the directory where the sources are and execute: 

cd ../mondrian-cy3-app

mvn clean install

- if it not failed (it fails for me...), the apps's JARs will be created in the mondrian-cy3-app/target/ and cbioportal-client/target/ sub-directories (e.g. cbioportal-client-0.0.1-SNAPSHOT.jar).

Now, start Cstoscape 3.0.2 (or 3.1 snapshot build), bring the Apps Manager UI (using Apps menu), and install the app(s) from JAR(s).

Hope it helps (otherwise wait for the authors to reply here or contact them directly; 

I suspect the app, as it is now, won't start in Cy3 due to possible dependencies issues...)

Igor R.

[B. Arman Aksoy]

Hi Karim,

Thanks for your interest in Mondrian! As Igor mentioned, a typical mvn install procedure for the cbio-client and the mondiran-cy3-apps would create the necessary JAR files under mondrian-cy3-app/target, which then can be used for installing the App on Cy3. However, the Mondrian development has somehow stalled after the Google Summer of Code program ended and unfortunately the App is not stable at the moment. 

We are planning to continue the development of the plug-in and release it on Cytoscape App to make the install procedure easy for everybody. Unfortunately I am not certain on the exact date of the release right now, but I am hoping this will happen by the end of this year -- so please stay tuned until we polish the App by then.

Sorry about the inconvenience, let me know if you need more information on this.

Best,

-- Arman

[kmezhoud]

Dear Dr Arman,
If mondrian is not yet ready, Can I suggest a student to work on it?
Thanks
Karim

[srikanth bezawada]

Hi all, 

Is this app available for use now ?

Thanks,

Srikanth.B.

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