Adapt to changes in main

.gitignore

@@ -4,3 +4,6 @@ site-config/*
 
 ## Ignore site configuration
 */docker-compose.override.yml
+
+## MAC OS
+.DS_Store

README.md

@@ -64,7 +64,7 @@ Additionally, your site might use its own proxy. You should discuss this with yo
 
 Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators.
 
-If there is a site firewall, this needs to be configured so that git and Docker can reach the outside world. Another job for the systems administrators.
+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.
 
 Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
 

bbmri/directory-sync.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-function dirSetup() {
-	if [ -n "$DS_DIRECTORY_USER_NAME" ]; then
-		log INFO "Directory sync setup detected -- will start directory sync service."
-		OVERRIDE+=" -f ./$PROJECT/directory-sync-compose.yml"
-	fi
-}

bbmri/docker-compose.yml

@@ -1,5 +1,7 @@
 version: "3.7"
 
+# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see vars.
+
 services:
   blaze:
     image: docker.verbis.dkfz.de/cache/samply/blaze:latest
@@ -19,42 +21,10 @@ services:
       - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
       - "traefik.http.routers.blaze_ccp.tls=true"
 
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
-    container_name: bridgehead-focus
-    environment:
-      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      BEAM_APP_ID_LONG: focus.${PROXY_ID}
-      PROXY_ID: ${PROXY_ID}
-      BLAZE_URL: "http://bridgehead-bbmri-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/root.crt.pem:/conf/root.crt.pem:ro
-
 volumes:
   blaze-data:
 
+# used in modules *-locator.yml
 secrets:
   proxy.pem:
     file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

bbmri/modules/directory-sync.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+if [ -n "${DS_DIRECTORY_USER_NAME}" ]; then
+	log INFO "Directory sync setup detected -- will start directory sync service."
+	OVERRIDE+=" -f ./$PROJECT/modules/directory-sync-compose.yml"
+fi

bbmri/modules/dnpm-setup.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM}" ]; then
-	log DEBUG "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
+	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect

bbmri/modules/eric-compose.yml

@@ -0,0 +1,36 @@
+version: "3.7"
+
+services:
+  focus-eric:
+    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    container_name: bridgehead-focus-eric
+    environment:
+      API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${ERIC_PROXY_ID}
+      PROXY_ID: ${ERIC_PROXY_ID}
+      BLAZE_URL: "http://blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy-eric:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+    depends_on:
+      - "beam-proxy-eric"
+      - "blaze"
+
+  beam-proxy-eric:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-beam-proxy-eric
+    environment:
+      BROKER_URL: ${ERIC_BROKER_URL}
+      PROXY_ID: ${ERIC_PROXY_ID}
+      APP_focus_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/bbmri/modules/eric.root.crt.pem:/conf/root.crt.pem:ro
+

bbmri/modules/eric-setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+if [ "${ENABLE_ERIC}" == "true" ]; then
+	log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
+	OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
+
+	# Set required variables
+	ERIC_BROKER_ID=broker.bbmri.samply.de
+	ERIC_BROKER_URL=https://${ERIC_BROKER_ID}
+	ERIC_PROXY_ID=${SITE_ID}.${ERIC_BROKER_ID}
+	ERIC_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+	ERIC_SUPPORT_EMAIL=bridgehead@helpdesk.bbmri-eric.eu
+fi

bbmri/modules/gbn-compose.yml

@@ -0,0 +1,36 @@
+version: "3.7"
+
+services:
+  focus-gbn:
+    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    container_name: bridgehead-focus-gbn
+    environment:
+      API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${GBN_PROXY_ID}
+      PROXY_ID: ${GBN_PROXY_ID}
+      BLAZE_URL: "http://blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy-gbn:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+    depends_on:
+      - "beam-proxy-gbn"
+      - "blaze"
+
+  beam-proxy-gbn:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-beam-proxy-gbn
+    environment:
+      BROKER_URL: ${GBN_BROKER_URL}
+      PROXY_ID: ${GBN_PROXY_ID}
+      APP_focus_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/bbmri/modules/gbn.root.crt.pem:/conf/root.crt.pem:ro
+

bbmri/modules/gbn-setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+if [ "${ENABLE_GBN}" == "true" ]; then
+	log INFO "GBN setup detected -- will start services for German Biobank Node."
+	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
+
+	# Set required variables
+	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=todo@verbis.dkfz.de
+fi

bbmri/modules/gbn.root.crt.pem

@@ -0,0 +1 @@
+#TODO#

bbmri/vars

@@ -1,9 +1,10 @@
-BROKER_ID=broker.bbmri.samply.de
+# Makes sense for all European Biobanks
-BROKER_URL=https://${BROKER_ID}
+: ${ENABLE_ERIC:=true}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
+
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+# Makes only sense for German Biobanks
+: ${ENABLE_GBN:=false}
+
 FOCUS_RETRY_COUNT=32
-SUPPORT_EMAIL=bridgehead@helpdesk.bbmri-eric.eu
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 for module in $PROJECT/modules/*.sh
@@ -12,6 +13,25 @@ do
     source $module
 done
 
-# This will load directory-sync setup.
+SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
-source $PROJECT/directory-sync.sh
+BROKER_URL_FOR_PREREQ=$ERIC_BROKER_URL
-dirSetup
+
+if [ -n "$GBN_SUPPORT_EMAIL" ]; then
+    SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL
+fi
+
+function do_enroll {
+    COUNT=0
+    if [ "$ENABLE_ERIC" == "true" ]; then
+        do_enroll_inner $ERIC_PROXY_ID $ERIC_SUPPORT_EMAIL
+        COUNT=$((COUNT+1))
+    fi
+    if [ "$ENABLE_GBN" == "true" ]; then
+        do_enroll_inner $GBN_PROXY_ID $GBN_SUPPORT_EMAIL
+        COUNT=$((COUNT+1))
+    fi
+    if [ $COUNT -ge 2 ]; then
+        echo
+        echo "You just received $COUNT certificate signing requests (CSR). Please send $COUNT e-mails, with 1 CSR each, to the respective e-mail address."
+    fi
+}

bridgehead

@@ -73,7 +73,6 @@ case "$ACTION" in
 		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 -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
 		;;
 	stop)
@@ -103,25 +102,17 @@ case "$ACTION" in
 	uninstall)
 		exec ./lib/uninstall-bridgehead.sh $PROJECT
 		;;
+	adduser)
+		loadVars
+		log "INFO" "Adding encrypted credentials in /etc/bridgehead/$PROJECT.local.conf"
+    		read -p "Please choose the component (LDM_AUTH|NNGM_AUTH) you want to add a user to : " COMPONENT
+    		read -p "Please enter a username: " USER
+    		read -s -p "Please enter a password (will not be echoed): "$'\n' PASSWORD
+    		add_basic_auth_user $USER $PASSWORD $COMPONENT $PROJECT
+		;;
 	enroll)
 		loadVars
-
+		do_enroll $PROXY_ID
-		MANUAL_PROXY_ID="${3:-$PROXY_ID}"
-		if [ -z "$MANUAL_PROXY_ID" ]; then
-			log ERROR "No Proxy ID set"
-			exit 1
-		else
-			log INFO "Enrolling Beam Proxy Id $MANUAL_PROXY_ID"
-		fi
-
-		if [ -z "$SUPPORT_EMAIL" ]; then
-			EMAIL_PARAM=""
-		else
-			EMAIL_PARAM="--admin-email $SUPPORT_EMAIL"
-		fi
-			
-		docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $EMAIL_PARAM
-		chmod 600 $PRIVATEKEYFILENAME
 		;;
 	preRun | preUpdate)
 		fixPermissions

ccp/docker-compose.yml

@@ -7,7 +7,6 @@ services:
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx4g"
-      LOG_LEVEL: "debug"
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"

ccp/modules/dnpm-setup.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM}" ]; then
-	log DEBUG "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
+	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect

ccp/modules/id-management-compose.yml

@@ -5,6 +5,7 @@ services:
     container_name: bridgehead-id-manager
     environment:
       TOMCAT_REVERSEPROXY_FQDN: ${HOST}
+      TOMCAT_REVERSEPROXY_SSL: "true"
       MAGICPL_SITE: ${IDMANAGEMENT_FRIENDLY_ID}
       MAGICPL_ALLOWED_ORIGINS: https://${HOST}
       MAGICPL_LOCAL_PATIENTLIST_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

ccp/modules/mtba-setup.sh

@@ -0,0 +1,13 @@
+#!/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 "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
+                      exit 1;
+              fi
+               OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
+       fi
+}

ccp/modules/nngm-compose.yml

@@ -18,7 +18,12 @@ services:
       - "traefik.http.middlewares.connector_strip.stripprefix.prefixes=/nngm-connector"
       - "traefik.http.services.connector.loadbalancer.server.port=8080"
       - "traefik.http.routers.connector.tls=true"
-      - "traefik.http.routers.connector.middlewares=connector_strip,auth"
+      - "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
     volumes:
       - nngm-rest:/var/log
 
+  traefik:
+    labels:
+      - "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"
+
+

ccp/modules/nngm-setup.sh

@@ -0,0 +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/nngm-setup.sh

@@ -1,24 +0,0 @@
-#!/bin/bash
-##nNGM vars:
-#NNGM_MAGICPL_APIKEY
-#NNGM_CTS_APIKEY
-#NNGM_CRYPTKEY
-
-function nngmSetup() {
-	if [ -n "$NNGM_CTS_APIKEY" ]; then
-		log INFO "nNGM setup detected -- will start nNGM Connector."
-		OVERRIDE+=" -f ./$PROJECT/nngm-compose.yml"
-	fi
-	}
-
-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 "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
-			exit 1;
-		fi
-		OVERRIDE+=" -f ./$PROJECT/mtba-compose.yml"
-	fi
-}

ccp/root.crt.pem

@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUMeGRSrNPhRdQ1tU7uK5+lUa4f38wDQYJKoZIhvcNAQEL
+MIIDNTCCAh2gAwIBAgIUN7yzueIZzwpe8PaPEIMY8zoH+eMwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjIwOTI5MTQxMjU1WhcNMzIw
+BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwNTIzMTAxNzIzWhcNMzMw
-OTI2MTQxMzI1WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
+NTIwMTAxNzUzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAMYyroOUeb27mYzClOrjCmgIceLalsFA0aVCh5mZ
+AQEBBQADggEPADCCAQoCggEBAN5JAj+HydSGaxvA0AOcrXVTZ9FfsH0cMVBlQb72
-KtP8+1U3oq/7exP30gXiJojxW7xoerfyQY9s0Sz5YYbxYbuskFOYEtyAILB/pxgd
+bGZgrRvkqtB011TNXZfsHl7rPxCY61DcsDJfFq3+8VHT+S9HE0qV1bEwP+oA3xc4
-+k+J3tlZKolpfmo7WT5tZiHxH/zjrtAYGnuB2xPHRMCWh/tHYrELgXQuilNol24y
+Opq77av77cNNOqDC7h+jyPhHcUaE33iddmrH9Zn2ofWTSkKHHu3PAe5udCrc2QnD
-GBa1plTlARy0aKEDUHp87WLhD2qH7B8sFlLgo0+gunE1UtR2HMSPF45w3VXszyG6
+4PLRF6gqiEY1mcGknJrXj1ff/X0nRY/m6cnHNXz0Cvh8oPOtbdfGgfZjID2/fJNP
-fJNrAj0yPnKy3Dm1BMO3jDO2e0A9lCQ71a4j4TeKePfCk1xCArSu6PpiwiacKplF
+fNoNKqN+5oJAZ+ZZ9id9rBvKj1ivW3F2EoGjZF268SgZzc5QrM/D1OpSBQf5SF/V
-c6CRR6KrWVm2g+8Y2hFcOBG/Py2xusm3PWbpylGq6vtFRkkCAwEAAaN7MHkwDgYD
+qUPcQTgt9ry3YR+SZYazLkfKMEOWEa0WsqJVgXdQ6FyergcCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFEFxD6BQwQO5
+VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFEa70kcseqU5
-xsJ+3cvZypsnh6dDMB8GA1UdIwQYMBaAFEFxD6BQwQO5xsJ+3cvZypsnh6dDMBYG
+bHx2zSt4bG21HokhMB8GA1UdIwQYMBaAFEa70kcseqU5bHx2zSt4bG21HokhMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQB5zTeIhV/3
+A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCGmE7NXW4T
-3Am6O144EFtnIeaZ2w0D6aEHqHAZp50vJv3+uQfOliCOzgw7VDxI4Zz2JALjlR/i
+6J4mV3b132cGEMD7grx5JeiXK5EHMlswUS+Odz0NcBNzhUHdG4WVMbrilHbI5Ua+
-uOYHsu3YIRMIOmPOjqrdDJa6auB0ufL4oUPfCRln7Fh0f3JVlz3BUoHsSDt949p4
+6jdKx5WwnqzjQvElP0MCw6sH/35gbokWgk1provOP99WOFRsQs+9Sm8M2XtMf9HZ
-g0nnsciL2JHuzlqjn7Jyt3L7dAHrlFKulCcuidG5D3cqXrRCbF83f+k3TC/HRiNd
+m3wABwU/O+dhZZ1OT1PjSZD0OKWKqH/KvlsoF5R6P888KpeYFiIWiUNS5z21Jm8A
-25oMi7I4MP/SOCdfQGUGIsHIf/0hSm3pNjDOrC/XuI/8gh2f5io+Y8V+hMwMBcm4
+ZcllJjiRJ60EmDwSUOQVJJSMOvtr6xTZDZLtAKSN8zN08lsNGzyrFwqjDwU0WTqp
-JbH8bdyBB+EIhsNbTwf2MWntD5bmg47sf7hh23aNvKXI67Li1pTI2t1CqiGnFR0U
+scMXEGBsWQjlvxqDnXyljepR0oqRIjOvgrWaIgbxcnu98tK/OdBGwlAPKNUW7Crr
-fCEpeaEAHs0k
+vO+eHxl9iqd4
 -----END CERTIFICATE-----

ccp/vars

@@ -1,4 +1,4 @@
-BROKER_ID=broker.dev.ccp-it.dktk.dkfz.de
+BROKER_ID=broker.ccp-it.dktk.dkfz.de
 BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
 FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
@@ -6,17 +6,15 @@ FOCUS_RETRY_COUNT=32
 SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
-# This will load id-management setup. Effective only if id-management configuration is defined.
+BROKER_URL_FOR_PREREQ=$BROKER_URL
-source $PROJECT/modules/id-management-setup.sh
-idManagementSetup
-# This will load nngm setup. Effective only if nngm configuration is defined.
-source $PROJECT/nngm-setup.sh
-nngmSetup
 
-mtbaSetup
 
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module
 done
+
+idManagementSetup
+nngmSetup
+mtbaSetup

lib/functions.sh

@@ -9,14 +9,6 @@ detectCompose() {
 	fi
 }
 
-getLdmPassword() {
-	if [ -n "$LDM_PASSWORD" ]; then
-		docker run --rm docker.verbis.dkfz.de/cache/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"
@@ -34,7 +26,7 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
 	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
@@ -180,6 +172,43 @@ function bk_is_running {
 	fi
 }
 
-##Setting Network properties
+function do_enroll_inner {
-# currently not needed
+	PARAMS=""
-#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 $1}');
+	
+	MANUAL_PROXY_ID="${1:-$PROXY_ID}"
+	if [ -z "$MANUAL_PROXY_ID" ]; then
+		log ERROR "No Proxy ID set"
+		exit 1
+	else
+		log INFO "Enrolling Beam Proxy Id $MANUAL_PROXY_ID"
+	fi
+
+	SUPPORT_EMAIL="${2:-$SUPPORT_EMAIL}"
+	if [ -n "$SUPPORT_EMAIL" ]; then
+		PARAMS+="--admin-email $SUPPORT_EMAIL"
+	fi
+
+	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
+}
+
+function do_enroll {
+	do_enroll_inner $@
+}
+
+add_basic_auth_user() {
+   USER="${1}"
+   PASSWORD="${2}"
+   NAME="${3}"
+   PROJECT="${4}"
+   FILE="/etc/bridgehead/${PROJECT}.local.conf"
+   ENCRY_CREDENTIALS="$(docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $USER $PASSWORD  | tr -d '\n' | tr -d '\r')"
+   if [ -f $FILE ] && grep -R -q "$NAME=" $FILE # if a specific basic auth user already exists:
+   then
+     sed -i "/$NAME/ s|='|='$ENCRY_CREDENTIALS,|" $FILE
+   else
+     echo -e "\n## Basic Authentication Credentials for:\n$NAME='$ENCRY_CREDENTIALS'" >> $FILE;
+   fi
+ 	log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
+   sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
+}

lib/install-bridgehead.sh

@@ -29,12 +29,16 @@ 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 "$LDM_PASSWORD" ]; then
+if [ -z "$LDM_AUTH" ]; then
-  log "INFO" "Now generating a password for the local data management. Please save the password for your ETL process!"
+  log "INFO" "Now generating basic auth for the local data management (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 $PROJECT $generated_passwd "LDM_AUTH" $PROJECT
+fi
 
