commit to trigger the switch

README.md

@@ -21,7 +21,7 @@ This repository is the starting point for any information and tools you will nee
     - [HTTPS Access](#https-access)
     - [TLS terminating proxies](#tls-terminating-proxies)
     - [File structure](#file-structure)
-    - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
+    - [BBMRI-ERIC Directory](#bbmri-eric-directory)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -51,41 +51,22 @@ Ensure the following software (or newer) is installed:
 - docker >= 20.10.1
 - docker-compose >= 2.xx (`docker-compose` and `docker compose` are both supported).
 - systemd
-- curl
 
 We recommend to install Docker(-compose) from its official sources as described on the [Docker website](https://docs.docker.com).
 
-> 📝 Note for Ubuntu: Snap versions of Docker are not supported.
+Note for Ubuntu: Please note that snap versions of Docker are not supported.
 
 ### Network
 
-A Bridgehead communicates to all central components via outgoing HTTPS connections.
+A running Bridgehead requires an outgoing HTTPS proxy to communicate with the central components.
 
-Your site might require an outgoing proxy (i.e. HTTPS forward proxy) to connect to external servers; you should discuss this with your local systems administration. In that case, you will need to note down the URL of the proxy. If the proxy requires authentication, you will also need to make a note of its username and password. This information will be used later on during the installation process. TLS terminating proxies are also supported, see [here](#tls-terminating-proxies). Apart from the Bridgehead itself, you may also need to configure the proxy server in [git](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker](https://docs.docker.com/network/proxy/).
+Additionally, your site might use its own proxy. You should discuss this with your local systems administration. If a proxy is being used, you will need to note down the URL of the proxy. If it is a secure proxy, then you will also need to make a note of its username and password. This information will be used later on during the installation process.
 
-The following URLs need to be accessible (prefix with `https://`):
-* To fetch code and configuration from git repositories
-  * github.com
-  * git.verbis.dkfz.de
-* To fetch docker images
-  * docker.verbis.dkfz.de
-  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
-    * hub.docker.com
-    * registry-1.docker.io
-    * production.cloudflare.docker.com
-* To report bridgeheads operational status
-  * healthchecks.verbis.dkfz.de
-* only for DKTK/CCP
-  * broker.ccp-it.dktk.dkfz.de
-* only for BBMRI-ERIC
-  * broker.bbmri.samply.de
-  * gitlab.bbmri-eric.eu
-* only for German Biobank Node
-  * broker.bbmri.de
+Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators.
 
-> 📝 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.
+If there is a site firewall, this needs to be configured so that outgoing calls to the following URLs are allowed: *.dkfz.de, github.com, docker.io, *.docker.io, *.samply.de.
 
-> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
+Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
 
 ## Deployment
 
@@ -254,21 +235,6 @@ Even within your internal network, the Bridgehead enforces HTTPS for all service
 
 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.
 
-To find the certificate file, first run the following:
-
-```
-curl -v https://broker.bbmri.samply.de/v1/health
-```
-
-In the output, look out for the line:
-
-
-```
-successfully set certificate verify locations:
-```
-
-Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exact location  will depend on your operating system. This is the file that you need to copy.
-
 ### 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.
@@ -281,29 +247,28 @@ Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exac
 
 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>`.
 
-### BBMRI-ERIC Directory entry needed
+### BBMRI-ERIC Directory
 
-If you run a biobank, you should be listed together with your collections with in the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
+If you run a biobank, you should register with the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
 
 To do this, contact the BBMRI-ERIC national node for the country where your biobank is based, see [the list of nodes](http://www.bbmri-eric.eu/national-nodes/).
 
-Once you have added your biobank to the Directory you got persistent identifier (PID) for your biobank and unique identifiers (IDs) for your collections. The collection IDs are necessary for the biospecimens assigning to the collections and later in the data flows between BBMRI-ERIC tools. In case you cannot distribute all your biospecimens within collections via assigning the collection IDs, **you should choose one of your sample collections as a default collection for your biobank**. This collection will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this default collection ID, you will need it later on in the installation process.
+Once you have registered, **you should choose one of your sample collections as a default collection for your biobank**. This is the collection that will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this ID, you will need it later on in the installation process.
 
-### Directory sync tool
-
-The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature.
+The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory url, username and password to enable this feature.
 
 Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
 
 To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
 
 ```
+### Directory sync service
 DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
 DS_DIRECTORY_USER_NAME=your_directory_username
 DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
 DS_TIMER_CRON="0 22 * * *"
 ```
-You must contact the Directory team for your national node to find the URL, and to register as a user.
+You must contact the Directory for your national node to find the URL, and to register as a user.
 
 Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.
 
@@ -354,28 +319,8 @@ Installation under WSL ought to work, but we have not tested this.
 
 ### 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, you'll need to configure the proxy inside the system unit of docker by creating the file `/etc/systemd/system/docker.service.d/proxy.conf` with the following content:
+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).
 
-``` ini
-[Service]
-Environment="HTTP_PROXY=http://proxy.example.com:3128"
-Environment="HTTPS_PROXY=https://proxy.example.com:3128"
-Environment="NO_PROXY=localhost,127.0.0.1,some-local-docker-registry.example.com,.corp"
-```
-
-After saving the configuration file, you'll need to reload the system daemon for the changes to take effect:
-
-``` shell
-sudo systemctl daemon-reload
-```
-
-and restart the docker daemon:
-
-``` shell
-sudo systemctl restart docker
-```
-
-For more information, please consult the [official documentation](https://docs.docker.com/config/daemon/systemd/#httphttps-proxy).
 
 ### Monitoring
 

bbmri/modules/dnpm-compose.yml

@@ -22,7 +22,7 @@ services:
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
     container_name: bridgehead-dnpm-beam-connect
     environment:
       PROXY_URL: http://dnpm-beam-proxy:8081
@@ -34,7 +34,6 @@ services:
       HTTPS_PROXY: http://forward_proxy:3128
       NO_PROXY: dnpm-beam-proxy,dnpm-backend
       RUST_LOG: ${RUST_LOG:-info}
-      NO_AUTH: "true"
     volumes:
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro

bbmri/modules/gbn-setup.sh

@@ -5,9 +5,9 @@ if [ "${ENABLE_GBN}" == "true" ]; then
 	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
 
 	# Set required variables
-	GBN_BROKER_ID=broker.bbmri.de
+	GBN_BROKER_ID='#TODO#'
 	GBN_BROKER_URL=https://${GBN_BROKER_ID}
 	GBN_PROXY_ID=${SITE_ID}.${GBN_BROKER_ID}
 	GBN_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-	GBN_SUPPORT_EMAIL=feedback@germanbiobanknode.de
+	GBN_SUPPORT_EMAIL=todo@verbis.dkfz.de
 fi

bbmri/modules/gbn.root.crt.pem

@@ -1,20 +1 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUckVOQQWZBTC0pWhn1X3lPxAWricwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwOTA0MDkwMTQ0WhcNMzMw
-OTAxMDkwMjEzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAOOD+CVvteBmu1hKV1QlfbHmiLCnuf6F+9k+1u/b
-6as6k7BURn8KZAxVLWSIwC6x2C7n9CHN9Jieb4DWpS0XmXQVUEpT1/yiLGBdxp2x
-nrbzm7caOunsWsPlGOcXPJKJpzAhcg58RDzXZ+2+shulSmsgPNlWBaLhNL5wj0sQ
-MzbwGVlGIJg18Ye/9WgQkO2ZcnTGb5cRsChKs4H43ZC34ZSSk7wqWg6P3e2xFam1
-YKXBOZzhwHoI4AxUQ+gd6upz5dqcwbaNZm10VP8fMac2dMLw9cOCS0ueDCS4viLd
-A69yds19AndBPMZhoEY1UHafjJ1uITRJQpaaB4vNliX+1rECAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFC74YIorSwWD
-/s5ozz3xvqUMDJ3qMB8GA1UdIwQYMBaAFC74YIorSwWD/s5ozz3xvqUMDJ3qMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCzcIccBzYr
-sHCGTGsSyLGBYsuI5yl+hvFOitYTha/mC+XBxq2R6By2WzbfSZtyZkUtC/+FqdCY
-VtMSjbDVXtBgsabfqODBobHmPyOEmNUX4IGcyn06rdM+rHQRah98lF+PhiPPO42F
-9Wj8dkq4/Gf+Yarq31ZbY0sed2sEPZ/bV26Og8Ft9qip5gKwklyakAiCnDIq+QBd
-ltvng3g08AQM0o5KIphP2/WU0UoSk1YPVMjRxuLiFg8xvr2EdCQQ9oA7xbhrmAXe
-242HVW/7KokjmowyWTQlIUGnuGdCOtTl8h74eHTID0YWO68hHkA0J5Ox2j4dZxvw
-HRFTxAR1gGKX
------END CERTIFICATE-----
+#TODO#

bbmri/vars

@@ -14,7 +14,7 @@ do
 done
 
 SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
-BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
+BROKER_URL_FOR_PREREQ=$ERIC_BROKER_URL
 
