Code to retrieve and display an XGMML file from a REST API

[Arun Kumar]

I have a REST based web service which outputs an XGMML file. I am able to import the url using File>Import>Network>URL an display the network.

I am trying to create an additional menu item under File which when clicked would automatically call the web service and display the XGMML output file. Could someone point me to the right classes in Cytoscape API to accomplish this? Thanks.

[Kei]

Hi.

You can do it by importing correct reader from OSGi service registry.  In your case, you need to get XGMMLReaderFactory from CyNetworkReaderManager:

http://chianti.ucsd.edu/cytoscape-3.2.1/API/org/cytoscape/io/read/CyNetworkReaderManager.html

So you can import this manager, and pass the stream to this.  It should return XGMMLReaderFactory.

Kei

2015年7月22日水曜日 12時52分29秒 UTC-7 Arun Kumar:

[Arun Kumar]

Thanks Kei. But I am looking at a simpler way to implement this using Task Factories.:

final TaskIterator ti = adapter.get_LoadNetworkURLTaskFactory().loadCyNetworks(restAPIURL);

adapter.getTaskManager().execute(ti);
SynchronousTaskManager<?> synTaskMan = adapter.getCyServiceRegistrar().getService(SynchronousTaskManager.class);           
synTaskMan.execute(ti);   

This does not work. I am not sure how to get from TaskManager to actually displaying the network data on Cytoscape.

[piet molenaar]

Hi Arun, 

If you're serious about building your own app to achieve this, I'd advice you to walk through our app developer ladder first:

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder

For your specific question you'd might consult the cookbook

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook

Hope this helps,
Piet

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Piet Molenaar
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Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
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[Arun Kumar]

Piet, I have already looked at the sites you mentioned. Most of the examples there are rudimentary. I could not find anything as simple as reading a network file and displaying the network.

On Wednesday, July 22, 2015 at 3:52:29 PM UTC-4, Arun Kumar wrote: