BBMRI Teiler default templates: bbmri (exporter) and bbmri-qb (reporter)

bbmri/docker-compose.yml

@@ -1,6 +1,6 @@
 version: "3.7"
 
-# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see vars.
+# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see ccp vars.
 
 services:
   blaze:

bbmri/modules/exporter-compose.yml

@@ -0,0 +1,67 @@
+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

@@ -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 +1,81 @@
+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

@@ -0,0 +1,9 @@
+#!/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

@@ -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

@@ -7,6 +7,18 @@
 FOCUS_RETRY_COUNT=32
 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

@@ -28,9 +28,6 @@ fi
 case "$PROJECT" in
 	ccp)
 		#nothing extra to do
-        ;;
-	leme)
-		#nothing extra to do
 		;;
 	bbmri)
 		#nothing extra to do

leme/docker-compose.yml

@@ -1,62 +0,0 @@
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
-    container_name: bridgehead-leme-blaze
-    environment:
-      BASE_URL: "http://bridgehead-leme-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
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_leme.rule=PathPrefix(`/leme-localdatamanagement`)"
-      - "traefik.http.middlewares.leme_b_strip.stripprefix.prefixes=/leme-localdatamanagement"
-      - "traefik.http.services.blaze_leme.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_leme.middlewares=leme_b_strip,auth"
-      - "traefik.http.routers.blaze_leme.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
-    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-leme-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/leme/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

leme/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUHtDdZ+L/Z1YmwlrHJRelJFLAGh0wDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwNTEzMTExMTQyWhcNMzQw
-NTExMTExMjExWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAMLGngURLDDleDC/jGUSU12z9nfJBFrHItWQkcQk
-uZPOhCB55mD18aMtLmpXcHQ4MZdDOCHjA7n3gZa04PvueuLht57z3Uyk+M9C1Oor
-9KpnJWLogWtVJ9iaLrIGGS+lwttpglISg+7nZIszrCVaq2/mLe/Il47D7EifmA8L
-T+/gNd470tvAWaFn3pmeNJ2CHZ0ld+6CSOweerfPHq44DrZeCO8nRl/+v/JTizLg
-Fxjr2N38TohL4S8/QLIWtyQLZJbshuWAMwd7WtMXWqGPrIIDC8NiIQW8Yb1zjdoD
-/Ghmw6yfr+/m02GpJTe4rVhYJT9WYZS6wUbRlK1WTuy8T2ECAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFMdNeYJQr5e5
-Cmh3NzSg/6eQF0IxMB8GA1UdIwQYMBaAFMdNeYJQr5e5Cmh3NzSg/6eQF0IxMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQBl3iQUJYKz
-E82f1SMyd9EHx4xs5fwVAKpndDkPBo4QbRHCeSfEnkxJHtluaDXJF0MaWMbvNps1
-99afOVjZCDa5UQUqneyBTbY1tHr3gyYV/doe4FIHA799D2dKlyxu6sPNzRZJGppT
-gaueKzc3jKINER1LcdOaPmSogNGNezCwOsAkmwuPQMrzMT8JPlLEGh0vfG4B994w
-ECxyC3PicjXvq5UOCwYiGSwawqTznLUb3FO6SFYS1mNv2inVaNfLzkuCkdIyyqeU
-dc/h6tuDSC+CKAy+/qoDNzG9KD+mI8kVyhhIrQ++vQ9bbRtWr5aQzaq+fyDJNXx3
-IQvYUuSR8Nab
------END CERTIFICATE-----

leme/vars

@@ -1,14 +0,0 @@
-BROKER_ID=broker-test.health-innovation-lab.eu
-BROKER_URL=http://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=32
-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

lib/prepare-system.sh

@@ -49,9 +49,6 @@ case "$PROJECT" in
 	ccp)
 		site_configuration_repository_middle="git.verbis.dkfz.de/bridgehead-configurations/bridgehead-config-"
 		;;
-    leme)
-		site_configuration_repository_middle="git.verbis.dkfz.de/bridgehead-configurations/bridgehead-config-"
-		;;
 	bbmri)
 		site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
 		;;

minimal/docker-compose.yml

@@ -46,15 +46,15 @@ services:
       # Wait 1s before marking this service healthy. Required for the oauth2-proxy to talk to the OIDC provider on startup which will fail if the forward proxy is not started yet.
       test: ["CMD", "sleep", "1"]
 
-  # landing:
+  landing:
-  #   container_name: bridgehead-landingpage
+    container_name: bridgehead-landingpage
-  #   image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
-  #   labels:
+    labels:
-  #     - "traefik.enable=true"
+      - "traefik.enable=true"
-  #     - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-  #     - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.services.landing.loadbalancer.server.port=80"
-  #     - "traefik.http.routers.landing.tls=true"
+      - "traefik.http.routers.landing.tls=true"
-  #   environment:
+    environment:
-  #     HOST: ${HOST}
+      HOST: ${HOST}
-  #     PROJECT: ${PROJECT}
+      PROJECT: ${PROJECT}
-  #     SITE_NAME: ${SITE_NAME}
+      SITE_NAME: ${SITE_NAME}

minimal/modules/bbmri vars

@@ -0,0 +1,2 @@
+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

@@ -0,0 +1,7 @@
+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"