Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/biopragmatics/biolookup-docker

🐋 A dockerfile for the frontend to the Biolookup Service

https://github.com/biopragmatics/biolookup-docker

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary

Keywords

biopragmatics docker
Last synced: 10 months ago · JSON representation

Repository

🐋 A dockerfile for the frontend to the Biolookup Service

Basic Info
  • Host: GitHub
  • Owner: biopragmatics
  • License: mit
  • Language: Shell
  • Default Branch: main
  • Homepage:
  • Size: 29.3 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
biopragmatics docker
Created over 5 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.md

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:

    shell $ 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:

shell $ 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:

shell $ 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:

shell $ 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:

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

🕵️ Logging

The logs can be shown with

shell $ 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.

Owner

  • Name: Biopragmatics Stack
  • Login: biopragmatics
  • Kind: organization

Software supporting biomedical semantics and pragmatics

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/ci.yml actions
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
  • docker/setup-qemu-action v1 composite
Dockerfile docker
  • python 3.9 build
docker-compose.yml docker
  • biopragmatics/biolookup latest
  • biopragmatics/postgres-biolookup latest