VirusSeq Gateway

Development of the back-end gateway service for the VirusSeq Portal-ui

Documentation

This file is meant as a quick introduction, WIP

• Getting Started
  • Development Setup

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Getting Started

This app has been tested using NodeJS v^18, yet should work with earlier versions.

- Data sources

This service depends on a Postgres instance of its own, as well as those owned by Singularity and Song. Make sure to provide the right environment variables for it to reach those correctly.

- Development Setup

Setting up the project, and prepare things to make changes

# 1. clone the repository
  git clone git@github.com:virusseq/portal-gateway.git

# 2. install the dependencies
  npm ci

Now you should be able to start the server from the project's root folder:

# run the server (on port 8080)
  npm run dev
  # or better yet
  npm run dev:nodemon
  # which also restarts if linked packages are updated (e.g. Arranger)

# NOTE: if using NodeJS v17+, you may have to do one of the following:
  NODE_OPTIONS=--openssl-legacy-provider npm run dev
  # or do this, before running the server
  export NODE_OPTIONS=--openssl-legacy-provider

The development server will start on port 4000 by default.

- Endpoint Documentation

There is API documentation provided by Swagger, available at /swagger.

- Database migrations

Leveraging Ley, this API is able to apply migrations every time it is deployed to one of our k8s environments. The changes are implemented in the sequential files contained in the migrations directory, and you may create new ones by running the following command:

npm run migrate new <short_migration_description>.ts

Each of these files should contain an up function that effects the changes, and a down function that rolls them back entirely.

// Example migration file
import { Sql } from 'postgres';

export const up = async (client: Sql) => {
	await client`create table example (...)`;
};

export const down = async (client: Sql) => {
	await client`drop table example`;
};