Pin the landing page to a version known to work

This command no longer disables the Bridgehead in systemctl, it
only stops it.

README.md

@@ -8,8 +8,8 @@ This repository is the starting point for any information and tools you will nee
     - [Hardware](#hardware)
     - [Software](#software)
     - [Network](#network)
-    - [EHDS2/ECDC](#ehds2-ecdc)
 2. [Deployment](#deployment)
+    - [EHDS2/ECDC](#ehds2-ecdc)
     - [Site name](#site-name)
     - [Projects](#projects)
     - [GitLab repository](#gitlab-repository)
@@ -88,37 +88,43 @@ The following URLs need to be accessible (prefix with `https://`):
   * gitlab.bbmri-eric.eu
 * only for German Biobank Node
   * broker.bbmri.de
+* only for EHDS2/ECDC
+  * ecdc-vm-ehds-test1.swedencentral.cloudapp.azure.com
 
 > 📝 This URL list is subject to change. Instead of the individual names, we highly recommend whitelisting wildcard domains: *.dkfz.de, github.com, *.docker.com, *.docker.io, *.samply.de, *.bbmri.de.
 
 > 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
 
+## Deployment
+
 ### EHDS2/ECDC
 
-ECDC data should be provided as a CSV file and placed in the directory /srv/docker/ecdc/data. The Bridgehead can be started without data, but obviously, any searches run from a Locator will return zero results for this site if you do that. Note that an empty data directory will automatically be inserted on the first start of the Bridgehead if you don't set one up yourself.
+The ECDC Bridgehead allows you to connect your site/node to the [AMR Explorer](http://ehds2-lens.swedencentral.cloudapp.azure.com/), a non-public central web site that allow certified researchers to search for information relating to antiobiotic resistance, Europe-wide. You can supply the Bridgehead with data from your site in the form of CSV files, which will then be made available to the Explorer for searching purposes.
 
-To get the right Beam certificate for your setup, you will need to edit the following files and comment/uncomment as appropriate:
+You will need to set up some configuration before you can start a Bridgehead. This can be done as follows:
 
-- bbmri/modules/ehds2.root.crt.pem
+```shell
-- bbmri/modules/ehds2.test.root.crt.pem
+sudo mkdir -p /etc/bridgehead
+sudo cp /srv/docker/bridgehead/bbmri/modules/bbmri.conf /etc/bridgehead
+```
 
-You will also need to edit:
+Now edit ```/etc/bridgehead/bbmri.conf``` and customize the following variables for your site:
 
-./bbmri/modules/ehds2-setup.sh
+- SITE_NAME
+- SITE_ID
+- OPERATOR_FIRST_NAME
+- OPERATOR_LAST_NAME
+- OPERATOR_EMAIL
 
-and set the broker address correctly for your site.
+If you run a proxy at your site, you will also need to give values to the ```HTTP*_PROXY*``` variables.
 
-When you first start the Bridgehead, it will clone two extra repositories into /srv/docker, namely, focus and transfair. It will automatically build local images of these repositories for you. These components have the following functionality that has been customized for ECDC:
+When you first start the Bridgehead, it will clone two extra repositories into /srv/docker, namely, ```focus``` and ```transfair```. It will automatically build local images of these repositories for you. These components have the following functionality that has been customized for ECDC:
 
-- *focus.* This component is responsible for completing the CQL that is used for running queries against the Blaze FHIR store. It uses a set of templates for doing this. Extra templates have been written for the ECDC use case.
+- *focus.* This component is responsible for completing the CQL that is used for running queries against the Blaze FHIR store. It uses a set of templates for doing this. Extra templates have been written for the ECDC use case. They can be found in /srv/docker/focus/resources/cql/EHDS2*.
-- *transfair.* This is an ETL component. It takes the CSV data that you provide, converts it to FHIR, and loads it to Blaze.
+- *transfair.* This is an ETL component. It takes the CSV data that you provide, converts it to FHIR, and loads it to Blaze. This will be run once, if there is data in /srv/docker/ecdc/data. A lock file in the data directory ensures that it does not get run again. Remove this lock file and restart the Bridgehead if you want to load new data.
 
 These images will normally be rebuilt every time you restart the Bridgehead. This is a workaround to fix a bug: if you don't rebuild these images for every start, then legacy versions will be used and you will lose the new ECDC functionality. The reason for this is still under investigation.
 
-Note that the /srv/docker/ecdc/data directory is also used as the home for a "lock" file, which will be created if your data has been successfully converted to FHIR by transfair. As long as this file exists, transfair will not be run again when you restart the Bridgehead. Hence, if you add or modify data, you will need to delete this file by hand before restarting the Bridgehead.
-
-## Deployment
-
 ### Site name
 
 You will need to choose a short name for your site. This is not a URL, just a simple identifying string. For the examples below, we will use "your-site-name", but you should obviously choose something that is meaningful to you and which is unique.
@@ -165,19 +171,14 @@ sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
 
 If this is an ECDC/EHDS2 installation, switch to the ```ehds2``` branch and copy the configuration file to the required location:
 ```shell
-cd
-git clone https://github.com/samply/transFAIR.git
-cd transFAIR
-docker build -t samply/transfair --no-cache .
 cd /srv/docker/bridgehead
 sudo git checkout ehds2
-sudo mkdir test data
 sudo mkdir -p /etc/bridgehead/
 sudo cp bbmri/modules/bbmri.conf /etc/bridgehead/
 sudo vi /etc/bridgehead/bbmri.conf # Modify to include national node name and admin contact details
 ```
 
-For an ECDC/EHDS2 installation, you will also need to copy your data in a comma-separated value (CSV) formatted file to ```/srv/docker/bridgehead/data```. Make sure it is readable by all. Only files with the ending ```.csv``` will be read in, all other files will be ignored.
+For an ECDC/EHDS2 installation, you will also need to copy your data in a comma-separated value (CSV) formatted file to ```/srv/docker/ecdc/data```. Make sure it is readable by all. Only files with the ending ```.csv``` will be read in, all other files will be ignored.
 
 If this is not an ECDC/EHDS2 installation, then download your site specific configuration repository:
 ```shell
@@ -232,6 +233,22 @@ pki-scripts/managepki list
 
 ### Starting and stopping your Bridgehead
 
+For an ECDC/EHDS2 installation, this is done with the help of specialized scripts:
+
+To start:
+
+```shell
+sudo /srv/docker/bridgehead/run.sh
+```
+
+To stop (you generally won't need to do this):
+
+```shell
+sudo /srv/docker/bridgehead/stop.sh
+```
+
+For regular installations, read on.
+
 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
@@ -377,6 +394,19 @@ There will be a delay before the effects of Directory sync become visible. First
 
 The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze).
 
+For an ECDC/EHDS2 installation, you need to provide your data as a table in a CSV (comma-separated value) files and place it in the directory /srv/docker/ecdc/data. You can provide as many data files as you like, and you can add new files incrementally over time.
+
+In order for this new data to be loaded, you will need to execute the ```run.sh``` script with the appropriate arguments:
+
+- To read just the most recently added data files: ```/srv/docker/bridgehead run.sh --upload```.
+- To read in all data from scratch: ```/srv/docker/bridgehead run.sh --upload-all```.
+
+These two variants give you the choice between uploading data in an incremental way that preserves the date used for statistics or as a single upload that date stamps everything with the current date.
+
+The Bridgehead can be started without data, but obviously, any searches run from the Explorer will return zero results for your site if you do that. Note that an empty data directory will automatically be inserted on the first start of the Bridgehead if you don't set one up yourself.
+
+For non-ECDC setups, read on.
+
 You can load data into this store by using its FHIR API:
 
 ```

bbmri/docker-compose.yml

@@ -4,7 +4,10 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    #image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    # Blaze versions 0.26 and 0.27 do not return anything when you run a
+    # CQL query, so I am pinning the version at 0.25.
+    image: samply/blaze:0.25
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"

bbmri/modules/bbmri.conf

@@ -19,18 +19,19 @@
 
 
 ### Common Configuration of all Components
-## This is the descriptive humanreadable name of your site (e.g. München LMU)
+## This is a descriptive human readable name of your site (e.g. Belgium)
-SITE_NAME=ECDC-Bridgehead-<National node>
+SITE_NAME=<National node>
-## This is the id for your site used in machine to machine communication (e.g. muenchen-lmu)
+## This is the id for your site used in machine to machine communication (should be
-SITE_ID=ecdc-bridgehead-<National node>
+## lower-case, e.g. belgium)
+SITE_ID=<National node>
 ## This server's hostname, for access from other computers within your institution
 ## (e.g. mybridgehead.intern.myinstitution.org)
 ## Optional. If left empty, this is auto-generated via the `hostname` command.
 HOST=
 
