A sample page matching the a function is: The CyREST API and CyREST Command API submenus document CyREST in a Swagger web application, which allows you to explore CyREST entrypoints by reading about them and invoking them directly (using a Try it out!) button.
PYTHON CYTOSCAPE HOW TO
Notably, Automation Examples contains a tutorial that explains how to explore CyREST Commands and Functions. Automation Examples leads to a web portal containing the bulk of documentation, samples and tutorials for Cytsocape Automation in general. The CyREST API submenu shows available Functions, and CyREST Command API shows available Commands.
Specify the port on the Cytoscape command line via the -R parameter:Įxploring CyREST Commands and Functions ¶Ĭytoscape makes a list of available Commands and Functions available via the Help → Automation submenus.Use the Edit → Preferences menu to alter the rest.port property to select a different port (e.g., 8888).If your workstation has port 1234 already in use, you can specify a different CyREST port in two ways: Note that the list of namespaces will vary depending on the apps you install – some apps provide Commands in namespaces of their own. The second form is a Command that returns a list of available Command namespaces: Your Cytoscape workstation and navigate to either or The first form is a Function that returns basic Cytoscape information as a JSON object: Cytsocape enables progamatic access to both its Commands and Functions via its CyREST interface.īy default, the CyREST interface is enabled and available on TCP/IP port 1234. Such languages enable complex Cytoscape-centric workflows or the integration of Cytoscape into larger workflows. In some cases, you may need to leverage the complex control and data structures available in a fully featured programming language,
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