mtba: fallback to keycloak test server pending migration

* Fixed: Authentik URL for Opal

* Removed: Unnecessary OIDC config in CCE and BBMRI

* KR with basic auth instead of OIDC

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

@@ -32,9 +32,6 @@ 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: "${OPERATOR_PHONE}"
@@ -42,8 +39,6 @@ services:
       EXPORTER_API_KEY: "${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"
 

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

@@ -35,6 +35,9 @@ case "$PROJECT" in
 	cce)
 		#nothing extra to do
 		;;
+	pscc)
+		#nothing extra to do
+		;;
 	itcc)
 		#nothing extra to do
 		;;
@@ -162,7 +165,7 @@ case "$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/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"
+
+  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"
+
+  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"
+    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/pscc-compose.yml

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

cce/modules/pscc-setup.sh

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

cce/modules/teiler-compose.yml

@@ -0,0 +1,64 @@
+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"
+      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: "${EXPORTER_API_KEY}"
+      TEILER_ORCHESTRATOR_URL: "/cce-teiler"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
+      REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
+      EXPORTER_DEFAULT_TEMPLATE_ID: "cce"
+
+
+  teiler-backend:
+    image: docker.verbis.dkfz.de/ccp/cce-teiler-backend:latest
+    container_name: bridgehead-teiler-backend
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_backend_cce.rule=PathPrefix(`/cce-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_cce.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_cce.tls=true"
+      - "traefik.http.middlewares.teiler_backend_cce_strip.stripprefix.prefixes=/cce-teiler-backend"
+      - "traefik.http.routers.teiler_backend_cce.middlewares=teiler_backend_cce_strip"
+    environment:
+      LOG_LEVEL: "INFO"
+      APPLICATION_PORT: "8085"
+      DEFAULT_LANGUAGE: "${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

cce/vars

@@ -1,6 +1,9 @@
 BROKER_ID=test-no-real-data.broker.samply.de
+BROKER_ID_PSCC=test-no-real-data.broker.samply.de
 BROKER_URL=https://${BROKER_ID}
+BROKER_URL_PSCC=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
+PROXY_ID_PSCC=${SITE_ID}.${BROKER_ID_PSCC}
 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=manoj.waikar@dkfz-heidelberg.de

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: "${OIDC_URL}"
+      OIDC_URL: "${OIDC_PRIVATE_URL}"
       OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
       OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
       OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
@@ -73,71 +73,12 @@ services:
       - beam-proxy
     volumes:
       - /tmp/bridgehead/opal-map/:/map/:ro
-    networks:
-      - default
-
-  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
-  forward_proxy:
-    networks:
-      - default
 
   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

ccp/modules/datashield-setup.sh

@@ -5,10 +5,6 @@ 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\")"
@@ -22,18 +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-node-compose.yml

@@ -43,7 +43,7 @@ services:
       - "traefik.http.routers.dnpm-auth.tls=true"
 
   dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:latest
+    image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-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:latest
+    image: ghcr.io/dnpm-dip/backend:{DNPM_IMAGE_TAG:-latest}
     environment:
       - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
       - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}

ccp/modules/id-management-compose.yml

@@ -14,6 +14,7 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
+      MAGICPL_OIDC_PROVIDER: ${OIDC_PRIVATE_URL}
     depends_on:
       - patientlist
       - traefik-forward-auth
@@ -71,12 +72,14 @@ services:
       - https_proxy=http://forward_proxy:3128
       - OAUTH2_PROXY_PROVIDER=oidc
       - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
-      - OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master
+      - OAUTH2_PROXY_OIDC_ISSUER_URL=${OIDC_PRIVATE_URL}
-      - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
+      - OAUTH2_PROXY_CLIENT_ID=${OIDC_PRIVATE_CLIENT_ID}
-      - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
+      - OAUTH2_PROXY_CLIENT_SECRET=${OIDC_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=.${HOST}
@@ -87,8 +90,8 @@ services:
       - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
       - OAUTH2_PROXY_SET_XAUTHREQUEST=true
       # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
-      - OAUTH2_PROXY_COOKIE_REFRESH=60s
+      - OAUTH2_PROXY_ALLOWED_GROUPS=${OIDC_PSP_GROUP}
-      - OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
+      - OAUTH2_PROXY_OIDC_GROUPS_CLAIM=${OIDC_GROUP_CLAIM}
       - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
     labels:
       - "traefik.enable=true"

