Remove remaining secret

README.md

@@ -85,8 +85,6 @@ The following URLs need to be accessible (prefix with `https://`):
     * hub.docker.com
     * registry-1.docker.io
     * production.cloudflare.docker.com
-  * GitHub Container Registry - (for use of DNPM:DIP)
-    * ghcr.io
 * To report bridgeheads operational status
   * healthchecks.verbis.dkfz.de
 * only for DKTK/CCP
@@ -97,7 +95,7 @@ The following URLs need to be accessible (prefix with `https://`):
 * only for German Biobank Node
   * broker.bbmri.de
 
-> 📝 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, *.ghcr.io, *.samply.de, *.bbmri.de.
+> 📝 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).
 

bbmri/docker-compose.yml

@@ -26,7 +26,3 @@ services:
 volumes:
   blaze-data:
 
-# used in modules *-locator.yml
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

bbmri/modules/eric-compose.yml

@@ -26,11 +26,11 @@ services:
       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/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 

bbmri/modules/exporter-compose.yml

@@ -36,7 +36,7 @@ services:
       - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
 
     volumes:
-      - "/var/cache/bridgehead/bbmri/exporter-files:/app/exporter-files/output"
+      - "/var/cache/bridgehead/bbmri/exporter-files:/app/exporter-files/output:z"
 
   exporter-db:
     image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
@@ -47,7 +47,7 @@ services:
       POSTGRES_DB: "exporter"
     volumes:
       # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/bbmri/exporter-db:/var/lib/postgresql/data"
+      - "/var/cache/bridgehead/bbmri/exporter-db:/var/lib/postgresql/data:Z"
 
   reporter:
     image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
@@ -69,7 +69,7 @@ services:
     # There is a risk that the bridgehead restarts, losing the already created export.
 
     volumes:
-      - "/var/cache/bridgehead/bbmri/reporter-files:/app/reports"
+      - "/var/cache/bridgehead/bbmri/reporter-files:/app/reports:z"
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.reporter_bbmri.rule=PathPrefix(`/bbmri-reporter`)"

bbmri/modules/gbn-compose.yml

@@ -26,11 +26,11 @@ services:
       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/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 

bbmri/modules/teiler-compose.yml

@@ -19,7 +19,7 @@ services:
       HTTP_RELATIVE_PATH: "/bbmri-teiler"
 
   teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
     container_name: bridgehead-teiler-dashboard
     labels:
       - "traefik.enable=true"
@@ -32,6 +32,9 @@ services:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
       TEILER_BACKEND_URL: "/bbmri-teiler-backend"
       TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
+      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
       TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
       TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -39,6 +42,8 @@ services:
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
       TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
+      TEILER_USER: "${OIDC_USER_GROUP}"
+      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
       REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb"
       EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"
 

bridgehead

@@ -35,9 +35,6 @@ case "$PROJECT" in
 	cce)
 		#nothing extra to do
 		;;
-	pscc)
-		#nothing extra to do
-		;;
 	itcc)
 		#nothing extra to do
 		;;

cce/docker-compose.yml

@@ -35,7 +35,7 @@ services:
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
-      - /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
+      - /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
     depends_on:
       - "beam-proxy"
       - "blaze"
@@ -57,12 +57,10 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 
 
 volumes:
   blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

cce/modules/exporter-compose.yml

@@ -37,7 +37,7 @@ services:
       - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
 
     volumes:
-      - "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output"
+      - "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output:z"
 
   exporter-db:
     image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
@@ -48,7 +48,7 @@ services:
       POSTGRES_DB: "exporter"
     volumes:
       # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/cce/exporter-db:/var/lib/postgresql/data"
+      - "/var/cache/bridgehead/cce/exporter-db:/var/lib/postgresql/data:Z"
 
   reporter:
     image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
@@ -70,7 +70,7 @@ services:
     # There is a risk that the bridgehead restarts, losing the already created export.
 
