Routine Operations

Administrative Web User Interface

Troubleshoot ontology submissions: Ontologies tab

See the Troubleshooting Submissions page for detailed instructions on troubleshooting ontology submissions.

See the Managing Ontologies page to learn more about basic operations like updating ontology metadata, deleting ontologies, and reparsing ontologies.

Caching

How can I clear the memcached-based UI cache?

If you are logged in as the admin user, simply visit http://{your_appliance_ip_or_domain_name}/admin and click the “Flush Memcache” button. There should be a response indicating success or failure.

Reset user’s API key

OntoPortal provides a Rake task to easily reset the API key of a user (if it has been exposed or abused).

Optionally view the list of available Rake tasks with their descriptions:

$ cd /srv/ontoportal/ncbo_cron
$ bundle exec rake -T
rake cache:clear                                         # Clear HTTP cache (redis and Rack::Cache)
rake group:add_ontology[group_acronym,ontology_acronym]  # Add ontology to a group
rake group:create[acronym,name]                          # Create a new ontology group
rake test                                                # Run tests
rake user:adminify[username]                             # Add administrator role to the user
rake user:apikey:get[username]                           # get APIKEY for the user
rake user:apikey:reset[username,apikey]                  # reset APIKEY for the user to random value or to specified value if API key is provided
rake user:artifacts[username]                            # Show all artifacts administrered by the user
rake user:create[username,email,password]                # Create a new user
rake user:resetpassword[username]                        # Reset password to a random value for the user
rake user:resetroles[username]                           # Reset all roles to LIBRARIAN for the user

Reset a user’s API key to a randomly generated value:

$ cd /srv/ontoportal/ncbo_cron
$ bundle exec rake user:apikey:reset[username]

OntoPortal uses UUID for API keys which can be generated with uuidgen command line untility and can be explicitly set when reseting API keys:

$ uuidgen
cf304210-4715-424a-a48d-7ec04fc8924f
$ cd /srv/ontoportal/ncbo_cron
$ bundle exec rake user:apikey:reset[username,cf304210-4715-424a-a48d-7ec04fc8924f]

Grant administrative privileges to a BioPortal user

cd /srv/ontoportal/ncbo_cron
bundle exec rake user:adminify[username]

Stopping and starting services

- Confirm and fix: This is likely outdated.
! Many of these services may now be controlled with 
   _sudo systemctl stop/start <service>_