Cytoscape Wiki|
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| 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 achine maximum modulality. | 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. |
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=== 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 |
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| === Interface-Based Programming === | |
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=== OSGi Service Management === Some of the functions in Cytoscape 3 will be implemented as ''OSGi Services''. This requires exporting |
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| ==== Benchmarking ==== |
Spring Dynamic Modules for Cytoscape
(Under construction) TableOfContents
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.