Merge pull request #42 from samply/develop

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##Ignore site configuration
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*/docker-compose.override.yml

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Apache License
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README.md
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# bridgehead
# Bridgehead
The Bridgehead is a secure, low-effort solution to connect your research institution to a federated research network. It bundles interoperable, open-source software components into a turnkey package for installation on one of your secure servers. The Bridgehead is pre-configured with sane defaults, centrally monitored and with an absolute minimum of "moving parts" on your side, making it an extremely low-maintenance gateway to data sharing.
This repository is the starting point for any information and tools you will need to deploy a Bridgehead. If you have questions, please [contact us](mailto:verbis-support@dkfz-heidelberg.de).
1. [Requirements](#requirements)
- [Hardware](#hardware)
- [System](#system)
- [Git](#git)
- [Docker](#docker)
2. [Deployment](#deployment)
- [Installation](#installation)
- [Register with Samply.Beam](#register-with-samplybeam)
- [Starting and stopping your Bridgehead](#starting-and-stopping-your-bridgehead)
- [Auto-starting your Bridgehead when the server starts](#auto-starting-your-bridgehead-when-the-server-starts)
3. [Additional Services](#additional-Services)
- [Monitoring](#monitoring)
- [Register with a Directory](#register-with-a-Directory)
4. [Site-specific configuration](#site-specific-configuration)
- [HTTPS Access](#https-access)
- [Locally Managed Secrets](#locally-managed-secrets)
- [Git Proxy Configuration](#git-proxy-configuration)
- [Docker Daemon Proxy Configuration](#docker-daemon-proxy-configuration)
- [Non-Linux OS](#non-linux-os)
5. [License](#license)
## Requirements
### Hardware
Hardware requirements strongly depend on the specific use-cases of your network as well as on the data it is going to serve. Most use-cases are well-served with the following configuration:
- 4 CPU cores
- 32 GB RAM
- 160GB Hard Drive, SSD recommended
### Software
You are strongly recommended to install the Bridgehead under a Linux operating system (but see the section [Non-Linux OS](#non-linux-os)). You will need root (administrator) priveleges on this machine in order to perform the deployment. We recommend the newest Ubuntu LTS server release.
Ensure the following software (or newer) is installed:
- git >= 2.0
- docker >= 20.10.1
- docker-compose >= 2.xx (`docker-compose` and `docker compose` are both supported).
- systemd
We recommend to install Docker(-compose) from its official sources as described on the [Docker website](https://docs.docker.com).
Note for Ubuntu: Please note that snap versions of Docker are not supported.
### Network
Since it needs to carry sensitive patient data, Bridgeheads are intended to be deployed within your institution's secure network and behave well even in networks in strict security settings, e.g. firewall rules. The only connectivity required is an outgoing HTTPS proxy. TLS termination is supported, too (see [below](#tls-terminating-proxies))
Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
## Deployment
### Base Installation
First, clone the repository to the directory `/srv/docker/bridgehead`:
```shell
sudo mkdir -p /srv/docker/
sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
```
Then, run the installation script:
```shell
cd /srv/docker/bridgehead
sudo ./bridgehead install <PROJECT>
```
... and follow the instructions on the screen. You should then be prompted to do the next step:
### Register with Samply.Beam
Many Bridgehead services rely on the secure, performant and flexible messaging middleware called [Samply.Beam](https://github.com/samply/beam). You will need to register ("enroll") with Samply.Beam by creating a cryptographic key pair for your bridgehead:
``` shell
cd /srv/docker/bridgehead
sudo ./bridgehead enroll <PROJECT>
```
... and follow the instructions on the screen. You should then be prompted to do the next step:
### Starting and stopping your Bridgehead
If you followed the above steps, your Bridgehead should already be configured to autostart (via systemd). If you would like to start/stop manually:
To start, run
```shell
sudo systemctl start bridgehead@<PROJECT>.service
```
To stop, run
```shell
sudo systemctl stop bridgehead@<PROJECT>.service
```
To enable/disable autostart, run
```shell
sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
```
## Site-specific configuration
### HTTPS Access
Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).
### TLS terminating proxies
All of the Bridgehead's outgoing connections are secured by transport encryption (TLS) and a Bridgehead will refuse to connect if certificate verification fails. If your local forward proxy server performs TLS termination, please place its CA certificate in `/etc/bridgehead/trusted-ca-certs` as a `.pem` file, e.g. `/etc/bridgehead/trusted-ca-certs/mylocalca.pem`. Then, all Bridgehead components will pick up this certificate and trust it for outgoing connections.
### File structure
- `/srv/docker/bridgehead` contains this git repository with the shell scripts and *project-specific configuration*. In here, all files are identical for all sites. You should not make any changes here.
- `/etc/bridgehead` contains your *site-specific configuration* synchronized from your site-specific git repository as part of the [base installation](#base-installation). To change anything here, please consult your git repository (find out its URL via `git -C /etc/bridgehead remote -v`).
