Merge pull request #314 from samply/develop

Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>

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 +382,36 @@ 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/modules/eric.acc.root.crt.pem

@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUE/wu6FmI+KSMOalI65b+lI3HI4cwDQYJKoZIhvcNAQEL
+MIIDNTCCAh2gAwIBAgIUFzdpDi1OLdXyogtCsktHFhCILtMwDQYJKoZIhvcNAQEL
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-8riQJIhY4huX
+GeWQ1wQNTEBX
------END CERTIFICATE-----
+-----END CERTIFICATE-----

bbmri/modules/exporter-compose.yml

@@ -0,0 +1,86 @@
+version: "3.7"
+
+services:
+  exporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
+    container_name: bridgehead-bbmri-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: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
+      HTTP_RELATIVE_PATH: "/bbmri-exporter"
+      SITE: "${SITE_ID}"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.exporter_bbmri.rule=PathPrefix(`/bbmri-exporter`)"
+      - "traefik.http.services.exporter_bbmri.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_bbmri.tls=true"
+      - "traefik.http.middlewares.exporter_bbmri_strip.stripprefix.prefixes=/bbmri-exporter"
+      - "traefik.http.routers.exporter_bbmri.middlewares=exporter_bbmri_strip"
+      # Main router
+      - "traefik.http.routers.exporter_bbmri.priority=20"
+
+      # API router
+      - "traefik.http.routers.exporter_bbmri_api.middlewares=exporter_bbmri_strip,exporter_auth"
+      - "traefik.http.routers.exporter_bbmri_api.rule=PathRegexp(`/bbmri-exporter/.+`)"
+      - "traefik.http.routers.exporter_bbmri_api.tls=true"
+      - "traefik.http.routers.exporter_bbmri_api.priority=25"
+
+      # Shared middlewares
+      - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
+
+    volumes:
+      - "/var/cache/bridgehead/bbmri/exporter-files:/app/exporter-files/output"
+
+  exporter-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-bbmri-exporter-db
+    environment:
+      POSTGRES_USER: "exporter"
+      POSTGRES_PASSWORD: "${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/bbmri/exporter-db:/var/lib/postgresql/data"
+
+  reporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
+    container_name: bridgehead-bbmri-reporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      CROSS_ORIGINS: "https://${HOST}"
+      HTTP_RELATIVE_PATH: "/bbmri-reporter"
+      SITE: "${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 bbmri 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/bbmri/reporter-files:/app/reports"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.reporter_bbmri.rule=PathPrefix(`/bbmri-reporter`)"
+      - "traefik.http.services.reporter_bbmri.loadbalancer.server.port=8095"
+      - "traefik.http.routers.reporter_bbmri.tls=true"
+      - "traefik.http.middlewares.reporter_bbmri_strip.stripprefix.prefixes=/bbmri-reporter"
+      - "traefik.http.routers.reporter_bbmri.middlewares=reporter_bbmri_strip"
+      - "traefik.http.routers.reporter_bbmri.priority=20"
+
+      - "traefik.http.routers.reporter_bbmri_api.middlewares=reporter_bbmri_strip,exporter_auth"
+      - "traefik.http.routers.reporter_bbmri_api.rule=PathRegexp(`/bbmri-reporter/.+`)"
+      - "traefik.http.routers.reporter_bbmri_api.tls=true"
+      - "traefik.http.routers.reporter_bbmri_api.priority=25"
+

bbmri/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

bbmri/modules/exporter.md

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

bbmri/modules/teiler-compose.yml

@@ -0,0 +1,70 @@
+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_bbmri.rule=PathPrefix(`/bbmri-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_bbmri.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_bbmri.tls=true"
+      - "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://${HOST}/bbmri-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
+      HTTP_RELATIVE_PATH: "/bbmri-teiler"
+
+  teiler-dashboard:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
+    container_name: bridgehead-teiler-dashboard
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_dashboard_bbmri.rule=PathPrefix(`/bbmri-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_bbmri.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_bbmri.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_bbmri_strip.stripprefix.prefixes=/bbmri-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_bbmri.middlewares=teiler_dashboard_bbmri_strip"
+    environment:
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/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: "${OPERATOR_PHONE}"
+      TEILER_PROJECT: "${PROJECT}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/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"
+
+
+  teiler-backend:
+    image: docker.verbis.dkfz.de/ccp/bbmri-teiler-backend:latest
+    container_name: bridgehead-teiler-backend
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_backend_bbmri.rule=PathPrefix(`/bbmri-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_bbmri.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_bbmri.tls=true"
+      - "traefik.http.middlewares.teiler_backend_bbmri_strip.stripprefix.prefixes=/bbmri-teiler-backend"
+      - "traefik.http.routers.teiler_backend_bbmri.middlewares=teiler_backend_bbmri_strip"
+    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://${HOST}/bbmri-teiler"
+      TEILER_DASHBOARD_DE_URL: "https://${HOST}/bbmri-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "https://${HOST}/bbmri-teiler-dashboard/en"
+      HTTP_PROXY: "http://forward_proxy:3128"

