Tests

This document explains the test strategy for this software. There are three layers:

1. Backend unit & API tests using Pytest for the Flask backend.
2. Frontend unit & component tests using Vitest and React Testing Library for React components.
3. End-to-end (E2E) tests using Playwright, executed in GitHub Actions against the hosted app, to validate full pipelines.

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1) Backend Unit & API Tests (Pytest)

Goal: Verify every Flask API endpoint and backend logic in isolation (fast, deterministic).

Scope

• Status codes, JSON schema, and error handling of all API endpoints.
• Auth/session flows (login, logout, protected routes).
• Validation of complex pipeline payloads (e.g., Scrinshot, MERFISH, SeqFISH).
• Pipeline submission/scheduling logic (mock long-running jobs & I/O).
• DB interactions (mock MongoDB in unit tests).

Running locally

# note: start database first
pytest flask
# with coverage:
pytest flask --cov=flask --cov-report=term-missing

or if using Docker:

# Start services with tests profile (optional, but recommended for consistency):
npm run docker:start:test
# or for development with hot reloading:
npm run docker:watch:test

# Then run backend tests:
docker compose run --rm --build odt-server pytest
# with coverage:
docker compose run --rm --build odt-server pytest --cov=. --cov-report=term-missing

Alternatively, you can start just the database and run tests:

docker compose up odt-db -d
docker compose run --rm --build odt-server pytest

Fixtures & notes

• Never execute real long-running pipelines in unit tests; mock them and assert:
  • request validation
  • scheduling trigger
  • persisted records / status initialization

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2) Frontend Unit & Component Tests (Vitest)

Goal: Verify React components render correctly and handle user interactions as expected (fast, deterministic).

Scope

• Component rendering and rendering with props.
• User interactions (clicks, form inputs, navigation).
• Component state management.
• Integration between React components.
• UI behavior and conditional rendering.

Running locally

# Run all frontend tests:
npm test
# Run tests in watch mode (for development):
npm run test:watch

Fixtures & notes

• Tests use Vitest as the test runner with React Testing Library for component testing.
• Tests run in a jsdom environment to simulate browser behavior.
• Test files should be named *.test.tsx or *.test.ts and placed alongside the components they test.

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3) End-to-End (E2E) Tests (Playwright)

Goal: Prove a real user can run a pipeline from the UI to a successful terminal state on the deployed app.

Scope

• Navigate to pipelines page, fill required fields, and submit.
• Optionally capture/display Run ID if shown (useful for debugging).
• Pass criteria: Visible terminal success signal (e.g., banner “Pipeline finished successfully”, or status badge COMPLETED).
• Smoke checks for key pages (render without severe console errors).

Running locally

# in the frontend root
npx playwright test
# test with ui:
npx playwright test --ui

or if using Docker:

The odt-tests container is only available when using the tests profile. To start the application with the test container available, use:

npm run docker:start:test
# or for development with hot reloading:
npm run docker:watch:test

See Using Docker for more details on Docker profiles.

Then run Playwright tests:

# run all tests:
docker compose run --rm odt-tests
# run a specific test:
docker compose run --rm odt-tests test tests/scrinshot.spec.ts --reporter=html
# inspect the test results:
docker compose run --rm odt-tests show-report

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Continuous Integration (GitHub Actions)

Backend tests (Pytest), Frontend tests (Vitest), and E2E tests (Playwright) run on every push/PR.
Set E2E_BASE_URL as a repository secret to point E2E tests to the hosted app.

You can find the configuration at:

• .github/workflows/pr_tests.yml - Backend and Frontend tests
• .github/workflows/e2e.yml - E2E tests
• .github/workflows/backend_tests.yml - Backend tests (legacy)