DevelopersGuide

This is a guide to installing, building and running the BioVeL Extension for OpenRefine.

The recommended method to work on the BioVeL Extension is to first first install OpenRefine and then include this project within the extensions directory.

Install Open Refine

The latest release version of OpenRefine is 2.6b1 (but it is not intended for production work).

	
	git clone https://github.com/OpenRefine/OpenRefine.git
	cd OpenRefine
	git checkout tags/2.6-beta.1	
	

The last stable (and recommended) release of OpenRefine is 2.5.

	
	git clone https://github.com/OpenRefine/OpenRefine.git
	cd OpenRefine
	git checkout tags/2.5
	

Install BioVeL Extension

The code base for the BioVeL Extension should be cloned in the OpenRefine/extensions directory. Also, rename the installed directory to biovel.

	
	git clone https://github.com/BioVeL/refine-ext.git 
	mv refine-ext biovel
	

Patches to Open Refine [for release 2.5]

The files that need to be patched in OpenRefine are,

• OpenRefine/build.xml : to remove the 'revision' variable since git does not have this information.
• OpenRefine/extensions/build.xml : to include the biovel extension in compilation tasks.
• OpenRefine/main/webapp/WEB-INF/butterfly.properties : to include the extension at load time when running refine.

The above patches are available in the patches directory in the extension.

Working with Eclipse

Setting up of the project for development with the Eclipse IDE requires adding the source path for the extension and the third-party dependent libraries.

• Import the OpenRefine directory as an existing project into an Eclipse workspace

• This will create a a project named grefine-all

• Configure the build path for the project

• Choose Add folder in the Source tab

• Select the src directory in the OpenRefine/extensions/biovel/src

• Choose Add Jars in the Libraries tab

• Select the jars in the directory in OpenRefine/extensions/biovel/module/MOD-INF/lib