Diff for "Cytoscape_3/UserManual/ProgrammaticAccess"

Differences between revisions 5 and 10 (spanning 5 versions)

Programmatic Access to Cytoscape Features

In this chapter, you will learn how to use Cytoscape from command line and scripts. These features replace Scripting module in the past versions of Cytoscape.

Topics

Commands
RESTful API
- Command REST API
- cyREST

Background

Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization. It is a great way for exploratory data analysis, but what happens if you have hundreds of data files or need to ask someone to execute your data analysis workflows? It is virtually impossible to apply same operations to hundreds of networks manually with GUI, and more importantly, although you can save your results as session files, you cannot save your workflows if your analysis is based on point-and-click GUI operation. Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape. The latest version of Cytoscape has several options to script and automate your workflows.

Options for Programmatic Access

There are two ways to access Cytoscape programmatically: Commands and RESTful API.

Commands

Commands is the built-in Cytoscape feature to automate your workflow as simple script. You can learn more about this feature in this section:

Command Tool

RESTful API

In some cases, you may need to use fully featured programming languages, such as Python, R, Ruby, or JavaScript,

REST API for Commands

In addition to running Command scripts, Command module has REST API to access those

By default, this feature is disables. To run REST server for Commands, please follow these steps:

Open a terminal session:
- PowerShell (For windows)
- Terminal or iTerm2 (For Mac)
- Terminal (For Linux)
Start Cytoscape from command-line. You need to specify port number as a parameter (In this example, port 8888 will be opened for Command):
- For Mac/Linux
```
./cytoscape.sh -R 8888
```
  For Windows
```
./cytoscape.bat -R 8888
```
Open the following URL with your web browser:
- ```
http://localhost:8888/cytoscape/commands
```
If yo see list of available commands, you are ready to use Command API

cyREST

cyREST is a language-agnostic, programmer-friendly RESTful API module for Cytoscape. If you want to build your own workflow with R, Python or other programming languages along with Cytoscape, this is the option for you.

Currently, cyREST is available as an App for Cytoscape 3.2.1 and later.

cyREST App Store page.

Debugging your workflows

(TBD)

Cytoscape_3/UserManual/ProgrammaticAccess (last edited 2016-04-26 22:22:57 by server2)

-  ← Revision 5 as of 2015-06-22 18:49:44 →
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+  ← Revision 10 as of 2015-06-22 20:29:24 →
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+Additions are marked like this.
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-In this section, you will learn how to use programmatic access features for advanced Cytoscape users.
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+Line 3:
-==== Topics ====
+In this chapter, you will learn how to use Cytoscape from command line and scripts.  These features replace ''Scripting'' module in the past versions of Cytoscape.
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+Line 5:
- * Commands

 * RESTful API

    * Command REST API

    * cyREST
+=== Topics ===



 * '''''Commands'''''

 * '''RESTful API'''

    * '''Command REST API'''

    * '''cyREST'''
-Line 13:
+Line 14:
-=== Background ===

Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization.  It is a great way to exploratory analyze your data sets, but what happens if you have hundreds of data files?  It is virtually impossible to apply same operations to hundreds of networks manually with GUI.



More importantly, although you can save your ''results'' as session files, you cannot save your '''''workflows''''' if your analysis is based on point-and-click GUI operation.  Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape.  Latest version of Cytoscape has several options to script and automate your workflows.
+== Background ==

Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization.  It is a great way for exploratory data analysis, but what happens if you have hundreds of data files or need to ask someone to execute your data analysis workflows?  It is virtually impossible to apply same operations to hundreds of networks manually with GUI, and more importantly, although you can save your ''results'' as session files, you cannot save your '''''workflows''''' if your analysis is based on point-and-click GUI operation.  Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape.  The latest version of Cytoscape has several options to script and automate your workflows.
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+Line 18:
-=== Options ===
+== Options for Programmatic Access ==
-Line 22:
+Line 21:
-==== Commands ====

'''''Commands''''' is the built-in Cytoscape feature to automate your workflow as a simple script.
+=== Commands ===



 {{attachment:CommandTool.png}}
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-===== Sample Scripts =====

{{{

(TBD)

}}}
+'''''Commands''''' is the built-in Cytoscape feature to automate your workflow as simple script.  You can learn more about this feature in this section:



 * [[Command_Tool|Command Tool]]
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+Line 31:
-==== RESTful API ====
+=== RESTful API ===
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+Line 34:
-===== Commands REST API =====

In addition to running scripts, Commands have REST API to access the
+==== REST API for Commands ====

In addition to running Command scripts, Command module has REST API to access those
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+Line 41:
-    * Terminal or [[|iTerm]] (For Mac)
+    * Terminal or [[https://www.iterm2.com/|iTerm2]] (For Mac)
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+Line 43:
-. Start Cytoscape from command-line:
+. Start Cytoscape from command-line.  You need to specify port number as a parameter (In this example, port 8888 will be opened for Command):
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+Line 47:
-./cytoscape.sh
+./cytoscape.sh -R 8888
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+Line 52:
-./cytoscape.bat
+./cytoscape.bat -R 8888
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+Line 55:
-.
+. Open the following URL with your web browser:
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+Line 57:
-{{{

}}}
+    {{{

http://localhost:8888/cytoscape/commands

    }}}
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-(TBD)
+. If yo see list of available commands, you are ready to use Command API



  {{attachment:CommandAPI.png}}
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+Line 66:
-===== cyREST =====
+==== cyREST ====
-Line 66:
+Line 68:
-cyREST is available from
+{{https://raw.githubusercontent.com/idekerlab/cyREST/master/docs/images/logo300.png}}



'''[[http://apps.cytoscape.org/apps/cyrest|cyREST]] is a language-agnostic, programmer-friendly RESTful API module for Cytoscape'''.  If you want to build your own workflow with [[http://www.r-project.org/|R]], [[https://www.python.org/|Python]] or other programming languages along with Cytoscape, this is the option for you.





 {{attachment:jupyter.png}}





Currently, cyREST is available as an App for Cytoscape 3.2.1 and later.



 * [[http://apps.cytoscape.org/apps/cyrest|cyREST App Store page]].