Galaxy Acceptance Tests

Playwright tests to confirm Galaxy is functioning as expected after deployment.

The tests directory contains Playwright test scripts that verify Galaxy functionality across two deployment scenarios:

• Terra-hosted Galaxy: Tests that manage the full lifecycle on Terra (launch, test, shutdown)
• External Galaxy: Tests against a standalone Galaxy instance running on a known URL

A complete end-to-end Terra test flow includes:

1. Launching a new Galaxy instance on Terra
2. Running functional tests:
   • Create, rename, and delete a history
   • Upload data by pasting text into the upload dialog
   • Upload datasets and run the fastp tool
   • Upload datasets, a reference genome, and run a variant calling workflow
3. Pausing the Galaxy instance (preserving disks)
4. Resuming and verifying data persistence
5. Shutting down and cleaning up resources

Test files are organized into two categories: Terra tests (platform operations) and Galaxy tests (application functionality).

Terra tests

The test files that target Terra functionality are:

• login.spec.ts
  performs the login flow to authenticate with a Google account.
• launch.spec.ts
  launches a Galaxy instance with the default configuration.
• open.spec.ts
  opens Galaxy in a new browser tab
• pause.spec.ts
  deletes the Galaxy instance but leaves the disks intact.
• shutdown.spec.ts
  deletes the Galaxy instance and persistent disks.

Galaxy tests

The test files that target Galaxy functionality:

• history.spec.ts
  create, rename, and delete a history
• paste.spec.ts
  upload text by pasting into the upload dialog
• fastp.spec.ts
  upload two datasets and run the fastp tool
• variant.spec.ts
  [WIP] upload datasets, a workflow, and runs the workflow

Administrative functions

Administrative test utilities:

• auth.setup.ts
  Authenticates to Terra and saves session to .auth/user.json. This allows subsequent tests to bypass Google OAuth login and avoid captchas. Run in headed mode: npx playwright test tests/auth.setup.ts --headed. For CI/CD, update the GitHub secret USER_JSON with the contents of this file.
• cleanup.spec.ts
  Cleans up orphaned persistent disks that sometimes linger after test failures.

Running the tests locally

Setup

1. Install dependencies:

   npm install
   npx playwright install

2. Configure environment variables: Create a .env.local file (or set environment variables) with the following:

   For Terra testing:

   TERRA_URL=test          # Options: 'test'/'dev', 'production', 'sarscov2'
   TERRA_WORKSPACE=acceptance-tests  # Or 'integration_tests'
   [email protected]
   TERRA_PASSWORD=your_password

   For external Galaxy testing:

   TERRA_URL=http://<IP_ADDRESS>:8000/galaxy/

3. Authentication setup (Terra only): To avoid Google captchas, run the authentication setup once:

   npx playwright test tests/auth.setup.ts --headed

   This saves your authenticated session to .auth/user.json, which is automatically reused by all subsequent tests.

Running tests

Test an external Galaxy instance:

TERRA_URL=http://35.196.87.134:8000/galaxy/ npx playwright test history paste fastp

Test against Terra (full lifecycle):

npx playwright test login launch    # Launch Galaxy on Terra
npx playwright test history paste fastp  # Run Galaxy functional tests
npx playwright test shutdown        # Clean up

Run all tests:

npx playwright test

Run specific test file:

npx playwright test tests/fastp.spec.ts

Debug tests (headed mode with inspector):

npx playwright test tests/fastp.spec.ts --debug

Run with visible browser:

npx playwright test --headed