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LAPIS-SILO End-to-End Testing

This repository contains end-to-end tests for the LAPIS API backed by SILO. It's designed to make adding new test cases easy and straightforward, while ensuring all endpoints and functionalities work as expected.

Features

  • Docker Integration: Utilizes Docker Compose to manage test environments for LAPIS and SILO.
  • Automated Testing: Runs tests using Vitest to ensure all endpoints and functionalities are working as expected.
  • Configuration Flexibility: Configurable test sets and environments through Docker and external YAML/JSON files.
  • Dynamic Test Set Detection: Automatically detects and runs tests for all test sets in the /testsets/ directory.

Prerequisites

Running tests

  1. Install dependencies:

    npm ci

  2. Run tests:

    npm test

    This command will start up the Docker containers and execute all defined tests.

  3. Stop Docker containers:

    npm run dockerDown

Also, tests can be rerun without restarting all containers by calling npm run testRunner after npm run dockerUp directly.

Configuration

Modify the database_config.yaml, reference_genomes.json, and any other configuration files in the testsets directory according to your test requirements.

Project Structure

  • /testsets/: Contains individual test sets. Each test set is a directory that includes:
    • data/: Input data for the test set
    • queries/: Test queries and expected responses
    • output/: Output directory for SILO preprocessing
  • docker-compose.yml: Defines the LAPIS and SILO services
  • bin/: Scripts to be executed via npm run
  • src/: Main code for the tests
    • src/testset.spec.ts: Main test script that runs all queries for all test sets
  • vitest.config.ts: Vitest configuration
  • package.json: Defines project dependencies and scripts
  • .prettierrc: Prettier configuration for code formatting

Adding New Test Sets

To add a new test set:

  1. Create a new directory under /testsets/
  2. Add necessary data files to the data/ subdirectory
  3. Create query files in the queries/ subdirectory (must end with .query.ts)
  4. Add expected response files if needed

The test runner will automatically detect and run tests for all test sets in the /testsets/ directory.

If the added queries contain test, whose expectedResponse-body is a sql: statement, the test files need to be generated before running npm test by running npm run generate.

Before changing the /testsets/ directory, always call npm run dockerDown. After modifying the directory this command might fail to take down all currently running containers, and they need to be stopped manually.

Notes

  • Test set directory names should only contain alphanumeric characters, hyphens, and underscores.
  • The test runner uses dynamic port allocation to avoid conflicts between test sets.

Contributing

Contributions to improve the test suite or add new scenarios are welcome. Please submit a pull request with your changes, adhering to the existing code structure and documentation style.

License

TBD