This sample adds TaskFactory instances to the OSGi context, which can then be executed as a Command using the Cytoscape Command Tool.
We recommended that you be familiar with concepts in Cytoscape 3.0 App Development.
The Work API defines the fundamental unit of work in Cytoscape: the Task. In our application, we have created two Tasks: SayHelloTask and ReturnAValueTask. To be able to execute a task within Cytoscape you must create a TaskFactory. In our example, we’ve created two TaskFactories: SayHelloTaskFactory and ReturnAValueTaskFactory. Each of these generate a TaskIterator, which contains an ordered list of Tasks to be completed, and in our case contains only one task for each factory.
Tunables are annotated fields within a Task. They act as parameters that affect the execution of the Task. For example, SayHelloTask contains a single tunable, defined by the code below:
@Tunable (description="The name of the person you want to greet.")
public String name = null;
When Cytoscape processes a Task, these tunables are set automatically, either via the contents of a dialog, or by assignment in the Command line.
If you open the Cytoscape Command Line Dialog (after installing this app), you can see the name tunable if you query the help utility by entering help sample_app say_hello. This should return the following output:
sample_app say_hello arguments:
name=<String>: The name of the person you want to greet.
In addition, Cytoscape can also generate a dialog to access SayHelloTask, which can be seen by accessing Sample App>Say Hello in the main Cytoscape menu.
Tasks can provide output to the Command Line Dialog through the TaskMonitor argument passed in the run(TaskMonitor arg0) method.
In SayHelloTask, the following code is responsible for printing a message to either the Command Line Dialog or the Cytoscape Task History window:
arg0.showMessage(Level.INFO, "Hello" + name + ".");
Tasks that implement ObservableTask, such as ReturnAValueTask must implement a method public <R> R getResults(Class<? extends R> type), which allows programmatic access to results after the Task has completed. Note that this implementation allows different return types. All ObservableTask implementations should allow String types to be returned. ReturnAValueTask also allows a Double type to be returned, which can be useful to other app developers wishing to access automation functions in your App.
For a TaskFactory to be available to Cytoscape users, the TaskFactory must be registered its the CyActivator. There are several things to note about our registrations.
The following code registers our TaskFactory as a Command:
import static org.cytoscape.work.ServiceProperties.COMMAND;
import static org.cytoscape.work.ServiceProperties.COMMAND_DESCRIPTION;
import static org.cytoscape.work.ServiceProperties.COMMAND_NAMESPACE;
...
public static final String SAMPLE_COMMAND_NAMESPACE = "sample_app";
...
String sayHelloDescription = "Say hello to the someone by name using the Task Monitor.";
...
sayHelloTaskFactoryProperties.setProperty(COMMAND_NAMESPACE, SAMPLE_COMMAND_NAMESPACE);
sayHelloTaskFactoryProperties.setProperty(COMMAND, "say_hello");
sayHelloTaskFactoryProperties.setProperty(COMMAND_DESCRIPTION, sayHelloDescription);
Every command requires a unique COMMAND_NAMESPACE property as well as a unique COMMAND property within that namespace. In addition, a COMMAND_DESCRIPTION property can be added to assist users. This description appears in the Command Line Dialog when help sample_app is entered, and should appear as below:
Available commands:
sample_app return_a_value Add two numbers (a and b) and return their value using ObservableTask.
sample_app say_hello Say hello to the someone by name using the Task Monitor.
TaskFactories registered as Commands can be accessed from an HTTP utility, such as curl or a wrapper library which provides access from within a scripting language, like python or R. There are three REST endpoints devoted to commands:
The exact functionality of these is documented in CyREST.
Some useful wrapper libraries for accessing Cytoscape’s REST automation are py2cytoscape and RCy3.
More detailed resources regarding Commands and Tasks can be found below: