GDI User Portal

This is a deployment example of all components needed for GDI User Portal, assuming a RHEL-based Linux distribution. For REMS, the keys for issuing Visas and passports are included, follow the instructions here https://github.com/GenomicDataInfrastructure/starter-kit-rems for the complete manual.

Important

This repository cannot be used directly for production. Please ensure you have carefully reviewed all requirements and environment variables, for each component, and have put all security measurements in place.

Preparatory steps on the VM

# Install some tools
sudo dnf install git 

# Install, start and enable Docker
dnf config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo
dnf install docker-ce docker-ce-cli containerd.io
sudo systemctl start docker
sudo systemctl enable docker

# You can also [create a user](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/4/html/system_administration_guide/s2-users-add)
# And [add her to a docker group](https://docs.docker.com/engine/install/linux-postinstall/) so that docker can be run without sudo.

# Configure firewall
firewall-cmd --permanent --zone=public --add-port=8443/tcp
# If you intend to run a reverse proxy on the machine as well, ensure 80/443 are open and nginx is configured to proxy connection to port 8443.

# Access to GDI Github packages 
Make sure that the VM has access to GitHub packages. Follow the manual here: https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#authenticating-with-a-personal-access-token-classic

Installation

# Prepare the project files
mkdir -p /srv
cd /srv
git clone https://github.com/GenomicDataInfrastructure/gdi-userportal-deployment.git
cd gdi-userportal-deployment/
cp .env.example .env

Configuration

Check and replace sensitive values in .env;
Replace NGINX SSL certificates.

Running

sudo su
cd /srv/gdi-userportal-deployment/
docker compose build
docker compose run --rm -e CMD="migrate;test-data" rems
docker compose up -d

If you want to test locally with another domain, you can generated a new self-signed certificate with the following command:

openssl req -new -newkey rsa:2048 -sha256 -days 365 -nodes -x509 -keyout ./nginx/ssl/server.key -out ./nginx/ssl/server.crt -config ./nginx/ssl/openssl.cnf

Post configuration

Add a new user to CKAN realm and REMS realm in Keycloak
Ensure both CKAN and frontend are pointing to the same Keycloak;

Contributing

We welcome contributions! If you would like to contribute, please follow these steps:

Fork the repository Create a new branch for your changes Make your changes Run the tests to ensure they pass Submit a pull request

License

This work is licensed under multiple licences. Here is a brief summary as of January 2024:

All original source code is licensed under Apache-2.0.
All documentation is licensed under CC-BY-4.0.
For more accurate information, check the individual files.