 if [ -n "$GBN_SUPPORT_EMAIL" ]; then
     SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL

bridgehead

@@ -65,7 +65,6 @@ loadVars() {
 	fi
 	detectCompose
 	setHostname
-	setupProxy
 }
 
 case "$ACTION" in

ccp/modules/adt2fhir-rest-compose.yml

@@ -1,18 +0,0 @@
-version: "3.7"
-
-services:
-  adt2fhir-rest:
-    container_name: bridgehead-adt2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/adt2fhir-rest:main
-    environment:
-      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SALT: ${LOCAL_SALT}
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.adt2fhir-rest.rule=PathPrefix(`/adt2fhir-rest`)"
-      - "traefik.http.middlewares.adt2fhir-rest_strip.stripprefix.prefixes=/adt2fhir-rest"
-      - "traefik.http.services.adt2fhir-rest.loadbalancer.server.port=8080"
-      - "traefik.http.routers.adt2fhir-rest.tls=true"
-      - "traefik.http.routers.adt2fhir-rest.middlewares=adt2fhir-rest_strip,auth"

ccp/modules/adt2fhir-rest-setup.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-function adt2fhirRestSetup() {
-  if [ -n "$ENABLE_ADT2FHIR_REST" ]; then
-    log INFO "ADT2FHIR-REST setup detected -- will start adt2fhir-rest API."
-    if [ ! -n "$IDMANAGER_LOCAL_PATIENTLIST_APIKEY" ]; then
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      exit 1;
-    fi
-    OVERRIDE+=" -f ./$PROJECT/modules/adt2fhir-rest-compose.yml"
-    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  fi
-}

ccp/modules/dnpm-compose.yml

@@ -6,7 +6,7 @@ services:
       APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
   dnpm-beam-connect:
     depends_on: [ beam-proxy ]
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
     container_name: bridgehead-dnpm-beam-connect
     environment:
       PROXY_URL: http://beam-proxy:8081
@@ -18,7 +18,6 @@ services:
       HTTPS_PROXY: "http://forward_proxy:3128"
       NO_PROXY: beam-proxy,dnpm-backend
       RUST_LOG: ${RUST_LOG:-info}
-      NO_AUTH: "true"
     volumes:
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro

ccp/modules/id-management-compose.yml

@@ -43,7 +43,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"

ccp/modules/id-management-setup.sh

@@ -39,7 +39,6 @@ function applySpecialCases() {
 	result="$1";
 	result="${result/Lmu/LMU}";
 	result="${result/Tum/TUM}";
-	result="${result/Dktk Test/Teststandort}";
 	echo "$result";
 }
 

ccp/modules/mtba-setup.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
 
 function mtbaSetup() {
+       # TODO: Check if ID-Management Module is activated!
        if [ -n "$ENABLE_MTBA" ];then
                log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
               if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+                      log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
                       exit 1;
               fi
                OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"

ccp/modules/nngm-setup.sh

@@ -1,6 +1,8 @@
 #!/bin/bash
 
+function nngmSetup() {
 	if [ -n "$NNGM_CTS_APIKEY" ]; then
 		log INFO "nNGM setup detected -- will start nNGM Connector."
 		OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
 	fi
+	}

ccp/vars

@@ -16,5 +16,5 @@ do
 done
 
 idManagementSetup
+nngmSetup
 mtbaSetup
-adt2fhirRestSetup

lib/functions.sh

@@ -9,33 +9,6 @@ detectCompose() {
 	fi
 }
 
-setupProxy() {
-	### Note: As the current data protection concepts do not allow communication via HTTP,
-	### we are not setting a proxy for HTTP requests.
-
-	local http="no"
-	local https="no"
-	if [ $HTTPS_PROXY_URL ]; then
-		local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
-		local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
-		local hostport=$(echo $HTTPS_PROXY_URL | sed -e "s,$proto,,g" | cut -d/ -f1)
-		HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
-		HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
-		if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
-			local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
-			local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
-			HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
-			https="authenticated"
-		else
-			HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
-			https="unauthenticated"
-		fi
-	fi
-
-	log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
-	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
-}
-
 exitIfNotRoot() {
   if [ "$EUID" -ne 0 ]; then
     log "ERROR" "Please run as root"
@@ -76,7 +49,7 @@ fetchVarsFromVault() {
 
 	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 docker.verbis.dkfz.de/cache/samply/bridgehead-vaultfetcher:latest $@)
+	PASS=$(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
@@ -215,7 +188,7 @@ function do_enroll_inner {
 		PARAMS+="--admin-email $SUPPORT_EMAIL"
 	fi
 
-	docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki docker.verbis.dkfz.de/cache/samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
+	docker run --rm -ti -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
 	chmod 600 $PRIVATEKEYFILENAME
 }
 

lib/monitoring.sh

@@ -47,8 +47,8 @@ function hc_send(){
 
     if [ -n "$2" ]; then
         MSG="$2\n\nDocker stats:\n$UPTIME"
-        echo -e "$MSG" | https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
+        echo -e "$MSG" | https_proxy=$HTTPS_PROXY_URL curl --max-time 5 -A "$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_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
+        https_proxy=$HTTPS_PROXY_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
     fi
 }

lib/prerequisites.sh

@@ -14,7 +14,7 @@ checkOwner /etc/bridgehead bridgehead || exit 1
 
 ## Check if user is a su
 log INFO "Checking if all prerequisites are met ..."
-prerequisites="git docker curl"
+prerequisites="git docker"
 for prerequisite in $prerequisites; do
   $prerequisite --version 2>&1
   is_available=$?
@@ -68,7 +68,7 @@ source /etc/bridgehead/${PROJECT}.conf
 source ${PROJECT}/vars
 
 set +e
-SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+SERVERTIME="$(https_proxy=$HTTPS_PROXY_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
 RET=$?
 set -e
 if [ $RET -ne 0 ]; then

lib/update-bridgehead.sh

@@ -30,7 +30,7 @@ source $CONFFILE
 assertVarsNotEmpty SITE_ID || fail_and_report 1 "Update failed: SITE_ID empty"
 export SITE_ID
 
-checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
+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"
@@ -50,12 +50,12 @@ for DIR in /etc/bridgehead $(pwd); do
     git -C $DIR config credential.helper "$CREDHELPER"
   fi
   old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
-  if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
+  if [ -z "$HTTP_PROXY_URL" ]; then
     log "INFO" "Git is using no proxy!"
     OUT=$(retry 5 git -C $DIR fetch 2>&1 && retry 5 git -C $DIR pull 2>&1)
   else
-    log "INFO" "Git is using proxy ${HTTPS_PROXY_URL} from ${CONFFILE}"
-    OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
+    log "INFO" "Git is using proxy ${HTTP_PROXY_URL} from ${CONFFILE}"
+    OUT=$(retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$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"
@@ -80,6 +80,12 @@ for DIR in /etc/bridgehead $(pwd); do
       log "INFO" "You can review all changes on the repository with $git_repository_url/compare?from=$old_git_hash&to=$new_git_hash"
     fi
     git_updated="true"
+    if [ "$DIR" == "/srv/docker/bridgehead" ]; then
+      git -C "$DIR" checkout main
+      REPORT_BRANCH_NAME=$(git -C "$DIR" branch --show-current)
+      REPORT_STATUS_CHECK=$(git -C "$DIR" status --porcelain)
+      report_error 7 "MAINTENANCE: Switched Branch to main, you are now on branch $REPORT_BRANCH_NAME \n see status \n $REPORT_STATUS_CHECK"
+    fi
   fi
 done
 
@@ -116,7 +122,7 @@ if [ -n "${BACKUP_DIRECTORY}" ]; then
     mkdir -p "$BACKUP_DIRECTORY"
     chown -R "$BACKUP_DIRECTORY" bridgehead;
   fi
-  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $BACKUP_DIRECTORY"
+  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $(pwd)"
   # Collect all container names that contain '-db'
   BACKUP_SERVICES="$(docker ps --filter name=-db --format "{{.Names}}" | tr "\n" "\ ")"
   log INFO "Performing automatic maintenance: Creating Backups for $BACKUP_SERVICES";

minimal/docker-compose.yml

@@ -35,8 +35,8 @@ services:
     image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
-      HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
-      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+      USERNAME: ${HTTPS_PROXY_USERNAME}
+      PASSWORD: ${HTTPS_PROXY_PASSWORD}
     tmpfs:
       - /var/log/squid
       - /var/spool/squid
@@ -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(`/`)"

minimal/modules/dnpm-compose.yml

@@ -22,7 +22,7 @@ services:
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
     container_name: bridgehead-dnpm-beam-connect
     environment:
       PROXY_URL: http://dnpm-beam-proxy:8081
@@ -34,7 +34,6 @@ services:
       HTTPS_PROXY: http://forward_proxy:3128
       NO_PROXY: dnpm-beam-proxy,dnpm-backend
       RUST_LOG: ${RUST_LOG:-info}
-      NO_AUTH: "true"
     volumes:
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro