Library for adding/modifying/deleting sequencing runs and associated metadata with a Flask site for viewing data.
To start with local development:
git clone https://github.com/PennChopMicrobiomeProgram/SampleRegistry.git
cd SampleRegistry
python -m venv env/
source env/bin/activate
pip install -r requirements.txt
pip install app/sample_registry
create_test_db
export FLASK_DEBUG=1 && flask --app app/app run
How you want to deploy this will depend on your needs, facilities, and ability. We have it deployed by a Kubernetes cluster but you could also 1) just run it in development mode from a lab computer or 2) setup Nginx/Apache on a dedicated server or 3) run it serverlessly in the cloud (e.g. with Zappa on AWS) or 4) do something else. There are lots of well documented examples of deploying Flask sites out there, look around and find what works best for you.
When running, it will default to using a SQLite3 database located in the root of this repository (automatically created if it doesn't already exist). You can change to a PostgreSQL backend by providing the environment variables DB_HOST, DB_NAME, DB_USER, and DB_PSWD. If you want to use a different backend, you'll have to do a bit of modification to app/sample_registry/src/sample_registry/__init__.py and be somewhat familiar with SQLAlchemy URI strings.
The sample_registry library can be installed and run anywhere by following the instructions in Development (you don't need to do the create_test_db and running the site (bottom two commands)). To connect it to a Postgres backend, you'll need to also set the environment variables DB_HOST, DB_USER, DB_NAME, and DB_PSWD.
If you want to iterate over a feature you can only test on the K8s deployment, you can manually build the Docker image instead of relying on the release workflow. Use docker build -t ctbushman/sample_registry:latest -f Dockerfile . to build the image and then docker push ctbushman/sample_registry:latest to push it to DockerHub. You can then trigger the K8s deployment to grab the new image.
N.B. You might want to use a different tag than latest if you're testing something volatile so that if someone else is trying to use the image as you're developing, they won't pull your wonky changes.