hvp_db

UPenn Human Virome Project sample database

Install

git clone https://github.com/Ulthran/hvp_db
cd hvp_db
python -m venv env
source env/bin/activate
pip install -e .[web]

Init db

The package installs a small CLI named hvp-db.

Initialize a new SQLite database:

hvp-db init sqlite:///hvp.db

Ingest data

Load samples from a CSV file:

hvp-db load sqlite:///hvp.db samples.csv

CSV columns should match the fields of the Sample model and dates must be in ISO format (YYYY-MM-DD).

View data

Run the Flask site in dev mode:

hvp-db web sqlite:///hvp.db password

Or put it into production as a system daemon with something like this (make sure to set the env vars HVP_DB_URI and HVP_DB_PASSWORD properly for your daemon):

gunicorn --workers 2 --bind unix:/run/hvp.sock hvp_db/wsgi:app