Added files for running a gbn project

.gitignore

@@ -0,0 +1,10 @@
+##Ignore site configuration
+.gitsubmodules
+site-config
+
+## Ignore site configuration
+config/**/*
+!config/**/*.default
+docker-compose.override.yml
+site-specific.conf
+

convenience/bridgehead@.service

@@ -1,23 +1,16 @@
 [Unit]
 Description=Bridgehead (%i) Service
-Requires=traefik.service
-After=traefik.service
 
 [Service]
 Restart=always
 RestartSec=30
 
-WorkingDirectory=/srv/docker/bridgehead
+WorkingDirectory=/srv/docker/bridgehead/%i
 
-ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/%i.env down
+ExecStartPre=/usr/local/bin/docker-compose --env-file ../site-config/%i.env down
-ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/%i.env rm
+ExecStart=/usr/local/bin/docker-compose --env-file ../site-config/%i.env up
-ExecStartPre=CONNECTOR_POSTGRES_PASSWORD=%i_CONNECTOR_POSTGRES_PASSWORD
-ExecStartPre=export CONNECTOR_POSTGRES_PASSWORD
-ExecStart=/usr/local/bin/docker-compose --env-file site-config/%i.env up
-ExecStart=CONNECTOR_POSTGRES_PASSWORD=
-ExecStart=export CONNECTOR_POSTGRES_PASSWORD
 
-ExecStop=/usr/local/bin/docker-compose --env-file site-config/%i.env down
+ExecStop=/usr/local/bin/docker-compose --env-file ../site-config/%i.env down
 
 [Install]
 WantedBy=multi-user.target

convenience/traefik.service

@@ -1,19 +0,0 @@
-[Unit]
-Description=Traefik Service
-Requires=docker.service
-After=docker.service
-
-[Service]
-Restart=always
-RestartSec=30
-
-WorkingDirectory=/srv/docker/bridgehead
-
-ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/start.env down
-ExecStartPre=/usr/local/bin/docker-compose --env-file site-config/start.env rm
-ExecStart=/usr/local/bin/docker-compose --env-file site-config/start.env up
-
-ExecStop=/usr/local/bin/docker-compose --env-file site-config/start.env down
-
-[Install]
-WantedBy=multi-user.target

gbn/docker-compose.yml

@@ -22,7 +22,7 @@ services:
       POSTGRES_HOST: "connector-db"
       POSTGRES_DB: "samply.connector"
       POSTGRES_USER: "samply"
-      POSTGRES_PASS: "samply"
+      POSTGRES_PASS: ${GBN_CONNECTOR_POSTGRES_PASS}
       STORE_URL: "http://store:8080/fhir"
       QUERY_LANGUAGE: "CQL"
       MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
@@ -37,7 +37,7 @@ services:
 
   connector-db:
     container_name: "connector-db"
-    image: "postgres:9.6"
+    image: "postgres:10.17"
     environment:
       POSTGRES_USER: "samply"
       POSTGRES_PASSWORD: "samply"

gbn/gbn.env.dev

@@ -0,0 +1,2 @@
+GBN_CONNECTOR_POSTGRES_PASS=samply
+

install-bridgehead.sh

@@ -33,7 +33,6 @@ echo "Starting Project ${project} "
     echo "Enabling nightly updates for bridgehead@${project}.service ..."
     sudo systemctl enable --now bridgehead-update@"${project}".timer
   fi
-done
 
 # Switch back to execution directory;
 cd -

prerequisites.sh

@@ -14,7 +14,8 @@ for prerequisite in $prerequisites; do
   fi
   # TODO: Check for specific version
 done
-echo "All prerequisites are installed. Now we can download the bridgehead from https://code.mitro.dkfz.de/scm/docker/c4.bk.docker.git."
+
+echo "Checking site.conf"
 
 #check if site.conf is created
 if [ ! -f site.conf ]; then
@@ -26,11 +27,11 @@ fi
 source site.conf
 
 if [ -z "$site_name" ]; then
-  echo "Site name is empty,please enter site name:"
+  echo "Please set site_name"
-  read -r site_name
-  site_name_lowercase=$(echo "$site_name" | tr '[:upper:]' '[:lower:]')
 fi
 
+echo "Checking site-config module"
+
 ## Download submodule
 if [ ! -d "site-config" ]; then
   echo "Please set up the site-config folder. Instruction are in the readme."
@@ -45,5 +46,9 @@ if [ -z "$project"  ]; then
   exit
 fi
 
-# Check for each project
+#check if project env is present
+if [ -d "site-config/${project}.env" ]; then
+   echo "Please copy the tempalte from ${project} and put it in the site-config folder"
+fi
+
 echo "All prerequisites meet! All systems are ready to go!"

site.dev.conf

@@ -0,0 +1,59 @@
+#!/bin/bash
+### This is the configuration file for secrets, only your site should know
+### Because the deployment via systemd is not possible in the current wsl environment,
+### developers need to export the necessary variables.
+### You can copy this file to site-specific.conf and run source site-specific.conf.
+### After this docker-compose up should use the environment variables defined in this file.
+
+### Connector configuration
+## The password the for your connector database
+export dktk_CONNECTOR_POSTGRES_PASSWORD=
+export c4_CONNECTOR_POSTGRES_PASSWORD=
+export gbn_CONNECTOR_POSTGRES_PASSWORD=
+
+### Local Datamanagenment configuration if necessary
+## Supply this, if you use samplystore
+# export LDM_DATABASE_PASSWORD=this-should-only-be-used-by-developers-ldm-database-password;
+
+### ID-Management configuration
+## provided by DKFZ with cooperation in Mainz
+export CCP_PATIENTLISTE_APIKEY=
+## provided by DKFZ with cooperation in Frankfurt
+export CCP_CONTROLLNUMBERGENERATOR_APIKEY=
+export LOCAL_IDMANAGER_LDM_APIKEY=
+## Additional new ID-Manager Configuration
+export LOCAL_IDMANAGER_MAINZELLISTE_APIKEY=
+export LOCAL_IDMANAGER_CONNECTOR_APIKEY=
+export LOCAL_PATIENTLIST_DBPASS=
+
+export dktk_CCP_OIDC_CLIENT_SECRET=
+export c4_CCP_OIDC_CLIENT_SECRET=
+### Mail Server username and password
+# export MAIL_USER=
+# export MAIL_PASSWORD=
+
+### Monitoring
+## by default, the bridgehead will report it's state to DKFZ monitoring. Change here to opt-out.
+# export MONITOR_OPTOUT=true
+
+### nNGM Configuration, only necessary if your site takes part in nNGM
+## The cts login data, that healex provided you
+# export NNGM_CTS_USER=<provided-by-healex>
+# export NNGM_CTS_PASSWORD=<provided-by-healex>
+## The idmanagement authentication data, that is provided by dkfz dataprotection office
+# export NNGM_MAGICPL_APIKEY=<provided-by-dkfz>
+# export NNGM_MAINZELLISTE_APIKEY=<provided-by-dkfz>
+
+### Workaround for local developers network environment
+## Note: MSYS_NO_PATHCONV is needed, because git bash and msys2 will otherwise convert /etc/hosts to a windows path
+#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 $1}');
+#export HOST=$(hostname)
+
+export HOSTIP=
+export HOST=
+
+export site_name=
+### Write the Project you want to start with the brigdehead
+##Exmaple project=gbn
+project=
+