NOMAD server

Server side code for NOMAD system made out of two main building blocks. These are two individual NPM projects that are in individual folders with corresponding names.

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nomad-front-end

React front-end bootstrapped with Vite JS.

nomad-rest-api

REST API built using Express JS Library.

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The third main component of the system nomad-spect-client is a JS app that runs on NMR spectrometer PC in Node.js runtime environment and enables communication of NOMAD server with Bruker IconNMR software. The code for the spectrometer client is stored in its own repository.

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Set up for development

The 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 all operating systems.

Clone nomad-server repository

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

To setup SMTP client for sending e-mails, following entries in /envs/dev/backend.env file need to be edited.

EMAIL_SUFFIX=''

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

You can possibly change the password for automatically generated admin user by editing the following entry.

ADMIN_PASSWORD='foo'

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

docker-compose up -d

To start after updating dependencies in any package.json file you have to build new Docker images by using command

docker-compose up -d --build

To stop use command

docker-compose down

Connecting spectrometer client in development environment

Clone nomad-spect-client repository in the same folder next to nomad-server repository.

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

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 on documentation website. Then you need rewrite INSTRUMENT_ID entry in /envs/dev/client.env file using actual instrument ID.

To start NOMAD together with the client, you need to navigate to nomad-server folder and run

docker-compose --profile client up -d

after updating dependencies you need to use

docker-compose --profile client up -d --build

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

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