Peregrine

Query interface to get insights into data in Gen3 Commons

API Documentation

YAML file for the OpenAPI documentation is found in the openapi folder (in the root directory); see the README in that folder for more details.

Developer Setup

Run

poetry install
./run.py

Test

python bin/setup_test_database.py --host postgres
mkdir -p tests/resources/keys; cd tests/resources/keys; openssl genrsa -out test_private_key.pem 2048; openssl rsa -in test_private_key.pem -pubout -out test_public_key.pem; cd -

If needed, set environment variables to point to a specific Postgres instance.

export GDC_PG_HOST=postgres
export GDC_PG_USER=postgres
export GDC_PG_PASSWORD=""

Run tests.

poetry run pytest -vv --cov=peregrine --cov-report xml tests

Quickstart with Helm

You can now deploy individual services via Helm! Please refer to the Helm quickstart guide HERE (https://github.com/uc-cdis/peregrine/blob/master/docs/quickstart_helm.md)