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

• Docker and Docker Compose
• Node.js (version specified in package.json)
• npm

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