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ontologies_api

ontologies_api provides a RESTful interface for accessing BioPortal (an open repository of biomedical ontologies). Supported services include downloads, search, access to terms and concepts, text annotation, and much more.

Run ontologies_api

Using OntoPortal api utilities script

See help

bin/ontoportal help
Usage: bin/ontoportal {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY]
  dev            : Start the Ontoportal API development server.
                  Example: bin/ontoportal dev --api-url http://localhost:9393
                  Use --reset-cache to remove volumes: bin/ontoportal dev --reset-cache
  test           : Run tests.
  run            : Run a command in the Ontoportal API Docker container.
  help           : Show this help message.

Description:
  This script provides convenient commands for managing an Ontoportal API
  application using Docker Compose. It includes options for starting the development server,
  running tests, and executing commands within the Ontoportal API Docker container.

Goals:
  - Simplify common tasks related to Ontoportal API development using Docker.
  - Provide a consistent and easy-to-use interface for common actions.

Run dev

bin/ontoportal dev

Run test with a local OntoPortal API

bin/ontoportal test

Manually

Prerequisites

  • Ruby 2.x (most recent patch level)
  • rbenv and ruby-build (optional)
    • If you need to switch Ruby versions for other projects, you may want to install something like rbenv to manage your Ruby environment.
  • Git
  • Bundler
    • Install with gem install bundler if you don't have it
    • To use local ontologies_linked_data gem: bundle config local.ontologies_linked_data ~/path_to/ontologies_linked_data/
  • 4store
    • NCBO code relies on 4store as the main datastore. There are several installation options, but the easiest is getting the binaries.
    • For starting, stopping, and restarting 4store easily, you can try setting up 4s-service
  • Redis
    • Used for caching (HTTP, query caching, Annotator cache)
  • Solr
    • BioPortal indexes ontology class and property content using Solr (a Lucene-based server)

Configuring Solr

To configure Solr for ontologies_api usage, modify the example project included with Solr by doing the following:

cd $SOLR_HOME
cp example ncbo
cd $SOLR_HOME/ncbo/solr
mv collection1 core1
cd $SOLR_HOME/ncbo/solr/core1/conf
# Copy NCBO-specific configuration files
cp `bundle show ontologies_linked_data`/config/solr/solrconfig.xml ./
cp `bundle show ontologies_linked_data`/config/solr/schema.xml ./
cd $SOLR_HOME/ncbo/solr
cp -R core1 core2
cp `bundle show ontologies_linked_data`/config/solr/solr.xml ./
# Edit $SOLR_HOME/ncbo/solr/solr.xml
# Find the following lines:
# <core name="NCBO1" config="solrconfig.xml" instanceDir="core1" schema="schema.xml" dataDir="data"/>
# <core name="NCBO2" config="solrconfig.xml" instanceDir="core2" schema="schema.xml" dataDir="data"/>
# Replace the value of `dataDir` in each line with: 
# /<your own path to data dir>/core1
# /<your own path to data dir>/core2
# Start solr
java -Dsolr.solr.home=solr -jar start.jar
# Edit the ontologieS_api/config/environments/{env}.rb file to point to your running instance:
# http://localhost:8983/solr/NCBO1

Installing

Clone the repository

$ git clone [email protected]:ncbo/ontologies_api.git
$ cd ontologies_api

Install the dependencies

$ bundle install

Create an environment configuration file

$ cp config/environments/config.rb.sample config/environments/development.rb

config.rb.sample can be copied and renamed to match whatever environment you're running, e.g.:

production.rb
development.rb
test.rb

Run the unit tests (optional)

Requires a configuration file for the test environment:

$ cp config/environments/config.rb.sample config/environments/test.rb

Execute the suite of tests from the command line:

$ bundle exec rake test

Run the application

$ bundle exec rackup --port 9393

Once started, the application will be available at localhost:9393.

Contributing

We encourage contributions! Please check out the contributing guide for guidelines on how to proceed.

Acknowledgements

The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-HG004028.

License

LICENSE.md