- `/etc/bridgehead/<PROJECT>.conf` is your main site-specific configuration, all bundled into one concise config file. Do not change it here but via the central git repository.
- `/etc/bridgehead/<PROJECT>.local.conf` contains site-specific parameters to be known to your Bridgehead only, e.g. local access credentials. The file is ignored via git, and you may edit it here via a text editor.
- `/etc/bridgehead/traefik-tls` contains your Bridgehead's reverse proxies TLS certificates for [HTTPS access](#https-access).
- `/etc/bridgehead/pki` contains your Bridgehead's private key (e.g., but not limited to Samply.Beam), generated as part of the [Samply.Beam enrollment](#register-with-samplybeam).
- `/etc/bridgehead/trusted-ca-certs` contains third-party certificates to be trusted by the Bridgehead. For example, you want to place the certificates of your [TLS-terminating proxy](#network) here.
Your Bridgehead's actual data is not stored in the above directories, but in named docker volumes, see `docker volume ls` and `docker volume inspect <volume_name>`.
## Things you should know
### Auto-Updates
Your Bridgehead will automatically and regularly check for updates. Whenever something has been updates (e.g., one of the git repositories or one of the docker images), your Bridgehead is automatically restarted. This should happen automatically and does not need any configuration.
If you would like to understand what happens exactly and when, please check the systemd units deployed during the [installation](#base-installation) via `systemctl cat bridgehead-update@<PROJECT>.service` and `systemctl cat bridgehead-update@<PROJECT.timer`.
### Monitoring
To keep all Bridgeheads up and working and detect any errors before a user does, a central monitoring
- Your Bridgehead itself will report relevant system events, such as successful/failed updates, restarts, performance metrics or version numbers.
- Your Bridgehead is also monitored from the outside by your network's central components. For example, the federated search will regularly perform a black-box test by sending an empty query to your Bridgehead and checking if the results make sense.
In all monitoring cases, obviously no sensitive information is transmitted, in particular not any patient-related data. Aggregated data, e.g. total amount of datasets, may be transmitted for diagnostic purposes.
## Troubleshooting
### Docker Daemon Proxy Configuration
Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, configure the proxy for this daemon as described in the [official documentation](https://docs.docker.com).
### Non-Linux OS
The installation procedures described above have only been tested under Linux.
Below are some suggestions for getting the installation to work on other operating systems. Note that we are not able to provide support for these routes!
We believe that it is likely that installation would also work with FreeBSD and MacOS.
Under Windows, you have 2 options:
- Virtual machine
- WSL
We have tested the installation procedure with an Ubuntu 22.04 guest system running on a VMware virtual machine. That worked flawlessly.
Installation under WSL ought to work, but we have not tested this.
## License
Copyright 2019 - 2022 The Samply Community
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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version: "3.7"
services:
traefik:
container_name: bridgehead-traefik
image: traefik:latest
command:
- --entrypoints.web.address=:80
- --entrypoints.websecure.address=:443
- --providers.docker=true
- --providers.docker.exposedbydefault=false
- --providers.file.directory=/configuration/
- --api.dashboard=true
- --accesslog=true
- --entrypoints.web.http.redirections.entrypoint.to=websecure
- --entrypoints.web.http.redirections.entrypoint.scheme=https
labels:
- "traefik.enable=true"
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
- "traefik.http.routers.dashboard.entrypoints=websecure"
- "traefik.http.routers.dashboard.service=api@internal"
- "traefik.http.routers.dashboard.tls=true"
- "traefik.http.routers.dashboard.middlewares=auth"
- "traefik.http.middlewares.auth.basicauth.users=${LDM_LOGIN}"
ports:
- 80:80
- 443:443
volumes:
- /etc/bridgehead/traefik-tls:/certs:ro
- ../lib/traefik-configuration/:/configuration:ro
- /var/run/docker.sock:/var/run/docker.sock:ro
forward_proxy:
container_name: bridgehead-forward-proxy
image: samply/bridgehead-forward-proxy:latest
environment:
HTTPS_PROXY: ${HTTPS_PROXY_URL}
USERNAME: ${HTTPS_PROXY_USERNAME}
PASSWORD: ${HTTPS_PROXY_PASSWORD}
volumes:
- /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
landing:
container_name: bridgehead-landingpage
image: samply/bridgehead-landingpage:master
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
environment:
HOST: ${HOST}
PROJECT: ${PROJECT}
SITE_NAME: ${SITE_NAME}
blaze:
image: "samply/blaze:0.18"
container_name: bridgehead-bbmri-blaze
environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx4g"
LOG_LEVEL: "debug"
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_ccp.rule=PathPrefix(`/bbmri-localdatamanagement`)"
- "traefik.http.middlewares.ccp_b_strip.stripprefix.prefixes=/bbmri-localdatamanagement"
- "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
- "traefik.http.routers.blaze_ccp.tls=true"
spot:
image: samply/spot:latest
container_name: bridgehead-spot
environment:
SECRET: ${SPOT_BEAM_SECRET_LONG}
APPID: spot
PROXY_ID: ${PROXY_ID}
LDM_URL: http://bridgehead-bbmri-blaze:8080/fhir
BEAM_PROXY: http://beam-proxy:8081
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: "samply/beam-proxy:develop"
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_0_ID: spot
APP_0_KEY: ${SPOT_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
RUST_LOG: debug
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

