Remove R-Studio

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.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.

bridgehead

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

@@ -1,87 +0,0 @@
-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

@@ -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

cce/modules/lens-compose.yml

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

cce/modules/teiler-compose.yml

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

cce/modules/teiler-setup.sh

@@ -1,8 +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=EN
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-fi

ccp/modules/datashield-compose.yml

@@ -73,12 +73,71 @@ 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

@@ -5,6 +5,10 @@ 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\")"
@@ -18,13 +22,18 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
     openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
   fi
   mkdir -p /tmp/bridgehead/opal-map
-  echo '{"sites": []}' >/tmp/bridgehead/opal-map/central.json
+  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
-  # Only allow connections from the central beam proxy that is used by all coder workspaces
+  echo "$sites" | docker_jq -n --args '{"sites": input | map({
-  echo '[{
+    "name": .,
-    "external": "'$SITE_ID':443",
+    "id": .,
+    "virtualhost": "\(.):443",
+    "beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
+  })}' $sites >/tmp/bridgehead/opal-map/central.json
+  echo "$sites" | docker_jq -n --args '[{
+    "external": "'"$SITE_ID"':443",
     "internal": "opal:8443",
-    "allowed": ["central-ds-orchestrator.'$BROKER_ID'"]
+    "allowed": input | map("\(.).'"$BROKER_ID"'")
-  }]' > /tmp/bridgehead/opal-map/local.json
+  }]' >/tmp/bridgehead/opal-map/local.json
   if [ "$USER" == "root" ]; then
     chown -R bridgehead:docker /tmp/bridgehead
     chmod g+wr /tmp/bridgehead/opal-map/*

ccp/modules/datashield-sites.json

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

itcc/modules/lens-compose.yml

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

lib/functions.sh

@@ -436,3 +436,7 @@ 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/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
 }
+
+docker_jq() {
+    docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
+}