martinteaching / phenoflow-server

Kithia Ngigi, 2023

Phenoflow (modified server)

Portable, workflow-based phenotype definitions.

Configuration

.env

1. Create a .env file in project root.

2. To this file, add the following,

##

## Environment variables

##

## Server port

PORT = 3000

## GitHub personal authentication token

AUTH_TOKEN =

## GitHub 'organization' name

OWNER =

## Phenoflow user details

USER_NAME =

USER_EMAIL =

3. Complete 'Organization' configuration.
4. Add the generated personal access token to AUTH_TOKEN =
5. Add the name of the created 'Organization' to personal access token to OWNER =
6. Add a name and email address to USER_NAME = USER_EMAIL = accordingly, which identify the commiter.

Organization

1. Visit https://github.com/settings/organizations.
2. Create a new 'Organization'. The Free tier is sufficient.
3. Visit https://github.com/settings/tokens.
4. Generate a new Fine-grained Personal Access Token. - Select the created 'Organization' as the Resource owner. - Select All repositories under Repository access. - Select Read and write on all repository permissions under Permissions.

Install and Run

This is a Node.js server written with Express.js.

Server

1. Install dependencies:

npm install

2. Run server:

node index.js 

or...

nodemon 

Tests

Development

• At the root directory, run all tests:

npm test

Usage

Development

The server runs by default on port 3000. Visit http://localhost:3000/[route] to test changes to GET endpoints and use software such as Postman to test changes to POST, PUT and DELETE endpoints.

Authors

Kĩthia Ngigĩ, King's College London Health Informatics