7
bbmri/vars Normal file
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BROKER_ID=broker.bbmri.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
SPOT_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
SPOT_BEAM_SECRET_LONG="ApiKey spot.${PROXY_ID} ${SPOT_BEAM_SECRET_SHORT}"
SUPPORT_EMAIL=bridgehead@helpdesk.bbmri-eric.eu
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem

107
bridgehead Executable file
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#!/bin/bash -e
baseDir() {
# see https://stackoverflow.com/questions/59895
SOURCE=${BASH_SOURCE[0]}
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
SOURCE=$(readlink "$SOURCE")
[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
echo $DIR
}
BASE=$(baseDir)
cd $BASE
source ./lib/functions.sh
ACTION=$1
export PROJECT=$2
if [[ -z $1 || -z $2 ]]; then
printUsage
exit 1
fi
case "$PROJECT" in
ccp)
#nothing extra to do
;;
bbmri)
#nothing extra to do
;;
*)
printUsage
exit 1
;;
esac
loadVars() {
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
set -a
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
fi
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
set +a
OVERRIDE=${OVERRIDE:=""}
if [ -f "$PROJECT/docker-compose.override.yml" ]; then
log INFO "Applying $PROJECT/docker-compose.override.yml"
OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
fi
detectCompose
setHostname
}
case "$ACTION" in
start)
loadVars
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
checkRequirements
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
export LDM_LOGIN=$(getLdmPassword)
exec $COMPOSE -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
;;
stop)
loadVars
exec $COMPOSE -f ./$PROJECT/docker-compose.yml $OVERRIDE down
;;
update)
loadVars
exec ./lib/update-bridgehead.sh $PROJECT
;;
install)
source ./lib/prepare-system.sh
loadVars
exec ./lib/install-bridgehead.sh $PROJECT
;;
uninstall)
exec ./lib/uninstall-bridgehead.sh $PROJECT
;;
enroll)
loadVars
if [ -e $PRIVATEKEYFILENAME ]; then
log ERROR "Private key already exists at $PRIVATEKEYFILENAME. Please delete first to proceed."
exit 1
fi
docker run --rm -ti -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $PROXY_ID --admin-email $SUPPORT_EMAIL
chmod 600 $PRIVATEKEYFILENAME
;;
preRun | preUpdate)
fixPermissions
;;
postRun | postUpdate)
;;
*)
printUsage
exit 1
;;
esac
exit 0

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version: "3.7"
services:
traefik:
container_name: bridgehead-traefik
image: traefik:latest
command:
- --entrypoints.web.address=:80
- --entrypoints.websecure.address=:443
- --providers.docker=true
- --providers.docker.exposedbydefault=false
- --providers.file.directory=/configuration/
- --api.dashboard=true
- --accesslog=true
- --entrypoints.web.http.redirections.entrypoint.to=websecure
- --entrypoints.web.http.redirections.entrypoint.scheme=https
labels:
- "traefik.enable=true"
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
- "traefik.http.routers.dashboard.entrypoints=websecure"
- "traefik.http.routers.dashboard.service=api@internal"
- "traefik.http.routers.dashboard.tls=true"
- "traefik.http.routers.dashboard.middlewares=auth"
- "traefik.http.middlewares.auth.basicauth.users=${LDM_LOGIN}"
ports:
- 80:80
- 443:443
volumes:
- /etc/bridgehead/traefik-tls:/certs:ro
- ../lib/traefik-configuration/:/configuration:ro
- /var/run/docker.sock:/var/run/docker.sock:ro
forward_proxy:
container_name: bridgehead-forward-proxy
image: samply/bridgehead-forward-proxy:latest
environment:
HTTPS_PROXY: ${HTTPS_PROXY_URL}
USERNAME: ${HTTPS_PROXY_USERNAME}
PASSWORD: ${HTTPS_PROXY_PASSWORD}
volumes:
- /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
landing:
container_name: bridgehead-landingpage
image: samply/bridgehead-landingpage:master
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
environment:
HOST: ${HOST}
PROJECT: ${PROJECT}
SITE_NAME: ${SITE_NAME}
blaze:
image: "samply/blaze:0.18"
container_name: bridgehead-ccp-blaze
environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx4g"
LOG_LEVEL: "debug"
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_ccp.rule=PathPrefix(`/ccp-localdatamanagement`)"
- "traefik.http.middlewares.ccp_b_strip.stripprefix.prefixes=/ccp-localdatamanagement"
- "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
- "traefik.http.routers.blaze_ccp.tls=true"
spot:
image: samply/spot:latest
container_name: bridgehead-spot
environment:
SECRET: ${SPOT_BEAM_SECRET_LONG}
APPID: spot
PROXY_ID: ${PROXY_ID}
LDM_URL: http://bridgehead-ccp-blaze:8080/fhir
BEAM_PROXY: http://beam-proxy:8081
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: "samply/beam-proxy:develop"
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_0_ID: spot
APP_0_KEY: ${SPOT_BEAM_SECRET_SHORT}
APP_1_ID: report-hub
APP_1_KEY: ${REPORTHUB_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
RUST_LOG: debug
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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version: "3.7"
services:
connector:
container_name: bridgehead-connector
image: docker.verbis.dkfz.de/ccp/connector:bk2
environment:
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASSWORD}
NNGM_MAGICPL_APIKEY: ${NNGM_MAGICPL_APIKEY}
NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
NNGM_CTS_APIKEY: ${NNGM_CTS_APIKEY}
NNGM_CRYPTKEY: ${NNGM_CRYPTKEY}
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.connector.rule=PathPrefix(`/ccp-connector`)"
- "traefik.http.services.connector.loadbalancer.server.port=8080"
- "traefik.http.routers.connector.tls=true"
connector_db:
image: postgres:9.5-alpine
container_name: bridgehead-ccp-connector-db
volumes:
- "connector_db_data:/var/lib/postgresql/data"
environment:
POSTGRES_DB: "samplyconnector"
POSTGRES_USER: "samplyconnector"
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASSWORD}
restart: always
volumes:
connector_db_data:

