Refactor ovis-compose.yml to add new services

ccp/modules/ovis-compose.yml

@@ -1,17 +1,6 @@
 version: "3.7"
 
 services:
-  fhir-transformer:
-    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-fhir-transformer:latest
-    container_name: bridgehead-ccp-ovis-fhir-transformer
-    restart: on-failure
-    environment:
-      FHIR_SERVER_URL: ${FHIR_SERVER_URL:-http://bridgehead-ccp-blaze:8080/fhir}
-      FHIR_USERNAME: ${FHIR_USERNAME}
-      FHIR_PASSWORD: ${FHIR_PASSWORD}
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/app/output
-
   mongo:
     image: mongo:${MONGO_VER:-latest}
     container_name: bridgehead-ccp-ovis-mongo
@@ -20,6 +9,88 @@ services:
     volumes:
       - /var/cache/bridgehead/ccp/ovis/mongo/init/init.js:/docker-entrypoint-initdb.d/init.js:ro
 
+  ovis-backend-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: ${APOLLO_PORT:-4001}
+      CREDOS_PORT: ${CREDOS_PORT:-4000}
+      HTTP_PROXY: ${OVIS_HTTP_PROXY:-}
+      HTTPS_PROXY: ${OVIS_HTTPS_PROXY:-}
+      NO_PROXY: ${OVIS_NO_PROXY:-}
+      http_proxy: ${OVIS_HTTP_PROXY:-}
+      https_proxy: ${OVIS_HTTPS_PROXY:-}
+      no_proxy: ${OVIS_NO_PROXY:-}
+      CORS_ORIGIN: ${OVIS_CORS_ORIGIN:-*}
+      DB: ${DB:-onc_test}
+      ADRESS: mongodb://mongo:27017
+      MONGO_VER: ${MONGO_VER:-latest}
+      OVIS_PREPROC_DECEASED_KEYWORDS: ${OVIS_PREPROC_DECEASED_KEYWORDS:-}
+      OVIS_PREPROC_REZIDIV_PREFIXES: ${OVIS_PREPROC_REZIDIV_PREFIXES:-}
+      OVIS_PREPROC_REZIDIV_CANONICAL: ${OVIS_PREPROC_REZIDIV_CANONICAL:-}
+      OVIS_PREPROC_REZIDIV_LYMPH_STATES: ${OVIS_PREPROC_REZIDIV_LYMPH_STATES:-}
+      OVIS_PREPROC_PROGRESS_LABELS: ${OVIS_PREPROC_PROGRESS_LABELS:-}
+      OVIS_PREPROC_COMPLETE_REMISSION_LABELS: ${OVIS_PREPROC_COMPLETE_REMISSION_LABELS:-}
+      OVIS_PREPROC_RCLASS_SUCCESS: ${OVIS_PREPROC_RCLASS_SUCCESS:-}
+      OVIS_PREPROC_LOCAL_RSTATE_SUCCESS: ${OVIS_PREPROC_LOCAL_RSTATE_SUCCESS:-}
+      OVIS_PREPROC_METASTASIS_PREFIXES: ${OVIS_PREPROC_METASTASIS_PREFIXES:-}
+      OVIS_PREPROC_METASTASIS_SPREAD_VALUES: ${OVIS_PREPROC_METASTASIS_SPREAD_VALUES:-}
+      OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON: ${OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON:-}
+      OVIS_PREPROC_METASTASIS_STRAT_NONE: ${OVIS_PREPROC_METASTASIS_STRAT_NONE:-}
+      OVIS_PREPROC_NULL_STUDY_PHASES: ${OVIS_PREPROC_NULL_STUDY_PHASES:-}
+      OVIS_PREPROC_PREV_THERAPY_SURGERY: ${OVIS_PREPROC_PREV_THERAPY_SURGERY:-}
+      OVIS_PREPROC_PREV_THERAPY_SYSTEMIC: ${OVIS_PREPROC_PREV_THERAPY_SYSTEMIC:-}
+      OVIS_PREPROC_PREV_THERAPY_RADIATION: ${OVIS_PREPROC_PREV_THERAPY_RADIATION:-}
+      OVIS_PREPROC_PREV_CONSULTATION_NUTRITION: ${OVIS_PREPROC_PREV_CONSULTATION_NUTRITION:-}
+      OVIS_PREPROC_PREV_CONSULTATION_SOCIAL: ${OVIS_PREPROC_PREV_CONSULTATION_SOCIAL:-}
+      OVIS_PREPROC_PREV_CONSULTATION_PSYCHO: ${OVIS_PREPROC_PREV_CONSULTATION_PSYCHO:-}
+      OVIS_PREPROC_PREV_CONSULTATION_GENETIC: ${OVIS_PREPROC_PREV_CONSULTATION_GENETIC:-}
+      OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE: ${OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE:-}
+      OVIS_PREPROC_TUMORBOARD_PATTERN_POST: ${OVIS_PREPROC_TUMORBOARD_PATTERN_POST:-}
+      OVIS_PREPROC_TUMORBOARD_PATTERN_MTB: ${OVIS_PREPROC_TUMORBOARD_PATTERN_MTB:-}
+      OVIS_PREPROC_ECOG_PREFIX: ${OVIS_PREPROC_ECOG_PREFIX:-}
+      OVIS_PREPROC_DISTRESS_TYPE: ${OVIS_PREPROC_DISTRESS_TYPE:-}
+      OVIS_PREPROC_DISTRESS_POSITIVE_VALUES: ${OVIS_PREPROC_DISTRESS_POSITIVE_VALUES:-}
+    depends_on:
+      - mongo
+    volumes:
+      - /var/cache/bridgehead/ccp/ovis/shared_data:/app/generated
+    healthcheck:
+      test: ["CMD-SHELL", "node -e \"require('http').get('http://localhost:9000/health', res => process.exit(res.statusCode===200?0:1)).on('error', () => process.exit(1));\""]
+      interval: 10s
+      timeout: 5s
+      retries: 6
+      start_period: 5s
+    command: ["node", "./Preprocessing/catalogue-service.mjs"]
+
+  ovis-backend-data-import:
+    image: docker.verbis.dkfz.de/ovis/ovis-backend-data-import-${OVIS_IMPORT_MODE:-demo}:latest
+    container_name: bridgehead-ccp-ovis-import
+    restart: on-failure
+    depends_on:
+      ovis-backend-data-preprocessing:
+        condition: service_healthy
+    environment:
+      # CCP mode: FHIR source configuration (ignored by DEMO image)
+      FHIR_SERVER_URL: ${FHIR_SERVER_URL:-http://bridgehead-ccp-blaze:8080/fhir}
+      FHIR_USERNAME: ${FHIR_USERNAME:-}
+      FHIR_PASSWORD: ${FHIR_PASSWORD:-}
+      ICD10_FILTER: ${ICD10_FILTER:-}
+      # Required for both CCP and DEMO: preprocessor upload endpoint
+      OVIS_PREPROCESSOR_URL: ${OVIS_PREPROCESSOR_URL:-http://ovis-backend-data-preprocessing:9000/omock}
+      # Proxy configuration
+      HTTP_PROXY: ${OVIS_HTTP_PROXY:-}
+      HTTPS_PROXY: ${OVIS_HTTPS_PROXY:-}
+      NO_PROXY: ${OVIS_NO_PROXY:-}
+      http_proxy: ${OVIS_HTTP_PROXY:-}
+      https_proxy: ${OVIS_HTTPS_PROXY:-}
+      no_proxy: ${OVIS_NO_PROXY:-}
+    volumes:
+      - /var/cache/bridgehead/ccp/ovis/shared_data:/shared
+
   backend:
     image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
     container_name: bridgehead-ccp-ovis-backend
@@ -31,27 +102,17 @@ services:
       CREDOS_PORT: ${CREDOS_PORT:-4000}
       CORS_ORIGIN: ${OVIS_CORS_ORIGIN:-*}
       DB: ${DB:-onc_test}
-      ADRESS: ${ADRESS:-mongodb://mongo:27017}
+      ADRESS: mongodb://mongo:27017
     depends_on:
       - mongo
-      - fhir-transformer
+      - ovis-backend-data-preprocessing
+      - ovis-backend-data-import
     healthcheck:
       test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"]
       interval: 5s
       timeout: 3s
       retries: 5
       start_period: 10s
-    entrypoint: >
-      sh -c "
-        while [ ! -f /shared/omock.json ]; do
-          echo 'Waiting for omock.json...'
-          sleep 5
-        done;
-        mkdir -p ./prep &&
-        cp /shared/omock.json ./prep/omock.json &&
-        node ./mgDB/prep/preprocessor.mjs &&
-        echo 'Processing complete' &&
-        exec node --watch index.js"
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.ovis-backend.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/graphql`)"
@@ -62,8 +123,6 @@ services:
       - "traefik.http.middlewares.ovis-backend-ccp-strip.stripprefix.prefixes=/ccp-ovis"
       - "traefik.http.routers.ovis-backend-ccp.middlewares=ovis-backend-ccp-strip,${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}"
       - "traefik.http.services.ovis-backend.loadbalancer.server.port=${APOLLO_PORT:-4001}"
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/shared
 
