feature: add github action for automated pull request for the pilot branch, after pull requests on main

fix: specify host for id-management login

.github/workflows/auto-pr.yml

@@ -0,0 +1,21 @@
+name: Automatically generate Pull Requests for feature/pilot-projects
+
+on:
+  pull_request:
+    types: [closed]
+    branches:
+      - main
+
+jobs:
+  create_pr:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Create Pull Request to feature/pilot-projects branch
+        run: gh pr create -B feature/pilot-projects -H main --title 'Create Pull Request to feature/pilot-projects branch' --body 'Created by Github action'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -200,7 +200,7 @@ sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
 After starting the Bridgehead, you can watch the initialization process with the following command:
 
 ```shell
-journalctl -u bridgehead@bbmri -f
+/srv/docker/bridgehead/bridgehead logs <project> -f
 ```
 
 if this exits with something similar to the following:
@@ -220,8 +220,9 @@ docker ps
 There should be 6 - 10 Docker proceses. If there are fewer, then you know that something has gone wrong. To see what is going on, run:
 
 ```shell
-journalctl -u bridgehead@bbmri -f
+/srv/docker/bridgehead/bridgehead logs <Project> -f
 ```
+This translates to a journalctl command so all the regular journalctl flags can be used.
 
 Once the Bridgehead has passed these checks, take a look at the landing page:
 
@@ -235,7 +236,7 @@ You can either do this in a browser or with curl. If you visit the URL in the br
 curl -k https://localhost
 ```
 
-If you get errors when you do this, you need to use ```docker logs``` to examine your landing page container in order to determine what is going wrong.
+Should the landing page not show anything, you can inspect the logs of the containers to determine what is going wrong. To do this you can use `./bridgehead docker-logs <Project> -f` to follow the logs of the container. This transaltes to a docker compose logs command meaning all the ususal docker logs flags work.
 
 If you have chosen to take part in our monitoring program (by setting the ```MONITOR_APIKEY``` variable in the configuration), you will be informed by email when problems are detected in your Bridgehead.
 
@@ -298,19 +299,19 @@ Once you have added your biobank to the Directory you got persistent identifier
 
 The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature.
 
+You should talk with your local data protection group regarding the information that is published by Directory sync.
+
 Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
 
 To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
 
 ```
-DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
 DS_DIRECTORY_USER_NAME=your_directory_username
-DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
+DS_DIRECTORY_USER_PASS=your_directory_password
-DS_TIMER_CRON="0 22 * * *"
 ```
-You must contact the Directory team for your national node to find the URL, and to register as a user.
+Please contact your National Node to obtain this information.
 
-Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.
+Optionally, you **may** change when you want Directory sync to run by specifying a [cron](https://crontab.guru) expression, e.g. `DS_TIMER_CRON="0 22 * * *"` for 10 pm every evening.
 
 Once you edited the gitlab config, the bridgehead will autoupdate the config with the values and will sync the data.
 

bbmri/docker-compose.yml

@@ -1,10 +1,10 @@
 version: "3.7"
 
-# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see ccp vars.
+# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see vars.
