Added files for running a gbn project
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##Ignore site configuration
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.gitsubmodules
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site-config
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## Ignore site configuration
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config/**/*
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!config/**/*.default
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docker-compose.override.yml
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site-specific.conf
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@ -1,23 +1,16 @@
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[Unit]
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Description=Bridgehead (%i) Service
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Requires=traefik.service
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After=traefik.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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WorkingDirectory=/srv/docker/bridgehead/%i
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ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/%i.env down
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ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/%i.env rm
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ExecStartPre=CONNECTOR_POSTGRES_PASSWORD=%i_CONNECTOR_POSTGRES_PASSWORD
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ExecStartPre=export CONNECTOR_POSTGRES_PASSWORD
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ExecStart=/usr/local/bin/docker-compose --env-file site-config/%i.env up
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ExecStart=CONNECTOR_POSTGRES_PASSWORD=
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ExecStart=export CONNECTOR_POSTGRES_PASSWORD
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ExecStartPre=/usr/local/bin/docker-compose --env-file ../site-config/%i.env down
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ExecStart=/usr/local/bin/docker-compose --env-file ../site-config/%i.env up
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ExecStop=/usr/local/bin/docker-compose --env-file site-config/%i.env down
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ExecStop=/usr/local/bin/docker-compose --env-file ../site-config/%i.env down
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[Install]
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WantedBy=multi-user.target
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@ -1,19 +0,0 @@
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[Unit]
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Description=Traefik Service
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Requires=docker.service
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After=docker.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=/usr/local/bin/docker-compose --env-file site-config/start.env down
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ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/start.env rm
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ExecStart=/usr/local/bin/docker-compose --env-file site-config/start.env up
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ExecStop=/usr/local/bin/docker-compose --env-file site-config/start.env down
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[Install]
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WantedBy=multi-user.target
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@ -22,7 +22,7 @@ services:
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POSTGRES_HOST: "connector-db"
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POSTGRES_DB: "samply.connector"
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POSTGRES_USER: "samply"
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POSTGRES_PASS: "samply"
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POSTGRES_PASS: ${GBN_CONNECTOR_POSTGRES_PASS}
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STORE_URL: "http://store:8080/fhir"
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QUERY_LANGUAGE: "CQL"
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MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
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@ -37,7 +37,7 @@ services:
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connector-db:
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container_name: "connector-db"
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image: "postgres:9.6"
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image: "postgres:10.17"
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environment:
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POSTGRES_USER: "samply"
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POSTGRES_PASSWORD: "samply"
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GBN_CONNECTOR_POSTGRES_PASS=samply
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@ -1,40 +1,39 @@
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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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./prerequisites.sh
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source site.conf
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echo "Installing bridgehead"
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cd /etc/systemd/system/
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echo "Installing bridgehead\@.service in systemd ..."
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sudo cp /srv/docker/bridgehead/convenience/bridgehead\@.service ./
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echo "Installing bridgehead\@.update.service in systemd ..."
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sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.service ./
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sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.timer ./
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echo "Loading the bridgehead and traefik service definitions in systemd"
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sudo systemctl daemon-reload
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echo "Starting Project ${project} "
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if [ ! -f "/etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf" ]; then
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echo "Can't find local configuration file for bridgehead@${project} service. Please ensure that the file /etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf exists"
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continue
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fi
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sudo systemctl is-active --quiet bridgehead@"${project}"
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if [ ! $? -eq 0 ]; then
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echo "Starting bridgehead@${project} service ..."
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sudo systemctl start bridgehead@"${project}"
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echo "Enabling autostart of bridgehead@${project}.service"
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sudo systemctl enable bridgehead@"${project}"
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echo "Enabling nightly updates for bridgehead@${project}.service ..."
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sudo systemctl enable --now bridgehead-update@"${project}".timer
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fi
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done
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# Switch back to execution directory;
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cd -
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# TODO: Configuration of the different modules
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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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./prerequisites.sh
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source site.conf
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echo "Installing bridgehead"
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cd /etc/systemd/system/
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echo "Installing bridgehead\@.service in systemd ..."
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sudo cp /srv/docker/bridgehead/convenience/bridgehead\@.service ./
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echo "Installing bridgehead\@.update.service in systemd ..."
