https://github.com/genspectrum/lapis-silo-e2e
https://github.com/genspectrum/lapis-silo-e2e
Last synced: 5 days ago
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- Host: GitHub
- URL: https://github.com/genspectrum/lapis-silo-e2e
- Owner: GenSpectrum
- Created: 2024-09-02T14:30:45.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2025-05-12T12:28:03.000Z (7 days ago)
- Last Synced: 2025-05-12T13:38:09.035Z (7 days ago)
- Language: TypeScript
- Size: 10.2 MB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
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README
# 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](https://www.docker.com/get-started) and Docker Compose
- [Node.js](https://nodejs.org/en/) (version specified in `package.json`)
- [npm](https://www.npmjs.com/get-npm)
## Running tests
1. Install dependencies:
```bash
npm ci
```
2. Run tests:
```bash
npm test
```
This command will start up the Docker containers and execute all defined tests.
3. Stop Docker containers:
```bash
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