Martin's change

Merge develop into main

.github/CODEOWNERS

@@ -0,0 +1 @@
+*  @samply/bridgehead-developers

README.md

@@ -76,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
   * 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))
+  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
     * hub.docker.com
     * registry-1.docker.io
     * production.cloudflare.docker.com
@@ -154,7 +154,7 @@ Pay special attention to:
 Clone the bridgehead repository:
 ```shell
 sudo mkdir -p /srv/docker/
-sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
+sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
 ```
 
 Then, run the installation script:

bbmri/docker-compose.yml

@@ -4,7 +4,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"

bridgehead

@@ -53,17 +53,44 @@ case "$PROJECT" in
 		;;
 esac
 
+# Loads config variables and runs the projects setup script
 loadVars() {
-	# Load variables from /etc/bridgehead and /srv/docker/bridgehead
 	set -a
+	# Source the project specific config file
 	source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
+	# Source the project specific local config file if present
+	# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
 	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
+	# Set execution environment on main default to prod else test
+	if [[ -z "${ENVIRONMENT+x}" ]]; then
+		if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
+			ENVIRONMENT="production"
+		else
+			ENVIRONMENT="test"
+		fi
+	fi
+	# Source the versions of the images components 
+	case "$ENVIRONMENT" in
+		"production")
+			source ./versions/prod
+			;;
+		"test")
+			source ./versions/test
+			;;
+		*)
+			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			source ./versions/prod
+			;;
+	esac
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
 	setHostname
 	optimizeBlazeMemoryUsage
+	# Run project specific setup if it exists
+	# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
+	# This is also where projects specify which modules to load
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -79,26 +106,6 @@ loadVars() {
 	fi
 	detectCompose
 	setupProxy
-
-	# Set some project-independent default values
-	: ${ENVIRONMENT:=production}
-	export ENVIRONMENT
-
-	case "$ENVIRONMENT" in
-		"production")
-			export FOCUS_TAG=main
-			export BEAM_TAG=main
-			;;
-		"test")
-			export FOCUS_TAG=develop
-			export BEAM_TAG=develop
-			;;
-		*)
-			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
-			export FOCUS_TAG=main
-			export BEAM_TAG=main
-			;;
-	esac
 }
 
 case "$ACTION" in

cce/docker-compose.yml

@@ -2,13 +2,14 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-cce-blaze
     environment:
       BASE_URL: "http://bridgehead-cce-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -31,6 +32,10 @@ services:
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    volumes:
+      - /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:
       - "beam-proxy"
       - "blaze"

cce/queries_to_cache.conf

@@ -0,0 +1,2 @@
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ccp/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
@@ -35,7 +35,7 @@ services:
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
-      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
+      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:
       - "beam-proxy"
       - "blaze"

ccp/modules/blaze-secondary-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze-secondary
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

ccp/modules/obds2fhir-rest-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
   obds2fhir-rest:
     container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
+    image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
     environment:
       IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
       MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

ccp/queries_to_cache.conf

@@ -1,2 +1,2 @@
-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
-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ccp/vars

@@ -30,3 +30,11 @@ idManagementSetup
 mtbaSetup
 obds2fhirRestSetup
 blazeSecondarySetup
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+transfairSetup

dhki/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-dhki-blaze
     environment:
       BASE_URL: "http://bridgehead-dhki-blaze:8080"
@@ -33,7 +33,7 @@ services:
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
     volumes:
-      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
+      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:
       - "beam-proxy"
       - "blaze"

dhki/vars

@@ -18,3 +18,11 @@ done
 
 idManagementSetup
 obds2fhirRestSetup
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+transfairSetup

itcc/docker-compose.yml

@@ -2,13 +2,14 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-itcc-blaze
     environment:
       BASE_URL: "http://bridgehead-itcc-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -31,6 +32,10 @@ services:
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    volumes:
+      - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:
       - "beam-proxy"
       - "blaze"

itcc/queries_to_cache.conf

@@ -0,0 +1,2 @@
+bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
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

kr/docker-compose.yml

@@ -6,7 +6,7 @@ services:
       replicas: 0 #deactivate landing page
 
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"

lib/functions.sh

@@ -313,15 +313,82 @@ function sync_secrets() {
         -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
         -e PROXY_ID=$PROXY_ID \
         -e BROKER_URL=$BROKER_URL \
-        -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
+        -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
         -e SECRET_DEFINITIONS=$secret_sync_args \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
 
     set -a # Export variables as environment variables
-    source /var/cache/bridgehead/secrets/*
+    source /var/cache/bridgehead/secrets/oidc
     set +a # Export variables in the regular way
 }
 