-  log "INFO" "Your generated credentials are:\n            user: $PROJECT\n            password: $generated_passwd"
+if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
-  echo -e "## Local Data Management Basic Authentication\n# User: $PROJECT\nLDM_PASSWORD=$generated_passwd" >> /etc/bridgehead/${PROJECT}.local.conf;
+  log "INFO" "Now generating basic auth for nNGM upload API (see adduser in bridgehead for more information). "
+  generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
+  add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
 fi
 
 log "INFO" "Registering system units for bridgehead and bridgehead-update"

lib/prepare-system.sh

@@ -71,8 +71,12 @@ if [ -d /etc/bridgehead ]; then
     fi
 elif [[ "$DEV_MODE" == "NODEV" ]]; then
     log "INFO" "Now cloning your site configuration repository for you."
+    if [ -z "$site" ]; then
         read -p "Please enter your site: " site
+    fi
+    if [ -z "$access_token" ]; then
         read -s -p "Please enter the bridgehead's access token for your site configuration repository (will not be echoed): " access_token
+    fi
     site_configuration_repository_url="https://bytoken:${access_token}@${site_configuration_repository_middle}$(echo $site | tr '[:upper:]' '[:lower:]').git"
     git clone $site_configuration_repository_url /etc/bridgehead
     if [ $? -gt 0 ]; then

lib/prerequisites.sh

@@ -62,6 +62,34 @@ if [ -e /etc/bridgehead/vault.conf ]; then
   fi
 fi
 
+log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
+
+source /etc/bridgehead/${PROJECT}.conf
+source ${PROJECT}/vars
+
+set +e
+SERVERTIME="$(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
+	log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
+	log WARN "Unable to check clock skew due to previous error."
+else
+	log INFO "Checking clock skew ..."
+
+	SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
+	MYTIME=$(date +%s)
+	SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
+	SKEW=$(echo $SKEW | awk -F- '{print $NF}')
+	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
+	elif [ $SKEW -ge 60 ]; then
+		log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
+	fi
+fi
+
 checkPrivKey() {
   if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
     log INFO "Success - private key found."
@@ -69,8 +97,6 @@ checkPrivKey() {
     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
 }
 
@@ -80,4 +106,7 @@ else
   checkPrivKey || exit 1
 fi
 
+log INFO "Success - all prerequisites are met!"
+hc_send log "Success - all prerequisites are met!"
+
 exit 0

lib/update-bridgehead.sh

@@ -139,6 +139,15 @@ else
   log WARN "Automated backups are disabled (variable AUTO_BACKUPS != \"true\")"
 fi
 
+#TODO: the following block can be deleted after successful update at all sites
+if [ ! -z "$LDM_PASSWORD" ]; then
+  FILE="/etc/bridgehead/$PROJECT.local.conf"
+  log "INFO" "Migrating LDM_PASSWORD to encrypted credentials in $FILE"
+  add_basic_auth_user $PROJECT $LDM_PASSWORD "LDM_AUTH" $PROJECT
+  add_basic_auth_user $PROJECT $LDM_PASSWORD "NNGM_AUTH" $PROJECT
+  sed -i "/LDM_PASSWORD/{d;}" $FILE
+fi
+
 exit 0
 
 # TODO: Print last commit explicit

minimal/docker-compose.yml

@@ -21,7 +21,7 @@ services:
       - "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=${LDM_LOGIN}"
+      - "traefik.http.middlewares.auth.basicauth.users=${LDM_AUTH}"
     ports:
       - 80:80
       - 443:443
@@ -37,6 +37,9 @@ services:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
       USERNAME: ${HTTPS_PROXY_USERNAME}
       PASSWORD: ${HTTPS_PROXY_PASSWORD}
+    tmpfs:
+      - /var/log/squid
+      - /var/spool/squid
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro