Using pyLODE for ontology documentation

Introduction

pyLODE is an OWL ontology documentation tool which ORR can use to improve visualization and therefore interpretation of various resources. This document provides a guide to deploy and use pyLODE in your orr-portal deployment.

Assumptions: that you will be serving orr-portal through an HTTPD server and that is already set up.

Crontab configuration

Edit the crontab as follows crontab -e and then add the following line

@reboot cd /path/to/pyLODE/ && gunicorn -b 0.0.0.0:8080 --chdir /path/to/pyLODE/pylode server:api & >> pyLODE.cronjob.out

This ensures that pyLODE is started whenever the machine is rebooted and also simply redirects std output to the pyLODE.cronjob.out

Add entry to HTTPD virtual host

Open /etc/httpd/conf.d/orr.conf and add the following four line entry within the <VirtualHost *:80> XML block

<VirtualHost *:80>

    # pyLODE Flask server running on 8080 started with 'gunicorn -b 0.0.0.0:8080 --chdir /path/to/pyLODE/pylode server:api &'
    # Source for pyLODE resides at https://github.com/RDFLib/pyLODE
    ProxyPass        /pylode http://localhost:8080
    ProxyPassReverse /pylode http://localhost:8080

You can then gracefully restart HTTPD sudo service httpd graceful

Start the pyLODE service

cd /path/to/pyLODE && gunicorn -D -b 0.0.0.0:8080 --chdir /path/to/pyLODE/pylode server:api &

This will start the pyLODE service in the background on port 8080 which can be accessed at http://${myhost}/pylode.

orr-portal configuration

grab a copy of the local.config.js file on the ORR host

docker cp orr:/path/to/tomcat/webapps/ont/js/local.config.js .

edit the file as follows

appConfig.externalTools.ontViewers = [{name: 'pyLODE', title: 'ESIP-hosted pyLODE server', srcUrlTemplate: 'http://cor.esipfed.org/pylode?url=$uri', moreInfoUrl: 'https://github.com/RDFLib/pyLODE'}]

...and then copy it back

docker cp local.config.js orr:/usr/local/tomcat/webapps/ont/js/

N.B. you may have to restart the ORR service.

Usage in orr-portal

When you navigate to a specific resource and scroll to the Data section and you will now be able to vizualize and browse the resource via pyLODE.