Cytoscape WikiIntroduction
[http://wiki.ops4j.org/confluence/display/ops4j/Pax Pax] is a project to develop tools for OSGi bundles. Pax-Construct, which is a part of Pax project, is a tool to create, build, manage and deploy OSGi bundles. The basic idea is that instead of writing all pom.xml files manually, generate those using simple shell commands.
Sample Projects
Create New Spring-OSGi Project
Install Pax-Construct - Essentially, Pax-Construct is a collection of scripts, so you can install this by uncompress the zip file somewhere on your local disk space, and set the path to the directory. For example, if you unzip the pax-construct version 1.3 to PAX_HOME, you need to set the path to:
PAX_HOME/pax-construct-1.3/bin
Create Project - You can run the following shell script to create a sample Spring-OSGi project named project1.
############################################## # Template for Spring-OSGi projects # ############################################## # (1) Create Project "project1" pax-create-project -g org.cytoscape -a project1 cd project1 # (2) Add SpringSource Enterprise Bundle Repositories pax-add-repository -i com.springsource.repository.bundles.release -u http://repository.springsource.com/maven/bundles/release pax-add-repository -i com.springsource.repository.bundles.external -u http://repository.springsource.com/maven/bundles/external # (3) Import required bundles pax-import-bundle -g org.springframework.osgi -a org.springframework.osgi.extender -v 1.1.0 -- -DimportTransitive -DwidenScope # (4) Create bundles pax-create-bundle -p org.cytoscape.helloservice1 -- -Djunit pax-create-bundle -p org.cytoscape.helloservice2 -- -Dspring=2.5.5 -Djunit pax-create-bundle -p org.cytoscape.helloserviceuser -- -Dspring=2.5.5 -Djunit # (5) Build and run the project mvn clean install pax:provision
Details
pax-create-project command creates a new OSGi project in the current working directory. By -g option, you can specify group id of this project.
In general, you CANNOT use existing library files (jar files registered at the maven central repository) as OSGi bundle. There are two options to solve this problem:
Wrap existing jar files by pax-wrap-jar command
- Use OSGi bundle repository instead of maven central repository
In this example, I used the second option. pax-add-repository command adds an additional maven repository location to the pom file. SpringSource manages a maven repository [http://www.springsource.com/repository/app/ SpringSource Enterprise Bundle Repository], which is a repository of OSGi bundles. All library files in this repository are wrapped as OSGi bundles.
pax-import-bundle command automatically generates <dependency> statement in the project pom file. In this example, bundles required to run [http://www.springframework.org/osgi Spring Dynamic Modules] are imported.
This section contains the actual statements to generate templates for your bundles. pax-create-bundle commands generates minimal set of files to start writing OSGi bundle. If you do not specify the option, a simple bundle with BundleActivator and an OSGi service will be created. If -Dspring option is specified, an example Spring Bean and XML files to setup Spring-based OSGi services will be created.
Pax is also available as maven plugin. Anytime after you build the bundles by mvn clean install command, you can run your bundles by mvn pax:provision. This command automatically setup [http://felix.apache.org/site/index.html Apache Felix] to run your bundles.
After you run the script, you will see the prompt (if not, hit enter). Type ps and you can check the current status of the bundles:
-> ps START LEVEL 6 ID State Level Name [ 0] [Active ] [ 0] System Bundle (1.0.4) [ 1] [Active ] [ 5] Spring DM Extender (1.1.0) [ 2] [Active ] [ 5] Apache Commons Logging (1.1.1) [ 3] [Active ] [ 5] Spring Beans (2.5.5.A) [ 4] [Active ] [ 5] Spring Context (2.5.5.A) [ 5] [Active ] [ 5] Spring Core (2.5.5.A) [ 6] [Active ] [ 5] Spring DM Core (1.1.0) [ 7] [Active ] [ 5] AOP Appliance API (1.0.0) [ 8] [Active ] [ 5] Spring AOP (2.5.5.A) [ 9] [Active ] [ 5] Spring DM IO (1.1.0) [ 10] [Active ] [ 5] org.cytoscape.helloservice1 (1.0.0.SNAPSHOT) [ 11] [Active ] [ 5] org.cytoscape.helloservice2 (1.0.0.SNAPSHOT) [ 12] [Active ] [ 5] org.cytoscape.helloserviceuser (1.0.0.SNAPSHOT) [ 13] [Active ] [ 1] osgi.compendium (4.0.1) [ 14] [Active ] [ 1] Apache Felix Shell Service (1.0.1) [ 15] [Active ] [ 1] Apache Felix Shell TUI (1.0.1)
At this point, all bundles you have created by the script are running and they are assigned IDs (13, 14, and 15). Type services 10:
-> services 10 org.cytoscape.helloservice1 (10) provides: ------------------------------------------ objectClass = org.cytoscape.helloservice1.ExampleService service.id = 23
services command in the Felix shell shows a list of services running now. The example above shows an OSGi service named ExampleService is successfully registered at the OSGi service repository.
Now you are ready to write your code for the bundles. If you use Eclipse, use
mvn pax:eclipse
and then import the project from File --> Import. You need to choose Maven Project for project type. The project looks like the following:
attachment:eclipseproject1.png
Create New Plugin in Cytoscape 3 Project
Since Cytoscape 3 SVN trunk is build as PAX project, you do not need to create new project. You can add your plugin as a new bundle(s).
- Checkout Cytoscape 3 trunk from SVN
- cd to the Cytoscape 3 project directory
- Run this script:
####################################################################### # Create new Spring DM bundle in Cytoscape 3 directory # ####################################################################### # Add SpringSource Enterprise Bundle Repositories pax-add-repository -i com.springsource.repository.bundles.release -u http://repository.springsource.com/maven/bundles/release pax-add-repository -i com.springsource.repository.bundles.external -u http://repository.springsource.com/maven/bundles/external # Import required bundles pax-import-bundle -g org.springframework.osgi -a org.springframework.osgi.extender -v 1.1.0 -- -DimportTransitive -DwidenScope # Create new plugin as a bundle pax-create-bundle -n sampleplugin1 -p org.cytoscape.sampleplugin1 -- -Dspring=2.5.5 -Djunit
cd to the new plugin directory (in this example, sampleplugin1)
Type mvn pax:eclipse
- Import ploject to Eclipse
Now it's ready to write your own code. To build the plugin, just type mvn clean install in your plugin directory.