cg-maven 0.1.6

Store quality control metrics for cases in Clinical Genomics

Maven

Maven: "one who is experienced or knowledgeable."

This repository holds the software interacting with the maven database. Maven is currently a work in progress.

Aims

The maven database will be used to store quality metrics for cases and their analysis that come through Clinical Genomics.

Developing Maven

Steps to start developing on Maven locally:

1. Clone the repo

   git clone https://github.com/Clinical-Genomics/maven
   

2. Create a working environment
   • Requires poetry to be installed: https://python-poetry.org/docs/

2a. Create a virtual python environment in the directory

# Go into the directory
cd ./maven
# Create a virtual environment
python3 -m venv maven
# Activate the virtual environment
source venv/bin/activate
# Install packages
poetry install

2b. If you are using pycharm setup a poetry interpreter

• https://www.jetbrains.com/help/pycharm/poetry.html#poetry-pyproject

3. Install a mongodb client locally (for now) follow steps outlined here

   • https://www.mongodb.com/docs/v7.0/tutorial/install-mongodb-on-os-x/#install-mongodb-community-edition

4. Start a mongo server locally that runs the database

      brew services start mongodb-community@7.0
   

   • to stop the service when wanted

   brew services stop mongodb-community@7.0
   

5. To establish a connection to the database with FastApi and uvicorn run:

python3 -m uvicorn --reload --app-dir ./api main:app

• If this step worked you should see "Connected to database." in the terminal

6. To view the database in Compass

   • https://www.mongodb.com/products/tools/compass
   • Setup a connection to the localhost
   • Create a new database called "maven"

7. Alternatively to the steps above one can also run maven using docker 7a. Install docker and start the docker application: https://docs.docker.com/engine/install/

   • After step 1

   cd ./maven
   docker compose up