Cytoscape WikiRFC Name : ... |
Editor(s): ... |
About this document
This is an official Request for Comment (RFC) for Cytoscape Headless Mode Operation
For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]
Status
"Not yet completely written"
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Proposal
Cytoscape currently runs only in window mode. There is need to access Cytoscape functionality in alternative ways, such as laying out graph images on a webserver or embedding a cytoscape window in a different application. In discussions of the various needs, we've identified several different modes of interacting with cytoscape.
#1 Window mode - This is how Cytoscape currently operates. # Text mode - This means running Cytoscape (generally from the command line) without opening the gui. The goal here is an application that provides access to Cytoscape features. For example, a user might specify a SIF file along with a vizmap.props file and rather than bringing up a window, simply create an image of the layed out graph using the specified vizmap.props. Text mode would allow calls to the cytoscape application to be embedded in scripts for other purposes, such as CGI scripts. # Library mode - This means providing a set of libraries that provide access to Cytoscape capabilities from other Java applications. For example, if a developer of a different application wanted to create a graph image based on some sort of network structure, instead of running a script in an external process to create the image, a developer could call specific Cytoscape methods directly to create the image. # Embedded Window mode - This means embedding one or more Cytoscape windows or panels in a separate application without creating all of the normal frames and panels. For instance, an application may want to show the network window without showing the menus or cytopanels. Interaction with the embedded window could be controlled through an external interface that calls various actions directly. # Daemon mode - This means having a single Cytoscape process running perpetually in the background. A program would interact with the daemon using some sort of IPC mechanism. The interface could be direct method calls or something like a [http://beanshell.org BeanShell] that allows command line interaction.
Biological Questions / Use Cases
General Notes
Requirements
Deferred Items
Open Issues
Cytoscape (on linux) currently needs an X11 process to be running before it can do anything. This is a result of PhoebeCanvas adding a DropTarget to itself to support Drag-n-drop operations. It is unclear how deeply rooted this behavior is and whether or not it can be turned on/off in a reasonable way.
- Exiting from Cytoscape currently calls System.exit(), which means that if it is embedded in another application, when Cytoscape is closed, the other application will be as well.
When Cytoscape is used as a library without calling CytoscapeInit (i.e. simply calling Cytoscape.getRootGraph() and a few other static methods), there is currently no way to specify the vizmap.props file. This means that applying visual properties fails.
Backward Compatibility
Proper support for headless mode would almost certainly imply significant changes to Cytoscape's current command line interface. It would be important to maintain the current options.
Expected growth and plan for growth
References
Implementation Plan
- ["/Implementation Plan"]