dktk-fed
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Patrick Skowronek
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24
README.md
24
README.md
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# bridgehead
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# bridgehead
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This repository contains all tools to deploy a bridgehead with docker. If you have any questions about deploying a bridgehead, please contact us.
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There are some prerequisites, which need to be meet before starting a bridgehead. If you running a Windows or Mac OS machine you should read starting a bridgehead. If you running a Linux machine you can start or install a bridgehead.
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## Setup
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Clone this repository to /srv/docker/
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The first step is to copy the site.conf. It contains some configuration and secrets for your bridgehead.
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With cp site.dev.conf site.conf you can clone the template. You need to set the project accoriding to the which bridgehead you want to start. It's either a GBN/BBMRI-ERIC, DKTK, DKTK-FED or C4 Bridgehead.
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Each Project needs a .env file where all the settings are located. Each Project has a template for it in their respective folder. We offer you to setup the file with and also to manage it.
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### DKTK-FED
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For the DKTK Federate Search put dkkt-fed as project in the site.conf.
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## Starting the bridgehead
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./install_bridgehead
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version: "3.7"
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services:
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traefik:
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container_name: bridgehead_traefik
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image: traefik:2.4
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command:
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- --api.insecure=true
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- --entrypoints.web.address=:80
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- --entrypoints.web-secure.address=:443
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- --providers.docker=true
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ports:
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- 80:80
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- 443:443
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- 8080:8080
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volumes:
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- /var/run/docker.sock:/var/run/docker.sock:ro
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- ../auth/:/auth
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extra_hosts:
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- "host.docker.internal:host-gateway"
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landing:
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container_name: bridgehead_landingpage
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image: nginx:stable
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volumes:
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- ../landing/:/usr/share/nginx/html
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
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- "traefik.http.services.landing.loadbalancer.server.port=80"
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blaze:
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image: "samply/blaze:0.15"
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container_name: bridgehead_dktk_blaze
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environment:
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BASE_URL: "http://blaze:8080"
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JAVA_TOOL_OPTIONS: "-Xmx4g"
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LOG_LEVEL: "debug"
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ENFORCE_REFERENTIAL_INTEGRITY: "false"
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volumes:
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- "blaze-data:/app/data"
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labels:
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- "traefik.enable=true"
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- "traefik.http.middlewares.test-auth.basicauth.usersfile=/auth/dktk"
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- "traefik.http.routers.blaze_dktk.rule=PathPrefix(`/dktk-localdatamanagement`)"
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- "traefik.http.middlewares.dktk_b_strip.stripprefix.prefixes=/dktk-localdatamanagement"
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- "traefik.http.services.blaze_dktk.loadbalancer.server.port=8080"
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- "traefik.http.routers.blaze_dktk.middlewares=dktk_b_strip,test-auth"
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volumes:
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blaze-data:
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#!/bin/bash
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### Note: Currently not complete, needs some features before useable for production
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source lib/functions.sh
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exitIfNotRoot
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if ! ./lib/prerequisites.sh; then
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log "Prerequisites failed, exiting"
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exit 1
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fi
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source site.conf
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echo -e "\nInstalling systemd units ..."
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cp -v \
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lib/systemd/bridgehead\@.service \
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lib/systemd/bridgehead-update\@.service \
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lib/systemd/bridgehead-update\@.timer \
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/etc/systemd/system/
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systemctl daemon-reload
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echo
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if ! systemctl is-active --quiet bridgehead@"${project}"; then
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echo "Enabling autostart of bridgehead@${project}.service"
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systemctl enable bridgehead@"${project}"
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echo "Enabling nightly updates for bridgehead@${project}.service ..."
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systemctl enable --now bridgehead-update@"${project}".timer
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fi
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echo -e "\nDone - now start your bridgehead by running\n\tsystemctl start bridgehead@${project}.service\nor by rebooting your machine."
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#!/bin/bash -e
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exitIfNotRoot() {
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if [ "$EUID" -ne 0 ]; then
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echo "Please run as root"
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exit 1
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fi
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}
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log() {
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echo "$(date +'%Y-%m-%d %T')" "$1:" "$2"
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}
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#!/bin/bash
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cat > ../landing/index.html <<EOL
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta name="description" content="">
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<title>Bridgehead Overview</title>
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<!-- Bootstrap core CSS -->
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<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet"
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integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
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<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js"
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integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p"
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crossorigin="anonymous"></script>
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</head>
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<body>
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<nav class="navbar navbar-light" style="background-color: #aad7f6;">
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<h2 class="pb-2 border-bottom">Bridgehead ${site_name}</h2>
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</nav>
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<div class="container px-4 py-5" id="featured-3">
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<div>
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<h2>Components</h2>
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<h3>Central</h3>
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<table class="table">
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<thead class="thead-dark">
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<tr>
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<th style="width: 50%">Group</th>
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<th style="width: 50%">Service</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>CCP-IT</td>
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<td><a href="https://patientlist.ccp-it.dktk.dkfz.de">Zentrale Patientenliste</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="https://decentralsearch.ccp-it.dktk.dkfz.de">Dezentrale Suche</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="https://centralsearch.ccp-it.dktk.dkfz.de">Zentrale Suche</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="https://deployment.ccp-it.dktk.dkfz.de">Deployment-Server</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="https://dktk-kne.kgu.de">Zentraler Kontrollnummernerzeuger</td>
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</tr>
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</tbody>
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</table>
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</div>
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<div>
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<h3>Local</h3>
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<table class="table">
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<thead class="thead-dark">
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<tr>
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<th style="width: 50%">Project</th>
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<th style="width: 50%">Services</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>Bridgehead</td>
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<td>Reverse Proxy <a href="http://e260-serv-05:8080/">Traefik</a></td>
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</tr>
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<tr>
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<td>DKTK</td>
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<td><a href="http://e260-serv-05/dktk-localdatamanagement/fhir/">Blaze</a></td>
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</tr>
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</tbody>
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</table>
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</div>
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<footer class="footer mt-auto py-3 ">
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<a href="https://dktk.dkfz.de/"><img src="https://www.oncoray.de/fileadmin/files/bilder_gruppen/DKTK/Logo_DKTK_neu_2016.jpg" height="10%" width="30%"></a> DKTK 2022
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</footer>
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</body>
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</html>
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EOL
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#!/bin/bash
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## Check if user is a su
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echo "Welcome to the starting a bridgehead. We will get your instance up and running in no time"
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echo "First we will check if all prerequisites are met ..."
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prerequisites="git docker docker-compose cat"
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for prerequisite in $prerequisites; do
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$prerequisite --version 2>&1
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is_available=$?
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if [ $is_available -gt 0 ]; then
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log "ERROR" "Prerequisite not fulfilled - $prerequisite is not available!"
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exit 79
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fi
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# TODO: Check for specific version
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done
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echo "Checking site.conf"
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#check if site.conf is created
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if [ ! -f site.conf ]; then
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echo "Please create your specific site.conf file from the site.dev.conf"
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exit
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fi
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#Load site specific variables
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source site.conf
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if [ -z "$site_name" ]; then
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echo "Please set site_name"
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fi
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echo "Checking site-config module"
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## Download submodule
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if [ ! -d "site-config" ]; then
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echo "Please set up the site-config folder. Instruction are in the readme."
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exit
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else
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echo "Site configuration is already loaded"
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fi
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#Check if a project is selected
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if [ -z "$project" ]; then
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echo "No project selected! Please add a Project in your local site.conf."
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exit
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fi
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#check if project env is present
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if [ -d "site-config/${project}.env" ]; then
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echo "Please copy the tempalte from ${project} and put it in the site-config folder"
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fi
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echo "All prerequisites are met!"
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[Unit]
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Description=Bridgehead (%i) Update Service
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[Service]
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Type=oneshot
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WorkingDirectory=/srv/docker/bridgehead/
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ExecStart=/bin/bash -c "/srv/docker/bridgehead/update-bridgehead.sh %i"
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[Install]
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WantedBy=multi-user.target
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[Unit]
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Description=Nightly Updates of Bridgehead (%i)
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[Timer]
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OnCalendar=*-*-* 03:00:00
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[Install]
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WantedBy=basic.target
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[Unit]
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Description=Bridgehead (%i) Service
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[Service]
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Restart=always
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RestartSec=30
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WorkingDirectory=/srv/docker/bridgehead/
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ExecStartPre=/bin/bash -c '`which docker-compose` -f %i/docker-compose.yml --env-file site-config/%i.env down'
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ExecStart=/bin/bash -c '`which docker-compose` -f %i/docker-compose.yml --env-file site-config/%i.env up'
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ExecStop=/bin/bash -c '`which docker-compose` -f %i/docker-compose.yml --env-file site-config/%i.env down'
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[Install]
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WantedBy=multi-user.target
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#!/bin/bash
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### This is the configuration file for secrets, only your site should know
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##Setting Network properties
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export HOSTIP=$(MSYS_NO_PATHCONV=1 docker run --rm --add-host=host.docker.internal:host-gateway ubuntu cat /etc/hosts | grep 'host.docker.internal' | awk '{print $1}');
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export HOST=
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export site_name=
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### Write the Project you want to start with the brigdehead
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##Exmaple project=dktk-fed
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export project=
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#!/bin/bash
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### Note: Currently not complete, needs some features before useable for production
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source lib/functions.sh
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if ! lib/prerequisites.sh; then
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log "Prerequisites failed, exiting"
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exit
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fi
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source site.conf
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./lib/generate.sh
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log "Starting bridgehead"
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docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env up -d
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log "The bridgehead should be in online in a few seconds"
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#!/bin/bash -e
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source lib/functions.sh
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source site.conf
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log "Stopping bridgehead"
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docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env down
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#!/bin/bash -e
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source site.conf
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source lib/functions.sh
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echo "Stopping systemd services and removing bridgehead ..."
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systemctl disable --now bridgehead@${project}.service bridgehead-update@${project}.timer bridgehead-update@${project}.service
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rm -v /etc/systemd/system/{bridgehead\@.service,bridgehead-update\@.timer,bridgehead-update\@.service}
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#!/bin/bash
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service="bridgehead"
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source lib/functions.sh
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if ! lib/prerequisites.sh; then
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log "Prerequisites failed, exiting"
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exit
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fi
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log "INFO" "Checking for updates of $service"
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# check prerequisites
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# check if updates are available
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old_git_hash="$(git rev-parse --verify HEAD)"
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git fetch 2>&1
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git pull 2>&1
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new_git_hash="$(git rev-parse --verify HEAD)"
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git_updated="false"
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if [ "$old_git_hash" != "$new_git_hash" ]; then
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log "INFO" "Pulled new changes from origin"
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git_updated="true"
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fi
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docker_updated="false"
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for image in $(docker ps --filter "name=$service" --format {{.Image}}); do
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log "INFO" "Checking for Updates of Image: $image"
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if docker pull $image | grep "Downloaded newer image"; then
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log "INFO" "$image updated."
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docker_updated="true"
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fi
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done
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if [ $git_updated = "true" ] || [ $docker_updated = "true" ]; then
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log "INFO" "Due to previous updates now restarting $service@$1"
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systemctl restart "$service@$1.service"
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fi
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log "INFO" "checking updates finished"
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exit 0
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