This command causes Cytoscape to exit. It is typically used at the end of a script file.

  • verbose print more


cyclient.command.pause(self, message=None, verbose=False)

The pause command displays a dialog with the text provided in the message argument and waits for the user to click OK

  • message a message to display. default=None
  • verbose print more,script_file,args=None,verbose=False)

The run command will execute a command script from the file pointed to by the file argument, which should contain Cytoscape commands, one per line. Arguments to the script are provided by the args argument.

  • script_file file to run
  • args: enter the script arguments as key value pairs separated by commas. eg. "arg1:value1,arg2:value2"
  • verbose print more


cyclient.command.echo(self, variableName, verbose=False)

The echo command will display the value of the variable specified by the variableName argument, or all variables if variableName is not provided.

  • variableName The name of the variable or '*' to display the value of all variables.
  • verbose print more



The sleep command will pause processing for a period of time as specified by duration seconds. It is typically used as part of a command script.

  • duration enter the time in seconds to sleep
  • verbose print more


cyclient.command.open_dialog(self, verbose=False)

The command line dialog provides a field to enter commands and view results. It also provides the help command to display namespaces, commands, and arguments.

  • verbose print more


cyclient.session.createSessionFile(file, verbose=None)

Saves the current session to a file. If successful, the session file location will be returned.

  • file Session file location as an absolute path
  • verbose print more

  • returns 200: successful operation



This deletes the current session and initializes a new one. A message is returned to indicate the success of the deletion.

  • verbose print more

  • returns 200: successful operation


cyclient.session.getSessionFromFile(file, verbose=None)

Loads a session from a local file and returns the session file name

  • file Session file location as an absolute path
  • verbose print more

  • returns 200: successful operation



Returns the file name for the current Cytoscape session.

  • verbose print more

  • returns 200: successful operation



Manually call Java's System.gc() to free up unused memory. This process happens automatically, but may be useful to call explicitly for testing or evaluation purposes.

  • verbose print more

  • returns 204: Successful Garbage Collection