Package org.cytoscape.work

Interface Task

All Known Subinterfaces:

CyNetworkReader, CyPropertyReader, CySessionReader, CyTableReader, CyWriter, ObservableTask, VizmapReader

All Known Implementing Classes:

AbstractCyNetworkReader, AbstractEdgeViewTask, AbstractLayoutTask, AbstractNetworkCollectionTask, AbstractNetworkTask, AbstractNetworkViewCollectionTask, AbstractNetworkViewTask, AbstractNodeViewTask, AbstractParallelPartitionLayoutTask, AbstractPartitionLayoutTask, AbstractRootNetworkCollectionTask, AbstractRowTask, AbstractTableCellTask, AbstractTableColumnTask, AbstractTableTask, AbstractTask

public interface Task

This interface specifies a unit of work to be executed asynchronously in its own Thread along with a user interface to display its progress, provide a means for the user to cancel the Task, and show information about any Exceptions thrown during its execution. Tasks are executed as part of a TaskIterator which will be passed into a TaskManager's execute method.

Some hints for writing a Task:

• Exceptions:
  • When an exception is thrown, the Task should not catch it and set a status message or the progress, even to provide explanatory messages for the user. A TaskManager may disregard status message and progress updates once an exception is thrown. Any helpful user messages regarding the exception should be contained solely in the exception.
  • If a Task throws a low level exception, it should catch it and throw an exception with a high level description. For example:

    
     try
     {
       ...
     }
     catch (IOException exception) // Low level exception
     {
       // Throw a high level exception that gives a high level explanation
       // that makes sense for a non-technical user.
       throw new Exception("Oops. Looks like you specified an invalid file.", exception)
     }
     

    Any helpful messages for the user should be contained in an exception.
  • When a Task encounters an error that is not in the form of an exception, like an invalid variable or incorrectly formatted parameter, the Task should not set the status message giving an explanation of the error and then exit. Instead, it should throw an exception.

    The wrong way:

    
     public void run(TaskMonitor taskMonitor)
     {
       if (myParameter == null)
       {
         taskMonitor.setStatusMessage("Whoa, looks like you didn't specified the parameter.");
         return;
       }
     }
     

    The right way:

    
     public void run(TaskMonitor taskMonitor) throws Exception
     {
       if (myParameter == null)
         throw new Exception("Whoa, looks like you didn't specified the parameter.");
     }
     

    This is done because it is possible for the TaskManager to close the Task's user interface when the Task returns before the user can read the message. Throwing an exception ensures the user will see the message.
• Status Messages:
  • The Task, when specifying its status message, should describe what it will do, not what it has done. Specifically, if the Task has several constituent parts, it should set its status message at the beginning of a part, not at the end. For example, assume a Task has two parts, A and B:

    
     public void run(TaskMonitor taskMonitor)
     {
       taskMonitor.setStatusMessage("Starting part A...");
       ... // do part A
       taskMonitor.setStatusMessage("Part A is done.");
    
       taskMonitor.setStatusMessage("Starting part B...");
       ... // do part B
       taskMonitor.setStatusMessage("Part B is done.");
     }
     

    Setting the status message after part A is unnecessary because the status message is immediately changed when part B starts. Setting the status message after part B is unnecessary because the Task ends immediately after part B finishes. Therefore, Tasks should set the status message at the beginning of a part.
  • Information regarding the result of the Task's should not be specified in the status message. For example:

    
     public void run(TaskMonitor taskMonitor)
     {
       int result = ... // some complicated computation
       taskMonitor.setStatusMessage("The result of the computation is " + result);
       // Give the user a chance to read the message:
       try
       {
         Thread.wait(1000);
       }
       catch (InterruptedException exception) { }
     }
     

    This is because the purpose of the status message is to inform the user what the Task is currently doing, not what it has done. If the Task wishes to provide any information regarding what it has done, it must do so through alternate means.
  • The Task should not set the status message or progress immediately before the Task finishes. This is because the TaskManager may close the Task's user interface before the user has a chance to read it. For example:

    
     public void run(TaskMonitor taskMonitor) throws Exception
     {
       ... // Some complicated calculation
       
       // This is unnecessary:
       taskMonitor.setStatusMessage("We're all done.");
       taskMonitor.setProgress(1.0);
     }
     

  • To specify an indefinite state in the progress bar, the Task should set its progress by using the setProgress method of TaskMonitor to a value less than 0.

Module: work-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>work-api</artifactId>
</dependency>

Cytoscape Backwards Compatibility (SPI Interface): We expect that this interface will be implemented. Therefore to maintain backwards compatibility this interface will only be modified for major version updates.

Method Summary

Modifier and Type	Method	Description
void	cancel()	This method is called by the TaskManager when the user chooses to cancel the Task.
void	run(TaskMonitor taskMonitor)	This method is called when the Task begins execution.

Method Detail

run

void run(TaskMonitor taskMonitor)
  throws Exception

This method is called when the Task begins execution. This method should not be called by the programmer, as it will be called by the TaskManager.

Parameters:

taskMonitor - The TaskMonitor provided by TaskManager. to allow the Task to modify its user interface.

Throws:

Exception - The Task is at liberty to throw an exception in run. The exception is caught by TaskManager and is displayed in the interface. If a Task does not throw an exception, the Task implementation does not need to specify the throws Exception clause for the run method. Moreover, exceptions should be the way the Task communicates the occurrence of a fatal error, like a low-level exception or an invalid parameter, to the TaskManager.

cancel

void cancel()

This method is called by the TaskManager when the user chooses to cancel the Task.

This method should not be called by the programmer, as it might be called by the TaskManager.

This method should inform the Task that it must terminate execution cleanly and do any necessary cleanup work required.

WARNING: this method is called by a different thread than the thread executing run. The programmer must be aware of concurrency issues!