     volumes:
-      - "/var/cache/bridgehead/cce/reporter-files:/app/reports"
+      - "/var/cache/bridgehead/cce/reporter-files:/app/reports:z"
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.reporter_cce.rule=PathPrefix(`/cce-reporter`)"

cce/modules/teiler-compose.yml

@@ -19,7 +19,7 @@ services:
       HTTP_RELATIVE_PATH: "/cce-teiler"
 
   teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
     container_name: bridgehead-teiler-dashboard
     labels:
       - "traefik.enable=true"
@@ -32,6 +32,9 @@ services:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
       TEILER_BACKEND_URL: "/cce-teiler-backend"
       TEILER_DASHBOARD_URL: "/cce-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
+      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
       TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
       TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -39,6 +42,8 @@ services:
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
       TEILER_ORCHESTRATOR_URL: "/cce-teiler"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
+      TEILER_USER: "${OIDC_USER_GROUP}"
+      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
       REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
       EXPORTER_DEFAULT_TEMPLATE_ID: "cce"
 

ccp/docker-compose.yml

@@ -35,7 +35,7 @@ services:
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
-      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
+      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
     depends_on:
       - "beam-proxy"
       - "blaze"
@@ -57,11 +57,9 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 
 volumes:
   blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

ccp/modules/datashield-compose.yml

@@ -25,7 +25,7 @@ services:
       APP_CONTEXT_PATH: "/opal"
       OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
       OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
-      OIDC_URL: "${OIDC_PRIVATE_URL}"
+      OIDC_URL: "${OIDC_URL}"
       OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
       OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
       OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
@@ -35,10 +35,10 @@ services:
       BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
       BEAM_DATASHIELD_PROXY: request-manager
     volumes:
-      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
-    secrets:
-      - opal-cert.pem
-      - opal-key.pem
+      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv:Z" # Opal metadata
+      # secrets don't seem to allow us to specify Z/z
+      - /tmp/bridgehead/opal-cert.pem:/run/secrets/opal-cert.pem:z
+      - /tmp/bridgehead/opal-key.pem:/run/secrets/opal-key.pem:Z
 
   opal-db:
     container_name: bridgehead-opal-db
@@ -48,7 +48,7 @@ services:
       POSTGRES_USER: "opal"
       POSTGRES_DB: "opal"
     volumes:
-      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
+      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data:Z" # Opal project data (imported from exporter)
 
   opal-rserver:
     container_name: bridgehead-opal-rserver
@@ -67,20 +67,14 @@ services:
       DISCOVERY_URL: "./map/central.json"
       LOCAL_TARGETS_FILE: "./map/local.json"
       NO_AUTH: "true"
-    secrets:
-      - opal-cert.pem
     depends_on:
       - beam-proxy
     volumes:
-      - /tmp/bridgehead/opal-map/:/map/:ro
+      - /tmp/bridgehead/opal-map/:/map/:ro,Z
+      # secrets don't seem to allow us to specify Z/z
+      - /tmp/bridgehead/opal-cert.pem:/run/secrets/opal-cert.pem:z
 
   beam-proxy:
     environment:
       APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
       APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
-
-secrets:
-  opal-cert.pem:
-    file: /tmp/bridgehead/opal-cert.pem
-  opal-key.pem:
-    file: /tmp/bridgehead/opal-key.pem

ccp/modules/dnpm-compose.yml

@@ -25,7 +25,7 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
+      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro,Z
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

ccp/modules/dnpm-node-compose.yml

@@ -12,13 +12,13 @@ services:
       MYSQL_ROOT_HOST: "%"
       MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
     volumes:
-      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
+      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql:Z
 
   dnpm-authup:
     image: authup/authup:latest
     container_name: bridgehead-dnpm-authup
     volumes:
-      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
+      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable:Z
     depends_on:
       dnpm-mysql:
         condition: service_healthy
@@ -43,7 +43,7 @@ services:
       - "traefik.http.routers.dnpm-auth.tls=true"
 
   dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:${DNPM_IMAGE_TAG:-latest}
+    image: ghcr.io/dnpm-dip/portal:latest
     container_name: bridgehead-dnpm-portal
     environment:
       - NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
 
   dnpm-backend:
     container_name: bridgehead-dnpm-backend
-    image: ghcr.io/dnpm-dip/backend:${DNPM_IMAGE_TAG:-latest}
+    image: ghcr.io/dnpm-dip/backend:latest
     environment:
       - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
       - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
@@ -68,7 +68,7 @@ services:
       - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
     volumes:
       - /etc/bridgehead/dnpm/config:/dnpm_config
-      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
+      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data:Z
     depends_on:
       dnpm-authup:
         condition: service_healthy

ccp/modules/exporter-compose.yml

@@ -24,7 +24,7 @@ services:
       - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
       - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
     volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
+      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output:z"
 
   exporter-db:
     image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
@@ -35,7 +35,7 @@ services:
       POSTGRES_DB: "exporter"
     volumes:
       # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
+      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data:Z"
 
   reporter:
     image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
@@ -57,7 +57,7 @@ services:
     # There is a risk that the bridgehead restarts, losing the already created export.
 
     volumes:
-      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
+      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports:z"
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"

ccp/modules/fhir2sql-compose.yml

@@ -22,7 +22,7 @@ services:
       POSTGRES_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
       POSTGRES_DB: "dashboard"
     volumes:
-      - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
+      - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data:Z"
 
   focus:
     environment:

ccp/modules/id-management-compose.yml

@@ -14,7 +14,6 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
-      MAGICPL_OIDC_PROVIDER: ${OIDC_PRIVATE_URL}
     depends_on:
       - patientlist
       - traefik-forward-auth
@@ -63,7 +62,7 @@ services:
     volumes:
       - "patientlist-db-data:/var/lib/postgresql/data"
       # NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
-      - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
+      - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/:Z"
 
   traefik-forward-auth:
     image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
@@ -72,14 +71,12 @@ services:
       - https_proxy=http://forward_proxy:3128
       - OAUTH2_PROXY_PROVIDER=oidc
       - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
-      - OAUTH2_PROXY_OIDC_ISSUER_URL=${OIDC_PRIVATE_URL}
-      - OAUTH2_PROXY_CLIENT_ID=${OIDC_PRIVATE_CLIENT_ID}
-      - OAUTH2_PROXY_CLIENT_SECRET=${OIDC_CLIENT_SECRET}
+      - OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master
+      - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
+      - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
       - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
       - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
       - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
-      - OAUTH2_PROXY_COOKIE_REFRESH=4m
-      - OAUTH2_PROXY_COOKIE_EXPIRE=24h
       - OAUTH2_PROXY_HTTP_ADDRESS=:4180
       - OAUTH2_PROXY_REVERSE_PROXY=true
       - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
@@ -90,8 +87,8 @@ services:
       - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
       - OAUTH2_PROXY_SET_XAUTHREQUEST=true
       # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
-      - OAUTH2_PROXY_ALLOWED_GROUPS=${OIDC_PSP_GROUP}
-      - OAUTH2_PROXY_OIDC_GROUPS_CLAIM=${OIDC_GROUP_CLAIM}
+      - OAUTH2_PROXY_COOKIE_REFRESH=60s
+      - OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
       - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
     labels:
       - "traefik.enable=true"

ccp/modules/id-management-setup.sh

@@ -14,8 +14,6 @@ function idManagementSetup() {
 
 		# Ensure old ids are working !!!
 		export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID")
-
-		add_private_oidc_redirect_url "/oauth2-idm/callback"
 	fi
 }
 