ccp/modules/id-management-setup.sh

@@ -14,6 +14,8 @@ 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

@@ -22,8 +22,14 @@ services:
       HTTP_RELATIVE_PATH: "/mtba"
       OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
       OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      # TODO: Add following variables after moving to Authentik:
-      OIDC_URL: "${OIDC_URL}"
+      #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"
 
     labels:
       - "traefik.enable=true"

ccp/vars

@@ -10,9 +10,11 @@ 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=${SITE_ID}-public
-OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
+OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
+OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
 OIDC_GROUP_CLAIM="groups"
 
 for module in $PROJECT/modules/*.sh

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/modules/exporter-compose.yml

@@ -1,9 +1,10 @@
 version: "3.7"
 
 services:
+
   exporter:
     image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-exporter
+    container_name: bridgehead-kr-exporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
       LOG_LEVEL: "INFO"
@@ -12,39 +13,51 @@ services:
       EXPORTER_DB_USER: "exporter"
       EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
       EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/ccp-exporter"
+      HTTP_RELATIVE_PATH: "/kr-exporter"
       SITE: "${SITE_ID}"
       HTTP_SERVLET_REQUEST_SCHEME: "https"
       OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
+      - "traefik.http.routers.exporter_kr.rule=PathPrefix(`/kr-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
+      - "traefik.http.services.exporter_kr.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
+      - "traefik.http.routers.exporter_kr.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
+      - "traefik.http.middlewares.exporter_kr_strip.stripprefix.prefixes=/kr-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
+      - "traefik.http.routers.exporter_kr.middlewares=exporter_kr_strip"
+      # Main router
+      - "traefik.http.routers.exporter_kr.priority=20"
+
+      # API router
+      - "traefik.http.routers.exporter_kr_api.middlewares=exporter_kr_strip,exporter_auth"
+      - "traefik.http.routers.exporter_kr_api.rule=PathRegexp(`/kr-exporter/.+`)"
+      - "traefik.http.routers.exporter_kr_api.tls=true"
+      - "traefik.http.routers.exporter_kr_api.priority=25"
+
+      # Shared middlewares
+      - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
+
     volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
+      - "/var/cache/bridgehead/kr/exporter-files:/app/exporter-files/output"
 
   exporter-db:
     image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-exporter-db
+    container_name: bridgehead-kr-exporter-db
     environment:
       POSTGRES_USER: "exporter"
       POSTGRES_PASSWORD: "${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"
+      - "/var/cache/bridgehead/kr/exporter-db:/var/lib/postgresql/data"
 
   reporter:
     image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-ccp-reporter
+    container_name: bridgehead-kr-reporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
       LOG_LEVEL: "INFO"
       CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/ccp-reporter"
+      HTTP_RELATIVE_PATH: "/kr-reporter"
       SITE: "${SITE_ID}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
       EXPORTER_URL: "http://exporter:8092"
@@ -52,16 +65,23 @@ 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 CCP sites, this volume seems to be very important. A report is
+    # However, in the first executions in the kr 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"
+      - "/var/cache/bridgehead/kr/reporter-files:/app/reports"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
+      - "traefik.http.routers.reporter_kr.rule=PathPrefix(`/kr-reporter`)"
-      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
+      - "traefik.http.services.reporter_kr.loadbalancer.server.port=8095"
-      - "traefik.http.routers.reporter_ccp.tls=true"
+      - "traefik.http.routers.reporter_kr.tls=true"
-      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
+      - "traefik.http.middlewares.reporter_kr_strip.stripprefix.prefixes=/kr-reporter"
-      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
+      - "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"
+

kr/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.

