Installation notes

Installation of shanoir-ng on a server (linux) Creation of a shanoir-ng user on the server (to run shanoir-ng), which is not sudoers.

The installation requires a sudoers user.

UBUNTU Version

• lsb_release -d Description: Ubuntu 18.04.1 LTS

Install GIT

• sudo apt-get install git

check

• git version git version 2.17.1

Install JAVA

• sudo apt-get install software-properties-common
• sudo add-apt-repository ppa:webupd8team/java
• sudo apt-get update
• sudo apt-get install oracle-java8-installer

check

• java -version java version "1.8.0_191" Java(TM) SE Runtime Environment (build 1.8.0_191-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)

Install MAVEN

• sudo apt-get install maven

check

• mvn -version Apache Maven 3.5.2 Maven home: /usr/share/maven Java version: 1.8.0_191, vendor: Oracle Corporation Java home: /usr/lib/jvm/java-8-oracle/jre Default locale: en_US, platform encoding: ISO-8859-1 OS name: "linux", version: "4.15.0-39-generic", arch: "amd64", family: "unix"

Install DOCKER

please refer to https://docs.docker.com/install/linux/docker-ce/ubuntu/

• sudo apt-get update

• sudo apt-get install \ apt-transport-https \ ca-certificates \ curl \ software-properties-common

• curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

• sudo add-apt-repository \ "deb [arch=amd64] https://download.docker.com/linux/ubuntu \ $(lsb_release -cs) \ stable"

• sudo apt-get update

• sudo apt-get install docker-ce

check

• sudo docker run hello-world Unable to find image 'hello-world:latest' locally latest: Pulling from library/hello-world d1725b59e92d: Pull complete Digest: sha256:0add3ace90ecb4adbf7777e9aacf18357296e799f81cabc9fde470971e499788 Status: Downloaded newer image for hello-world:latest

Hello from Docker! This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:

1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub. (amd64)
3. The Docker daemon created a new container from that image which runs the executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it to your terminal.

To try something more ambitious, you can run an Ubuntu container with:

• docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID: https://hub.docker.com/

For more examples and ideas, visit: https://docs.docker.com/get-started/

• sudo usermod -aG docker shanoir-ng
• sudo systemctl enable docker

MAKE SURE DOCKER HAS ENOUGH MEMORY TO RUN SHANOIR: 6Gb should be enough

On mac: docker dashboard > preferences > resources > increase the memory and the number of CPU cores.

Install DOCKER-COMPOSE

• sudo curl -L "https://github.com/docker/compose/releases/download/1.23.1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
• sudo chmod +x /usr/local/bin/docker-compose

check

• docker-compose --version docker-compose version 1.23.1, build b02f1306

Install NPM AND NODEJS

• sudo apt-get update
• sudo apt-get install nodejs npm

check

• nodejs --version v8.10.0
• npm --version 3.5.2

CHANGE hosts

• sudo vi /etc/hosts add 127.0.0.1

INSTALL SHANOIR-NG

Change user

• su - shanoir-ng

in /home/shanoir-ng/

• git clone https://github.com/fli-iam/shanoir-ng.git

For Preclinical mode ONLY

• git checkout appning

Compile

• cd shanoir-ng-parent
• mvn clean install -DskipTests

For Preclinical mode ONLY:

load bruker dicomifier image, eg. the dicomifier.ws.img is located in /home/shanoir-ng

• cd /home/shanoir-ng
• docker load -i dicomifier.ws.img

check

• docker images REPOSITORY TAG IMAGE ID CREATED SIZE hello-world latest 4ab4c602aa5e 2 months ago 1.84kB dicomifier.ws latest be2095d78858 5 months ago 499MB

Change files

See readme

• Keycloak: Open /docker-compose/keycloak/cfg/shanoir-ng-realm.json and change redirectUris and webOrigins
• Spring Boot: Open /.env and change the host and scheme of all three properties in the file
• Docker Compose: Open /docker-compose.yml and change the container_name of Nginx to e.g. shanoir-ng.irisa.fr This is necessary, that e.g. ms users and the Keycloak CLI client can access to Keycloak (resolve the host name)
• Angular: Open /shanoir-ng-front/config/webpack.config.js and change SHANOIR_NG_URL_SCHEME and SHANOIR_NG_URL_HOST
• /shanoir-ng/docker-compose/users/ssl.sh : replacing -subj "/CN=shanoir-ng-nginx" by -subj "/CN="
• /shanoir-ng/docker-compose/users/Dockerfile : replacing -alias shanoir-ng-nginx by ​-alias
• .env : spring.jpa.hibernate.ddl-auto=validate spring.datasource.initialize=false
• mail server : cf. readme : .env :replace SMTP_HOST by your mail server url

compile

• cd /home/shanoir-ng/shanoir-ng/shanoir-ng-parent
• mvn clean install -DskipTests

##run docker-compose

• cd /home/shanoir-ng/shanoir-ng/
• docker-compose up -d --build

NB. to stop the server

• docker-compose down

TESTS

https://

Keycloack :

=> ssh tunnel ssh -L18080:localhost:8080 @ http://localhost:18080/auth/admin

#default admin pwd Please choose a default admin pwd for your installation

FEDORA 36 VERSION

Please see above. Shanoir-NG runs on Fedora, at least as development environment, but two issues have to be solved before:

1. Microservices can not connect to Keycloak: Connection refused on Keycloak URL can be found in the log files (the local /etc/hosts is wrongly copied into the containers, what leads to errors with URL name resolving) Solution: remove Podman entirely from your OS and only install docker+docker-compose following the docker installation guide here install docker on fedora

2. MySQL servers use 20Gb of RAM and slow down the entire machine Solution: add in docker-compose.yml to database and keycloak-database solves the issue

ulimits: nofile: soft: 262144 hard: 262144

(known issue: MySQL issues)