9
ccp/nngm-setup.sh Normal file
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#!/bin/bash
function nngmSetup() {
if [ -n "$NNGM_CTS_APIKEY" ]; then
log INFO "nNGM setup detected -- will start nNGM Connector."
OVERRIDE+=" -f ./$PROJECT/nngm-compose.yml"
fi
CONNECTOR_POSTGRES_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
}

13
ccp/vars Normal file
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BROKER_ID=broker.dev.ccp-it.dktk.dkfz.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
SPOT_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
SPOT_BEAM_SECRET_LONG="ApiKey spot.${PROXY_ID} ${SPOT_BEAM_SECRET_SHORT}"
REPORTHUB_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
REPORTHUB_BEAM_SECRET_LONG="ApiKey report-hub.${PROXY_ID} ${REPORTHUB_BEAM_SECRET_SHORT}"
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
# This will load nngm setup. Effective only if nngm configuration is defined.
source $PROJECT/nngm-setup.sh
nngmSetup

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lib/functions.sh Normal file
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#!/bin/bash -e
detectCompose() {
if [[ "$(docker compose version 2>/dev/null)" == *"Docker Compose version"* ]]; then
COMPOSE="docker compose"
else
COMPOSE="docker-compose"
# This is intended to fail on startup in the next prereq check.
fi
}
getLdmPassword() {
if [ -n "$LDM_PASSWORD" ]; then
docker run --rm httpd:alpine htpasswd -nb $PROJECT $LDM_PASSWORD | tr -d '\n' | tr -d '\r'
else
echo -n ""
fi
}
exitIfNotRoot() {
if [ "$EUID" -ne 0 ]; then
log "ERROR" "Please run as root"
fail_and_report 1 "Please run as root"
fi
}
checkOwner(){
COUNT=$(find $1 ! -user $2 |wc -l)
if [ $COUNT -gt 0 ]; then
log ERROR "$COUNT files in $1 are not owned by user $2. Run find $1 ! -user $2 to see them, chown -R $2 $1 to correct this issue."
return 1
fi
return 0
}
printUsage() {
echo "Usage: bridgehead start|stop|update|install|uninstall|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri"
}
checkRequirements() {
if ! lib/prerequisites.sh $@; then
log "ERROR" "Validating Prerequisites failed, please fix the error(s) above this line."
fail_and_report 1 "Validating prerequisites failed."
else
return 0
fi
}
fetchVarsFromVault() {
[ -e /etc/bridgehead/vault.conf ] && source /etc/bridgehead/vault.conf
if [ -z "$BW_MASTERPASS" ] || [ -z "$BW_CLIENTID" ] || [ -z "$BW_CLIENTSECRET" ]; then
log "ERROR" "Please supply correct credentials in /etc/bridgehead/vault.conf."
return 1
fi
set +e
PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy samply/bridgehead-vaultfetcher $@)
RET=$?
if [ $RET -ne 0 ]; then
echo "Code: $RET"
echo $PASS
return $RET
fi
eval $(echo -e "$PASS" | sed 's/\r//g')
set -e
return 0
}
fetchVarsFromVaultByFile() {
VARS_TO_FETCH=""
for line in $(cat $@); do
if [[ $line =~ .*=[\"]*\<VAULT\>[\"]*.* ]]; then
VARS_TO_FETCH+="$(echo -n $line | sed 's/=.*//') "
fi
done
if [ -z "$VARS_TO_FETCH" ]; then
return 0
fi
log INFO "Fetching $(echo $VARS_TO_FETCH | wc -w) secrets from Vault ..."
fetchVarsFromVault $VARS_TO_FETCH
return 0
}
assertVarsNotEmpty() {
MISSING_VARS=""
for VAR in $@; do
if [ -z "${!VAR}" ]; then
MISSING_VARS+="$VAR "
fi
done
if [ -n "$MISSING_VARS" ]; then
log "ERROR" "Mandatory variables not defined: $MISSING_VARS"
return 1
fi
return 0
}
fixPermissions() {
CHOWN=$(which chown)
sudo $CHOWN -R bridgehead /etc/bridgehead /srv/docker/bridgehead
}
source lib/monitoring.sh
report_error() {
CODE=$1
shift
log ERROR "$@"
hc_send $CODE "$@"
}
fail_and_report() {
report_error $@
exit $1
}
setHostname() {
if [ -z "$HOST" ]; then
export HOST=$(hostname -f)
log DEBUG "Using auto-detected hostname $HOST."
fi
}
##Setting Network properties
# currently not needed
#export HOSTIP=$(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}');