kr/modules/teiler-compose.yml

@@ -7,73 +7,58 @@ services:
     container_name: bridgehead-teiler-orchestrator
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
+      - "traefik.http.routers.teiler_orchestrator_kr.rule=PathPrefix(`/kr-teiler`)"
-      - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
+      - "traefik.http.services.teiler_orchestrator_kr.loadbalancer.server.port=9000"
-      - "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
+      - "traefik.http.routers.teiler_orchestrator_kr.tls=true"
-      - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
+      - "traefik.http.middlewares.teiler_orchestrator_kr_strip.stripprefix.prefixes=/kr-teiler"
-      - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
+      - "traefik.http.routers.teiler_orchestrator_kr.middlewares=teiler_orchestrator_kr_strip"
     environment:
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_BACKEND_URL: "/kr-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/kr-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
-      HTTP_RELATIVE_PATH: "/ccp-teiler"
+      HTTP_RELATIVE_PATH: "/kr-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.routers.teiler_dashboard_kr.rule=PathPrefix(`/kr-teiler-dashboard`)"
-      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
+      - "traefik.http.services.teiler_dashboard_kr.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
+      - "traefik.http.routers.teiler_dashboard_kr.tls=true"
-      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
+      - "traefik.http.middlewares.teiler_dashboard_kr_strip.stripprefix.prefixes=/kr-teiler-dashboard"
-      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
+      - "traefik.http.routers.teiler_dashboard_kr.middlewares=teiler_dashboard_kr_strip"
     environment:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_BACKEND_URL: "/kr-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/kr-teiler-dashboard"
-      OIDC_URL: "${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: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "/kr-teiler"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-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/dktk-teiler-backend:latest
+    image: docker.verbis.dkfz.de/ccp/kr-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.routers.teiler_backend_kr.rule=PathPrefix(`/kr-teiler-backend`)"
-      - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
+      - "traefik.http.services.teiler_backend_kr.loadbalancer.server.port=8085"
-      - "traefik.http.routers.teiler_backend_ccp.tls=true"
+      - "traefik.http.routers.teiler_backend_kr.tls=true"
-      - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
+      - "traefik.http.middlewares.teiler_backend_kr_strip.stripprefix.prefixes=/kr-teiler-backend"
-      - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
+      - "traefik.http.routers.teiler_backend_kr.middlewares=teiler_backend_kr_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: "/kr-teiler"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "/kr-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_DE_URL: "/kr-teiler-dashboard/de"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "/kr-teiler-dashboard/en"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
       HTTP_PROXY: "http://forward_proxy:3128"
-      ENABLE_MTBA: "${ENABLE_MTBA}"
-      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-    secrets:
-      - ccp.conf
-
-secrets:
-  ccp.conf:
-    file: /etc/bridgehead/ccp.conf

kr/modules/teiler-setup.sh

@@ -3,7 +3,6 @@
 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=EN
   TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-  add_public_oidc_redirect_url "/ccp-teiler/*"
 fi

kr/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.

lib/functions.sh

@@ -301,19 +301,33 @@ 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 $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-        -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
+        -v $root_crt_file:/run/secrets/root.crt.pem:ro \
         -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
         -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
         -e NO_PROXY=localhost,127.0.0.1 \
         -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-        -e PROXY_ID=$PROXY_ID \
+        -e PROXY_ID=$proxy_id \
-        -e BROKER_URL=$BROKER_URL \
+        -e BROKER_URL=$broker_url \
-        -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
+        -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
         -e SECRET_DEFINITIONS=$secret_sync_args \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
 
@@ -436,7 +450,3 @@ 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/prepare-system.sh

@@ -55,6 +55,9 @@ 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

@@ -59,3 +59,4 @@ services:
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
       ENVIRONMENT: ${ENVIRONMENT}
+    profiles: [deactivated]

minimal/modules/dnpm-node-compose.yml

@@ -43,7 +43,7 @@ services:
       - "traefik.http.routers.dnpm-auth.tls=true"
 
   dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:latest
+    image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-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:latest
+    image: ghcr.io/dnpm-dip/backend:{DNPM_IMAGE_TAG:-latest}
     environment:
       - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
       - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}

pscc/docker-compose.yml

@@ -0,0 +1,65 @@
+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

@@ -0,0 +1,34 @@
+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

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

pscc/root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

pscc/vars

@@ -0,0 +1,14 @@
+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