Start and configure nimbus-image

start_nimbus.sh

export GIRDER_PORT=8080
export VUE_PORT=8081
SCREEN_NAME=nimbusimage_docker
DOCKER_NAME=girder
SERVICE_NAME="NimbusImage Docker"

pushd /home/ubuntu/UPennContrast

case "$1" in
    install)
        cd /home/ubuntu
        sudo apt-get update
        sudo apt-get install -y \
          ca-certificates \
          curl \
          gnupg \
          lsb-release \
          unzip \
          nginx 
        sudo mkdir -p /etc/apt/keyrings
        curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
        echo   "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
        sudo apt-get update
        sudo apt-get install -y \
          docker-ce \
          docker-ce-cli \
          containerd.io \
          docker-compose-plugin
        sudo groupadd docker
        sudo usermod -aG docker $USER
        sudo apt-get upgrade --auto-remove -y
        # reboot here

        # sudo snap install --classic certbot
        # sudo ln -s /snap/bin/certbot /usr/bin/certbot
        # vim /etc/nginx/conf.d/girder.conf
        # /etc/nginx/conf.d/girder.conf /tmp/.
        # service nginx start
        # vim /etc/nginx/conf.d/base.conf
        # certbot certonly --nginx --email "admin@www.nimbus-domain.org" --agree-tos --no-eff-email --cert-name www.nimbus-domain.org --domains www.nimbus-domain.org --rsa-key-size 4096 --keep-until-expiring --non-interactive
        # service nginx restart
        # certbot renew --dry-run
        # chmod 600 /swap
        # mkswap /swap
        # swapon /swap
        # vim /etc/fstab
        # swapon -a
        # curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
        # unzip awscliv2.zip
        # sudo ./aws/install
        # rm -r aws
        curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.3/install.sh | bash
        export NVM_DIR="$HOME/.nvm"
        [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
        [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This loads nvm bash_completion
        nvm install 12
        nvm alias default 12
        nvm use default
        git clone https://github.com/Kitware/UPennContrast.git
        pushd UPennContrast
        git pull
        popd
        ;;	    
    start)
        if ! docker ps -a | grep -q "$DOCKER_NAME"; then
            echo "Starting $SERVICE_NAME"
            start_service=true
        fi
        ;;
    restart)
        start_service=true
        if ! docker ps -a | grep -q "$DOCKER_NAME"; then
            echo "Starting $SERVICE_NAME"
        else
            echo "Restarting $SERVICE_NAME"
            stop_service=true
        fi
        ;;
    stop)
        if docker ps -a | grep -q "$DOCKER_NAME"; then
            echo "Stopping $SERVICE_NAME"
            stop_service=true
        fi
        ;;
    pull)
        docker compose pull
        ;;
    build)
        docker compose build --no-cache
        ;;
    log)
        docker compose logs -f
        ;;
    logs)
        docker compose logs -f
        ;;
    tail)
        docker compose logs -f
        ;;
    update)
        pushd /home/ubuntu/UPennContrast
        git pull
        popd
        docker compose pull
        ;;
    *)
        if ! docker ps -a | grep -q "$DOCKER_NAME"; then
            echo "Starting $SERVICE_NAME"
            start_service=true
        else
            echo "Already running $SERVICE_NAME"
        fi
        ;;
esac
if [ "$stop_service" = true ]; then
    docker compose down
    # Remove unused anonymous volumes
    docker volume rm $(docker volume ls -q | grep -e '.\{64\}') 2>/dev/null
    /usr/bin/screen -X -S $SCREEN_NAME quit
    /usr/bin/screen -wipe >/dev/null 2>&1
fi
if [ "$start_service" = true ]; then
    docker compose up -d
    . ~/.nvm/nvm.sh
    nvm use 12
    npm ci
    /usr/bin/screen -S $SCREEN_NAME -d -m /bin/bash -c 'npm run serve -- --port $VUE_PORT >/tmp/nimbus_output.log 2>&1'
    until curl --silent "http://localhost:$GIRDER_PORT/api/v1/system/version" >/dev/null 2>/dev/null; do echo -n .; sleep 1; done; echo ""
    until curl --silent --max-time 1 --connect-timeout 1 "http://localhost:$VUE_PORT" >/dev/null 2>/dev/null; do echo -n .; sleep 1; done; echo ""
    echo "Available on port $GIRDER_PORT, $VUE_PORT"
fi
popd