opencloning-db 1.9.5

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 postgres

# Load required local runtime config
source .env.dev

# Apply schema migrations (creates tables on an empty database)
uv run opencloning-cli db migrate

# Optional: load the deterministic demo/test baseline
OPENCLONING_TESTING=1 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.

Database migrations (Alembic)

Schema changes are defined in opencloning_db.models and applied with Alembic in this package (alembic/, alembic.ini). Edit the models first, generate or adjust the revision under alembic/versions/, then run migrations against each database.

Alembic reads the database URL from OPENCLONING_DB_URL (same as the app; load .env.dev for local work). Revision history is stored in the database table alembic_version, not in git.

From the repository root, pass the config file explicitly (or cd packages/opencloning-db and omit -c):

ALEMBIC_CFG=packages/opencloning-db/alembic.ini
# Use -c "$ALEMBIC_CFG" (quoted). Do not put -c inside the variable: zsh does not
# split $ALEMBIC on spaces, so `ALEMBIC="-c …"; alembic $ALEMBIC` breaks.

Autogenerate a migration

With Postgres running and .env.dev loaded:

source .env.dev
ALEMBIC_CFG=packages/opencloning-db/alembic.ini

# Optional: see which revision the database is at
uv run alembic -c "$ALEMBIC_CFG" current

# 1. Change src/opencloning_db/models.py first (desired end state).
# 2. Generate a revision by diffing models against the live database:
uv run alembic -c "$ALEMBIC_CFG" revision --autogenerate -m "short description of the change"

# 3. Open the new file under packages/opencloning-db/alembic/versions/ and review it.
#    Autogenerate can miss or mis-handle partial indexes, renames, and data backfills.

The database you point at must reflect the previous migration state (run alembic upgrade head first, or use a fresh DB). If the schema already matches your models but alembic_version is empty, stamp instead of upgrading (see below).

Run migrations

source .env.dev
ALEMBIC_CFG=packages/opencloning-db/alembic.ini

# Apply all pending revisions (CLI wrapper or Alembic directly)
uv run opencloning-cli db migrate
# uv run alembic -c "$ALEMBIC_CFG" upgrade head

# Confirm
uv run alembic -c "$ALEMBIC_CFG" current

To migrate a different database (for example the test DB), set OPENCLONING_DB_URL to that database before running Alembic.

Schema already up to date? If the live database already has the objects a migration would add (for example after a manual change or an older deploy), upgrade may fail with “already exists”. Mark the database as migrated without running SQL:

uv run alembic -c "$ALEMBIC_CFG" stamp head

Use stamp only when you are sure the live schema matches the migration chain at head.

Useful commands

Command	Purpose
uv run alembic -c "$ALEMBIC_CFG" history	List revisions
uv run alembic -c "$ALEMBIC_CFG" downgrade -1	Revert the last revision
uv run alembic -c "$ALEMBIC_CFG" upgrade head --sql	Print SQL without executing (offline preview)

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 reseeding after tests that modify the database. This is done 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, and it delegates to the guarded opencloning-cli db seed command.

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 .
# or
docker buildx build -f docker/opencloning.Dockerfile --build-arg APP_TARGET=db -t manulera/opencloning-db-backend:prod --platform linux/amd64,linux/arm64 .

Then run it for development:

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

Database backup worker

To create backups, you can use this dockerfile for a worker.

To build it:

docker build -f docker/postgres-aws-cli.Dockerfile -t manulera/postgres-aws-cli .