OmicsDM_v2

Holds sources for the version 2 of Omics Data Management platform

Run Server

Python Environment

cd server/
python3 -m venv venv
source venv/bin/activate
pip3 install "biodm[kubernetes] @ git+https://github.com/bag-cnag/biodm"
pip3 install -r requirements.txt

Dependencies

docker compose up --build -d

Configuration

Populate server/.env file with desired configuration.

Run

After those pre-requisite steps you may either use the provided VSCode run and debug entry or run manually

python3 app.py 

Warning: You should run the python it in the immediate directory of app.py so that .env is accounted for.

Run Client

Client is developped using node v23.1.0, assuming you're using nvm you should preface with this command.

cd client/
nvm use 23
npm install

Configuration

You should populate client/static/config.json with appropriate configuration, in partocular your server endpoint.

Fetch client

Once your server is running and configuration is populated, you should run the following command in order to generate a type safe client based on the OpenAPI description of the server.

npx @hey-api/openapi-ts

Run

npm run dev