opencloning-db 1.5.0

Database for OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.

opencloning-db

opencloning-db is the database/API companion package for the OpenCloning backend. It provides the app and local data workflows used for OpenCloning database features.

Run locally

From the repository root:

# Install or update workspace dependencies
uv sync

# If you are using mac, you may have to stop any local Postgres instances running on port 5432
brew services stop postgresql

# Start local Postgres with dev/test/e2e databases plus Garage for object storage
docker compose \
    -f docker/docker-compose.postgres.yml \
    -f docker/docker-compose.garage.yml \
    up -d postgres garage

# Load required local runtime config
source .env.dev

# Seed the local baseline
uv run opencloning-cli db seed

# Run both the cloning and the database API - this what the OpenCloningDB frontend expects
uv run uvicorn opencloning_db.combined:app --reload --reload-exclude='.venv'

# Run the opencloning-db API (only database, not cloning. This is not used when running with the frontend)
uv run uvicorn opencloning_db.api:app --reload --reload-exclude='.venv'

That will serve the cloning API at http://127.0.0.1:8000/cloning and the database API at http://127.0.0.1:8001/db. That's what the OpenCloningDB frontend expects.

When the cloning app is served through opencloning_db.combined, the entire /cloning mount is protected by the same bearer-token authentication used by the db API.

Running tests locally

From the repository root:

# Install or update workspace dependencies
uv sync

# Run the tests
uv run pytest packages/opencloning-db/tests -v -ks

Frontend testing

Frontend testing using the database requires reseting after tests that modify the database. You can do this by calling the /__test/reset-db endpoint with the X-Test-Reset-Token header set to RESET-TOKEN. That endpoint is only available if the OPENCLONING_TESTING environment variable is set to 1.

Building and running the Docker image

The Dockerfile is shared with the cloning app, and the build arg APP_TARGET determines which app to build. So you can build the image by running:

docker build -f docker/opencloning.Dockerfile --build-arg APP_TARGET=db -t manulera/opencloning-db-backend .

Then run it for development:

# Run the containers (Postgres + Garage + db API)
docker compose \
    -f docker/docker-compose.postgres.yml \
    -f docker/docker-compose.garage.yml \
    -f docker/docker-compose.opencloning-db.yml \
    up -d

That stack exposes Garage's S3-compatible API at http://127.0.0.1:9000. Garage does not provide a MinIO-style browser console in this setup, so use an S3 client such as awscli or mc if you need to inspect the local bucket. The local defaults in .env.dev point host-side uv run ... commands at the same Garage bucket used by the containerized db API.