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"

bbmri/modules/directory-sync-compose.yml

@@ -4,7 +4,13 @@ services:
   directory_sync_service:
     image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
     environment:
-      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL}
+      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
       DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
-      DS_DIRECTORY_PASS_CODE: ${DS_DIRECTORY_PASS_CODE}
+      DS_DIRECTORY_USER_PASS: ${DS_DIRECTORY_USER_PASS}
-      DS_TIMER_CRON: ${DS_TIMER_CRON}
+      DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
+      DS_DIRECTORY_ALLOW_STAR_MODEL: ${DS_DIRECTORY_ALLOW_STAR_MODEL:-true}
+      DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK}
+      DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID}
+      DS_DIRECTORY_COUNTRY: ${DS_DIRECTORY_COUNTRY}
+    depends_on:
+      - "blaze"

bbmri/modules/exporter-compose.yml

@@ -1,67 +0,0 @@
-version: "3.7"
-
-services:
-  exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-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: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/ccp-exporter"
-      SITE: "${SITE_ID}"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
-    volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-exporter-db
-    environment:
-      POSTGRES_USER: "exporter"
-      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      POSTGRES_DB: "exporter"
-    volumes:
-      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
-
-  reporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-ccp-reporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/ccp-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 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/ccp/reporter-files:/app/reports"
-    labels:
-      - "traefik.enable=true"
-      - "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"

bbmri/modules/exporter-setup.sh

@@ -1,8 +0,0 @@
-#!/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

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/teiler-compose.yml

@@ -1,81 +0,0 @@
-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_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: "https://${HOST}/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
-      HTTP_RELATIVE_PATH: "/ccp-teiler"
-
-  teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
-    container_name: bridgehead-teiler-dashboard
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
-      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
-      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
-    environment:
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${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: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
-      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_USER: "${OIDC_USER_GROUP}"
-      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
-      REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb"
-      EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"
-
-
-  teiler-backend:
-    image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
-    container_name: bridgehead-teiler-backend
-    labels:
-      - "traefik.enable=true"
-      - "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}"
-      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://${HOST}/ccp-teiler-dashboard/en"
-      CENTRAX_URL: "${CENTRAXX_URL}"
-      HTTP_PROXY: "http://forward_proxy:3128"
-      ENABLE_MTBA: "${ENABLE_MTBA}"
-      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-    secrets:
-      - ccp.conf
-
-secrets:
-  ccp.conf:
-    file: /etc/bridgehead/ccp.conf

bbmri/modules/teiler-setup.sh

@@ -1,9 +0,0 @@
-#!/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=DE
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-  add_public_oidc_redirect_url "/ccp-teiler/*"
-fi

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.

bbmri/vars

@@ -4,21 +4,9 @@
 # Makes only sense for German Biobanks
 : ${ENABLE_GBN:=false}
 
-FOCUS_RETRY_COUNT=32
+FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
-OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
-OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
-OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
-OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
-# Use "test-realm-01" for testing
-OIDC_REALM="${OIDC_REALM:-master}"
-OIDC_URL="https://login.verbis.dkfz.de"
-OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
-OIDC_GROUP_CLAIM="groups"
-
-POSTGRES_TAG=15.6-alpine
-
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

bridgehead

@@ -70,6 +70,7 @@ loadVars() {
 
 	# Set some project-independent default values
 	: ${ENVIRONMENT:=production}
+	export ENVIRONMENT
 
 	case "$ENVIRONMENT" in
 		"production")
@@ -107,6 +108,11 @@ case "$ACTION" in
 		exit $?
 		;;
 	logs)
+		loadVars
+		shift 2
+		exec journalctl -u bridgehead@$PROJECT -u bridgehead-update@$PROJECT -a $@
+		;;
+	docker-logs)
 		loadVars
 		shift 2
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@

ccp/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
@@ -21,7 +21,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -31,6 +31,9 @@ services:
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+    volumes:
+      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
     depends_on:
       - "beam-proxy"
       - "blaze"

ccp/modules/adt2fhir-rest-compose.yml

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

ccp/modules/adt2fhir-rest-setup.sh

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

ccp/modules/blaze-secondary-compose.yml

@@ -0,0 +1,32 @@
+version: "3.7"
+
+services:
+  blaze-secondary:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    container_name: bridgehead-ccp-blaze-secondary
+    environment:
+      BASE_URL: "http://bridgehead-ccp-blaze-secondary: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
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-secondary-data:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze-secondary_ccp.rule=PathPrefix(`/ccp-localdatamanagement-secondary`)"
+      - "traefik.http.middlewares.ccp_b-secondary_strip.stripprefix.prefixes=/ccp-localdatamanagement-secondary"
+      - "traefik.http.services.blaze-secondary_ccp.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze-secondary_ccp.middlewares=ccp_b-secondary_strip,auth"
+      - "traefik.http.routers.blaze-secondary_ccp.tls=true"
+
+  obds2fhir-rest:
+    environment:
+      STORE_PATH: ${STORE_PATH:-http://blaze:8080/fhir}
+
+  exporter:
+    environment:
+      BLAZE_HOST: "blaze-secondary"
+
+volumes:
+  blaze-secondary-data:

ccp/modules/blaze-secondary-setup.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+function blazeSecondarySetup() {
+  if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
+    log INFO "Secondary Blaze setup detected -- will start second blaze."