 ## Proxy Configuration
-# leave empty if not applyable
+# leave empty if not applicable
-# ex.: http://my-proxy-host:my-proxy-port
+# eg.: http://my-proxy-host:my-proxy-port
 HTTP_PROXY_URL=
 HTTP_PROXY_USERNAME=
 HTTP_PROXY_PASSWORD=

bbmri/modules/ehds2-compose.yml

@@ -12,6 +12,7 @@ services:
       BLAZE_URL: "http://blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy-ehds2:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+      OBFUSCATE: "no"
     depends_on:
       - "beam-proxy-ehds2"
       - "blaze"
@@ -55,11 +56,11 @@ services:
     command: bash -c " \
              echo listing /app/data && \
              ls -la /app/data && \
-             [ -f /app/data/*.[cC][sS][vV] ] && \
+             ls /app/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && \
              [ ! -f /app/data/lock ] && \
              ( \
                  echo 'Wait for Blaze to finish initializing' ; \
-                 sleep 60 ; \
+                 sleep 360 ; \
                  echo 'Remove old output files' ; \
                  rm -rf /app/test/* ; \
                  cd /app ; \
@@ -77,5 +78,5 @@ services:
   test-data-loader:
     container_name: test-data-loader
     image: samply/test-data-loader
-    command: sh -c "sleep 300 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"
+    command: sh -c "sleep 420 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"
 

bbmri/modules/ehds2-setup.sh

@@ -8,18 +8,15 @@ if [ "${ENABLE_EHDS2}" == "true" ]; then
 	case "$ENVIRONMENT" in
 		"production")
 			export EHDS2_BROKER_ID=broker.bbmri.samply.de
-			#export EHDS2_BROKER_ID=ecdc-vm-ehds-test1.swedencentral.cloudapp.azure.com
 			export EHDS2_ROOT_CERT=ehds2
 			;;
 		"test")
 			export EHDS2_BROKER_ID=broker.test.bbmri.samply.de
-			#export EHDS2_BROKER_ID=ecdc-vm-ehds-test1.swedencentral.cloudapp.azure.com
 			export EHDS2_ROOT_CERT=ehds2.test
 			;;
 		*)
 			report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
 			export EHDS2_BROKER_ID=broker.bbmri.samply.de
-			#export EHDS2_BROKER_ID=ecdc-vm-ehds-test1.swedencentral.cloudapp.azure.com
 			export EHDS2_ROOT_CERT=ehds2
 			;;
 	esac

bbmri/modules/ehds2.root.crt.pem

@@ -20,25 +20,3 @@ cBYgkKJTjwdRhc+ehI3kFo7b/a/Z/jl9szKsAPHozMixSi8lGnsYwN80oqeRvT7h
 wcMUK+igv3/K
 -----END CERTIFICATE-----
 
-# EHDS2/ECDC certificate
-#-----BEGIN CERTIFICATE-----
-#MIIDNTCCAh2gAwIBAgIUamQJB/Uevzf3+qrDQOqA8mwkwX8wDQYJKoZIhvcNAQEL
-#BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMjA3MTQ1MTQxWhcNMzQw
-#MjA0MTQ1MjExWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-#AQEBBQADggEPADCCAQoCggEBAKvI2XT0os20vG7d8FjRuMq9mALcQgLZvjAbQZbm
-#JyeVxRQP5HsSrBlBwaZWgmXWFfIPlwsEsTAUsCneAl4ZL3gQ6831nbmmpgThOEVy
-#rGBsbL6qlEWWplD/AGpcdEbAuDmuMSO9tKR6iRm+acTHJcXqsDm2HUUS7U+ManWY
-#S0dG10beJE2eVtEv5/fnFlVSn72VgAVgXVl7UA5E77zXK9GUAyQ6Oo7MET9zifZ/
-#EifeSoEvLk+U7HRLgQbKz2ti6ABh0wnK7Ec2DjekMBXyeQz0tR+8dS53s5pqti7c
-#SUQMHmL4jKxvfQr7fr5wbJpFDu37Vif9GdND9WSDRcufuM8CAwEAAaN7MHkwDgYD
-#VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFKMF6QgDV4cV
-#WyQZn3EHKLUumXzuMB8GA1UdIwQYMBaAFKMF6QgDV4cVWyQZn3EHKLUumXzuMBYG
-#A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQAhhE0ht7Sp
-#inKLJSVZrdFHbAbRXnYcUz/3oyy/uw0YvF0dJAHz2sgbtCLMHzKU7NwotaEqZedA
-#I7688nI42aHggIkwa1CzmFo9ybQ2afgrYNeF+TcTQI6G+fFpeRT5I+FvA9hUI3r4
-#Kp63Si7cpQS5uiHs90sv2SNMedo2Gf9VyJKB7NOReQJWsrw32ITi4QLNKHcHciKm
-#cpi/OqbR1YTJRoUrcC655G7bSKENzccdTWo8kBJgYLVbe+FohqgheqPqWpdH2zoR
-#OxOwviutfJTNvDyhXu8FrDc5tr9f5VjXv1hK2szYuvggwbybUBB9bLsx+fV79oZe
-#3zR0j5YwB28G
-#-----END CERTIFICATE-----
-

bbmri/modules/ehds2.test.root.crt.pem

@@ -20,25 +20,3 @@ UNe/254bc0vqHEPT6VI/86c7qAmk1xR0RUfrnKAEqZtUeuoj2fe1L/6yOB16fxt5
 vZdXnV1qjlM2
 -----END CERTIFICATE-----
 
-# EHDS2/ECDC certificate
-#-----BEGIN CERTIFICATE-----
-#MIIDNTCCAh2gAwIBAgIUamQJB/Uevzf3+qrDQOqA8mwkwX8wDQYJKoZIhvcNAQEL
-#BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMjA3MTQ1MTQxWhcNMzQw
-#MjA0MTQ1MjExWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-#AQEBBQADggEPADCCAQoCggEBAKvI2XT0os20vG7d8FjRuMq9mALcQgLZvjAbQZbm
-#JyeVxRQP5HsSrBlBwaZWgmXWFfIPlwsEsTAUsCneAl4ZL3gQ6831nbmmpgThOEVy
-#rGBsbL6qlEWWplD/AGpcdEbAuDmuMSO9tKR6iRm+acTHJcXqsDm2HUUS7U+ManWY
-#S0dG10beJE2eVtEv5/fnFlVSn72VgAVgXVl7UA5E77zXK9GUAyQ6Oo7MET9zifZ/
-#EifeSoEvLk+U7HRLgQbKz2ti6ABh0wnK7Ec2DjekMBXyeQz0tR+8dS53s5pqti7c
-#SUQMHmL4jKxvfQr7fr5wbJpFDu37Vif9GdND9WSDRcufuM8CAwEAAaN7MHkwDgYD
-#VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFKMF6QgDV4cV
-#WyQZn3EHKLUumXzuMB8GA1UdIwQYMBaAFKMF6QgDV4cVWyQZn3EHKLUumXzuMBYG
-#A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQAhhE0ht7Sp
-#inKLJSVZrdFHbAbRXnYcUz/3oyy/uw0YvF0dJAHz2sgbtCLMHzKU7NwotaEqZedA
-#I7688nI42aHggIkwa1CzmFo9ybQ2afgrYNeF+TcTQI6G+fFpeRT5I+FvA9hUI3r4
-#Kp63Si7cpQS5uiHs90sv2SNMedo2Gf9VyJKB7NOReQJWsrw32ITi4QLNKHcHciKm
-#cpi/OqbR1YTJRoUrcC655G7bSKENzccdTWo8kBJgYLVbe+FohqgheqPqWpdH2zoR
-#OxOwviutfJTNvDyhXu8FrDc5tr9f5VjXv1hK2szYuvggwbybUBB9bLsx+fV79oZe
-#3zR0j5YwB28G
-#-----END CERTIFICATE-----
-