bbmri/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

bbmri/modules/teiler.md

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

bbmri/vars

@@ -1,3 +1,9 @@
+BROKER_ID=broker-test.bbmri-test.samply.de
+BROKER_URL=https://${BROKER_ID}
+PROXY_ID=${SITE_ID}.${BROKER_ID}
+PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
+BROKER_URL_FOR_PREREQ=$BROKER_URL
+
 # Makes sense for all European Biobanks
 : ${ENABLE_ERIC:=true}
 
@@ -5,7 +11,6 @@
 : ${ENABLE_GBN:=false}
 
 FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 for module in $PROJECT/modules/*.sh
 do

bridgehead

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

cce/modules/pscc-compose.yml

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

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

cce/vars

@@ -1,9 +1,6 @@
 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

@@ -45,7 +45,6 @@ services:
       OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
       OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
       OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
       OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
       OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
       OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
@@ -141,7 +140,7 @@ services:
       --client-id="${OIDC_PRIVATE_CLIENT_ID}"
       --client-secret="${OIDC_CLIENT_SECRET}"
       --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
-      --oidc-issuer-url="${OIDC_ISSUER_URL}"
+      --oidc-issuer-url="${OIDC_URL}"
       --scope="openid email profile"
       --code-challenge-method="S256"
       --skip-provider-button=true

ccp/modules/mtba-compose.yml

@@ -23,7 +23,6 @@ services:
       OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
       OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
       OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      OIDC_REALM: "${OIDC_REALM}"
       OIDC_URL: "${OIDC_URL}"
 
     labels:

ccp/modules/teiler-compose.yml

@@ -33,7 +33,6 @@ services:
       TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
       TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
       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} ${OPERATOR_LAST_NAME}"
@@ -64,7 +63,6 @@ services:
       APPLICATION_PORT: "8085"
       APPLICATION_ADDRESS: "${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://${HOST}/ccp-teiler-dashboard/de"
@@ -73,9 +71,3 @@ services:
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
       IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active
-    secrets:
-      - ccp.conf
-
-secrets:
-  ccp.conf:
-    file: /etc/bridgehead/ccp.conf

ccp/vars

@@ -12,14 +12,9 @@ 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=${SITE_ID}-public
-# Use "test-realm-01" for testing
+OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
-OIDC_REALM="${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"

dhki/vars

@@ -8,8 +8,6 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-POSTGRES_TAG=15.6-alpine
-
 for module in ccp/modules/*.sh
 do
     log DEBUG "sourcing $module"

kr/modules/teiler-compose.yml

@@ -33,7 +33,6 @@ services:
       TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
       TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
       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}"

lib/install-bridgehead.sh

@@ -49,6 +49,12 @@ if [ -z "$TRANSFAIR_AUTH" ]; then
   fi
 fi
 
+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)."
+  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
+
 log "INFO" "Registering system units for bridgehead and bridgehead-update"
 cp -v \
     lib/systemd/bridgehead\@.service \

lib/prepare-system.sh

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

pscc/docker-compose.yml

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

pscc/modules/lens-compose.yml

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

pscc/modules/lens-setup.sh

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

pscc/root.crt.pem

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

pscc/vars

@@ -1,14 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.de
-BROKER_URL=https://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=denis.koether@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in $PROJECT/modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done

versions/acceptance

@@ -1,3 +1,4 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=main
+BLAZE_TAG=main
+POSTGRES_TAG=15.13-alpine

versions/prod

@@ -1,3 +1,4 @@
 FOCUS_TAG=main
 BEAM_TAG=main
-BLAZE_TAG=0.32
+BLAZE_TAG=0.32
+POSTGRES_TAG=15.13-alpine

versions/test

@@ -1,3 +1,4 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=main
+BLAZE_TAG=main
+POSTGRES_TAG=15.13-alpine