Open Genes API

Open Genes API is based on FastAPI framework and provides data for genes and experiments in Open Genes database.

Architecture

• api - API application root

  • main.py - entry point
  • endpoints - api endpoints
  • db - domain access object (DAO) logic for DB
  • entities - domain entities

• scripts - maintenance scripts root

  • aging_mechanisms -
  • clocks -
  • icd -
  • translations -
  • uniprot -

Development

Before you start working on a project, you need a database dump which you can download from our website or you can roll up a test database in Docker container from this repository.

Build local development image

./open-genes-backend.sh build

Run API app in development mode

./open-genes-backend.sh run api

Get the shell to run scripts

./open-genes-backend.sh run scripts

Dependencies

All dependencies are listed in ./requirements_dev.txt

Linters

Please use linter and code auto formatting when contributing to this repository.

Configs:

• .pylintrc
• pyproject.toml