biolookup-docker

This repository uses Docker to containerize the Biolookup Service web application, built on top of PyOBO. A public instance maintained by the INDRA Lab is served at http://biolookup.io.

Running the Biolookup Service

Before running the Biolookup Service, you'll need to prepare either a local database or get a connection string to a remote database. See here for instructions on loading the database.

🌐 Running Locally from Source

A dockerfile for pulling the latest Biolookup service and running its web app. Run with:

1. Make an .env file with BIOLOOKUP_SQLALCHEMY_URI. If you're on Mac and trying to connect to localhost, use host.docker.internal instead (ref) .

2. Run the following code:

   $ git clone https://github.com/biopragmatics/biolookup-docker.git
   $ cd biolookup-docker
   $ docker-compose up

   In case you're using a non-standard named docker-compose.yml, you can pass the -f flag to give the name of the file like in docker-compose -f biolookup-compose.yml up --detach.

🏗️ Building and Running Locally from Docker

After cloning, the image can be built locally with:

$ docker build -t biolookup:latest .
$ docker run --name biolookup -d -p 8765:8765 --env-file biolookup.env biolookup:latest

Where -d means "detached" mode. You'll need an environment file the same as described above. Alternatively, environment variables can be passed with --env (or -e for short) like in:

$ docker build -t biolookup:latest .
$ docker run --name biolookup -d -p 8765:8765 --env BIOLOOKUP_SQLALCHEMY_URI=foo biolookup:latest

🐋 Running Locally from Docker

The image is hosted on Docker Hub under biopragmatics/biolookup:latest and can be run with:

$ docker run -id --name biolookup -p 8765:8765 --env-file biolookup.env biopragmatics/biolookup:latest

The default port run by the app is 8765, but the -p option lets you map it to another port. You'll need an environment file the same as described above. Alternatively, environment variables can be passed with --env (or -e for short) like in:

$ docker run -id --name biolookup -p 8765:8765 --env BIOLOOKUP_SQLALCHEMY_URI=foo biopragmatics/biolookup:latest

🕵️ Logging

The logs can be shown with

$ docker exec $(docker ps --filter "name=biolookup" -q) /usr/bin/tail -f /root/.data/pyobo/biolookup/log.txt

📡 Pushing to Docker Hub

This repository is set up with a GitHub Action to build the dockerfile and push to Docker Hub.

🎁 Support

The Biolookup Service was developed by the INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

💰 Funding

The development of the Biolookup Service is funded by the DARPA Automating Scientific Knowledge Extraction (ASKE) program under award HR00111990009.