41
lib/gitpassword.sh Executable file
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#!/bin/bash
if [ "$1" != "get" ]; then
echo "Usage: $0 get"
exit 1
fi
baseDir() {
# see https://stackoverflow.com/questions/59895
SOURCE=${BASH_SOURCE[0]}
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
SOURCE=$(readlink "$SOURCE")
[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
echo $DIR
}
BASE=$(baseDir)
cd $BASE
source lib/functions.sh
assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
PARAMS="$(cat)"
GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
fetchVarsFromVault GIT_PASSWORD
if [ -z "${GIT_PASSWORD}" ]; then
fail_and_report 1 "gitpassword.sh failed: Git password not found."
fi
cat <<EOF
protocol=https
host=$GITHOST
username=bk-${SITE_ID}
password=${GIT_PASSWORD}
EOF

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#!/bin/bash -e
source lib/functions.sh
exitIfNotRoot
if [ $# -eq 0 ]; then
log "ERROR" "Please provide a Project as argument"
exit 1
fi
export PROJECT=$1
checkRequirements noprivkey
log "INFO" "Allowing the bridgehead user to start/stop the bridgehead."
cat <<EOF > /etc/sudoers.d/bridgehead-"${PROJECT}"
# This has been added by the Bridgehead installer. Remove with bridgehead uninstall.
Cmnd_Alias BRIDGEHEAD${PROJECT^^} = \\
/bin/systemctl start bridgehead@${PROJECT}.service, \\
/bin/systemctl stop bridgehead@${PROJECT}.service, \\
/bin/systemctl restart bridgehead@${PROJECT}.service, \\
/bin/systemctl restart bridgehead@*.service, \\
/bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead, \\
/usr/bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
bridgehead ALL= NOPASSWD: BRIDGEHEAD${PROJECT^^}
EOF
# TODO: Determine whether this should be located in setup-bridgehead (triggered through bridgehead install) or in update bridgehead (triggered every hour)
if [ -z "$LDM_PASSWORD" ]; then
log "INFO" "Now generating a password for the local data management. Please save the password for your ETL process!"
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
log "INFO" "Your generated credentials are:\n user: $PROJECT\n password: $generated_passwd"
echo -e "## Local Data Management Basic Authentication\n# User: $PROJECT\nLDM_PASSWORD=$generated_passwd" >> /etc/bridgehead/${PROJECT}.local.conf;
fi
log "INFO" "Registering system units for bridgehead and bridgehead-update"
cp -v \
lib/systemd/bridgehead\@.service \
lib/systemd/bridgehead-update\@.service \
lib/systemd/bridgehead-update\@.timer \
/etc/systemd/system/
systemctl daemon-reload
log INFO "Trying to update your bridgehead ..."
systemctl start bridgehead-update@"${PROJECT}".service
log "INFO" "Enabling autostart of bridgehead@${PROJECT}.service"
systemctl enable bridgehead@"${PROJECT}".service
log "INFO" "Enabling auto-updates for bridgehead@${PROJECT}.service ..."
systemctl enable --now bridgehead-update@"${PROJECT}".timer
STR="\n\n systemctl start bridgehead@${PROJECT}.service\n\nor by rebooting your machine."
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
STR="Success. Next, start your bridgehead by running$STR"
else
STR="Success. Next, enroll into the $PROJECT broker by creating a cryptographic certificate. To do so, run\n\n /srv/docker/bridgehead/bridgehead enroll $PROJECT\n\nThen, you may start the bridgehead by running$STR"
fi
log "INFO" "$STR"

