refactor: align Bridgehead OVIS CCP overlay with upstream runtime contracts

Apply the PR #375 review feedback by removing Bridgehead-specific compose/setup overrides that duplicated upstream OVIS behavior and by switching to the upstream-built Mongo image that already contains init logic. - rename CCP OVIS services to consistent upstream-style names (`ovis-*`) and update internal dependencies - switch Mongo service image from direct `mongo:latest` + host-mounted init script to `docker.verbis.dkfz.de/ovis/ovis-backend-mongodb:latest` - remove obsolete Mongo init bind mount (`/docker-entrypoint-initdb.d/init.js`) from compose - drop redundant runtime overrides from compose (`restart`, `command`, `user`, `working_dir`) - remove duplicated app-default/preprocessor env overrides (`OVIS_PREPROC_*`, misc backend defaults) and keep deployment wiring only - fix Mongo connection env usage to `ADDRESS` and point services to `ovis-backend-database-mongodb` - remove temporary root-compat Traefik redirect shim and keep mounted `/ccp-ovis` routing labels - remove setup-time generation of Mongo init.js and related cache directory prep from `ccp/modules/ovis-setup.sh`
2026-03-25 13:10:14 +01:00 · 2026-03-23 11:28:27 +01:00
parent 921bac11d2
commit 191f5f24da
2 changed files with 13 additions and 102 deletions
--- a/ccp/modules/ovis-compose.yml
+++ b/ccp/modules/ovis-compose.yml
@@ -1,77 +1,36 @@
 version: "3.7"

 services:
-  mongo:
-    image: mongo:latest
+  ovis-backend-database-mongodb:
+    image: docker.verbis.dkfz.de/ovis/ovis-backend-mongodb:latest
    container_name: bridgehead-ccp-ovis-mongo
-    restart: always
-    command: mongod
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/mongo/init/init.js:/docker-entrypoint-initdb.d/init.js:ro

-  ovis-backend-data-preprocessing:
+  ovis-backend-mongodb-data-preprocessing:
    image: docker.verbis.dkfz.de/ovis/ovis-backend-preprocessor:latest
    container_name: bridgehead-ccp-ovis-preprocessing
-    restart: on-failure
-    user: root
-    working_dir: /app
    environment:
-      APOLLO_PORT: "4001"
-      CREDOS_PORT: "4000"
+      ADDRESS: mongodb://ovis-backend-database-mongodb:27017
      HTTP_PROXY: ""
      HTTPS_PROXY: ""
      NO_PROXY: ""
      http_proxy: ""
      https_proxy: ""
      no_proxy: ""
-      CORS_ORIGIN: "*"
-      DB: onc_test
-      ADRESS: mongodb://mongo:27017
-      MONGO_VER: latest
-      OVIS_PREPROC_DECEASED_KEYWORDS: '["verstorben","dead","deceased","not alive","gestorben"]'
-      OVIS_PREPROC_REZIDIV_PREFIXES: '["Rezidiv"]'
-      OVIS_PREPROC_REZIDIV_CANONICAL: Rezidiv
-      OVIS_PREPROC_REZIDIV_LYMPH_STATES: '["Rezidiv","Neu"]'
-      OVIS_PREPROC_PROGRESS_LABELS: '["Progression","Divergentes Geschehen","Rezidiv"]'
-      OVIS_PREPROC_COMPLETE_REMISSION_LABELS: '["Vollremission / Tumorfrei (complete remission)"]'
-      OVIS_PREPROC_RCLASS_SUCCESS: '["R0"]'
-      OVIS_PREPROC_LOCAL_RSTATE_SUCCESS: '["R0"]'
-      OVIS_PREPROC_METASTASIS_PREFIXES: '["Rezidiv","Neu"]'
-      OVIS_PREPROC_METASTASIS_SPREAD_VALUES: '["Neu","Rezidiv","Tumornachweis"]'
-      OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON: Synchrone Metastasierung
-      OVIS_PREPROC_METASTASIS_STRAT_NONE: keine synchrone Metastasierung
-      OVIS_PREPROC_NULL_STUDY_PHASES: '["NOPH","KA"]'
-      OVIS_PREPROC_PREV_THERAPY_SURGERY: '["operation"]'
-      OVIS_PREPROC_PREV_THERAPY_SYSTEMIC: '["systemic"]'
-      OVIS_PREPROC_PREV_THERAPY_RADIATION: '["radiation"]'
-      OVIS_PREPROC_PREV_CONSULTATION_NUTRITION: '["nutrition"]'
-      OVIS_PREPROC_PREV_CONSULTATION_SOCIAL: '["social"]'
-      OVIS_PREPROC_PREV_CONSULTATION_PSYCHO: '["psycho"]'
-      OVIS_PREPROC_PREV_CONSULTATION_GENETIC: '["genetic"]'
-      OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE: prae|prä|pre
-      OVIS_PREPROC_TUMORBOARD_PATTERN_POST: post
-      OVIS_PREPROC_TUMORBOARD_PATTERN_MTB: mtb
-      OVIS_PREPROC_ECOG_PREFIX: ECOG
-      OVIS_PREPROC_DISTRESS_TYPE: distress
-      OVIS_PREPROC_DISTRESS_POSITIVE_VALUES: '["Positiv"]'
+
    depends_on:
-      - mongo
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/app/generated
+      - ovis-backend-database-mongodb
    healthcheck:
      test: ["CMD-SHELL", "node -e \"require('http').get('http://localhost:9000/health', res => process.exit(res.statusCode===200?0:1)).on('error', () => process.exit(1));\""]
      interval: 10s
      timeout: 5s
      retries: 6
      start_period: 5s
-    command: ["node", "./Preprocessing/catalogue-service.mjs"]

