pgx server -> Cytoscape automation -> Cytoscape js

[davidcod...@gmail.com]

Hi, new to Cytoscape and had some questions.

Looking to set up a Oracle PGX server and use Cytoscape automation with its RestApi's to get Cytoscape js out from it for UI development.

I assume Cytoscape automation makes a call to the PGX server and then formats the data into a nice json?

What are the limitations of the Cytoscape automation such as how many requests can it process? Size of data being requested?

Thanks

[David Otasek]

Hi David,

Cytoscape is designed as a UI application; each instance is designed primarily to process requests one at a time. Requests and responses will be limited by memory and processing power made available to Cytoscape.

Interacting with a PGX server would require exchanging JSON data with a running instance of Cytoscape. This has been be done via R, Python or JavaScript, but can be done with any language that can communicate via REST. You can familiarize yourself with the data structures by  exploring Cytoscape's Swagger documentation via the instructions in the Cytoscape Automation wiki. The Cytoscape Automation wiki and its associated GitHub repository are also a good starting place for using automation.

Of particular interest to you if you're interested in getting Cytoscape JS data will be the GET /v1/networks/{networkId}/views/{viewId} endpoint, and other endpoints branching from the /v1/networks/ root of the REST API.

Once you have Cytoscape JS JSON, the Cytoscape JS documentation can provide you with a means to manipulate and display it: http://js.cytoscape.org/

I hope this helps get you started. If you have any other specific questions, please let us know.

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[davidcod...@gmail.com]

Thank you, I had a chance to play around with some of those samples.  I'm looking for something that scales more, do to the fact that Cytoscape processes requests one at a time I may have to use something else.  

Are there other API's which I could utilize which would give me back a Cytoscape JS or a usable Graph JSON to be displayed in a UI?

[David Otasek]

This concerns Cytoscape.JS more than it does Cytoscape. For better support, check out the existing questions and answers for Cytoscape.js at stackoverflow, or ask for what you need there.