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Loculus

This website uses Astro for static site generation and React for dynamic components.

Getting started

Local Development

  • Set up your .env file, e.g. by copying .env.example with cp .env.example .env
  • Install packages: npm ci (ci as opposed to install makes sure to install the exact versions specified in package-lock.json)
  • Generate config files for local testing (requires Helm installed): ../generate_local_test_config.sh. If you are not running the backend locally, run ../generate_local_test_config.sh --from-live to point to the backend from the live server (preview of the main branch).
  • Run npm run start to start a local development server with hot reloading.

Unit Tests

Run npm run test to execute the unit tests.

End-to-end Tests

We use Playwright for end-to-end tests. The e2e tests assume that the website is running on http://localhost:3000, e.g. by running npm run start. Run npm run e2e to execute the end-to-end tests.

If you run Playwright for the first time, you might need to run npx playwright install and npx playwright install-deps first. Playwright will tell you if that's the case.

(!) Note: The e2e tests require a running LAPIS instance with test data. This will be prepared automatically, when the LAPIS instance is empty and otherwise skipped. Some e2e tests assume, this prepared data was the first data to be released. If you run the e2e tests for the first time on a LAPIS instance with existing data that is NOT the prepared data, tests will fail ,and you need to delete the data first.

Running The Application

Run npm run start-server to build and run the application with the Astro dev server.

Configuration

The website is configured via environment variables. They are most conveniently set in the .env file. Note that Astro requires the environment variables already at build time. See .env.docker for the required variables.

Furthermore, the website requires config files that need to be present at runtime in the directory specified in the CONFIG_DIR environment variable:

  • config.json: Contains configuration on the underlying organism. It's similar to the database config file that LAPIS uses.
  • reference_genomes.json: Defines names for segments of the genome and amino acids. It's equal to the file that LAPIS uses.
  • runtime_config.json: Contains configuration that specific for a deployed instance of the website.

Check our tests and examples for working config files.

Logging

The website writes logs to stdout. If the environment variable LOG_DIR is set, it will also store them in LOG_DIR/website.log.

Development environment

Editor

Setup

  • Install node version from .nvmrc with nvm install

General tips