Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder/Intro_To_App_Dev

Introduction to Cytoscape App Development

Overview

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