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NFDI4Health LDH Deployment

Deployment instructions and resources for an NFDI4Health Local Data Hub.

Disclaimer

This project and it's components are subject to heavy development. However, if you wish to participate in the development of the software, you are strongly encouraged to do so. Feel free to submit bug reports and suggestions in the issue tracker.

Prerequisites

Hardware / Operating System / License Costs

Hardware is not demanding; you may start with 16GB RAM, 100 GB Filespace; either a standalone PC/server or preferably as part of a VM infrastructure. We recommend the use of root-less operated docker in a Linux host.

FAIRDOM-SEEK/LDH and Docker-engine is free of charge. The use of "Docker Desktop" is relevant for Windows/MacOS hosts - no need for Linux. Even here: "Docker Desktop is free for small businesses (fewer than 250 employees AND less than $10 million in annual revenue), personal use, education, and non-commercial open source projects"

Docker

  • Docker must be installed on the system (Windows/Linux/MacOS). Please follow the official installation instructions
  • docker-compose is deprecated; please ensure that you can use docker compose (compose beeing option for docker)
  • You need a compose version v2 - test with docker compose version
  • LDH works perfectly with root-less docker; there is no need to have root right on the host; we recommend this
  • Consider allowing your non-root Linux user to use docker by adding to the docker group (see docker docs) otherwise only a root user will be able to execute docker

Download and Install

For a first and simple glimpse of what an LDH will look like follow the steps below.

  • Clone this repository
git clone https://github.com/nfdi4health/ldh-deployment.git
cd ldh-deployment

Configuration

  • Basic configuration is done in .env. Copy .env.tpl to .env and change variables in .env as you like
cp .env.tpl .env

* COMPOSE_PROJECT_NAME is a prefix for all container names; useful if you have multiple instances of LDH on your host; e.g. N4H. Default is the name of the enclosing file directory.
* SEEK_PORT is the port you will reach LDH on this host. Default is "3000"; e.g http://localhost:3000
* DHO_TERMS is the basename of an file overriding the standard term in the user interface - useful e.g. if you prefer "Sponsor" over "Programme" oder "Trial Project" instead of "Project" as in included "clinical-trials.en.yml". Default is "standard.en.yml".
* LDH_RELEASE is the relase to load, e.g. v0.2.2. Default is "latest".
* NGINX_CONF is overrinding the SEEK intername configuration for nginx; see below. Default is "nginx.conf.http".
  • Database configuration is specified in docker-compose.env. This is created by copying docker-compose.env.tpl to docker-compose.env and replace <some-password> with a password- either manually or using the openssl command, e.g.
cat docker-compose.env.tpl \
  | sed "s|<db-password>|$(openssl rand -base64 21)|" \
  | sed "s|<root-password>|$(openssl rand -base64 21)|" \
  > docker-compose.env
  • Create Volumes (internal Volumes are created automatically) using prefix in COMPOSE_PROJECT_NAME in .env
source .env
docker volume create ${COMPOSE_PROJECT_NAME}_filestore
docker volume create ${COMPOSE_PROJECT_NAME}_db

Startup the LDH

docker compose up -d

Wait a minute and direct browser to http://localhost:3000 to reach signup page. If you get a "502 Bad Gateway" wait a litte longer. You can watch the logs with

docker compose logs -f seek

Backup & Restore

There is a simple backup script backup.sh include which will dump your database and filestore to a backup directory. You can configure the number of copies to be held in backup.

bash backup.sh

You may destroy all data, including passwords. The only thing you need is to keep a valid copy of filestore and database. To restore all, startup the LDH and type

bash restore.sh <database.sql.gz_from_backup> <filestore.tar.gz_from_backup>

Update image

Follow "Upgrading between versions" in https://docs.seek4science.org/tech/docker/docker-compose.html But use LDH image name "ghcr.io/nfdi4health/ldh:latest" (or release like ghcr.io/nfdi4health/ldh:v0.2.1, see https://github.com/nfdi4health/ldh/releases) instead of "fairdom/seek:1.14".

Destroy all

  • If you like to completely destroy your testing installation including data and password
source .env
docker compose down -v
docker volume rm ${COMPOSE_PROJECT_NAME}_filestore ${COMPOSE_PROJECT_NAME}_db
rm docker-compose.env

Advance: Configure for https use

We recommend the use of a reverse proxy to make the LDH publicly and securely visible via https. Here, a SSL certificate can be presented to the outside and the communication to the inside, to the LDH, can run via HTTP. Additional header parameters are required in SEEK inbuild nginx for communication:

proxy_set_header X-Forwarded-Proto https;
proxy_set_header X-Forwarded-Ssl on;

"nginx.conf.https" contains these parameters and overwrites the original configuration ("nginx.conf.http"), which is default here.

Go further

The above working setting can be altered in many ways:

  • like to use an undockered, external mysql database? (configure docker-compose.env; remove db from docker-compose.yml)
  • like to put the filestore on external undockered file space? (use bind mounts)
  • like to use Container-Orchestration like Kubernetes?
  • want to expose your LDH to the internet - ask you local sysadmin!
  • Backup/Restore can be based on volumes too
  • see https://docs.docker.com/ from more