covid19

An interface to submit, serve, and analyze COVID19 related gene and drug sets.

Development

The entrypoint of the application is in covid19/app/app.py; do not change the name of the file or directory.

Getting Started

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Running in development

source venv/bin/activate
python run.py

And visit http://localhost:8080/covid19.

Installing new dependencies

Python dependencies

Ensure you update requirements.txt whenever installing a new dependency with pip.

System dependencies

In the case of extra (debian) system dependencies, add them to deps.txt.

Database

The .env.example and docker-compose.yml can be used to establish a local database.

• docker-compose up -d database: will start the database
• alembic current: will show you the current migrations on the active database (defined in .env)
• alembic upgrade +1: apply single database migration on the active database (defined in .env)
• alembic upgrade head: apply all database migrations on the active database (defined in .env)
• alembic downgrade -1: revert database migrations on the active database (defined in .env)
• python ./manage.py dump > your_data.dump: Dump the contents of the database to a file
• python ./manage.py load < your_data.dump: Load contents of the database from a file

Testing

Run pytest in the root folder to run unit tests.

Deployment

Build for deployment

docker-compose build app

Deploy

docker-compose push app

Execute locally

docker-compose run app