+function secret_sync_gitlab_token() {
+    # Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
+    local gitlab
+    case "$(git -C /etc/bridgehead remote get-url origin)" in
+        *git.verbis.dkfz.de*) gitlab=verbis;;
+        *gitlab.bbmri-eric.eu*) gitlab=bbmri;;
+        *)
+            log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
+            return
+            ;;
+    esac
+
+    if [ "$PROJECT" == "bbmri" ]; then
+        # If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
+        proxy_id=$ERIC_PROXY_ID
+        broker_url=$ERIC_BROKER_URL
+        broker_id=$ERIC_BROKER_ID
+        root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
+    else
+        proxy_id=$PROXY_ID
+        broker_url=$BROKER_URL
+        broker_id=$BROKER_ID
+        root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
+    fi
+
+    # Create a temporary directory for Secret Sync that is valid per boot
+    secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
+    mkdir -p $secret_sync_tempdir
+
+    # Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
+    # If it is missing or expired, Secret Sync will create a new token and write it to the file.
+    # The git credential helper reads the token from the file during git pull.
+    log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
+    docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
+    docker run --rm \
+        -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
+        -v $root_crt_file:/run/secrets/root.crt.pem:ro \
+        -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
+        -v $secret_sync_tempdir:/secret-sync/ \
+        -e CACHE_PATH=/secret-sync/gitlab-token \
+        -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
+        -e NO_PROXY=localhost,127.0.0.1 \
+        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
+        -e PROXY_ID=$proxy_id \
+        -e BROKER_URL=$broker_url \
+        -e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
+        -e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
+        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
+    if [ $? -eq 0 ]; then
+        log "INFO" "Secret Sync was successful"
+        # In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
+        CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
+        git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
+        # Set the git credential helper
+        git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
+    else
+        log "WARN" "Secret Sync failed"
+        # Remove the git credential helper
+        git -C /etc/bridgehead config --unset credential.helper
+    fi
+
+    # In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
+    # Let's remove it to avoid confusion. This line can be removed at some point the future when we
+    # believe that it was removed on all/most production servers.
+    git -C /srv/docker/bridgehead config --unset credential.helper
+}
+
 capitalize_first_letter() {
     input="$1"
     capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"

lib/gitlab-token-helper.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+[ "$1" = "get" ] || exit
+
+source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
+
+# Any non-empty username works, only the token matters
+cat << EOF
+username=bk
+password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
+EOF

lib/gitpassword.sh

@@ -1,41 +0,0 @@
-#!/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

lib/install-bridgehead.sh

@@ -41,6 +41,14 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
   add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
 fi
 
+if [ -z "$TRANSFAIR_AUTH" ]; then
+  if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
+    log "INFO" "Now generating basic auth user for transfair API (see adduser in bridgehead for more information). "
+    generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
+    add_basic_auth_user "transfair" $generated_passwd "TRANSFAIR_AUTH" $PROJECT
+  fi
+fi
+
 log "INFO" "Registering system units for bridgehead and bridgehead-update"
 cp -v \
     lib/systemd/bridgehead\@.service \

lib/update-bridgehead.sh

@@ -19,7 +19,7 @@ fi
 
 hc_send log "Checking for bridgehead updates ..."
 
-CONFFILE=/etc/bridgehead/$1.conf
+CONFFILE=/etc/bridgehead/$PROJECT.conf
 
 if [ ! -e $CONFFILE ]; then
   fail_and_report 1 "Configuration file $CONFFILE not found."
@@ -33,7 +33,7 @@ export SITE_ID
 checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
 checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
 
-CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
+secret_sync_gitlab_token
 
 CHANGES=""
 
@@ -45,10 +45,6 @@ for DIR in /etc/bridgehead $(pwd); do
   if [ -n "$OUT" ]; then
     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 $DIR rev-parse --verify HEAD)"
   if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
     log "INFO" "Git is using no proxy!"

modules/ssh-tunnel-compose.yml

@@ -0,0 +1,17 @@
+version: "3.7"
+
+services:
+  ssh-tunnel:
+    image: docker.verbis.dkfz.de/cache/samply/ssh-tunnel
+    container_name: bridgehead-ccp-ssh-tunnel
+    environment:
+      SSH_TUNNEL_USERNAME: "${SSH_TUNNEL_USERNAME}"
+      SSH_TUNNEL_HOST: "${SSH_TUNNEL_HOST}"
+      SSH_TUNNEL_PORT: "${SSH_TUNNEL_PORT:-22}"
+    volumes:
+      - "/etc/bridgehead/ssh-tunnel.conf:/ssh-tunnel.conf:ro"
+    secrets:
+      - privkey
+secrets:
+  privkey:
+    file: /etc/bridgehead/pki/ssh-tunnel.priv.pem

modules/ssh-tunnel-setup.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_SSH_TUNNEL" ]; then
+	log INFO "SSH Tunnel setup detected -- will start SSH Tunnel."
+	OVERRIDE+=" -f ./$PROJECT/modules/ssh-tunnel-compose.yml"
+fi

modules/ssh-tunnel.md

@@ -0,0 +1,19 @@
+# SSH Tunnel Module
+
+This module enables SSH tunneling capabilities for the Bridgehead installation.
+The primary use case for this is to connect bridgehead components that are hosted externally due to security concerns.
+To connect the new components to the locally running bridgehead infra one is supposed to write a docker-compose.override.yml changing the urls to point to the corresponding forwarded port of the ssh-tunnel container.
+
+## Configuration Variables
+
+- `ENABLE_SSH_TUNNEL`: Required to enable the module
+- `SSH_TUNNEL_USERNAME`: Username for SSH connection
+- `SSH_TUNNEL_HOST`: Target host for SSH tunnel
+- `SSH_TUNNEL_PORT`: SSH port (defaults to 22)
+
+## Configuration Files
+
+The module requires the following files to be present:
+
+- `/etc/bridgehead/ssh-tunnel.conf`: SSH tunnel configuration file. Detailed information can be found [here](https://github.com/samply/ssh-tunnel?tab=readme-ov-file#configuration).
+- `/etc/bridgehead/pki/ssh-tunnel.priv.pem`: The SSH private key used to connect to the `SSH_TUNNEL_HOST`. **Passphrases for the key are not supported!**

modules/transfair-compose.yml

@@ -0,0 +1,82 @@
+
+services:
+  transfair:
+    image: docker.verbis.dkfz.de/cache/samply/transfair:latest
+    container_name: bridgehead-transfair
+    environment:
+      # NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
+      - TTP_URL
+      - TTP_ML_API_KEY
+      - TTP_GW_SOURCE
+      - TTP_GW_DOMAIN
+      - TTP_TYPE
+      - TTP_AUTH
+      - PROJECT_ID_SYSTEM
+      - FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
+      - FHIR_INPUT_URL=${FHIR_INPUT_URL}
+      - FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
+      - FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
+      - FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
+      - FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
+      - EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
+      - DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
+      - RUST_LOG=${RUST_LOG:-info}
+      - TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
+    volumes:
+      - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.middlewares.transfair-strip.stripprefix.prefixes=/transfair"
+      - "traefik.http.routers.transfair.middlewares=transfair-strip,transfair-auth"
+      - "traefik.http.routers.transfair.rule=PathPrefix(`/transfair`)"
+      - "traefik.http.services.transfair.loadbalancer.server.port=8080"
+      - "traefik.http.routers.transfair.tls=true"
+  
+  traefik:
+    labels:
+      - "traefik.http.middlewares.transfair-auth.basicauth.users=${TRANSFAIR_AUTH}"
+
+  transfair-input-blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-transfair-input-blaze
+    environment:
+      BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1024m"
+      DB_BLOCK_CACHE_SIZE: 1024
+      CQL_EXPR_CACHE_SIZE: 8
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "transfair-input-blaze-data:/app/data"
+    profiles: ["transfair-input-blaze"]
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
+      - "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
+      - "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
+      - "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
+      - "traefik.http.routers.transfair-input-blaze.tls=true"
+
+  transfair-request-blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-transfair-requests-blaze
+    environment:
+      BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1024m"
+      DB_BLOCK_CACHE_SIZE: 1024
+      CQL_EXPR_CACHE_SIZE: 8
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "transfair-request-blaze-data:/app/data"
+    profiles: ["transfair-request-blaze"]
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.transfair-request-blaze.rule=PathPrefix(`/data-requests`)"
+      - "traefik.http.middlewares.transfair-request-strip.stripprefix.prefixes=/data-requests"
+      - "traefik.http.services.transfair-request-blaze.loadbalancer.server.port=8080"
+      - "traefik.http.routers.transfair-request-blaze.middlewares=transfair-request-strip,transfair-auth"
+      - "traefik.http.routers.transfair-request-blaze.tls=true"
+
+volumes:
+  transfair-input-blaze-data:
+  transfair-request-blaze-data:

modules/transfair-setup.sh

@@ -0,0 +1,31 @@
+#!/bin/bash -e
+
+function transfairSetup() {
+    if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
+        echo "Starting transfair."
+	    OVERRIDE+=" -f ./modules/transfair-compose.yml"
+	    if [ -n "$FHIR_INPUT_URL" ]; then
+		    log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
+	    else
+		    log INFO "TransFAIR input fhir store not set writing to internal blaze"
+		    FHIR_INPUT_URL="http://transfair-input-blaze:8080"
+		    OVERRIDE+=" --profile transfair-input-blaze"
+	    fi
+	    if [ -n "$FHIR_REQUEST_URL" ]; then
+		    log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
+	    else
+		    log INFO "TransFAIR request fhir store not set writing to internal blaze"
+		    FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
+		    OVERRIDE+=" --profile transfair-request-blaze"
+	    fi
+	    if [ -n "$TTP_GW_SOURCE" ]; then
+		    log INFO "TransFAIR configured with greifswald as ttp"
+		    TTP_TYPE="greifswald"
+	    elif [ -n "$TTP_ML_API_KEY" ]; then
+		    log INFO "TransFAIR configured with mainzelliste as ttp"
+		    TTP_TYPE="mainzelliste"
+        else
+		    log INFO "TransFAIR configured without ttp"
+	    fi
+    fi
+}

versions/prod

@@ -0,0 +1,3 @@
+FOCUS_TAG=main
+BEAM_TAG=main
+BLAZE_TAG=0.32

versions/test

@@ -0,0 +1,3 @@
+FOCUS_TAG=develop
+BEAM_TAG=develop
+BLAZE_TAG=main