Remove remaining secret

* Added Exporter to CCE

* Add Teiler to CCE

* Add EXPORTER_USER to adduser function

README.md

@@ -24,6 +24,9 @@ This repository is the starting point for any information and tools you will nee
     - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
     - [Directory sync tool](#directory-sync-tool)
     - [Loading data](#loading-data)
+    - [Teiler (Frontend)](#teiler-frontend)
+    - [Data Exporter Service](#data-exporter-service)
+      - [Data Quality Report](#data-quality-report)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -379,6 +382,37 @@ Normally, you will need to build your own ETL to feed the Bridgehead. However, t
 
 You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
 
+### Teiler (Frontend)
+
+Teiler is the web-based frontend of the Bridgehead, providing access to its various internal, and external services and components.   
+To learn how to integrate your custom module into Teiler, please refer to https://github.com/samply/teiler-dashboard.
+- To activate Teiler, set the following environment variable in your `<PROJECT>.conf` file:  
+
+```bash
+ENABLE_TEILER=true
+```
+
+### Data Exporter Service
+
+The Exporter is a dedicated service for extracting and exporting Bridgehead data in (tabular) formats such as Excel, CSV, Opal, JSON, XML, ...  
+- To enable the Exporter service, set the following environment variable in your `<PROJECT>.conf` file:  
+
+```bash
+ENABLE_EXPORTER=true
+```
+
+#### Data Quality Report
+To assess the quality and plausibility of your imported data, the Reporter component is pre-configured to generate Excel reports with data quality metrics and statistical analyses. Reporter is part of the Exporter and can be enabled by setting the same environment variable in your `<PROJECT>.conf` file:
+```bash
+ENABLE_EXPORTER=true
+```
+
+For convenience, it's recommended to enable the Teiler web frontend alongside the Exporter to access export and quality control features via a web interface: set the following environment varibles in your `<PROJECT>.conf` file:
+```bash
+ENABLE_TEILER=true
+ENABLE_EXPORTER=true
+```
+
 ## Things you should know
 
 ### Auto-Updates

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/eric.acc.root.crt.pem

@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUE/wu6FmI+KSMOalI65b+lI3HI4cwDQYJKoZIhvcNAQEL
+MIIDNTCCAh2gAwIBAgIUFzdpDi1OLdXyogtCsktHFhCILtMwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwOTE2MTUyMzU0WhcNMzQw
+BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjUwNjEwMTQzNjE1WhcNMzUw
-OTE0MTUyNDI0WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
+NjA4MTQzNjQ1WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAOt1I1FQt2bI4Nnjtg8JBYid29cBIkDT4MMb45Jr
+AQEBBQADggEPADCCAQoCggEBALpJCWE9Qe19R9DqotdkPV6jfiuJSKI3UYkCWdWG
-ays24y4R3WO7VJK9UjNduSq/A1jlA0W0A/szDf8Ojq6bBtg+uL92PTDjYH1QXwX0
+nRfkKB6OaY5t3JCHDqaEME9FwSd2nFXhTp5F6snG/K7g8MCLIEzGzuSnrdjGqINq
-c7eMo2tvvyyrs/cb2/ovDBQ1lpibcxVmVAv042ASmil3SdqKKXpv3ATnF9I7V4cv
+zXLfgqnxvQpPR4ARLNNgnKxZaq7m4Q3T/l+QAshK6CnCUWFQ6q5x3g/pZHFP2USd
-fwB56FChaGIov5EK+9JOMjTx6oMlBEgUFR6qq/lSqM9my0HYwUFbX2W+nT9EKEIP
+/G2FtDHX6YK4bHbbnigIPG6PdY2RYy60i30XGdIPBNf82XGkAtPUBz731gHOV5Vg
-9UP1eyfRZR3E/+oticnm/cS20BGCbjoYrNgLthXKyaASuhGoElKs8EZ3h9MiI+u0
+d+jfAqTwZAhYC2CcNmswFw1H9GrvTI/9KZWKcZNUIqemc0A/FyEyONUM18/vjQ7D
-DpR0KpePhAkMLugBrgYWqkMwwD1684LfC4YVQrsLwzo5OW8CAwEAAaN7MHkwDgYD
+lUwOcQsgAg44QTOUPgqXv3sJPQM5EnGuv3yYV9u6Y2i78M8CAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFPbXs3g3lMjH
+VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFPrDeNWgtEyZ
-1JMe0a5aVbN7lB92MB8GA1UdIwQYMBaAFPbXs3g3lMjH1JMe0a5aVbN7lB92MBYG
+VM0yeoRZdK2QGjyvMB8GA1UdIwQYMBaAFPrDeNWgtEyZVM0yeoRZdK2QGjyvMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQBM5RsXb2HN
+A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQAD2S0kqL18
-FpC1mYfocXAn20Zu4d603qmc/IqkiOWbp36pWo+jk1AxejyRS9hEpQalgSnvcRPQ
+laewh+qnyZ0WMq12mLV/Rwll6ZuShCx2uAu3UZuIGWk3l7gG5zlws+i+zbaNcn4o
-1hPEhGU+wvI0WWVi/01iNjVbXmJNPQEouXQWAT17dyp9vqQkPw8LNzpSV/qdPgbT
+HsS3WG9kiNLOMKp8LXGkjErl6RaQr+kb8qgYFTPjOr6v0OdVn6ve9RDNYB5Hd+zE
-Z9o3sZrjUsSLsK7A7Q5ky4ePkiJBaMsHeAD+wqGwpiJ4D2Xhp8e1v36TWM0qt2EA
+9jAWmS8PfS2AldE4VAd0C4pWTAinhnKGrKdn1YAX5x+LMq1y0lc1Pd4CDgsjD6SS
-gySx9isx/jeGGPBmDqYB9BCal5lrihPN56jd+5pCkyXeZqKWiiXFJKXwcwxctYZc
+3td7JtenXqCX0mN0XSeck7vvFGa6QpcQoVcN9tRENctHZTwyeGA21IkXylpFPUkE
-ADHIiTLLPXE8LHTUJAO51it1NAZ1S24aMzax4eWDXcWO7/ybbx5pkYkMd6EqlKHd
+LT60k48fNC8TZkBlfvtVGRebpm5krXIKEaVy5LniEpSuOR4hTqsgoQDntBjW4zHA
-8riQJIhY4huX
+GeWQ1wQNTEBX
------END CERTIFICATE-----
+-----END CERTIFICATE-----

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/exporter.md

@@ -1,15 +0,0 @@
-# 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.

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

@@ -13,8 +13,8 @@ services:
       - "traefik.http.middlewares.teiler_orchestrator_bbmri_strip.stripprefix.prefixes=/bbmri-teiler"
       - "traefik.http.routers.teiler_orchestrator_bbmri.middlewares=teiler_orchestrator_bbmri_strip"
     environment:
-      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_BACKEND_URL: "/bbmri-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/bbmri-teiler"
 
@@ -30,8 +30,8 @@ services:
       - "traefik.http.routers.teiler_dashboard_bbmri.middlewares=teiler_dashboard_bbmri_strip"
     environment:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_BACKEND_URL: "/bbmri-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard"
       OIDC_URL: "${OIDC_URL}"
       OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
       OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
@@ -40,7 +40,7 @@ services:
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler"
+      TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
       TEILER_USER: "${OIDC_USER_GROUP}"
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@@ -61,10 +61,9 @@ services:
     environment:
       LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
-      APPLICATION_ADDRESS: "${HOST}"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler"
+      TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/bbmri-teiler-dashboard/de"
+      TEILER_DASHBOARD_DE_URL: "/bbmri-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/bbmri-teiler-dashboard/en"
+      TEILER_DASHBOARD_EN_URL: "/bbmri-teiler-dashboard/en"
       HTTP_PROXY: "http://forward_proxy:3128"

bbmri/modules/teiler.md

@@ -1,19 +0,0 @@
-# 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.

bridgehead

@@ -162,7 +162,7 @@ case "$ACTION" in
 	adduser)
 		loadVars
 		log "INFO" "Adding encrypted credentials in /etc/bridgehead/$PROJECT.local.conf"
-    		read -p "Please choose the component (LDM_AUTH|NNGM_AUTH) you want to add a user to : " COMPONENT
+    		read -p "Please choose the component (LDM_AUTH|NNGM_AUTH|EXPORTER_USER) 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

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

@@ -0,0 +1,87 @@
+version: "3.7"
+
+services:
+
+  exporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
+    container_name: bridgehead-cce-exporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      CROSS_ORIGINS: "https://${HOST}"
+      EXPORTER_DB_USER: "exporter"
+      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
+      HTTP_RELATIVE_PATH: "/cce-exporter"
+      SITE: "${SITE_ID}"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.exporter_cce.rule=PathPrefix(`/cce-exporter`)"
+      - "traefik.http.services.exporter_cce.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_cce.tls=true"
+      - "traefik.http.middlewares.exporter_cce_strip.stripprefix.prefixes=/cce-exporter"
+      - "traefik.http.routers.exporter_cce.middlewares=exporter_cce_strip"
+      # Main router
+      - "traefik.http.routers.exporter_cce.priority=20"
+
+      # API router
+      - "traefik.http.routers.exporter_cce_api.middlewares=exporter_cce_strip,exporter_auth"
+      - "traefik.http.routers.exporter_cce_api.rule=PathRegexp(`/cce-exporter/.+`)"
+      - "traefik.http.routers.exporter_cce_api.tls=true"
+      - "traefik.http.routers.exporter_cce_api.priority=25"
+
+      # Shared middlewares
+      - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
+
+    volumes:
+      - "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output:z"
+
+  exporter-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-cce-exporter-db
+    environment:
+      POSTGRES_USER: "exporter"
+      POSTGRES_PASSWORD: "${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/cce/exporter-db:/var/lib/postgresql/data:Z"
+
+  reporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
+    container_name: bridgehead-cce-reporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      CROSS_ORIGINS: "https://${HOST}"
+      HTTP_RELATIVE_PATH: "/cce-reporter"
+      SITE: "${SITE_ID}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      EXPORTER_URL: "http://exporter:8092"
+      LOG_FHIR_VALIDATION: "false"
+      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 cce 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/cce/reporter-files:/app/reports:z"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.reporter_cce.rule=PathPrefix(`/cce-reporter`)"
+      - "traefik.http.services.reporter_cce.loadbalancer.server.port=8095"
+      - "traefik.http.routers.reporter_cce.tls=true"
+      - "traefik.http.middlewares.reporter_cce_strip.stripprefix.prefixes=/cce-reporter"
+      - "traefik.http.routers.reporter_cce.middlewares=reporter_cce_strip"
+      - "traefik.http.routers.reporter_cce.priority=20"
+
+      - "traefik.http.routers.reporter_cce_api.middlewares=reporter_cce_strip,exporter_auth"
+      - "traefik.http.routers.reporter_cce_api.rule=PathRegexp(`/cce-reporter/.+`)"
+      - "traefik.http.routers.reporter_cce_api.tls=true"
+      - "traefik.http.routers.reporter_cce_api.priority=25"
+

cce/modules/exporter-setup.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_EXPORTER" == true ]; then
+  log INFO "Exporter setup detected -- will start Exporter service."
+  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
+  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
+fi

cce/modules/lens-compose.yml

@@ -17,7 +17,6 @@ services:
       BEAM_PROXY_ID: ${SITE_ID}
       BEAM_BROKER_ID: ${BROKER_ID}
       BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "cce_supervisors"
     depends_on:
       - "beam-proxy"
     labels:
@@ -30,4 +29,4 @@ services:
       - "traefik.http.routers.spot.rule=Host(`${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"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"

cce/modules/teiler-compose.yml

@@ -0,0 +1,69 @@
+version: "3.7"
+
+services:
+
+  teiler-orchestrator:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
+    container_name: bridgehead-teiler-orchestrator
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_orchestrator_cce.rule=PathPrefix(`/cce-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_cce.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_cce.tls=true"
+      - "traefik.http.middlewares.teiler_orchestrator_cce_strip.stripprefix.prefixes=/cce-teiler"
+      - "traefik.http.routers.teiler_orchestrator_cce.middlewares=teiler_orchestrator_cce_strip"
+    environment:
+      TEILER_BACKEND_URL: "/cce-teiler-backend"
+      TEILER_DASHBOARD_URL: "/cce-teiler-dashboard"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
+      HTTP_RELATIVE_PATH: "/cce-teiler"
+
+  teiler-dashboard:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
+    container_name: bridgehead-teiler-dashboard
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_dashboard_cce.rule=PathPrefix(`/cce-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_cce.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_cce.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_cce_strip.stripprefix.prefixes=/cce-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_cce.middlewares=teiler_dashboard_cce_strip"
+    environment:
+      DEFAULT_LANGUAGE: "${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: "${OPERATOR_PHONE}"
+      TEILER_PROJECT: "${PROJECT}"
+      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: "${OIDC_ADMIN_GROUP}"
+      REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
+      EXPORTER_DEFAULT_TEMPLATE_ID: "cce"
+
+
+  teiler-backend:
+    image: docker.verbis.dkfz.de/ccp/cce-teiler-backend:latest
+    container_name: bridgehead-teiler-backend
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_backend_cce.rule=PathPrefix(`/cce-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_cce.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_cce.tls=true"
+      - "traefik.http.middlewares.teiler_backend_cce_strip.stripprefix.prefixes=/cce-teiler-backend"
+      - "traefik.http.routers.teiler_backend_cce.middlewares=teiler_backend_cce_strip"
+    environment:
+      LOG_LEVEL: "INFO"
+      APPLICATION_PORT: "8085"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
+      TEILER_ORCHESTRATOR_URL: "/cce-teiler"
+      TEILER_DASHBOARD_DE_URL: "/cce-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "/cce-teiler-dashboard/en"
+      HTTP_PROXY: "http://forward_proxy:3128"

cce/modules/teiler-setup.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+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_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
+fi

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

@@ -1,25 +1,6 @@
 version: "3.7"
 
 services:
-  rstudio:
-    container_name: bridgehead-rstudio
-    image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
-    environment:
-      #DEFAULT_USER: "rstudio" # This line is kept for informational purposes
-      PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
-      DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
-      HTTP_RELATIVE_PATH: "/rstudio"
-      ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
-      - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
-      - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
-      - "traefik.http.routers.rstudio_ccp.tls=true"
-      - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
-    networks:
-      - rstudio
-
   opal:
     container_name: bridgehead-opal
     image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
@@ -54,10 +35,10 @@ services:
       BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
       BEAM_DATASHIELD_PROXY: request-manager
     volumes:
-      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
+      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv:Z" # Opal metadata
-    secrets:
+      # secrets don't seem to allow us to specify Z/z
-      - opal-cert.pem
+      - /tmp/bridgehead/opal-cert.pem:/run/secrets/opal-cert.pem:z
-      - opal-key.pem
+      - /tmp/bridgehead/opal-key.pem:/run/secrets/opal-key.pem:Z
 
   opal-db:
     container_name: bridgehead-opal-db
@@ -67,7 +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
@@ -86,85 +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
-    networks:
+      # secrets don't seem to allow us to specify Z/z
-      - default
+      - /tmp/bridgehead/opal-cert.pem:/run/secrets/opal-cert.pem:z
-      - rstudio
-
-  traefik:
-    labels:
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2-proxy:4180/"
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
-    networks:
-      - default
-      - rstudio
-  forward_proxy:
-    networks:
-      - default
-      - rstudio
 
   beam-proxy:
     environment:
       APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
       APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
-
-  # TODO: Allow users of group /DataSHIELD and OIDC_USER_GROUP at the same time:
-  # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/configuration/oauth_provider):
-  # --allowed-groups=/DataSHIELD,OIDC_USER_GROUP
-  oauth2-proxy:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
-    container_name: bridgehead-oauth2proxy
-    command: >-
-      --allowed-group=DataSHIELD
-      --oidc-groups-claim=${OIDC_GROUP_CLAIM}
-      --auth-logging=true
-      --whitelist-domain=${HOST}
-      --http-address="0.0.0.0:4180"
-      --reverse-proxy=true
-      --upstream="static://202"
-      --email-domain="*"
-      --cookie-name="_BRIDGEHEAD_oauth2"
-      --cookie-secret="${OAUTH2_PROXY_SECRET}"
-      --cookie-expire="12h"
-      --cookie-secure="true"
-      --cookie-httponly="true"
-      #OIDC settings
-      --provider="keycloak-oidc"
-      --provider-display-name="VerbIS Login"
-      --client-id="${OIDC_PRIVATE_CLIENT_ID}"
-      --client-secret="${OIDC_CLIENT_SECRET}"
-      --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
-      --oidc-issuer-url="${OIDC_URL}"
-      --scope="openid email profile"
-      --code-challenge-method="S256"
-      --skip-provider-button=true
-      #X-Forwarded-Header settings - true/false depending on your needs
-      --pass-basic-auth=true
-      --pass-user-headers=false
-      --pass-access-token=false
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
-      - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
-      - "traefik.http.routers.oauth2_proxy.tls=true"
-    environment:
-      http_proxy: "http://forward_proxy:3128"
-      https_proxy: "http://forward_proxy:3128"
-    depends_on:
-      forward_proxy:
-        condition: service_healthy
-
-secrets:
-  opal-cert.pem:
-    file: /tmp/bridgehead/opal-cert.pem
-  opal-key.pem:
-    file: /tmp/bridgehead/opal-key.pem
-
-networks:
-  rstudio:

ccp/modules/datashield-setup.sh

@@ -5,17 +5,12 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
   if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then
     log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'."
   fi
-  OAUTH2_CALLBACK=/oauth2/callback
-  OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
-  add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
-
   log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
   OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
   EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
   TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
   OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
   OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")"
-  RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")"
   DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)"
   TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
   if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
@@ -23,18 +18,13 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
     openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
   fi
   mkdir -p /tmp/bridgehead/opal-map
-  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
+  echo '{"sites": []}' >/tmp/bridgehead/opal-map/central.json
-  echo "$sites" | docker_jq -n --args '{"sites": input | map({
+  # Only allow connections from the central beam proxy that is used by all coder workspaces
-    "name": .,
+  echo '[{
-    "id": .,
+    "external": "'$SITE_ID':443",
-    "virtualhost": "\(.):443",
-    "beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
-  })}' $sites >/tmp/bridgehead/opal-map/central.json
-  echo "$sites" | docker_jq -n --args '[{
-    "external": "'"$SITE_ID"':443",
     "internal": "opal:8443",
-    "allowed": input | map("\(.).'"$BROKER_ID"'")
+    "allowed": ["central-ds-orchestrator.'$BROKER_ID'"]
-  }]' >/tmp/bridgehead/opal-map/local.json
+  }]' > /tmp/bridgehead/opal-map/local.json
   if [ "$USER" == "root" ]; then
     chown -R bridgehead:docker /tmp/bridgehead
     chmod g+wr /tmp/bridgehead/opal-map/*

ccp/modules/datashield-sites.json

@@ -1,15 +0,0 @@
-[
-    "berlin",
-    "muenchen-lmu",
-    "dresden",
-    "freiburg",
-    "muenchen-tum",
-    "tuebingen",
-    "mainz",
-    "frankfurt",
-    "essen",
-    "dktk-datashield-test",
-    "dktk-test",
-    "mannheim",
-    "central-ds-orchestrator"
-]

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
@@ -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

@@ -22,8 +22,8 @@ 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:
-      POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"
+      POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"

ccp/modules/id-management-compose.yml

@@ -62,7 +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

ccp/modules/mtba-compose.yml

@@ -32,8 +32,8 @@ services:
       - "traefik.http.routers.mtba_ccp.tls=true"
 
     volumes:
-      - /var/cache/bridgehead/ccp/mtba/input:/app/input
+      - /var/cache/bridgehead/ccp/mtba/input:/app/input:z
-      - /var/cache/bridgehead/ccp/mtba/persist:/app/persist
+      - /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

@@ -13,8 +13,8 @@ services:
       - "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: "https://${HOST}/ccp-teiler-backend"
+      TEILER_BACKEND_URL: "/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/ccp-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/ccp-teiler"
 
@@ -30,8 +30,8 @@ services:
       - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
     environment:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_BACKEND_URL: "/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/ccp-teiler-dashboard"
       OIDC_URL: "${OIDC_URL}"
       OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
       OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
@@ -40,7 +40,7 @@ services:
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "/ccp-teiler"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
       TEILER_USER: "${OIDC_USER_GROUP}"
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@@ -61,12 +61,11 @@ services:
     environment:
       LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
-      APPLICATION_ADDRESS: "${HOST}"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "/ccp-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
+      TEILER_DASHBOARD_DE_URL: "/ccp-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
+      TEILER_DASHBOARD_EN_URL: "/ccp-teiler-dashboard/en"
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"

dhki/docker-compose.yml

@@ -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:ro
+      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
     depends_on:
       - "beam-proxy"
       - "blaze"
@@ -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

itcc/modules/lens-compose.yml

@@ -17,7 +17,6 @@ services:
       BEAM_PROXY_ID: ${SITE_ID}
       BEAM_BROKER_ID: ${BROKER_ID}
       BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "dktk_supervisors"
     depends_on:
       - "beam-proxy"
     labels:
@@ -30,4 +29,4 @@ services:
       - "traefik.http.routers.spot.rule=Host(`${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"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"

kr/docker-compose.yml

@@ -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

@@ -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`)"

kr/modules/teiler-compose.yml

@@ -71,9 +71,6 @@ services:
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-    secrets:
+    volumes:
-      - ccp.conf
+      # secrets don't seem to allow us to specify Z
-
+      - /etc/bridgehead/ccp.conf:/run/secrets/ccp.conf:ro
-secrets:
-  ccp.conf:
-    file: /etc/bridgehead/ccp.conf

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"
@@ -436,7 +462,3 @@ generate_simple_password(){
   local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
   echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
 }
-
-docker_jq() {
-    docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
-}

lib/install-bridgehead.sh

@@ -3,6 +3,7 @@
 source lib/functions.sh
 
 exitIfNotRoot
+checkAndSetSelinux
 
 if [ $# -eq 0 ]; then
     log "ERROR" "Please provide a Project as argument"
@@ -49,8 +50,8 @@ if [ -z "$TRANSFAIR_AUTH" ]; then
   fi
 fi
 
-if [ -z "$EXPORTER_USER" ]; then
+if [ "$ENABLE_EXPORTER" == "true" ] && [ -z "$EXPORTER_USER" ]; then
-  log "INFO" "Now generating basic auth for the exporter and reporter (see adduser in bridgehead for more information). "
+  log "INFO" "Now generating basic auth for the exporter and reporter (see adduser in bridgehead for more information)."
   generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
   add_basic_auth_user $PROJECT $generated_passwd "EXPORTER_USER" $PROJECT
 fi

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

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
@@ -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:
+      - "/etc/bridgehead/pki/ssh-tunnel.priv.pem:/run/secrets/privkey:ro"
-      - privkey
-secrets:
-  privkey:
-    file: /etc/bridgehead/pki/ssh-tunnel.priv.pem

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"