OntoBrowser-Docker

Dockerized OntoBrowser

Deployment

Create docker-compose.env with PostgreSQL credentials (see docker-compose.env.tpl).

cp docker-compose.env.tpl docker-compose.env
docker-compose up --build -d

After starting the containers, the web application is running at http://localhost:8080/ontobrowser

Connect to an existing PostgreSQL DB

In case you already have a running database, you can modify the environment variables POSTGRES_HOST, POSTGRES_DB, and POSTGRES_PORT in docker-compose.env accordingly. The variables default to the values given in docker-compose.env.tpl. You may also need to modify the pg_hba.conf file of your PostgreSQL database (see https://www.postgresql.org/docs/current/auth-pg-hba-conf.html).

Use the sql files in the backend folder to initialize the database.

It may be reasonable to strike the unused backend service from the docker-compose.yml file.

Upload Example OBO File

curl -s -S -O -L http://purl.obolibrary.org/obo/ma.obo
curl -s -S -H "Content-Type: application/obo;charset=utf-8" -X PUT --data-binary "@ma.obo" -u SYSTEM "http://localhost:8080/ontobrowser/ontologies/Mouse%20adult%20gross%20anatomy"

Notes

There is no authentication for uploading OBO files, so please don't use the frontend Docker image in productive environments. If you want to enable authentication, edit the Dockerfile in the frontend folder and remove sed -i 's/return username/return "SYSTEM"/g' src/main/java/com/novartis/pcs/ontology/rest/servlet/OntologiesServlet.java