  ovis-backend-data-import:
    image: docker.verbis.dkfz.de/ovis/ovis-backend-data-import-ccp:latest
    container_name: bridgehead-ccp-ovis-import
-    restart: on-failure
    depends_on:
-      ovis-backend-data-preprocessing:
+      ovis-backend-mongodb-data-preprocessing:
        condition: service_healthy
    environment:
      # CCP mode: FHIR source configuration (ignored by DEMO image)
@@ -79,8 +38,6 @@ services:
      FHIR_USERNAME: ""
      FHIR_PASSWORD: ""
      ICD10_FILTER: ""
-      # Required for both CCP and DEMO: preprocessor upload endpoint
-      OVIS_PREPROCESSOR_URL: http://ovis-backend-data-preprocessing:9000/omock
      # Proxy configuration
      HTTP_PROXY: ""
      HTTPS_PROXY: ""
@@ -88,24 +45,15 @@ services:
      http_proxy: ""
      https_proxy: ""
      no_proxy: ""
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/shared

-  backend:
+  ovis-backend-apollo:
    image: docker.verbis.dkfz.de/ovis/ovis-backend-apollo:latest
    container_name: bridgehead-ccp-ovis-backend
-    restart: always
-    user: root
-    working_dir: /app
    environment:
-      APOLLO_PORT: "4001"
-      CREDOS_PORT: "4000"
-      CORS_ORIGIN: "*"
-      DB: onc_test
-      ADRESS: mongodb://mongo:27017
+      ADDRESS: mongodb://ovis-backend-database-mongodb:27017
    depends_on:
-      - mongo
-      - ovis-backend-data-preprocessing
+      - ovis-backend-database-mongodb
+      - ovis-backend-mongodb-data-preprocessing
      - ovis-backend-data-import
    healthcheck:
      test: ["CMD-SHELL", "test -d /app/node_modules/mongodb"]
@@ -124,16 +72,14 @@ services:
      - "traefik.http.routers.ovis-backend-ccp.service=ovis-backend"
      - "traefik.http.services.ovis-backend.loadbalancer.server.port=4001"