bbmri/vars

@@ -7,7 +7,7 @@
 # Makes only sense for EHDS2 project
 : ${ENABLE_EHDS2:=false}
 
-FOCUS_RETRY_COUNT=32
+FOCUS_RETRY_COUNT=128
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 for module in $PROJECT/modules/*.sh

bridgehead

@@ -88,7 +88,11 @@ case "$ACTION" in
 	start)
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
+		chown -R bridgehead ${BASE}
 		checkRequirements
+		# Note: changes to "bridgehead" script will only take effect after next start.
+		su bridgehead -c "git pull"
+		chown -R bridgehead ${BASE}
                 # Local versions of focus and transfair are needed by EHDS2
                 clone_focus_if_nonexistent ${BASE}/..
                 build_focus ${BASE}/..

ecdc.service

@@ -0,0 +1,14 @@
+[Unit]
+Description=Start ECDC Bridgehead
+
+[Service]
+Type=simple
+ExecStart=/srv/docker/bridgehead/restart_service.sh
+ExecStop=/srv/docker/bridgehead/shutdown_service.sh
+Restart=always
+RestartSec=36000
+KillMode=mixed
+
+[Install]
+WantedBy=default.target
+

lib/functions.sh

@@ -258,8 +258,8 @@ function clone_repo_if_nonexistent() {
     cd "$target_dir"
 
     # Checkout the specified branch
-    git checkout "$branch_name"
+    chown -R bridgehead .
-    echo "Checked out branch '$branch_name'."
+    su bridgehead -c "git checkout $branch_name"
 
     cd -
 }
@@ -267,7 +267,7 @@ function clone_repo_if_nonexistent() {
 function clone_transfair_if_nonexistent() {
     local base_dir="$1"
 
-    clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2
+    clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2_develop
 }
 
 function clone_focus_if_nonexistent() {
@@ -282,11 +282,13 @@ function build_transfair() {
 
     # We only take the touble to build transfair if:
     #
-    # 1. There is no data lock file (which means that no ETL has yet been run) and
+    # 1. There is data available (any CSV files) and
-    # 2. There is data available.
+    # 2. There is no data lock file (which means that no ETL has yet been run).
-    if [ -f ../ecdc/data/*.[cC][sS][vV] ] && [ ! -f ../ecdc/data/lock ]; then
+    if ls ../ecdc/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && [ ! -f ../ecdc/data/lock ]; then
         cd $base_dir/transfair
+        su bridgehead -c "git pull"
         docker build --progress=plain -t samply/transfair --no-cache .
+        chown -R bridgehead .
         cd -
     fi
 }
@@ -295,7 +297,9 @@ function build_focus() {
     local base_dir="$1"
 
     cd $base_dir/focus
+    su bridgehead -c "git pull"
     docker build --progress=plain -f DockerfileWithBuild -t samply/focus --no-cache .
+    chown -R bridgehead .
     cd -
 }
 

lib/prerequisites.sh

@@ -84,7 +84,7 @@ else
 	SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
 	if [ $SKEW -ge 300 ]; then
 		report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
-		exit 1
+		log WARN "Server Time Error"
 	elif [ $SKEW -ge 60 ]; then
 		log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
 	fi

minimal/docker-compose.yml

@@ -45,7 +45,7 @@ services:
 
   landing:
     container_name: bridgehead-landingpage
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"

restart_service.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# Start a running Bridgehead. If there is already a Bridgehead running,
+# stop it first.
+# This is intended to be used by systemctl.
+
+cd /srv/docker/bridgehead
+
+echo "git status before stop"
+git status
+
+echo "Stopping running Bridgehead, if present"
+./bridgehead stop bbmri
+
+# If "flush_blaze" is present, delete the Blaze volume before starting
+# the Bridgehead again. This allows a user to upload all data, if
+# requested.
+if [ -f "/srv/docker/ecdc/data/flush_blaze" ]; then
+    docker volume rm bbmri_blaze-data
+    rm -f /srv/docker/ecdc/data/flush_blaze
+fi
+
+echo "git status before start"
+git status | systemd-cat -p info
+
+echo "Start the Bridgehead anew"
+./bridgehead start bbmri
+
+echo "Bridgehead has unexpectedly terminated"
+