ccp/modules/mtba-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   mtba:
-    image: docker.verbis.dkfz.de/cache/samply/mtba:${MTBA_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/mtba:develop
     container_name: bridgehead-mtba
     environment:
       BLAZE_STORE_URL: http://blaze:8080
@@ -22,14 +22,8 @@ services:
       HTTP_RELATIVE_PATH: "/mtba"
       OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
       OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      # TODO: Add following variables after moving to Authentik:
-      #OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      #OIDC_URL: "${OIDC_URL}"
-      # TODO: Remove following variables after moving to Authentik:
-      # Please add KECLOAK_CLIENT_SECRET in ccp.conf
-      OIDC_CLIENT_SECRET: "${KEYCLOAK_CLIENT_SECRET}"
-      OIDC_URL: "https://login.verbis.dkfz.de/realms/test-realm-01"
-      OIDC_ADMIN_URL: "https://login.verbis.dkfz.de/admin/realms/test-realm-01"
+      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      OIDC_URL: "${OIDC_URL}"
 
     labels:
       - "traefik.enable=true"
@@ -38,8 +32,8 @@ services:
       - "traefik.http.routers.mtba_ccp.tls=true"
 
     volumes:
-      - /var/cache/bridgehead/ccp/mtba/input:/app/input
-      - /var/cache/bridgehead/ccp/mtba/persist:/app/persist
+      - /var/cache/bridgehead/ccp/mtba/input:/app/input:z
+      - /var/cache/bridgehead/ccp/mtba/persist:/app/persist:z
 
   # TODO: Include CBioPortal in Deployment ...
   # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!

ccp/modules/teiler-compose.yml

@@ -19,7 +19,7 @@ services:
       HTTP_RELATIVE_PATH: "/ccp-teiler"
 
   teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
     container_name: bridgehead-teiler-dashboard
     labels:
       - "traefik.enable=true"

ccp/vars

@@ -10,11 +10,9 @@ BROKER_URL_FOR_PREREQ=$BROKER_URL
 
 OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
 OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
-OIDC_PSP_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_PSP"
 OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
 OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
-OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
-OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
+OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
 OIDC_GROUP_CLAIM="groups"
 
 for module in $PROJECT/modules/*.sh

dhki/docker-compose.yml

@@ -33,13 +33,13 @@ services:
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
     volumes:
-      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
+      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
     depends_on:
       - "beam-proxy"
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
@@ -55,12 +55,10 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 
 
 volumes:
   blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

itcc/docker-compose.yml

@@ -35,7 +35,7 @@ services:
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
-      - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
+      - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
     depends_on:
       - "beam-proxy"
       - "blaze"
@@ -51,18 +51,14 @@ services:
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
       ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
     depends_on:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 
 
 volumes:
   blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

kr/docker-compose.yml

@@ -40,7 +40,7 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
@@ -56,12 +56,10 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 
 
 volumes:
   blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

kr/modules/exporter-compose.yml

@@ -1,10 +1,9 @@
 version: "3.7"
 
 services:
-
   exporter:
     image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-kr-exporter
+    container_name: bridgehead-ccp-exporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
       LOG_LEVEL: "INFO"
@@ -13,51 +12,39 @@ services:
       EXPORTER_DB_USER: "exporter"
       EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
       EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/kr-exporter"
+      HTTP_RELATIVE_PATH: "/ccp-exporter"
       SITE: "${SITE_ID}"
       HTTP_SERVLET_REQUEST_SCHEME: "https"
       OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.exporter_kr.rule=PathPrefix(`/kr-exporter`)"
-      - "traefik.http.services.exporter_kr.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_kr.tls=true"
-      - "traefik.http.middlewares.exporter_kr_strip.stripprefix.prefixes=/kr-exporter"
-      - "traefik.http.routers.exporter_kr.middlewares=exporter_kr_strip"
-      # Main router
-      - "traefik.http.routers.exporter_kr.priority=20"
-
-      # API router
-      - "traefik.http.routers.exporter_kr_api.middlewares=exporter_kr_strip,exporter_auth"
-      - "traefik.http.routers.exporter_kr_api.rule=PathRegexp(`/kr-exporter/.+`)"
-      - "traefik.http.routers.exporter_kr_api.tls=true"
-      - "traefik.http.routers.exporter_kr_api.priority=25"
-
-      # Shared middlewares
-      - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
-
+      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
+      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_ccp.tls=true"
+      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
+      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
     volumes:
-      - "/var/cache/bridgehead/kr/exporter-files:/app/exporter-files/output"
+      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output:z"
 
   exporter-db:
     image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-kr-exporter-db
+    container_name: bridgehead-ccp-exporter-db
     environment:
       POSTGRES_USER: "exporter"
       POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
       POSTGRES_DB: "exporter"
     volumes:
       # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/kr/exporter-db:/var/lib/postgresql/data"
+      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data:Z"
 
   reporter:
     image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-kr-reporter
+    container_name: bridgehead-ccp-reporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
       LOG_LEVEL: "INFO"
       CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/kr-reporter"
+      HTTP_RELATIVE_PATH: "/ccp-reporter"
       SITE: "${SITE_ID}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
       EXPORTER_URL: "http://exporter:8092"
@@ -65,23 +52,16 @@ services:
       HTTP_SERVLET_REQUEST_SCHEME: "https"
 
     # In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
-    # However, in the first executions in the kr sites, this volume seems to be very important. A report is
+    # However, in the first executions in the CCP sites, this volume seems to be very important. A report is
     # a process that can take several hours, because it depends on the exporter.
     # There is a risk that the bridgehead restarts, losing the already created export.
 
     volumes:
-      - "/var/cache/bridgehead/kr/reporter-files:/app/reports"
+      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports:z"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.reporter_kr.rule=PathPrefix(`/kr-reporter`)"
-      - "traefik.http.services.reporter_kr.loadbalancer.server.port=8095"
-      - "traefik.http.routers.reporter_kr.tls=true"
-      - "traefik.http.middlewares.reporter_kr_strip.stripprefix.prefixes=/kr-reporter"
-      - "traefik.http.routers.reporter_kr.middlewares=reporter_kr_strip"
-      - "traefik.http.routers.reporter_kr.priority=20"
-
-      - "traefik.http.routers.reporter_kr_api.middlewares=reporter_kr_strip,exporter_auth"
-      - "traefik.http.routers.reporter_kr_api.rule=PathRegexp(`/kr-reporter/.+`)"
-      - "traefik.http.routers.reporter_kr_api.tls=true"
-      - "traefik.http.routers.reporter_kr_api.priority=25"
-
+      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
+      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
+      - "traefik.http.routers.reporter_ccp.tls=true"
+      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
+      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"

kr/modules/exporter.md

@@ -0,0 +1,15 @@
+# Exporter and Reporter
+
+
+## Exporter
+The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
+It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
+
+## Exporter-DB
+It is a database to save queries for its execution in the exporter. 
+The exporter manages also the different executions of the same query in through the database.
+
+## Reporter
+This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
+It is compatible with different template engines as Groovy, Thymeleaf,...
+It is perfect to generate a document as our traditional CCP quality report.

kr/modules/teiler-compose.yml

@@ -7,58 +7,70 @@ services:
     container_name: bridgehead-teiler-orchestrator
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.teiler_orchestrator_kr.rule=PathPrefix(`/kr-teiler`)"
-      - "traefik.http.services.teiler_orchestrator_kr.loadbalancer.server.port=9000"
-      - "traefik.http.routers.teiler_orchestrator_kr.tls=true"
-      - "traefik.http.middlewares.teiler_orchestrator_kr_strip.stripprefix.prefixes=/kr-teiler"
-      - "traefik.http.routers.teiler_orchestrator_kr.middlewares=teiler_orchestrator_kr_strip"
+      - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
+      - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
     environment:
-      TEILER_BACKEND_URL: "/kr-teiler-backend"
-      TEILER_DASHBOARD_URL: "/kr-teiler-dashboard"
+      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
-      HTTP_RELATIVE_PATH: "/kr-teiler"
+      HTTP_RELATIVE_PATH: "/ccp-teiler"
 
   teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
     container_name: bridgehead-teiler-dashboard
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.teiler_dashboard_kr.rule=PathPrefix(`/kr-teiler-dashboard`)"
-      - "traefik.http.services.teiler_dashboard_kr.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_dashboard_kr.tls=true"
-      - "traefik.http.middlewares.teiler_dashboard_kr_strip.stripprefix.prefixes=/kr-teiler-dashboard"
-      - "traefik.http.routers.teiler_dashboard_kr.middlewares=teiler_dashboard_kr_strip"
+      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
     environment:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "/kr-teiler-backend"
-      TEILER_DASHBOARD_URL: "/kr-teiler-dashboard"
+      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
+      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
       TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
       TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "/kr-teiler"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-teiler"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_USER: "${OIDC_USER_GROUP}"
+      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
       REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
       EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
 
 
   teiler-backend:
-    image: docker.verbis.dkfz.de/ccp/kr-teiler-backend:latest
+    image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
     container_name: bridgehead-teiler-backend
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.teiler_backend_kr.rule=PathPrefix(`/kr-teiler-backend`)"
-      - "traefik.http.services.teiler_backend_kr.loadbalancer.server.port=8085"
-      - "traefik.http.routers.teiler_backend_kr.tls=true"
-      - "traefik.http.middlewares.teiler_backend_kr_strip.stripprefix.prefixes=/kr-teiler-backend"
-      - "traefik.http.routers.teiler_backend_kr.middlewares=teiler_backend_kr_strip"
+      - "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
+      - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
     environment:
       LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
+      APPLICATION_ADDRESS: "${HOST}"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-teiler"
-      TEILER_ORCHESTRATOR_URL: "/kr-teiler"
-      TEILER_DASHBOARD_DE_URL: "/kr-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "/kr-teiler-dashboard/en"
+      CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
       HTTP_PROXY: "http://forward_proxy:3128"
+      ENABLE_MTBA: "${ENABLE_MTBA}"
+      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+    volumes:
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/ccp.conf:/run/secrets/ccp.conf:ro

kr/modules/teiler-setup.sh

@@ -3,6 +3,7 @@
 if [ "$ENABLE_TEILER" == true ];then
   log INFO "Teiler setup detected -- will start Teiler services."
   OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
-  TEILER_DEFAULT_LANGUAGE=EN
+  TEILER_DEFAULT_LANGUAGE=DE
   TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
+  add_public_oidc_redirect_url "/ccp-teiler/*"
 fi

kr/modules/teiler.md

@@ -0,0 +1,19 @@
+# Teiler
+This module orchestrates the different microfrontends of the bridgehead as a single page application.  
+
+## Teiler Orchestrator
+Single SPA component that consists on the root HTML site of the single page application and a javascript code that
+gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
+resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. 
+
+The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
+This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
+There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
+
+## Teiler Dashboard
+It consists on the main dashboard and a set of embedded services.
+### Login
+user and password in ccp.local.conf
+
+## Teiler Backend
+In this component, the microfrontends are configured.

lib/functions.sh

@@ -36,6 +36,32 @@ setupProxy() {
 	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
 }
 