-  frontend:
+  ovis-frontend:
    image: docker.verbis.dkfz.de/ovis/ovis-frontend:latest
    container_name: bridgehead-ccp-ovis-frontend
-    restart: always
    environment:
      OVIS_PUBLIC_BASE_PATH: /ccp-ovis
      PUBLIC_GRAPHQL_URL: https://${HOST}/ccp-ovis/graphql
      PUBLIC_LOGIN_ENABLED: "false"
      PUBLIC_OVIS_IMPORT: ccp
-      OVIS_CATALOGUE_UPSTREAM_URL: http://ovis-backend-data-preprocessing:9000/catalogue
      HTTP_PROXY: ""
      HTTPS_PROXY: ""
      NO_PROXY: ""
@@ -141,21 +87,10 @@ services:
      https_proxy: ""
      no_proxy: ""
    depends_on:
-      backend:
+      ovis-backend-apollo:
        condition: service_healthy
-    volumes:
-      # Dynamic catalogue from preprocessing service
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/app/dynamic-catalogue:ro
    labels:
      - "traefik.enable=true"
-      - "traefik.http.routers.ovis-frontend-root-compat.tls=true"
-      - "traefik.http.routers.ovis-frontend-root-compat.rule=PathRegexp(`^/(icons|svg|fonts|api|downloads|Ovis_logo.svg|CCP_logo.svg|patient-cohort|patient-single|filter-edit|survival-definition|footer-version|user-management|tumorboard|tnm|therapy|therapy-systemic|therapy-radiation|therapy-general|therapy-operation|survival|supplementary|study|settings|status|progress|molecular-marker|footer-licensing|footer-privacy|footer-imprint|footer-issues|footer-contact|footer-cite|diagnosis|bio-material|consultation)(/.*)?$`)"
-      - "traefik.http.routers.ovis-frontend-root-compat.priority=900"
-      - "traefik.http.routers.ovis-frontend-root-compat.middlewares=ovis-frontend-root-compat-redirect"
-      - "traefik.http.routers.ovis-frontend-root-compat.service=ovis-frontend"
-      - "traefik.http.middlewares.ovis-frontend-root-compat-redirect.redirectregex.regex=^https?://([^/]+)/(.*)$"
-      - "traefik.http.middlewares.ovis-frontend-root-compat-redirect.redirectregex.replacement=https://$${1}/ccp-ovis/$${2}"
-      - "traefik.http.middlewares.ovis-frontend-root-compat-redirect.redirectregex.permanent=false"
      - "traefik.http.routers.ovis-frontend-ccp-slash.tls=true"
      - "traefik.http.routers.ovis-frontend-ccp-slash.rule=Path(`/ccp-ovis`)"
      - "traefik.http.routers.ovis-frontend-ccp-slash.priority=1000"
--- a/ccp/modules/ovis-setup.sh
+++ b/ccp/modules/ovis-setup.sh
@@ -4,30 +4,6 @@ if [ -n "$ENABLE_OVIS" ]; then
  if declare -F log >/dev/null 2>&1; then
    log INFO "OVIS setup detected -- will start OVIS services."
  fi
-  mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
-  mkdir -p "/var/cache/bridgehead/ccp/ovis/shared_data"
-
-  cat >"/var/cache/bridgehead/ccp/ovis/mongo/init/init.js" <<'EOF'
-db = db.getSiblingDB("onc_test");
-db.createCollection("user");
-db.user.updateOne(
-  { _id: "OVIS-Root" },
-  {
-    $setOnInsert: {
-      _id: "OVIS-Root",
-      createdAt: new Date(),
-      createdBy: "system",
-      role: "super-admin",
-      status: "active",
-      pseudonymization: false,
-      darkMode: false,
-      colorTheme: "CCCMunich",
-      language: "de"
-    }
-  },
-  { upsert: true }
-);
-EOF

  OVERRIDE+=" -f ./$PROJECT/modules/ovis-compose.yml"
 fi