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sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.service ./
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sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.timer ./
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echo "Loading the bridgehead and traefik service definitions in systemd"
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sudo systemctl daemon-reload
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echo "Starting Project ${project} "
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if [ ! -f "/etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf" ]; then
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echo "Can't find local configuration file for bridgehead@${project} service. Please ensure that the file /etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf exists"
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continue
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fi
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sudo systemctl is-active --quiet bridgehead@"${project}"
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if [ ! $? -eq 0 ]; then
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echo "Starting bridgehead@${project} service ..."
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sudo systemctl start bridgehead@"${project}"
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echo "Enabling autostart of bridgehead@${project}.service"
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sudo systemctl enable bridgehead@"${project}"
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echo "Enabling nightly updates for bridgehead@${project}.service ..."
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sudo systemctl enable --now bridgehead-update@"${project}".timer
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fi
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# Switch back to execution directory;
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cd -
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# TODO: Configuration of the different modules
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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"
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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 - $prerequisite is not available!"
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exit 79
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fi
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# TODO: Check for specific version
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done
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echo "All prerequisites are installed. Now we can download the bridgehead from https://code.mitro.dkfz.de/scm/docker/c4.bk.docker.git."
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#check if site.conf is created
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if [ ! -f site.conf ]; then
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echo "Please create your specific site.conf file from the site.dev.conf"
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exit
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fi
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#Load site specific variables
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source site.conf
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if [ -z "$site_name" ]; then
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echo "Site name is empty,please enter site name:"
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read -r site_name
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site_name_lowercase=$(echo "$site_name" | tr '[:upper:]' '[:lower:]')
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fi
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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 for each project
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echo "All prerequisites meet! All systems are ready to go!"
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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"
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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 meet! All systems are ready to go!"
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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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### Because the deployment via systemd is not possible in the current wsl environment,
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### developers need to export the necessary variables.
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### You can copy this file to site-specific.conf and run source site-specific.conf.
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### After this docker-compose up should use the environment variables defined in this file.
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### Connector configuration
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## The password the for your connector database
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export dktk_CONNECTOR_POSTGRES_PASSWORD=
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export c4_CONNECTOR_POSTGRES_PASSWORD=
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export gbn_CONNECTOR_POSTGRES_PASSWORD=
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### Local Datamanagenment configuration if necessary
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## Supply this, if you use samplystore
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# export LDM_DATABASE_PASSWORD=this-should-only-be-used-by-developers-ldm-database-password;
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### ID-Management configuration
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## provided by DKFZ with cooperation in Mainz
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export CCP_PATIENTLISTE_APIKEY=
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## provided by DKFZ with cooperation in Frankfurt
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export CCP_CONTROLLNUMBERGENERATOR_APIKEY=
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export LOCAL_IDMANAGER_LDM_APIKEY=
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## Additional new ID-Manager Configuration
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export LOCAL_IDMANAGER_MAINZELLISTE_APIKEY=
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export LOCAL_IDMANAGER_CONNECTOR_APIKEY=
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export LOCAL_PATIENTLIST_DBPASS=
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export dktk_CCP_OIDC_CLIENT_SECRET=
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export c4_CCP_OIDC_CLIENT_SECRET=
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### Mail Server username and password
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# export MAIL_USER=
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# export MAIL_PASSWORD=
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### Monitoring
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## by default, the bridgehead will report it's state to DKFZ monitoring. Change here to opt-out.
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# export MONITOR_OPTOUT=true
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### nNGM Configuration, only necessary if your site takes part in nNGM
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## The cts login data, that healex provided you
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# export NNGM_CTS_USER=<provided-by-healex>
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# export NNGM_CTS_PASSWORD=<provided-by-healex>
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## The idmanagement authentication data, that is provided by dkfz dataprotection office
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# export NNGM_MAGICPL_APIKEY=<provided-by-dkfz>
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# export NNGM_MAINZELLISTE_APIKEY=<provided-by-dkfz>
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### Workaround for local developers network environment
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## Note: MSYS_NO_PATHCONV is needed, because git bash and msys2 will otherwise convert /etc/hosts to a windows path
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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 $1}');
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#export HOST=$(hostname)
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export HOSTIP=
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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=gbn
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project=
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