Diff for "Cytoscape_3/UserManual/ProgrammaticAccess"

Differences between revisions 6 and 12 (spanning 6 versions)

Programmatic Access to Cytoscape Features

In this chapter, you will learn how to use Cytoscape from the 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 you perform your data analysis with point-and-click GUI operations. To resolve this issue, recording workflows is the key feature for reproducible data analysis workflows, 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 to script your workflow. For such use cases, accessing Cytoscape via REST API is the right option.

1. REST API for Commands

In addition to running Command scripts, Command module has REST API to access available commands.

By default, this feature is disabled. To run REST API 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 you see list of available commands, you are ready to use Command API

2. 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. You can use popular tools, including IPython/Jupyter Notebook and RStudio as your orchestration tool for your data visualization workflow with Cytoscape.

(Sample Jupyter Notebook written with cyREST and py2cytoscape)

Currently, cyREST is available as an App for Cytoscape 3.2.1 and later. Please visit the link below for more information.

cyREST App Store page

Debugging your workflows

(TBD)

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

-  ← Revision 6 as of 2015-06-22 19:14:47 →
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+  ← Revision 12 as of 2015-06-22 20:57:24 →
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  Editor: KeiichiroOno
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-Deletions are marked like this.
+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 the 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.
+== 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 you perform your data analysis with point-and-click GUI operations.  To resolve this issue, recording workflows is the key feature for reproducible data analysis workflows, 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.
-Line 16:
+Line 17:
-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.
+== Options for Programmatic Access ==

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



=== Commands ===



 {{attachment:CommandTool.png}}
-Line 19:
+Line 25:
-=== Options ===

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



==== Commands ====



[[attachment:CommandTool.png]]





'''''Commands''''' is the built-in Cytoscape feature to automate your workflow as a simple script.  You can learn more about this feature in this section:
+'''''Commands''''' is the built-in Cytoscape feature to automate your workflow as simple script.  You can learn more about this feature in this section:
-Line 32:
+Line 30:
-===== Sample Scripts =====

{{{

(TBD)

}}}
+=== RESTful API ===

In some cases, you may need to use fully featured programming languages, such as Python, R, Ruby, or JavaScript to script your workflow.  For such use cases, accessing Cytoscape via REST API is the right option.
-Line 37:
+Line 33:
+==== 1. REST API for Commands ====

In addition to running Command scripts, Command module has REST API to access available commands.
-Line 38:
+Line 36:
-==== RESTful API ====

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



===== Commands REST API =====

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



By default, this feature is disables.  To run REST server for Commands, please follow these steps:
+By default, this feature is disabled.  To run REST API server for Commands, please follow these steps:
-Line 48:
+Line 40:
-    * Terminal or [[|iTerm]] (For Mac)
+    * Terminal or [[https://www.iterm2.com/|iTerm2]] (For Mac)
-Line 50:
+Line 42:
-. 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):
-Line 54:
+Line 46:
-./cytoscape.sh
+./cytoscape.sh -R 8888
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+Line 51:
-./cytoscape.bat
+./cytoscape.bat -R 8888
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+Line 54:
-.
+. Open the following URL with your web browser:
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+Line 56:
-{{{

}}}
+    {{{

http://localhost:8888/cytoscape/commands

    }}}
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+Line 60:
-(TBD)
+. If you see list of available commands, you are ready to use Command API



  {{attachment:CommandAPI.png}}
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+Line 65:
-===== cyREST =====
+==== 2. cyREST ====
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+Line 67:
-cyREST is available from
+{{https://raw.githubusercontent.com/idekerlab/cyREST/master/docs/images/logo300.png}}
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+'''[[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.  You can use popular tools, including IPython/Jupyter Notebook and RStudio as your orchestration tool for your data visualization workflow with Cytoscape.





 {{attachment:jupyter.png}}

(Sample [[http://jupyter.org/|Jupyter Notebook]] written with cyREST and [[https://github.com/idekerlab/py2cytoscape|py2cytoscape]])





Currently, cyREST is available as an App for Cytoscape 3.2.1 and later.  Please visit the link below for more information.



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





----