Diff for "Scripting" - Cytoscape Wiki

Differences between revisions 2 and 3

RFC Name : Scripting in Cytoscape

Editor(s): Keiichiro Ono

Status: Open for Comments

Proposal

Implementing scripting (Python, Ruby, Java Script, etc.) functionality for Cytoscape. Scripting languages provide an alternative interface to Cytoscape functionality. By providing scripting support we will enable more users to take advantage of Cytoscape in new ways. There are two alternative scenarios to consider:

Start cytoscape normally and then load a script to execute.
Run a script normally within the operating system that then starts cytoscape or uses cytoscape functionality.

Biological Questions / Use Cases

Apply the same operation to a large number of networks/files. Often users want to perform the same set of operations on a large number of networks. Scripting this sort of task is an obvious solution to reducing redundant work.

Open Issues

The Cytoscape interface is currently WIDE open, meaning any plugin can call any public method. This causes all manner of problems and by providing the same access for scripts, we will be exacerbating the problem.

Implementation Plan

Java provides support for running scripting languages from within the Java Virtual Machine using the [http://jakarta.apache.org/bsf/ Bean Scripting Framework]. Using this framework, access to the following scripting languages:

Javascript
NetRexx (an extension of the IBM REXX scripting language in Java)
Python
Tcl
XSLT Stylesheets
Groovy
JLog (PROLOG implemented in Java)
Ruby
JudoScript
ObjectScript
ooRexx (Open Object Rexx), using BSF4Rexx.

One possible implementation strategy would be to add the [http://jakarta.apache.org/bsf/ Bean Scripting Framework] functionality to the core and then provide plugins for each scripting language. For instance, if a user was interested in writing a Python script to perform some task in Cytoscape, the user would first load the Python scripting plugin. Then the user would be able to load and execute scripts from the (as yet undefined) scripting user interface. This would allow users to load only the scripting languages they choose and help avoid (excessive) bloat.

-  ← Revision 2 as of 2007-07-24 22:56:27 →
  Size: 1702
  Editor: KeiichiroOno
  Comment:
+  ← Revision 3 as of 2007-07-24 23:15:23 →
  Size: 2800
  Editor: nebbiolo
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-Implementing scripting functionality for Cytoscape.  This is for both support for general scripting language (Python, Ruby, Java Script, etc.) and Cytoscape specific simple scripting.
+Implementing scripting (Python, Ruby, Java Script, etc.) functionality for Cytoscape.  Scripting languages provide an alternative interface to Cytoscape functionality.  By providing scripting support we will enable more users to take advantage of Cytoscape in new ways. There are two alternative scenarios to consider:



 1. Start cytoscape normally and then load a script to execute.

 1. Run a script normally within the operating system that then starts cytoscape or uses cytoscape functionality.
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+Line 21:
-== General Notes ==



== Requirements ==



== Deferred Items ==
+. Apply the same operation to a large number of networks/files.  Often users want to perform the same set of operations on a large number of networks.  Scripting this sort of task is an obvious solution to reducing redundant work.
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-== Backward Compatibility ==



== Expected growth and plan for growth ==



== References ==
+The  Cytoscape interface is currently WIDE open, meaning any plugin can call any public method.  This causes all manner of problems and by providing the same access for scripts, we will be exacerbating the problem.
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+Line 29:
-##If you want to create a separate subpage for the Implementation Plan, then provide this link:  ["/Implementation Plan"]
+Java provides support for running scripting languages from within the Java Virtual Machine using the  [http://jakarta.apache.org/bsf/ Bean Scripting Framework]. Using this framework, access to the following scripting languages:



    * Javascript

    * NetRexx (an extension of the IBM REXX scripting language in Java)

    * Python 

    * Tcl 

    * XSLT Stylesheets 

    * Groovy

    * JLog (PROLOG implemented in Java)

    * Ruby

    * JudoScript

    * ObjectScript

    * ooRexx (Open Object Rexx), using BSF4Rexx.



One possible implementation strategy would be to add the [http://jakarta.apache.org/bsf/ Bean Scripting Framework] functionality to the core and then provide plugins for each scripting language.  For instance, if a user was interested in writing a Python script to perform some task in Cytoscape, the user would first load the Python scripting plugin.  Then the user would be able to load and execute scripts from the (as yet undefined) scripting user interface. This would allow users to load only the scripting languages they choose and help avoid (excessive) bloat.
-Line 38:
+Line 48:
-=== How to Comment ===

Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records.  Be sure to include today's date and your name for each comment.  '''Try to keep your comments as concrete and constructive as possible.  For example, if you find a part of the RFC makes no sense, please say so, but don't stop there.  Take the extra step and propose alternatives.'''