opencloning-db 1.4.0

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
docker compose -f docker/docker-compose.postgres.yml up -d

# 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.

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/opencloningbackend-db .

Then run it for development:

# Create the file storage directories
mkdir -p docker/file_storage/sequence_files docker/file_storage/sequencing_files

# Run the containers
docker compose \
    -f docker/docker-compose.postgres.yml \
    -f docker/docker-compose.opencloning-db.yml \
    up -d