Introduction to Cytoscape App Development

Overview

This step is designed to introduce you to Cytoscape App Development concepts and technology.

Cytoscape and OSGi

Cytoscape 3 design goals:

• Scalability
• Performance
• Stability
  • Application stability
  • API stability
  • Modularity (Enforced by OSGi)

Definition of OSGi from Wikipedia:

"The OSGi framework is a module system and service platform for the Java programming language that implements a complete and dynamic component model, something that does not exist in standalone Java/VM environments. Applications or components (coming in the form of bundles for deployment) can be remotely installed, started, stopped, updated, and uninstalled without requiring a reboot; management of Java packages/ classes is specified in great detail. Application life cycle management (start, stop, install, etc.) is done via APIs that allow for remote downloading of management policies. The service registry allows bundles to detect the addition of new services, or the removal of services, and adapt accordingly."

Important definitions:

• OSGi is service-oriented

• A bundle is the unit of access

• Bundles can be started and stopped independently
• Bundles implement services
  • Can be registered and unregistered
  • Generally, inter-bundle access is through a service
• Enforced separation of API and Implementation – Rules are that you can depend on API bundles, but not implementation bundles

Anatomy of a Bundle

A bundle is a JAR with extra metadata:

• Imports: The Java packages used by the bundle
• Exports: Java packages in the bundle that other bundles are allowed to use (usually just API)
• Activator: Triggered when bundle is started/stopped

Cytoscape 3 Architecture

• Service-oriented microkernel
• OSGi core
  • Dynamically loads and unloads modules, a.k.a. bundles
• Each subsystem in Cy3 has separate OSGi bundle(s)
• Apps can also be packaged as bundles

Example: HelloWorld

• pom.xml!
  • Maven project descriptor
  • Maven identifier
    • Group id
    • Artifact id
    • Version
  • OSGi identifier

    • Bundle-SymbolicName

  • Describes imports/ exports
• Activator.java! - Bundle activator

Maven Project Layout

• pom.xml!
  • Project descriptor
• src/main/java! - Bundle code
• src/test/java!
  • Test code
  • Not included in bundle JAR
• src/main/resources! - Non-code files that should be included in bundle JAR

Core Bundles

• app
• application
• command-executor
• core-task
• custom-graphics
• datasource
• equations
• event
• group
• io
• layout
• model
• presentation
• property
• service
• session
• swing-u/l
• viewmodel
• vizmap
• vizmap-gui
• webservice
• work

Core Bundles usually come in sets:

• API (optional) - No activator
• Implementation
  • At least one per API bundle
  • No exports
• Separate API so we can keep implementation modular
  • Desktop application
  • Console application, for scripts
• Nothing should import implementation bundles, unless it’s for unit testing

Task bundles

• work-api
• work-swing-api
• work-impl
• work-swing-impl
• work-headless-impl

VizMapper bundles

• vizmap-api
• vizmap-gui-api
• vizmap-gui-core-impl
• vizmap-gui-impl
• vizmap-impl

OSGi Services

• Service: An instance of a Java interface
  • The glue behind API and implementation bundles

  • Usually registered by a BundleActivator

• In Cytoscape 3:
  • Defined by an API bundle
  • Registered by an implementation bundle

• Interface: interface MyService { ... }!

• Implementation: class MyServiceImpl implements MyService { ... }!

• Properties: (“title”, “My Service”)! (“preferredMenu”, “Apps”)!
  • Arbitrary key-value pairs

Cytoscape API

Available as OSGi services. Two main types:

• API: Applica/on Programming Interface

  • Just fetch and use: MyService service = getService(context, MyService.class);!

• SPI: Service Provider Interface

  • Implement/extend and register: registerService(context, new MyServiceImpl(),MyService.class, properties);!

OSGi Services

Most common types of services:

• Factories: Create new instances
• Managers: Track, provide access to, or operate on collections of objects
• Utilities: Collections of utility functions

Cytoscape TaskFactories

TO-DO: Insert graphic for Tasks

TaskFactories:

• Main unit of work in Cytoscape is a “Task”

• Tasks are created by TaskFactories

• TaskFactories are OSGi services

  • Can be registered in your CyActivator: TaskFactory factory = registerService(bc, myFactory, TaskFactory.class, properties); where myFactory is the task factory you want to register

  • properties provide meta-data about the factory
• Java Properties

Cytoscape TaskFactory Properties:

• Properties have special meaning in Cytoscape

• Defined in org.cytoscape.work.ServiceProperties

• Key properties
  • TITLE – If used as a menu, this is the menu title
  • PREFERRED_MENU – Where this will be added
  • ENABLE_FOR – When this menu is active
  • IN_TOOL_BAR – is it in the tool bar?
  • IN_MENU_BAR – is it in the top-level menus?
  • MENU_GRAVITY – The specific gravity of this item.

Example

import org.cytoscape.work.AbstractTaskFactory; import org.cytoscape.work.TaskIterator; class MyTaskFactory extends AbstractTaskFactory {

• public MyTaskFactory() {

super(); } public TaskIterator !createTaskIterator() {

• return null; // Fill in

} public boolean isReady() { return true; } }

in CyActivator MyTaskFactory myFactory = new MyTaskFactory(); Properties props= new Properties(); // Note the “.” notation for cascading menus props.setProperty(PREFERRED_MENU, "Apps.cddApp"); props.setProperty(TITLE, "Load CDD Domains for Node"); // Not all task factories will be commands props.setProperty(COMMAND, "loadCDDDomains4node"); props.setProperty(COMMAND_NAMESPACE, "cddApp"); props.setProperty(IN_MENU_BAR, "true"); // Usually means the second menu item props.setProperty(MENU_GRAVITY, "2.0"); registerService(bc, loadCDDDomainNodeView,

• NodeViewTaskFactory.class, nodeViewProps);