   frontend:
     image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest
@@ -71,7 +130,18 @@ services:
     restart: always
     environment:
       PUBLIC_GRAPHQL_URL: https://${HOST:-localhost}/ccp-ovis/graphql
-      PUBLIC_LOGIN_ENABLED: "false"
+      PUBLIC_LOGIN_ENABLED: ${PUBLIC_LOGIN_ENABLED:-false}
+      PUBLIC_OVIS_IMPORT: ${OVIS_IMPORT_MODE:-demo}
+      OVIS_CATALOGUE_UPSTREAM_URL: ${OVIS_CATALOGUE_UPSTREAM_URL:-http://ovis-backend-data-preprocessing:9000/catalogue}
+      EXPRESS_AUTH_URL: ${EXPRESS_AUTH_URL:-http://express-auth:5000}
+      EXPRESS_AUTH_USERNAME: ${EXPRESS_AUTH_USERNAME:-admin}
+      EXPRESS_AUTH_PASSWORD: ${EXPRESS_AUTH_PASSWORD:-admin}
+      HTTP_PROXY: ${OVIS_HTTP_PROXY:-}
+      HTTPS_PROXY: ${OVIS_HTTPS_PROXY:-}
+      NO_PROXY: ${OVIS_NO_PROXY:-}
+      http_proxy: ${OVIS_HTTP_PROXY:-}
+      https_proxy: ${OVIS_HTTPS_PROXY:-}
+      no_proxy: ${OVIS_NO_PROXY:-}
     depends_on:
       backend:
         condition: service_healthy