SBP Portal Backend Server

FastAPI backend for handling Seqera Platform workflow launches.

Prerequisites

• Python 3.10+
• UV package manager

Setup

1. Install UV (if not already installed):

   # macOS/Linux
   curl -LsSf https://astral.sh/uv/install.sh | sh
   
   # Windows
   powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

2. Install dependencies:

   uv sync --all-extras

3. Configure environment variables:

   cp .env.example .env
   # Edit .env with your Seqera Platform credentials

4. Run the API locally:

   uv run uvicorn app.main:app --reload --host 0.0.0.0 --port 3000

API Endpoints

• GET /health — Lightweight health probe
• POST /api/workflows/launch — Launch a Seqera workflow (send the same payload previously expected by the Express server)
• POST /api/workflows/{runId}/cancel — Placeholder response for cancelling a run
• GET /api/workflows/runs — Placeholder list endpoint mirroring the previous Node API
• GET /api/workflows/{runId}/logs — Placeholder log endpoint
• GET /api/workflows/{runId}/details — Placeholder details endpoint
• POST /api/workflows/datasets/upload — Create a Seqera dataset and upload submitted form data as a CSV

Testing

Run the test suite with coverage:

# Run all tests with coverage report
uv run pytest --cov=app --cov-report=term-missing --cov-report=html

# Run tests with verbose output
uv run pytest -v

# Run specific test file
uv run pytest tests/test_main.py

# Check coverage threshold (90%)
uv run coverage report --fail-under=90

View HTML coverage report:

open htmlcov/index.html  # macOS
xdg-open htmlcov/index.html  # Linux
start htmlcov/index.html  # Windows (Command Prompt / PowerShell)

Linting and Code Quality

# Run ruff linter
uv run ruff check app tests

# Run black formatter
uv run black app tests

# Run type checking with mypy
uv run mypy app --ignore-missing-imports

# Install pre-commit hooks
uv run pre-commit install

# Run pre-commit on all files
pre-commit run --all-files

Environment Variables

Required entries in .env:

• SEQERA_API_URL — Seqera Platform API endpoint (e.g., https://api.seqera.io)
• SEQERA_ACCESS_TOKEN — API access token
• COMPUTE_ID — Default compute environment ID
• WORK_DIR — Default work directory
• WORK_SPACE — Seqera workspace identifier
• ALLOWED_ORIGINS — (Optional) comma-separated list of origins allowed via CORS (defaults to https://dev.sbp.test.biocommons.org.au)
• PORT — (Optional) uvicorn port when running python -m app.main
• UVICORN_RELOAD — (Optional) set to true to enable reload when running via python -m app.main

Containerization

1. Build the image from the repository root:

   docker build -t sbp-backend .

2. Run the container, passing your .env file (or explicit -e overrides) so the API can reach Seqera:

   docker run --rm -p 3000:3000 --env-file .env sbp-backend

   Override PORT or uvicorn flags in the env file if you need different bindings. Any value defined in .env becomes available to the app inside the container.

Notes

• Requests fail fast with 500 if mandatory environment variables are missing.
• Downstream Seqera API failures surface as a 502 response with the original error message for easier debugging.