cbio-ingest

REST API endpoints to ingest study and panel data into a cBioPortal instance. It requires the Docker installation of cBioPortal.

Prerequisites

Development

• Python==3.12
• uv
• Redis

Docker

• Docker Compose

Installation

Development

make install

This creates a virtual environment in .env that can be either activated, or indirectly by using uv run ....

source .venv/bin/activate

Then, start the server and worker:

# Terminal 1
make serve

# Terminal 2
make worker

Docker

Container registry (once)

docker run -d -p 5000:5000 --name registry registry:2

If the container is not running anymore (because of system restart or similar):

docker start registry

Build

bash docker/build.sh

This builds and pushes the image to your local registry.

Pull

docker pull localhost:5000/cbio-ingest:dev

Docker Compose

To use the installation with the cBioPortal docker compose, copy the override and env file to the cbioPortal Docker compose:

cp docker/docker-compose.override.yml ../cbioportal-docker-compose
cp docker/env.example ../cbioportal-docker-compose/.env.cbio-ingest

Access

The server in development instance is reachable via http://localhost:8000.

To access the API schema, navigate to http://localhost:8000/docs.

Database Migrations

We use alembic to manage database migrations and keep a history of changes to the database.

A typical workflow looks like this:

# 1. change a model in models.py, then:
make db-migration msg="add new_field to study"

# 2. review the generated file in migrations/versions/, fill in downgrade()

# 3. apply it
make db-migrate

# 4. if something's wrong
make db-rollback

To see the history of migrations, do:

make db-history

To see where in the history the database currently is, do:

bash db-current