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#!/bin/bash
log() {
SEVERITY="$1"
shift
echo -e "$(date +'%Y-%m-%d %T')" "$SEVERITY:" "$@"
}

54
lib/monitoring.sh Executable file
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#!/bin/bash
source lib/log.sh
function hc_set_uuid(){
HCUUID="$1"
}
function hc_set_service(){
HCSERVICE="$1"
}
UPTIME=
USER_AGENT=
function hc_send(){
BASEURL="https://healthchecks.verbis.dkfz.de/ping"
if [ -n "$MONITOR_APIKEY" ]; then
hc_set_uuid $MONITOR_APIKEY
fi
if [ -n "$HCSERVICE" ]; then
HCURL="$BASEURL/$PING_KEY/$HCSERVICE"
fi
if [ -n "$HCUUID" ]; then
HCURL="$BASEURL/$HCUUID"
fi
if [ ! -n "$HCURL" ]; then
log WARN "Did not report Healthcheck: Neither Healthcheck UUID nor service set. Please define MONITOR_APIKEY in /etc/bridgehead."
return 0
fi
if [ -z "$UPTIME" ]; then
UPTIME=$(docker ps -a --format 'table {{.Names}} \t{{.RunningFor}} \t {{.Status}} \t {{.Image}}' --filter name=bridgehead || echo "Unable to get docker statistics")
fi
if [ -z "$USER_AGENT" ]; then
if [ "$USER" != "root" ]; then
COMMIT_ETC=$(git -C /etc/bridgehead rev-parse HEAD | cut -c -8)
COMMIT_SRV=$(git -C /srv/docker/bridgehead rev-parse HEAD | cut -c -8)
else
COMMIT_ETC=$(su -c 'git -C /etc/bridgehead rev-parse HEAD' bridgehead | cut -c -8)
COMMIT_SRV=$(su -c 'git -C /srv/docker/bridgehead rev-parse HEAD' bridgehead | cut -c -8)
fi
USER_AGENT="srv:$COMMIT_SRV etc:$COMMIT_ETC"
fi
if [ -n "$2" ]; then
MSG="$2\n\nDocker stats:\n$UPTIME"
echo -e "$MSG" | https_proxy=$HTTPS_PROXY_URL curl -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
else
https_proxy=$HTTPS_PROXY_URL curl -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
fi
}

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#!/bin/bash -e
source lib/log.sh
source lib/functions.sh
log "INFO" "Preparing your system for bridgehead installation ..."
# Create the bridgehead user
if id bridgehead &>/dev/null; then
log "INFO" "Existing user with id $(id -u bridgehead) will be used by the bridgehead system units."
else
log "INFO" "Now creating a system user to own the bridgehead's files."
useradd -M -g docker -N bridgehead || fail_and_report ""
fi
# Clone the OpenSource repository of bridgehead
bridgehead_repository_url="https://github.com/samply/bridgehead.git"
if [ -d "/srv/docker/bridgehead" ]; then
current_owner=$(stat -c '%U' /srv/docker/bridgehead)
if [ "$(su -c 'git -C /srv/docker/bridgehead remote get-url origin' $current_owner)" == "$bridgehead_repository_url" ]; then
log "INFO" "Bridgehead's open-source repository has been found at /srv/docker/bridgehead"
else
log "ERROR" "The directory /srv/docker/bridgehead seems to exist, but doesn't contain a clone of $bridgehead_repository_url\nPlease delete the directory and try again."
exit 1
fi
else
log "INFO" "Cloning $bridgehead_repository_url to /srv/docker/bridgehead"
mkdir -p /srv/docker/
git clone bridgehead_repository_url /srv/docker/bridgehead -b feature/samplyBeam
fi
case "$PROJECT" in
ccp)
site_configuration_repository_middle="git.verbis.dkfz.de/bridgehead-configurations/bridgehead-config-"
;;
bbmri)
site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
;;
*)
log ERROR "Internal error, this should not happen."
exit 1
;;
esac
# Clone the site-configuration
if [ -d /etc/bridgehead ]; then
current_owner=$(stat -c '%U' /etc/bridgehead)
if [ "$(su -c 'git -C /etc/bridgehead remote get-url origin' $current_owner | grep $site_configuration_repository_middle)" ]; then
log "INFO" "Your site config repository in /etc/bridgehead seems to be installed correctly."
else
log "WARN" "Your site configuration repository in /etc/bridgehead seems to have another origin than git.verbis.dkfz.de. Please check if the repository is correctly cloned!"
fi
else
log "INFO" "Now cloning your site configuration repository for you."
read -p "Please enter your site: " site
read -s -p "Please enter the bridgehead's access token for your site configuration repository (will not be echoed): " access_token
site_configuration_repository_url="https://bytoken:${access_token}@${site_configuration_repository_middle}$(echo $site | tr '[:upper:]' '[:lower:]').git"
git clone $site_configuration_repository_url /etc/bridgehead
if [ $? -gt 0 ]; then
log "ERROR" "Unable to clone your configuration repository. Please obtain correct access data and try again."
fi
fi
chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
log INFO "System preparation is completed and private key is present."

83
lib/prerequisites.sh Executable file
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#!/bin/bash
source lib/functions.sh
detectCompose
if ! id "bridgehead" &>/dev/null; then
log ERROR "User bridgehead does not exist. Please run bridgehead install $PROJECT"
exit 1
fi
checkOwner /srv/docker/bridgehead bridgehead || exit 1
checkOwner /etc/bridgehead bridgehead || exit 1
## Check if user is a su
log INFO "Checking if all prerequisites are met ..."
prerequisites="git docker"
for prerequisite in $prerequisites; do
$prerequisite --version 2>&1
is_available=$?
if [ $is_available -gt 0 ]; then
fail_and_report 79 "Prerequisite not fulfilled - $prerequisite is not available!"
fi
# TODO: Check for specific version
done
log INFO "Checking if sudo is installed ..."
if [ ! -d /etc/sudoers.d ]; then
fail_and_report 1 "/etc/sudoers.d does not exist. Please install sudo package."
fi
log INFO "Checking configuration ..."
## Download submodule
if [ ! -d "/etc/bridgehead/" ]; then
fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
fi
# TODO: Check all required variables here in a generic loop
#check if project env is present
if [ -d "/etc/bridgehead/${PROJECT}.conf" ]; then
fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under /etc/bridgehead-config/${PROJECT}.conf."
fi
# TODO: Make sure you're in the right directory, or, even better, be independent from the working directory.
log INFO "Checking ssl cert for accessing bridgehead via https"
if [ ! -d "/etc/bridgehead/traefik-tls" ]; then
log WARN "TLS certs for accessing bridgehead via https missing, we'll now create a self-signed one. Please consider getting an officially signed one (e.g. via Let's Encrypt ...) and put into /etc/bridgehead/traefik-tls"
mkdir -p /etc/bridgehead/traefik-tls
fi
if [ ! -e "/etc/bridgehead/traefik-tls/fullchain.pem" ]; then
openssl req -x509 -newkey rsa:4096 -nodes -keyout /etc/bridgehead/traefik-tls/privkey.pem -out /etc/bridgehead/traefik-tls/fullchain.pem -days 3650 -subj "/CN=$HOST"
fi
if [ -e /etc/bridgehead/vault.conf ]; then
if [ "$(stat -c "%a %U" /etc/bridgehead/vault.conf)" != "600 bridgehead" ]; then
fail_and_report 1 "/etc/bridgehead/vault.conf has wrong owner/permissions. To correct this issue, run chmod 600 /etc/bridgehead/vault.conf && chown bridgehead /etc/bridgehead/vault.conf."
fi
fi
checkPrivKey() {
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
log INFO "Success - private key found."
else
log ERROR "Unable to find private key at /etc/bridgehead/pki/${SITE_ID}.priv.pem. To fix, please run\n bridgehead enroll ${PROJECT}\nand follow the instructions."
return 1
fi
log INFO "Success - all prerequisites are met!"
hc_send log "Success - all prerequisites are met!"
return 0
}
if [[ "$@" =~ "noprivkey" ]]; then
log INFO "Skipping check for private key for now."
else
checkPrivKey || exit 1
fi
exit 0

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[Unit]
Description=Bridgehead (%i) Update Service
[Service]
Type=oneshot
User=bridgehead
ExecStartPre=-/srv/docker/bridgehead/bridgehead preUpdate %i
ExecStart=/srv/docker/bridgehead/bridgehead update %i
ExecStopPost=-/srv/docker/bridgehead/bridgehead postUpdate %i
[Install]
WantedBy=multi-user.target

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[Unit]
Description=Hourly Updates of Bridgehead (%i)
[Timer]
OnCalendar=*-*-* *:00:00
[Install]
WantedBy=basic.target

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[Unit]
Description=Bridgehead (%i)
Requires=docker.service
[Service]
User=bridgehead
Restart=always
RestartSec=30
ExecStartPre=-/srv/docker/bridgehead/bridgehead preRun %i
ExecStart=/srv/docker/bridgehead/bridgehead start %i
ExecStop=/srv/docker/bridgehead/bridgehead stop %i
ExecStopPost=-/srv/docker/bridgehead/bridgehead postRun %i
[Install]
WantedBy=multi-user.target

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tls:
stores:
default:
defaultCertificate:
certFile: /certs/fullchain.pem
keyFile: /certs/privkey.pem

24
lib/uninstall-bridgehead.sh Executable file
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#!/bin/bash -e
source lib/functions.sh
if [ $# -eq 0 ]; then
log "ERROR" "Please provide a Project as argument"
exit 1
fi
export PROJECT=$1
#checkRequirements // not needed when uninstalling
log INFO "Removing bridgehead sudoers permissions."
rm -vf /etc/sudoers.d/bridgehead-${PROJECT}
log "INFO" "Stopping system units and removing bridgehead for ${PROJECT} ..."
systemctl disable --now bridgehead@${PROJECT}.service bridgehead-update@${PROJECT}.timer bridgehead-update@${PROJECT}.service
rm -v /etc/systemd/system/{bridgehead\@.service,bridgehead-update\@.timer,bridgehead-update\@.service}
log "INFO" "Successfully removed bridgehead for ${PROJECT} from your system"

109
lib/update-bridgehead.sh Executable file
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#!/bin/bash
source lib/functions.sh
AUTO_HOUSEKEEPING=${AUTO_HOUSEKEEPING:-true}
if [ "$AUTO_HOUSEKEEPING" == "true" ]; then
A="Performing automatic maintenance: Cleaning docker images."
hc_send log "$A"
log INFO "$A"
docker system prune -a -f
else
log WARN "Automatic housekeeping disabled (variable AUTO_HOUSEKEEPING != \"true\")"
fi
hc_send log "Checking for bridgehead updates ..."
CONFFILE=/etc/bridgehead/$1.conf
if [ ! -e $CONFFILE ]; then
fail_and_report 1 "Configuration file $CONFFILE not found."
fi
source $CONFFILE
assertVarsNotEmpty SITE_ID || fail_and_report 1 "Update failed: SITE_ID empty"
export SITE_ID
checkOwner . bridgehead || fail_and_report 1 "Update failed: Wrong permissions in $(pwd)"
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
CHANGES=""
# Check git updates
git_updated="false"
for DIR in /etc/bridgehead $(pwd); do
log "INFO" "Checking for updates to git repo $DIR ..."
OUT="$(git -C $DIR status --porcelain)"
if [ -n "$OUT" ]; then
log WARN "The working directory $DIR is modified. Changed files: $OUT"
report_error log "The working directory $DIR is modified. Changed files: $OUT"
fi
if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
log "INFO" "Configuring repo to use bridgehead git credential helper."
git -C $DIR config credential.helper "$CREDHELPER"
fi
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
if [ -z "$HTTP_PROXY_URL" ]; then
log "INFO" "Git is using no proxy!"
OUT=$(git -C $DIR fetch 2>&1 && git -C $DIR pull 2>&1)
else
log "INFO" "Git is using proxy ${HTTP_PROXY_URL} from ${CONFFILE}"
OUT=$(git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR fetch 2>&1 && git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR pull 2>&1)
fi
if [ $? -ne 0 ]; then
report_error log "Unable to update git $DIR: $OUT"
fi
new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
if [ "$old_git_hash" != "$new_git_hash" ]; then
CHANGE="Updated git repository in ${DIR} from commit $old_git_hash to $new_git_hash"
CHANGES+="- $CHANGE\n"
log "INFO" "$CHANGE"
# NOTE: Link generation doesn't work on repositories placed at an self-hosted instance of bitbucket.
# See: https://community.atlassian.com/t5/Bitbucket-questions/BitBucket-4-14-diff-between-any-two-commits/qaq-p/632974
git_repository_url="$(git -C $DIR remote get-url origin)"
git_repository_url=${git_repository_url/.git/}
if [ "$( echo $git_repository_url | grep "github.com")" ]; then
# Ensure web link even if ssh is used
git_repository_url="${git_repository_url/git@github.com/https:\/\/github.com\/}"
log "INFO" "You can review all changes on the repository with $git_repository_url/compare/$old_git_hash...$new_git_hash"
elif [ "$( echo $git_repository_url | grep "git.verbis.dkfz.de")" ]; then
git_repository_url="${git_repository_url/ssh:\/\/git@git.verbis.dkfz.de/https:\/\/git.verbis.dkfz.de\/}"
git_repository_url="https://$(echo $git_repository_url | awk -F '@' '{print $2}')"
log "INFO" "You can review all changes on the repository with $git_repository_url/compare?from=$old_git_hash&to=$new_git_hash"
fi
git_updated="true"
fi
done
# Check docker updates
log "INFO" "Checking for updates to running docker images ..."
docker_updated="false"
for IMAGE in $(cat $PROJECT/docker-compose.yml | grep -v "^#" | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
log "INFO" "Checking for Updates of Image: $IMAGE"
if docker pull $IMAGE | grep "Downloaded newer image"; then
CHANGE="Image $IMAGE updated."
CHANGES+="- $CHANGE\n"
log "INFO" "$CHANGE"
docker_updated="true"
fi
done
# If anything is updated, restart service
if [ $git_updated = "true" ] || [ $docker_updated = "true" ]; then
RES="Updates detected, now restarting bridgehead:\n$CHANGES"
log "INFO" "$RES"
hc_send log "$RES"
sudo /bin/systemctl restart bridgehead@*.service
else
RES="Nothing updated, nothing to restart."
log "INFO" "$RES"
hc_send log "$RES"
fi
exit 0
# TODO: Print last commit explicit