Spring Dynamic Modules for Cytoscape

Introduction

From Cytoscape 3.0, the entire system is based on OSGi, and this modularizes Cytoscape into a collection of bundles. OSGi bundles are just regular jar files plus a simple metadata file (MANIFEST.MF) and they can be used in other non-OSGi systems. However, once we use raw OSGi API, the bundle is coupled with OSGi environment, and it is not easy to port the bundle to non-OSGi environments. [http://www.springframework.org/osgi Spring Dynamic Modules] is one of the solutions to achive maximum modulality.

Usecases

Service Management

In OSGi environment, objects shared by multiple bundles are usually managed by [http://www.knopflerfish.org/osgi_service_tutorial.html OSGi Service Registory]. In Cytoscape, there are lots of objects

Testing

Good starting point to use Spring for Cytoscape. We can use DI to make mock objects to do integration test.

Integration Test

Mock Object

Interface-Based Programming

Aspect Oriented Programming

Logging

Benchmarking

Example: Command Parameter Intercepter

Managing Instances by Setter Injection

Open Issues / Problems

Inter-bundle aspect management.

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