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Added files for running a gbn project

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root 2021-12-21 13:48:28 +01:00
parent c683bb76bc
commit ed2f2ad590
8 changed files with 170 additions and 121 deletions
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10
.gitignore vendored Normal file
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##Ignore site configuration
.gitsubmodules
site-config
## Ignore site configuration
config/**/*
!config/**/*.default
docker-compose.override.yml
site-specific.conf

15
convenience/bridgehead@.service
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@ -1,23 +1,16 @@
[Unit] [Unit]
Description=Bridgehead (%i) Service Description=Bridgehead (%i) Service
Requires=traefik.service
After=traefik.service
[Service] [Service]
Restart=always Restart=always
RestartSec=30 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] [Install]
WantedBy=multi-user.target WantedBy=multi-user.target

19
convenience/traefik.service
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@ -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

4
gbn/docker-compose.yml
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@ -22,7 +22,7 @@ services:
POSTGRES_HOST: "connector-db" POSTGRES_HOST: "connector-db"
POSTGRES_DB: "samply.connector" POSTGRES_DB: "samply.connector"
POSTGRES_USER: "samply" POSTGRES_USER: "samply"
POSTGRES_PASS: "samply" POSTGRES_PASS: ${GBN_CONNECTOR_POSTGRES_PASS}
STORE_URL: "http://store:8080/fhir" STORE_URL: "http://store:8080/fhir"
QUERY_LANGUAGE: "CQL" QUERY_LANGUAGE: "CQL"
MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr" MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
@ -37,7 +37,7 @@ services:
connector-db: connector-db:
container_name: "connector-db" container_name: "connector-db"
image: "postgres:9.6" image: "postgres:10.17"
environment: environment:
POSTGRES_USER: "samply" POSTGRES_USER: "samply"
POSTGRES_PASSWORD: "samply" POSTGRES_PASSWORD: "samply"

2
gbn/gbn.env.dev Normal file
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GBN_CONNECTOR_POSTGRES_PASS=samply

79
install-bridgehead.sh Normal file → Executable file
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@ -1,40 +1,39 @@
#!/bin/bash #!/bin/bash
### Note: Currently not complete, needs some features before useable for production ### Note: Currently not complete, needs some features before useable for production
./prerequisites.sh ./prerequisites.sh
source site.conf source site.conf
echo "Installing bridgehead" echo "Installing bridgehead"
cd /etc/systemd/system/ cd /etc/systemd/system/
echo "Installing bridgehead\@.service in systemd ..." echo "Installing bridgehead\@.service in systemd ..."
sudo cp /srv/docker/bridgehead/convenience/bridgehead\@.service ./ sudo cp /srv/docker/bridgehead/convenience/bridgehead\@.service ./
echo "Installing bridgehead\@.update.service in systemd ..." echo "Installing bridgehead\@.update.service in systemd ..."
sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.service ./ sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.service ./
sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.timer ./ sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.timer ./
echo "Loading the bridgehead and traefik service definitions in systemd" echo "Loading the bridgehead and traefik service definitions in systemd"
sudo systemctl daemon-reload sudo systemctl daemon-reload
echo "Starting Project ${project} " echo "Starting Project ${project} "
if [ ! -f "/etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf" ]; then if [ ! -f "/etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf" ]; then
echo "Can't find local configuration file for bridgehead@${project} service. Please ensure that the file /etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf exists" echo "Can't find local configuration file for bridgehead@${project} service. Please ensure that the file /etc/systemd/system/bridgehead@${project}.service.d/bridgehead.conf exists"
continue continue
fi fi
sudo systemctl is-active --quiet bridgehead@"${project}" sudo systemctl is-active --quiet bridgehead@"${project}"
if [ ! $? -eq 0 ]; then if [ ! $? -eq 0 ]; then
echo "Starting bridgehead@${project} service ..." echo "Starting bridgehead@${project} service ..."
sudo systemctl start bridgehead@"${project}" sudo systemctl start bridgehead@"${project}"
echo "Enabling autostart of bridgehead@${project}.service" echo "Enabling autostart of bridgehead@${project}.service"
sudo systemctl enable bridgehead@"${project}" sudo systemctl enable bridgehead@"${project}"
echo "Enabling nightly updates for bridgehead@${project}.service ..." echo "Enabling nightly updates for bridgehead@${project}.service ..."
sudo systemctl enable --now bridgehead-update@"${project}".timer sudo systemctl enable --now bridgehead-update@"${project}".timer
fi fi
done
# Switch back to execution directory;
# Switch back to execution directory; cd -
cd - # TODO: Configuration of the different modules
# TODO: Configuration of the different modules

103
prerequisites.sh Normal file → Executable file
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@ -1,49 +1,54 @@
#!/bin/bash #!/bin/bash
## Check if user is a su ## Check if user is a su
echo "Welcome to the starting a bridgehead. We will get your instance up and running in no time" echo "Welcome to the starting a bridgehead. We will get your instance up and running in no time"
echo "First we will check if all prerequisites are met ..." echo "First we will check if all prerequisites are met ..."
prerequisites="git docker docker-compose" prerequisites="git docker docker-compose"
for prerequisite in $prerequisites; do for prerequisite in $prerequisites; do
$prerequisite --version 2>&1 $prerequisite --version 2>&1
is_available=$? is_available=$?
if [ $is_available -gt 0 ]; then if [ $is_available -gt 0 ]; then
log "ERROR" "Prerequisite not fulfilled - $prerequisite is not available!" log "ERROR" "Prerequisite not fulfilled - $prerequisite is not available!"
exit 79 exit 79
fi fi
# TODO: Check for specific version # TODO: Check for specific version
done done
echo "All prerequisites are installed. Now we can download the bridgehead from https://code.mitro.dkfz.de/scm/docker/c4.bk.docker.git."
echo "Checking site.conf"
#check if site.conf is created
if [ ! -f site.conf ]; then #check if site.conf is created
echo "Please create your specific site.conf file from the site.dev.conf" if [ ! -f site.conf ]; then
exit echo "Please create your specific site.conf file from the site.dev.conf"
fi exit
fi
#Load site specific variables
source site.conf #Load site specific variables
source site.conf
if [ -z "$site_name" ]; then
echo "Site name is empty,please enter site name:" if [ -z "$site_name" ]; then
read -r site_name echo "Please set site_name"
site_name_lowercase=$(echo "$site_name" | tr '[:upper:]' '[:lower:]') fi
fi
echo "Checking site-config module"
## Download submodule
if [ ! -d "site-config" ]; then ## Download submodule
echo "Please set up the site-config folder. Instruction are in the readme." if [ ! -d "site-config" ]; then
exit echo "Please set up the site-config folder. Instruction are in the readme."
else exit
echo "Site configuration is already loaded" else
fi echo "Site configuration is already loaded"
fi
#Check if a project is selected
if [ -z "$project" ]; then #Check if a project is selected
echo "No project selected! Please add a Project in your local site.conf." if [ -z "$project" ]; then
exit echo "No project selected! Please add a Project in your local site.conf."
fi exit
fi
# Check for each project
echo "All prerequisites meet! All systems are ready to go!" #check if project env is present
if [ -d "site-config/${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!"

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site.dev.conf Normal file
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#!/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=