j-christoffersen/genomic-variants

Genomic Variants

This project is a simple app where you can search for information on various genomic variants.

Table of Contents

1. Requirements
2. Usage
   1. Installing Dependencies
   2. Environment Variables
   3. Database Setup
   4. Starting the Application

Requirements

• NodeJS v9.1.2
• NPM v5.6.0
• Mocha npm install -g mocha v5.0.5
• Postgres v9.5.12

Usage

Installing Dependencies

npm install

Environment Variables

There are a few environment variables that are required to run the app.

• PORT: the port the server will listen on
• TEST_PORT: the port the server will listen on during testing, must be different from PORT in order to run tests while the server is running.
• NODE_ENV: either development or test
• DB_FILE_PATH: the path to the file where the data will be loaded from. See Database Setup
• DB_USER: the user who has access to the created database
• DB_PASSWORD: see above
• DB_NAME_DEVELOPMENT: name of the development database on your machine
• DB_NAME_TEST: see above

This repo makes use of the dotenv package to help specify environment variables. To use dotenv, fill in your environment variables in sample.env, and then rename the file to .env.

Database Setup

To set up the development and testing databases, create new PostgreSQL databases and add names to the .env file, or use the default names clinvitae and clinvitae-test.

To run migrations on the database, run npm run db:migrate

To load the developmnet database, download and the file containing the variant data here. Once you've specified the path to the file, run the command npm run db:load. This may take a few minutes.

To seed the test database, run knex seed:run. Be sure that NODE_ENV is set to test.

Starting the Application

To compile the app, run npm run build, or npm run build-dev if you wish to have webpack watch for changes.

To run the server, simply run npm start.

To run tests, make sure NODE_ENV is set to test and run npm test.