This service implementation has been archived.

NCBO Bioportal RDF CTS2 Plugin

A CTS2 implementation based on the NCBO BioPortal SPARQL endpoint.

Installation

Download the CTS2 Framework - (download page)

You can download either as a stand-alone server or a war.

Starting the Stand-alone Server

java -jar cts2framework-standalone.jar

The server should start and open up a browser window.

NOTE: Port 8080 will be assumed in further URLs. Change if configured differently.

Click the 'Admin Console' button or navigate to

http://localhost:8080/system/console/bundles

NOTE: Default username/password is admin/admin

Getting the Plugin

A pre-built plugin can be downloaded, or can be build from source code.

Download

Download the plugin from the Maven repository.

Build From Source

Ensure 'MAVEN_OPTS' envirnoment variables are set. For example:

export MAVEN_OPTS="-Xmx500m -XX:MaxPermSize=500m"

Building/Compiling:

git clone https://github.com/cts2/bioportal-rdf-service.git
cd bioportal-rdf-service
maven clean install -Dmaven.test.skip=true

NOTE: -Dmaven.test.skip=true will optionally skip the tests and only assemble the plugin. To run the tests, remove this parameter. If you choose to run the tests, you must specify your Bioportal API Key as a command line parameter: -DapiKey=xxxxxx

Installing the Plugin

In the 'Admin Console,' click the 'Install/Update...' button. In the dialog, browse to the bioportal-rdf-service plugin jar. Once selected, click 'Install Or Update.' Ensure that the 'Start Bundle' checkbox is unchecked. Next, click the 'Configuration Manager' tab:

http://localhost:8080/system/console/configMgr

Click the 'Bioportal RDF Service' row. Specify your Bioportal API Key and click 'Save.'

Navigate back to the 'Bundles' tab:

 http://localhost:8080/system/console/bundles

Find the 'NCBO Bioportal RDF CTS2 Service' bundle and click the 'start' button. This should start the service.

For a simple test:

http://localhost:8080/codesystems