diff --git a/ccp/modules/ovis-compose.yml b/ccp/modules/ovis-compose.yml index b58eb737..743dd6ac 100644 --- a/ccp/modules/ovis-compose.yml +++ b/ccp/modules/ovis-compose.yml @@ -2,7 +2,7 @@ version: "3.7" services: mongo: - image: mongo:${MONGO_VER:-latest} + image: mongo:latest container_name: bridgehead-ccp-ovis-mongo restart: always command: mongod @@ -16,44 +16,44 @@ services: 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} + APOLLO_PORT: "4001" + CREDOS_PORT: "4000" + HTTP_PROXY: "" + HTTPS_PROXY: "" + NO_PROXY: "" + http_proxy: "" + https_proxy: "" + no_proxy: "" + CORS_ORIGIN: "*" + 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: ${OVIS_PREPROC_DISTRESS_POSITIVE_VALUES:-} + MONGO_VER: latest + OVIS_PREPROC_DECEASED_KEYWORDS: '["verstorben","dead","deceased","not alive","gestorben"]' + OVIS_PREPROC_REZIDIV_PREFIXES: '["Rezidiv"]' + OVIS_PREPROC_REZIDIV_CANONICAL: Rezidiv + OVIS_PREPROC_REZIDIV_LYMPH_STATES: '["Rezidiv","Neu"]' + OVIS_PREPROC_PROGRESS_LABELS: '["Progression","Divergentes Geschehen","Rezidiv"]' + OVIS_PREPROC_COMPLETE_REMISSION_LABELS: '["Vollremission / Tumorfrei (complete remission)"]' + OVIS_PREPROC_RCLASS_SUCCESS: '["R0"]' + OVIS_PREPROC_LOCAL_RSTATE_SUCCESS: '["R0"]' + OVIS_PREPROC_METASTASIS_PREFIXES: '["Rezidiv","Neu"]' + OVIS_PREPROC_METASTASIS_SPREAD_VALUES: '["Neu","Rezidiv","Tumornachweis"]' + OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON: Synchrone Metastasierung + OVIS_PREPROC_METASTASIS_STRAT_NONE: keine synchrone Metastasierung + OVIS_PREPROC_NULL_STUDY_PHASES: '["NOPH","KA"]' + OVIS_PREPROC_PREV_THERAPY_SURGERY: '["operation"]' + OVIS_PREPROC_PREV_THERAPY_SYSTEMIC: '["systemic"]' + OVIS_PREPROC_PREV_THERAPY_RADIATION: '["radiation"]' + OVIS_PREPROC_PREV_CONSULTATION_NUTRITION: '["nutrition"]' + OVIS_PREPROC_PREV_CONSULTATION_SOCIAL: '["social"]' + OVIS_PREPROC_PREV_CONSULTATION_PSYCHO: '["psycho"]' + OVIS_PREPROC_PREV_CONSULTATION_GENETIC: '["genetic"]' + OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE: prae|prä|pre + OVIS_PREPROC_TUMORBOARD_PATTERN_POST: post + OVIS_PREPROC_TUMORBOARD_PATTERN_MTB: mtb + OVIS_PREPROC_ECOG_PREFIX: ECOG + OVIS_PREPROC_DISTRESS_TYPE: distress + OVIS_PREPROC_DISTRESS_POSITIVE_VALUES: '["Positiv"]' depends_on: - mongo volumes: @@ -67,7 +67,7 @@ services: command: ["node", "./Preprocessing/catalogue-service.mjs"] ovis-backend-data-import: - image: docker.verbis.dkfz.de/ovis/ovis-backend-data-import-${OVIS_IMPORT_MODE:-demo}:latest + image: docker.verbis.dkfz.de/ovis/ovis-backend-data-import-demo:latest container_name: bridgehead-ccp-ovis-import restart: on-failure depends_on: @@ -75,83 +75,69 @@ services: 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:-} + FHIR_SERVER_URL: http://bridgehead-ccp-blaze:8080/fhir + FHIR_USERNAME: your-fhir-username + FHIR_PASSWORD: your-fhir-password + ICD10_FILTER: "" # Required for both CCP and DEMO: preprocessor upload endpoint - OVIS_PREPROCESSOR_URL: ${OVIS_PREPROCESSOR_URL:-http://ovis-backend-data-preprocessing:9000/omock} + 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:-} + HTTP_PROXY: "" + HTTPS_PROXY: "" + NO_PROXY: "" + http_proxy: "" + https_proxy: "" + no_proxy: "" volumes: - /var/cache/bridgehead/ccp/ovis/shared_data:/shared backend: - image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest + 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: ${APOLLO_PORT:-4001} - CREDOS_PORT: ${CREDOS_PORT:-4000} - CORS_ORIGIN: ${OVIS_CORS_ORIGIN:-*} - DB: ${DB:-onc_test} + APOLLO_PORT: "4001" + CREDOS_PORT: "4000" + CORS_ORIGIN: "*" + DB: onc_test ADRESS: mongodb://mongo:27017 depends_on: - mongo - ovis-backend-data-preprocessing - ovis-backend-data-import healthcheck: - test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"] - interval: 5s - timeout: 3s + test: ["CMD-SHELL", "test -d /app/node_modules/mongodb"] + interval: 10s + timeout: 5s retries: 5 - start_period: 10s - labels: - - "traefik.enable=true" - - "traefik.http.routers.ovis-backend.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/graphql`)" - - "traefik.http.routers.ovis-backend.tls=true" - - "traefik.http.routers.ovis-backend.middlewares=${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" - - "traefik.http.routers.ovis-backend-ccp.rule=PathPrefix(`/ccp-ovis/graphql`)" - - "traefik.http.routers.ovis-backend-ccp.tls=true" - - "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}" frontend: - image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest + image: docker.verbis.dkfz.de/ovis/ovis-frontend:latest container_name: bridgehead-ccp-ovis-frontend restart: always environment: - PUBLIC_GRAPHQL_URL: https://${HOST:-localhost}/ccp-ovis/graphql - 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: ${OVIS_NO_PROXY:-} + PUBLIC_GRAPHQL_URL: https://${HOST}/ccp-ovis/graphql + PUBLIC_LOGIN_ENABLED: "false" + PUBLIC_OVIS_IMPORT: demo + OVIS_CATALOGUE_UPSTREAM_URL: http://ovis-backend-data-preprocessing:9000/catalogue + HTTP_PROXY: "" + HTTPS_PROXY: "" + NO_PROXY: "" + http_proxy: "" + https_proxy: "" + no_proxy: "" depends_on: backend: 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.tls=true" - - "traefik.http.routers.ovis-frontend.rule=Host(`${HOST:-localhost}`)" - - "traefik.http.routers.ovis-frontend.middlewares=${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" - - "traefik.http.routers.ovis-frontend-ccp.rule=PathPrefix(`/ccp-ovis`)" - "traefik.http.routers.ovis-frontend-ccp.tls=true" + - "traefik.http.routers.ovis-frontend-ccp.rule=PathPrefix(`/ccp-ovis`)" - "traefik.http.middlewares.ovis-frontend-ccp-strip.stripprefix.prefixes=/ccp-ovis" - - "traefik.http.routers.ovis-frontend-ccp.middlewares=ovis-frontend-ccp-strip,${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" + - "traefik.http.routers.ovis-frontend-ccp.middlewares=ovis-frontend-ccp-strip" - "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173"