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For Developers

System overview​

NOMAD is a web application that has been built using Javascript MERN stack. The whole app is composed of three main components.

nomad-front-end​

This part of the system works as graphical user interface of the main part of the system. It is a single page application (SPA) that was built using REACT JS library. The compiled production build is served by a webserver (NGINX) as static content web site, runs in web browser on user's computer and communicates with the application back-end via standard Internet communication protocols (HTTP/HTTPS).

nomad-rest-api​

The back-end code of the NOMAD system built using Express JS library. It runs on the application server in Node.js runtime environment and serves as REST API with the purpose to fetch and store application data using MongoDB. It also provides an end point for automatic NMR data upload. The communication with clients over HTTP/HTTPS protocol is facilitated by reverse proxy provided by a webserver (NGINX)

nomad-spect-client​

The spectrometer client is a Javascript code that runs on spectrometer PC in Node.js runtime environment and enables communication of NOMAD back-end with Bruker IconNMR. It parses status and history HTML file(s) and outputs files in external setup folder to control automated run of the NMR spectrometer.

Technical Overview

Set up for development​

The whole code base is split between two repositories. The repository nomad-server is the server side code composed of three parts nomad-front-end, nomad-nmrium and nomad-rest-api. The spectrometer client has its own repository.

The nomad-server repository contains all necessary configuration files to get you started in Docker environment. You will need to install both docker engine and docker compose. The easiest way to achieve that is to install Docker Desktop available for wide variety of Linux platforms, mcOS, Windows 10.

Clone both nomad-server and nomad-spect-client repositories

git clone https://github.com/nomad-nmr/nomad-server.git
git clone https://github.com/nomad-nmr/nomad-spect-client.git

You can skip the latter if you want to leave the client out and work only with the server code. In that case, you need to comment out the client block in nomad-server/docker-compose.yaml file.

Before you start, the environmental variables needs to be set up in env folder. You can create the folder and copy content of env-example folder in it.

cd nomad-server
mkdir env
cp env-example/* env/

The system shall start without editing environmental variables. To achieve full functionality, following entries in backend.env file need to be edited.

#Password for automatically generated admin user
ADMIN_PASSWORD=''

#Secret word for generating JWT
JWT_SECRET=''

EMAIL_SUFFIX=''

#SMTP configuration
SMTP_HOST=''
SMTP_USER=''
SMTP_PASS=''
SMTP_SENDER=''

To connect the spectrometer client, you need to login using admin username and the backdoor password that was set up in environmental variables and add an instrument into database. More information can be found in Tips & Tricks. Then you need to enter instrument ID in client.env file and restart the Docker containers.

To start NOMAD you need to navigate to nomad-server folder and run

docker-compose up -d

To stop use command

docker-compose down

Database dumps​

To dump database

docker exec -i nomad-server_mongodb_1 sh -c 'mongodump --archive' > mongodb.dump

To restore from dump

docker exec -i nomad-server_mongodb_1 sh -c 'mongorestore --archive --drop' < mongodb.dump

More useful info about developing in a Docker Container can be found here.

Automatic testing​

Automatic testing is currently work in progress. So far, there is setup for integration tests of backend api using SuperTest and Vitest.

To perform a single run without watch mode

cd nomad-rest-api
npm run test-once

You can also run test in watch mode or run it with coverage analysis by using following commands, respectively.

npm test
npm run coverage