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OpenBEL API on Docker

The openbel-api repository includes both production and local configurations.

OpenBEL API consists of the following images:

  • MongoDB 3.2
  • JRuby 9.1 (OpenBEL API)

First you will need to install Docker.

  • Linux: Install docker and docker-compose from your package manager.
  • Mac OSX / Windows: Install Docker and Docker Compose by following the instructions on the Docker site.

Getting started

The following bash command will do the following:

  • check for the docker, docker-compose commands

  • git clone or git pull depending on if 'openbel-api' director exists

  • download the needed datasets from datasets.openbel.org

  • copy /config/config.yml.example to /config/config.yml (you need to review this file!)

  • provide commands to run to build and start dev or prod docker

    bash <(curl -s https://raw.githubusercontent.com/OpenBEL/openbel-api/master/bin/setup-docker.sh)

Production docker

The production docker compose file is defined in docker-compose-prod.yml.

Run the following commands to start the production docker containers

docker-compose -f docker-compose-prod.yml build
docker-compose -f docker-compose-prod.yml up

You can then access the REST api at http://localhost:9292/api

The openbel-api on docker is successful when you see mongodb_1 and api_1 start up successfully:

openbel-api_1   | Puma starting in single mode...
openbel-api_1   | * Version 3.1.0 (jruby 2.3.1), codename: El Niño Winter Wonderland
openbel-api_1   | * Min threads: 1, max threads: 2
openbel-api_1   | * Environment: development
mongodb_1       | 2016-11-22T01:14:40.986+0000 I NETWORK  [initandlisten] connection accepted from 172.19.0.4:54350 #1 (1 connection now open)
mongodb_1       | 2016-11-22T01:14:41.049+0000 I NETWORK  [conn1] end connection 172.19.0.4:54350 (0 connections now open)
mongodb_1       | 2016-11-22T01:14:41.052+0000 I NETWORK  [initandlisten] connection accepted from 172.19.0.4:54352 #2 (1 connection now open)
mongodb_1       | 2016-11-22T01:14:41.058+0000 I NETWORK  [conn2] end connection 172.19.0.4:54352 (0 connections now open)
mongodb_1       | 2016-11-22T01:14:41.064+0000 I NETWORK  [initandlisten] connection accepted from 172.19.0.4:54354 #3 (1 connection now open)
openbel-api_1   | log4j:WARN No appenders could be found for logger (org.apache.jena.info).
openbel-api_1   | log4j:WARN Please initialize the log4j system properly.
openbel-api_1   | log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
mongodb_1       | 2016-11-22T01:14:41.795+0000 I NETWORK  [conn3] end connection 172.19.0.4:54354 (0 connections now open)
openbel-api_1   | * Listening on tcp://0.0.0.0:9292
openbel-api_1   | Use Ctrl-C to stop

To stop the docker containers

docker-compose -f docker-compose-prod.yml stop

To change the port that production docker is running on, add -- --port <portnumber> to the production Dockerfile at the end of the CMD:

CMD ["openbel-api", "--file", "/config/config.yml", "--", "--port", "9393"]

Development docker

To start development: docker-compose build docker-compose up

You can then access the REST API at http://localhost:9292/api

Now with docker development you can change the code in the following directories and have it automatically reload:

  • app/ (openbel-api)
  • lib/ (openbel-api)
  • subprojects/
    • bel/
    • bel_parser/
    • bel-rdf-jena/
    • bel-search-sqlite/

Development Docker commands

Access running docker api container

docker-compose exec openbel-api /bin/bash
docker-compose exec mongodb /bin/bash

Logs

docker-compose logs openbel-api

Clean up docker containers

docker kill $(docker ps -q)
docker rmi -f $(docker images -q -f dangling=true)

Notes

You may have to set a longer COMPOSE_HTTP_TIMEOUT if you receive this error:

ERROR: An HTTP request took too long to complete. Retry with --verbose to obtain debug information.
If you encounter this issue regularly because of slow network conditions, consider setting COMPOSE_HTTP_TIMEOUT to a higher value (current value: 60).

This can be done with the command: export COMPOSE_HTTP_TIMEOUT=300 (5 minutes)