+    OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml"
+    #make oBDS2FHIR ignore ID-Management and replace target Blaze
+    PATIENTLIST_URL=" "
+    STORE_PATH="http://blaze-secondary:8080/fhir"
+  fi
+}

ccp/modules/datashield-compose.yml

@@ -151,7 +151,7 @@ services:
       --pass-access-token=false
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`, `/oauth2/callback`)"
+      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
       - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
       - "traefik.http.routers.oauth2_proxy.tls=true"
     environment:

ccp/modules/datashield.md

@@ -1,5 +1,5 @@
 # DataSHIELD
-This module constitutes the infrastructure to run DataSHIELD within the bridghead. 
+This module constitutes the infrastructure to run DataSHIELD within the bridgehead. 
 For more information about DataSHIELD, please visit https://www.datashield.org/
 
 ## R-Studio

ccp/modules/fhir2sql-compose.yml

@@ -0,0 +1,25 @@
+version: "3.7"
+
+services:
+  fhir2sql:
+    depends_on:
+      - "dashboard-db"
+      - "blaze"
+    image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
+    container_name: bridgehead-ccp-dashboard-fhir2sql
+    environment:
+      BLAZE_BASE_URL: "http://bridgehead-ccp-blaze:8080"
+      PG_HOST: "dashboard-db"
+      PG_USERNAME: "dashboard"
+      PG_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
+      PG_DBNAME: "dashboard"
+
+  dashboard-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-ccp-dashboard-db
+    environment:
+      POSTGRES_USER: "dashboard"
+      POSTGRES_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
+      POSTGRES_DB: "dashboard"
+    volumes:
+      - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"

ccp/modules/fhir2sql-setup.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_FHIR2SQL" == true ]; then
+  log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
+  OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
+  DASHBOARD_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the Dashboard database. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+fi

ccp/modules/fhir2sql.md

@@ -0,0 +1,36 @@
+# fhir2sql
+fhir2sql connects to Blaze, retrieves data, and syncs it with a PostgreSQL database. The application is designed to run continuously, syncing data at regular intervals.
+The Dashboard module is a optional component of the Bridgehead CCP setup. When enabled, it starts two Docker services: **fhir2sql** and **dashboard-db**. Data held in PostgreSQL is only stored temporarily and Blaze is considered to be the 'leading system' or 'source of truth'.
+
+## Services
+### fhir2sql
+* Image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
+* Container name: bridgehead-ccp-dashboard-fhir2sql
+* Depends on: dashboard-db
+* Environment variables:
+  - BLAZE_BASE_URL: The base URL of the Blaze FHIR server (set to http://blaze:8080/fhir/)
+  - PG_HOST: The hostname of the PostgreSQL database (set to dashboard-db)
+  - PG_USERNAME: The username for the PostgreSQL database (set to dashboard)
+  - PG_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
+  - PG_DBNAME: The name of the PostgreSQL database (set to dashboard)
+
+### dashboard-db
+
+* Image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+* Container name: bridgehead-ccp-dashboard-db
+* Environment variables:
+  - POSTGRES_USER: The username for the PostgreSQL database (set to dashboard)
+  - POSTGRES_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
+  - POSTGRES_DB: The name of the PostgreSQL database (set to dashboard)
+* Volumes:
+  - /var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data
+
+The volume used by dashboard-db can be removed safely and should be restored to a working order by re-importing data from Blaze.
+
+### Environment Variables
+* DASHBOARD_DB_PASSWORD: A generated password for the PostgreSQL database, created using a salt string and the SHA1 hash function.
