Fix GitLab token syncing for BBMRI

Merge develop into main

bbmri/docker-compose.yml

@@ -4,7 +4,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"

cce/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-cce-blaze
     environment:
       BASE_URL: "http://bridgehead-cce-blaze:8080"

cce/modules/export-and-qb.curl-templates

@@ -1,6 +0,0 @@
-# Full Excel Export
-curl --location --request POST 'https://${HOST}/cce-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
---header 'x-api-key: ${EXPORT_API_KEY}'
-
-# QB
-curl --location --request POST 'https://${HOST}/cce-reporter/generate?template-id=ccp'

cce/modules/exporter-compose.yml

@@ -1,72 +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: "${EXPORTER_OPAL_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_cce.rule=PathPrefix(`/cce-exporter`)"
-      - "traefik.http.services.exporter_cce.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_cce.tls=true"
-      - "traefik.http.middlewares.exporter_cce_strip.stripprefix.prefixes=/cce-exporter"
-      - "traefik.http.routers.exporter_cce.middlewares=exporter_cce_strip"
-    volumes:
-      - "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${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"
-
-  focus:
-    environment:
-      EXPORTER_URL: "http://exporter:8092"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

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/teiler-compose.yml

@@ -1,89 +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: "https://${HOST}/cce-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/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: "https://${HOST}/cce-teiler-backend"
-      OIDC_URL: "${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}/cce-teiler"
-      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/cce-teiler-dashboard"
-      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/dktk-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"
-      APPLICATION_ADDRESS: "${HOST}"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      CONFIG_ENV_VAR_PATH: "/run/secrets/cce.conf"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/cce-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/cce-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/cce-teiler-dashboard/en"
-      CENTRAX_URL: "${CENTRAXX_URL}"
-      HTTP_PROXY: "http://forward_proxy:3128"
-      ENABLE_MTBA: "${ENABLE_MTBA}"
-      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-      TEILER_APP16_BACKENDURL: "https://${HOST}/cce-exporter"
-      TEILER_APP17_BACKENDURL: "https://${HOST}/cce-exporter"
-      TEILER_APP18_BACKENDURL: "https://${HOST}/cce-exporter"
-      TEILER_APP35_BACKENDURL: "https://${HOST}/cce-exporter"
-      TEILER_APP36_BACKENDURL: "https://${HOST}/cce-exporter"
-      TEILER_APP26_BACKENDURL: "https://${HOST}/cce-reporter"
-
-
-    secrets:
-      - cce.conf
-
-secrets:
-  cce.conf:
-    file: /etc/bridgehead/cce.conf

cce/modules/teiler-setup.sh

@@ -1,9 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_TEILER" == true ];then
-  log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
-  TEILER_DEFAULT_LANGUAGE=DE
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-  add_public_oidc_redirect_url "/cce-teiler/*"
-fi

cce/vars

@@ -7,18 +7,6 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-POSTGRES_TAG=15.6-alpine
-
-OIDC_USER_GROUP="CCE_$(capitalize_first_letter ${SITE_ID})"
-OIDC_ADMIN_GROUP="CCE_$(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:-test-realm-01}"
-OIDC_URL="https://login.verbis.dkfz.de"
-OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
-OIDC_GROUP_CLAIM="groups"
-
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

ccp/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"

ccp/modules/blaze-secondary-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze-secondary
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

dhki/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-dhki-blaze
     environment:
       BASE_URL: "http://bridgehead-dhki-blaze:8080"

itcc/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-itcc-blaze
     environment:
       BASE_URL: "http://bridgehead-itcc-blaze:8080"

kr/docker-compose.yml

@@ -6,7 +6,7 @@ services:
       replicas: 0 #deactivate landing page
 
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"

lib/functions.sh

@@ -334,6 +334,19 @@ function secret_sync_gitlab_token() {
             ;;
     esac
 
+    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
+
     # Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
     # If it is missing or expired, Secret Sync will create a new token and write it to the file.
     # The git credential helper reads the token from the file during git pull.
@@ -344,14 +357,14 @@ function secret_sync_gitlab_token() {
     docker run --rm \
         -v /var/cache/bridgehead/secrets/gitlab_token:/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 GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
+        -e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
         -e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
     if [ $? -eq 0 ]; then

modules/transfair-compose.yml

@@ -17,11 +17,13 @@ services:
       - EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
       - DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
       - RUST_LOG=${RUST_LOG:-info}
+      - TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
     volumes:
       - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
 
   transfair-input-blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-transfair-input-blaze
     environment:
       BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
@@ -34,7 +36,7 @@ services:
     profiles: ["transfair-input-blaze"]
 
   transfair-request-blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-transfair-requests-blaze
     environment:
       BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"

versions/prod

@@ -1,2 +1,3 @@
 FOCUS_TAG=main
-BEAM_TAG=main
+BEAM_TAG=main
+BLAZE_TAG=0.32

versions/test

@@ -1,2 +1,3 @@
 FOCUS_TAG=develop
-BEAM_TAG=develop
+BEAM_TAG=develop
+BLAZE_TAG=main