+checkAndSetSelinux() {
+	# This is needed for the systemd service to start on SELinux systems.
+	if ! command -v sestatus > /dev/null 2>&1; then
+	 	echo "SELinux not available; nothing to do"
+	 	return
+	fi
+	if ! sestatus | grep "SELinux status:" | grep enabled > /dev/null; then
+		echo "SELinux disabled; nothing to do"
+		return
+	fi
+	current_mode="$(sestatus | grep 'Current mode:' | tr -s ' ' | cut -d' ' -f 3)"
+	echo "SELinux is active and ${current_mode}, checking for labels..."
+	# TODO: perhaps split this into checkSelinux (without the need for root) and setSelinux (needing root)
+	# "stat /srv/docker/bridgehead/bridgehead --printf %C" could be used for a check that doesn't need root
+	exitIfNotRoot
+	labels_for_srv="$(semanage fcontext --list | grep -e ^/srv)"
+	echo "Found the following labels for /srv:"
+	echo "${labels_for_srv}"
+	if ! echo "${labels_for_srv}" | grep -e ^/srv/docker/bridgehead/bridgehead > /dev/null; then
+		echo "Adding a label for /srv/docker/bridgehead/bridgehead..."
+		semanage fcontext --add --type bin_t /srv/docker/bridgehead/bridgehead
+	fi
+	restorecon -v /srv/docker/bridgehead/bridgehead  # this survives a reboot
+	# TODO: check if this survives updates
+}
+
 exitIfNotRoot() {
   if [ "$EUID" -ne 0 ]; then
     log "ERROR" "Please run as root"
@@ -301,33 +327,19 @@ function sync_secrets() {
     if [[ $secret_sync_args == "" ]]; then
         return
     fi
-
-    if [ "$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
-
     mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
     touch /var/cache/bridgehead/secrets/oidc
     docker run --rm \
         -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
         -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-        -v $root_crt_file:/run/secrets/root.crt.pem:ro \
+        -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
         -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
         -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=$broker_url \
-        -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
+        -e PROXY_ID=$PROXY_ID \
+        -e BROKER_URL=$BROKER_URL \
+        -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
 

lib/install-bridgehead.sh

@@ -3,6 +3,7 @@
 source lib/functions.sh
 
 exitIfNotRoot
+checkAndSetSelinux
 
 if [ $# -eq 0 ]; then
     log "ERROR" "Please provide a Project as argument"

lib/prepare-system.sh

@@ -55,9 +55,6 @@ case "$PROJECT" in
 	cce)
 		site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
 		;;
-	pscc)
-		site_configuration_repository_middle="git.verbis.dkfz.de/pscc-sites/"
-		;;
 	itcc)
 		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
         ;;

minimal/docker-compose.yml

@@ -25,6 +25,12 @@ services:
     ports:
       - 80:80
       - 443:443
+    security_opt:
+      # allow access to the docker socket on systems with SELinux
+      - "label:type:container_runtime_t"
+    cap_add:
+      # Allow binding to ports <1024 without root
+      - NET_BIND_SERVICE
     volumes:
       - /etc/bridgehead/traefik-tls:/certs:ro
       - ../lib/traefik-configuration/:/configuration:ro
@@ -59,4 +65,3 @@ services:
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
       ENVIRONMENT: ${ENVIRONMENT}
-    profiles: [deactivated]

minimal/modules/dnpm-compose.yml

@@ -12,13 +12,13 @@ services:
       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/ccp/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro,Z
+      # secrets don't seem to allow us to specify Z
+      - /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
@@ -41,7 +41,7 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
+      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro,Z
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
@@ -53,7 +53,3 @@ services:
   dnpm-echo:
     image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
     container_name: bridgehead-dnpm-echo
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

minimal/modules/dnpm-node-compose.yml

@@ -12,13 +12,13 @@ services:
       MYSQL_ROOT_HOST: "%"
       MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
     volumes:
-      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
+      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql:Z
 
   dnpm-authup:
     image: authup/authup:latest
     container_name: bridgehead-dnpm-authup
     volumes:
-      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
+      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable:Z
     depends_on:
       dnpm-mysql:
         condition: service_healthy
@@ -43,7 +43,7 @@ services:
       - "traefik.http.routers.dnpm-auth.tls=true"
 
   dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:${DNPM_IMAGE_TAG:-latest}
+    image: ghcr.io/dnpm-dip/portal:latest
     container_name: bridgehead-dnpm-portal
     environment:
       - NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
 
   dnpm-backend:
     container_name: bridgehead-dnpm-backend
-    image: ghcr.io/dnpm-dip/backend:${DNPM_IMAGE_TAG:-latest}
+    image: ghcr.io/dnpm-dip/backend:latest
     environment:
       - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
       - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
@@ -68,7 +68,7 @@ services:
       - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
     volumes:
       - /etc/bridgehead/dnpm/config:/dnpm_config
-      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
+      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data:Z
     depends_on:
       dnpm-authup:
         condition: service_healthy

modules/ssh-tunnel-compose.yml

@@ -10,8 +10,4 @@ services:
       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
+      - "/etc/bridgehead/pki/ssh-tunnel.priv.pem:/run/secrets/privkey:ro"

modules/transfair-compose.yml

@@ -27,7 +27,7 @@ services:
       - NO_PROXY=${TRANSFAIR_NO_PROXIES}
       - ALL_PROXY=http://forward_proxy:3128
     volumes:
-      - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
+      - /var/cache/bridgehead/${PROJECT}/transfair:/transfair:Z
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
     labels:
       - "traefik.enable=true"

pscc/docker-compose.yml

@@ -1,65 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
-    container_name: bridgehead-pscc-blaze
-    environment:
-      BASE_URL: "http://bridgehead-pscc-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
-      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_pscc.rule=PathPrefix(`/pscc-localdatamanagement`)"
-      - "traefik.http.middlewares.pscc_b_strip.stripprefix.prefixes=/pscc-localdatamanagement"
-      - "traefik.http.services.blaze_pscc.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_pscc.middlewares=pscc_b_strip,auth"
-      - "traefik.http.routers.blaze_pscc.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    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-pscc-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/pscc/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

pscc/modules/lens-compose.yml

@@ -1,34 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/dashboard/pscc-explorer
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=5173"
-      - "traefik.http.routers.landing.middlewares=auth"
-      - "traefik.http.routers.landing.tls=true"
-
-#  spot:
-#    image: docker.verbis.dkfz.de/ccp-private/central-spot
-#    environment:
-#      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-#      BEAM_URL: http://beam-proxy:8081
-#      BEAM_PROXY_ID: ${SITE_ID}
-#      BEAM_BROKER_ID: ${BROKER_ID}
-#      BEAM_APP_ID: "focus"
-#      PROJECT_METADATA: "cce_supervisors"
-#    depends_on:
-#      - "beam-proxy"
-#    labels:
-#      - "traefik.enable=true"
-#      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-#      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-#      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-#      - "traefik.http.routers.spot.tls=true"
-#      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

pscc/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

pscc/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
-MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
-TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
-OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
-XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
-pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
-K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
-poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
-AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
-fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
-3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
-7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
-Rtup0MTxSJtN
------END CERTIFICATE-----

pscc/vars

@@ -1,14 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.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)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=denis.koether@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in $PROJECT/modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done

versions/acceptance

@@ -2,5 +2,3 @@ FOCUS_TAG=develop
 BEAM_TAG=develop
 BLAZE_TAG=main
 POSTGRES_TAG=15.13-alpine
-TEILER_DASHBOARD_TAG=develop
-MTBA_TAG=develop

versions/prod

@@ -2,5 +2,3 @@ FOCUS_TAG=main
 BEAM_TAG=main
 BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
-TEILER_DASHBOARD_TAG=main
-MTBA_TAG=main

versions/test

@@ -2,5 +2,3 @@ FOCUS_TAG=develop
 BEAM_TAG=develop
 BLAZE_TAG=main
 POSTGRES_TAG=15.13-alpine
-TEILER_DASHBOARD_TAG=develop
-MTBA_TAG=develop