+* POSTGRES_TAG: The tag of the PostgreSQL image to use (not set in this module, but required by the dashboard-db service).
+
+
+### Setup
+To enable the Dashboard module, set the ENABLE_FHIR2SQL environment variable to true. The dashboard-setup.sh script will then start the fhir2sql and dashboard-db services, using the environment variables and volumes defined above.

ccp/modules/id-management-compose.yml

@@ -14,15 +14,15 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
-      MAGICPL_OIDC_CLIENT_ID: ${IDMANAGER_AUTH_CLIENT_ID}
-      MAGICPL_OIDC_CLIENT_SECRET: ${IDMANAGER_AUTH_CLIENT_SECRET}
     depends_on:
       - patientlist
+      - traefik-forward-auth
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
       - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
       - "traefik.http.routers.id-manager.tls=true"
+      - "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
 
   patientlist:
     image: docker.verbis.dkfz.de/bridgehead/mainzelliste
@@ -56,5 +56,41 @@ services:
       # NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
       - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
 
+  traefik-forward-auth:
+    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
+    environment:
+      - http_proxy=http://forward_proxy:3128
+      - https_proxy=http://forward_proxy:3128
+      - OAUTH2_PROXY_PROVIDER=oidc
+      - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
+      - 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=${IDMANAGER_AUTH_COOKIE_SECRET}
+      - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
+      - OAUTH2_PROXY_HTTP_ADDRESS=:4180
+      - OAUTH2_PROXY_REVERSE_PROXY=true
+      - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
+      - OAUTH2_PROXY_UPSTREAMS=static://202
+      - OAUTH2_PROXY_EMAIL_DOMAINS=*
+      - OAUTH2_PROXY_SCOPE=openid profile email
+      # Pass Authorization Header and some user information to backend services
+      - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
+      - OAUTH2_PROXY_SET_XAUTHREQUEST=true
+      # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
+      - OAUTH2_PROXY_COOKIE_REFRESH=60s
+      - OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
+      - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4180"
+      - "traefik.http.routers.traefik-forward-auth.rule=Host(`${HOST}`) && PathPrefix(`/oauth2-idm`)"
+      - "traefik.http.routers.traefik-forward-auth.tls=true"
+      - "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.address=http://traefik-forward-auth:4180"
+      - "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.authResponseHeaders=Authorization"
+    depends_on:
+      forward_proxy:
+        condition: service_healthy
+
 volumes:
   patientlist-db-data:

ccp/modules/mtba-setup.sh

@@ -5,7 +5,6 @@ function mtbaSetup() {
     log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
     if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
       log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      exit 1;
     fi
     OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
     add_private_oidc_redirect_url "/mtba/*"

ccp/modules/obds2fhir-rest-compose.yml

@@ -0,0 +1,20 @@
+version: "3.7"
+
+services:
+  obds2fhir-rest:
+    container_name: bridgehead-obds2fhir-rest
+    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
+    environment:
+      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
+      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      SALT: ${LOCAL_SALT}
+      KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
+      MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
+      - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
+      - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
+      - "traefik.http.routers.obds2fhir-rest.tls=true"
+      - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"

ccp/modules/obds2fhir-rest-setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+function obds2fhirRestSetup() {
+  if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
+    log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
