System Requirements

The requirements for running an Ontoserver instance are heavily dependent on the intended usage. For the basic usage pattern (< 20 concurrent users, syndicating a small number of binary indexes but not building indexes from source), the following resource levels are recommended (on top of a 64-bit docker machine)

Building indexes from sources (e.g. RF2) is very demanding on memory - in these cases, at least 16GB of RAM is recommended.

Set up your environment

• Install Docker

  In order to run Ontoserver, you first need a Docker Machine. This will allow you to control the hosts (whether real or virtual, local or remote) on which Ontoserver and its database will run.

  The simplest method is to download and install Docker Toolbox https://www.docker.com/products/docker-toolbox

  This should provide you with both the docker and docker-compose commands.

  If you wish to run Ontoserver on a remote virtual host, you may need to configure the appropriate drivers

• Establish an account with Docker Hub at https://hub.docker.com
• Obtain an appropriate Licence:
  • Within Australia, email help@digitalhealth.gov.au to request a (free) Ontoserver licence. ADHA will then arrange authorisation for your Docker Hub account.
  • Elsewhere, email ontoserver-support@csiro.au to discuss licensing terms (both evaluation and production licences are available for single and multiple instances, no limit on number of users). Once the licence is established, CSIRO will register your Docker Hub account name to enable access to their repository
• Log in to Docker Hub with:

  docker login

Basic Configuration

• Create a text file called docker-compose.yml with the following contents (or download ./docker-compose.yml).
• Details on configuring NCTS_CLIENT_ID and NCTS_CLIENT_SECRET can be found here.
• You will almost certainly want to set the JVM maximum heap via JAVA_OPTS=-Xmx as per below, as the defaults can be unreliable.
• NOTE: By default, Ontoserver will run using SSL/TLS (i.e. https://). To disable SSL/TLS, add - ONTOSERVER_INSECURE=true to the environment section of the ontoserver container in the docker-compose.yml file.

  version: '3'
  volumes:
    onto:
      driver: local
    pgdata:
      driver: local
  services:
    db:
      image: postgres:12
      volumes:
        - pgdata:/var/lib/postgresql/data
      healthcheck:
        test: ["CMD-SHELL", "pg_isready -U postgres"]
        interval: 10s
        timeout: 5s
        retries: 5
      environment:
        - POSTGRES_HOST_AUTH_METHOD=trust
    ontoserver:
      image: aehrc/ontoserver:ctsa-5.8
      container_name: ontoserver
      depends_on:
        - db
      ports:
        - "8443:8443"
        - "8080:8080"
      environment:
        - authentication.oauth.endpoint.client_id.0=NCTS_ACCESS_CODE
        - authentication.oauth.endpoint.client_secret.0=NCTS_CLIENT_SECRET
        - JAVA_OPTS=-Xmx2G        # Minimum
  #      - JAVA_OPTS=-Xmx8G      # Preferred
      volumes:
        - onto:/var/onto
  
  

Running Ontoserver

docker-compose up -d

docker-compose stop

docker exec ontoserver /index.sh

docker exec ontoserver /index.sh -v 20191231

docker exec ontoserver /index.sh -h

docker logs ontoserver

docker logs -f ontoserver