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OntoPortal Documentation
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Overview

This section offers more advanced information on reconfiguring your OntoPortal Virtual Appliance environment.

You may wish to defer these steps until after you register your system and confirm it runs well in your environment.

# This section needs further review for accuracy.

Configuration introduction

Changing the configuration of appliance is a two step process:

  1. Modify any configuration files you want to change.
  2. Run deployment scripts to deploy application with updated configuration settings.

Most of the minor configuration changes, such as setting the hostname URI, should be set in the configuration files located in the distribution at /srv/ontoportal/virtual_appliance/appliance_config/site_config.rb.

  • For the Ontoportal UI: /srv/ontoportal/virtual_appliance/appliance_config/bioportal_web_ui/config/bioportal_config_appliance.rb
  • For API: /srv/ontoportal/virtual_appliance/appliance_config/ontologies_api/config/environments/appliance.rb
  • For NCBO_CRON: /srv/ontoportal/virtual_appliance/appliance_config/ncbo-cron/config/config.rb

Please note that both of those files import the site_config.rb file but would overwrite those settings if you set them in applicaiton specific configuration file.

Deploying the UI and API code

Once the necessary configuration adjustments are made, run the Appliance as follows:

[centos@appliance ]$ sudo su - ontoportal
[ontoportal@appliance ]$ cd /srv/ontoportal/virtual_appliance/deployment/
[ontoportal@appliance deployment]$ ./setup_deploy_env.sh
Setting up deployment environment
Setting up deployment env for UI
Cloning into 'bioportal_web_ui'...
remote: Enumerating objects: 557, done.
remote: Counting objects: 100% (557/557), done.
...
...
HEAD is now at 751e2b9... Gemfile.lock update
/srv/ontoportal/virtual_appliance/deployment
[ontoportal@appliance deployment]$ ./deploy_api.sh
[ontoportal@appliance deployment]$ ./deploy_ncbo_cron.sh
[ontoportal@appliance deployment]$ ./deploy_ui.sh
[ontoportal@appliance deployment]$ sudo oprestart

Updating the deployment scripts

- This section needs review and almost certainly an update

This is an optional step. If you want to pull in the latest deployment scripts— these will enable deployment of the latest OntoPortal application code— and run the Appliance with them, perform the following steps.

Update deployment environment

git pull will pull in latest deployment scripts to enable deployment of latest compatible OntoPortal application code.

Set up deployment environment

sh setup_deploy_env.sh gets latest compatible for the version of the appliance you are running UI and API code and installs necessary utilities for the deployment such as Capistrano.

Deploy the user interface

./deploy_ui Deploy API: ./deploy_api Deploy ncbo_cron: ./deploy_ncbo_cron

More advanced customization

Overwrite application files

It is possible to overwrite specific application files by simply dropping modified versions of those files in /srv/ontoportal/virtual_appliance/appliance_config/bioportal_web_ui and then running the deployment script. The deployment script will sync all files from configuration directory overwriting files in the directory from which application is deployed.

Set up ontology analytics

To make the ontology popularity statistics work, including the front page graphs, the browse page popularity sort order, and the search and recommender prioritizations, the Google Analytics has to be set up per the instructions on the Google Analytics Management page.

Next step

If you haven’t yet registered your system, go to the Registration Process step for detailed instructions.