+    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+      PATIENTLIST_URL=" "
+    fi
+    OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml"
+    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  fi
+}

ccp/queries_to_cache.conf

@@ -0,0 +1,2 @@
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
+bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwoKY29kZXN5c3RlbSBsb2luYzogJ2h0dHA6Ly9sb2luYy5vcmcnCmNvZGVzeXN0ZW0gaWNkMTA6ICdodHRwOi8vZmhpci5kZS9Db2RlU3lzdGVtL2JmYXJtL2ljZC0xMC1nbScKY29kZXN5c3RlbSBtb3JwaDogJ3VybjpvaWQ6Mi4xNi44NDAuMS4xMTM4ODMuNi40My4xJwoKY29udGV4dCBQYXRpZW50CgoKREtUS19TVFJBVF9HRU5ERVJfU1RSQVRJRklFUgoKREtUS19TVFJBVF9QUklNQVJZX0RJQUdOT1NJU19OT19TT1JUX1NUUkFUSUZJRVIKREtUS19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgoKREtUS19TVFJBVF9ERUNFQVNFRF9TVFJBVElGSUVSCgpES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCgpES1RLX1NUUkFUX1NQRUNJTUVOX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfUFJPQ0VEVVJFX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfTUVESUNBVElPTl9TVFJBVElGSUVSCgogIERLVEtfU1RSQVRfSElTVE9MT0dZX1NUUkFUSUZJRVIKREtUS19TVFJBVF9ERUZfSU5fSU5JVElBTF9QT1BVTEFUSU9OKGV4aXN0cyBbQ29uZGl0aW9uOiBDb2RlICdDNjEnIGZyb20gaWNkMTBdKSBhbmQgCigoZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzgxNDAvMycpIG9yIAooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzgxNDcvMycpIG9yIAooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzg0ODAvMycpIG9yIAooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzg1MDAvMycpKQ==

ccp/vars

@@ -2,7 +2,7 @@ BROKER_ID=broker.ccp-it.dktk.dkfz.de
 BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
 FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=32
+FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
 SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
@@ -28,4 +28,5 @@ done
 
 idManagementSetup
 mtbaSetup
-adt2fhirRestSetup
+obds2fhirRestSetup
+blazeSecondarySetup

lib/functions.sh

@@ -53,7 +53,7 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
 	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
@@ -299,33 +299,18 @@ function sync_secrets() {
     if [[ $secret_sync_args == "" ]]; then
         return
     fi
-    
-    if [ "${ENABLE_ERIC}" == "true" ]; then
-        BROKER_ROOT_CERT=/srv/docker/bridgehead/bbmri/$ERIC_ROOT_CERT.crt.pem
-        PROXY_ID=$ERIC_PROXY_ID
-        BROKER_ID=$ERIC_BROKER_ID
-    elif [ "${ENABLE_GBN}" == "true" ]; then
-        BROKER_ROOT_CERT=/srv/docker/bridgehead/bbmri/$GBN_ROOT_CERT.crt.pem
-        PROXY_ID=$GBN_PROXY_ID
-        BROKER_ID=$GBN_BROKER_ID
-    elif [ "${PROJECT}" == "ccp"]; then
-        BROKER_ROOT_CERT=/srv/docker/bridgehead/ccp/root.crt.pem
-    else
-        fail_and_report 1 "Could not start secret sync as the configuration does not seem to use beam"
-    fi
-    local broker_url="https://$BROKER_ID"
     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 $BROKER_ROOT_CERT:/run/secrets/root.crt.pem:ro \
+        -v /srv/docker/bridgehead/$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=$broker_url \
+        -e BROKER_URL=$BROKER_URL \
         -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
         -e SECRET_DEFINITIONS=$secret_sync_args \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest

lib/systemd/bridgehead-update@.timer

@@ -1,8 +1,9 @@
 [Unit]
-Description=Hourly Updates of Bridgehead (%i)
+Description=Daily Updates at 6am of Bridgehead (%i)
 
 [Timer]
-OnCalendar=*-*-* *:00:00
+OnCalendar=*-*-* 06:00:00
+Persistent=true
 
 [Install]
 WantedBy=basic.target

minimal/docker-compose.yml

@@ -58,3 +58,4 @@ services:
       HOST: ${HOST}
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
+      ENVIRONMENT: ${ENVIRONMENT}

minimal/modules/bbmri vars

@@ -1,2 +0,0 @@
-OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
-OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"

minimal/modules/ccp vars

@@ -1,7 +0,0 @@
-OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
-OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
-# Use "test-realm-01" for testing
-OIDC_REALM="${OIDC_REALM:-master}"
-OIDC_URL="https://login.verbis.dkfz.de"
-OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
-OIDC_GROUP_CLAIM="groups"