run.sh

@@ -0,0 +1,83 @@
+#!/usr/bin/env bash
+
+# Start a Bridgehead from the command line. Upload data if requested.
+# Behind the scenes we use systemctl to do the work.
+
+# Function to print usage
+print_usage() {
+    echo "Start a Bridghead, optionally upload data"
+    echo "Usage: $0 [--upload | --upload-all | --help | -h]"
+    echo "Options:"
+    echo "  --upload       Run Bridgehead and upload just the new CSV data files."
+    echo "  --upload-all   Run Bridgehead and upload all CSV data files."
+    echo "  --help, -h     Display this help message."
+    echo "  No options     Run Bridgehead only."
+}
+
+# Initialize variables
+UPLOAD=false
+UPLOAD_ALL=false
+
+# Parse arguments
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        --upload)
+            UPLOAD=true
+            ;;
+        --upload-all)
+            UPLOAD_ALL=true
+            ;;
+        --help|-h)
+            print_usage
+            exit 0
+            ;;
+        *)
+            echo "Error: Unknown argument '$1'"
+            print_usage
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+# Check for conflicting options
+if [ "$UPLOAD" = true ] && [ "$UPLOAD_ALL" = true ]; then
+    echo "Error: you must specify either --upload or --upload-all, specifying both is not permitted."
+    print_usage
+    exit 1
+fi
+
+# Disable/stop standard Bridgehead systemctl services, if present
+sudo systemctl disable bridgehead@bbmri.service >& /dev/null
+sudo systemctl disable system-bridgehead.slice >& /dev/null
+sudo systemctl disable bridgehead-update@bbmri.timer >& /dev/null
+sudo systemctl stop bridgehead@bbmri.service >& /dev/null
+sudo systemctl stop system-bridgehead.slice >& /dev/null
+sudo systemctl stop bridgehead-update@bbmri.timer >& /dev/null
+
+# Set up systemctl for EHDS2/ECDC if necessary
+cp /srv/docker/bridgehead/ecdc.service /etc/systemd/system
+systemctl daemon-reload
+systemctl enable ecdc.service
+
+# Use systemctl to stop the Bridgehead if it is running
+sudo systemctl stop ecdc.service
+
+# Use files to tell the Bridgehead what to do with any data present
+if [ "$UPLOAD" = true ] || [ "$UPLOAD_ALL" = true ]; then
+    if [ -f /srv/docker/ecdc/data/lock ]; then
+        rm /srv/docker/ecdc/data/lock
+    fi
+fi
+if [ "$UPLOAD_ALL" = true ]; then
+    echo "All CSV files in /srv/docker/ecdc/data will be uploaded"
+    touch /srv/docker/ecdc/data/flush_blaze
+fi
+
+# Start up the Bridgehead
+sudo systemctl start ecdc.service
+
+# Show status of Bridgehead service
+sleep 10
+systemctl status ecdc.service
+

shutdown_service.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Shut down a running Bridgehead.
+# This is intended to be used by systemctl.
+
+cd /srv/docker/bridgehead
+
+echo "git status before stop"
+git status
+
+echo "Stopping running Bridgehead, if present"
+./bridgehead stop bbmri
+

stop.sh

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+
+# Shut down a running Bridgehead.
+# Behind the scenes we use systemctl to do the work.
+
+# Function to print usage
+print_usage() {
+    echo "Stop the running Bridgehead"
+    echo "Usage: $0 [--help | -h]"
+    echo "Options:"
+    echo "  --help, -h     Display this help message."
+    echo "  No options     Stop Bridgehead only."
+}
+
+# Parse arguments
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        --help|-h)
+            print_usage
+            exit 0
+            ;;
+        *)
+            echo "Error: Unknown argument '$1'"
+            print_usage
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+# Set up systemctl for EHDS2/ECDC if necessary
+cp /srv/docker/bridgehead/ecdc.service /etc/systemd/system
+systemctl daemon-reload
+systemctl enable ecdc.service
+
+# Use systemctl to stop the Bridgehead if it is running
+sudo systemctl stop ecdc.service
+
+# Show status of Bridgehead service
+sleep 20
+systemctl status ecdc.service
+docker ps
+