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Refactor environment variables and image tags

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Updated environment variables and image tags in ovis-compose.yml for consistency and clarity.
This commit is contained in:
tm16-medma
2026-03-17 20:54:00 +01:00
committed by GitHub
parent b7d1adf91d
commit b2865d1b4d
1 changed files with 74 additions and 74 deletions
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ccp/modules/ovis-compose.yml
+74 -74
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@@ -2,7 +2,7 @@ version: "3.7"
services: services:
mongo: mongo:
image: mongo:${MONGO_VER:-latest} image: mongo:latest
container_name: bridgehead-ccp-ovis-mongo container_name: bridgehead-ccp-ovis-mongo
restart: always restart: always
command: mongod command: mongod
@@ -16,44 +16,44 @@ services:
user: root user: root
working_dir: /app working_dir: /app
environment: environment:
APOLLO_PORT: ${APOLLO_PORT:-4001} APOLLO_PORT: "4001"
CREDOS_PORT: ${CREDOS_PORT:-4000} CREDOS_PORT: "4000"
HTTP_PROXY: ${OVIS_HTTP_PROXY:-} HTTP_PROXY: ""
HTTPS_PROXY: ${OVIS_HTTPS_PROXY:-} HTTPS_PROXY: ""
NO_PROXY: ${OVIS_NO_PROXY:-} NO_PROXY: ""
http_proxy: ${OVIS_HTTP_PROXY:-} http_proxy: ""
https_proxy: ${OVIS_HTTPS_PROXY:-} https_proxy: ""
no_proxy: ${OVIS_NO_PROXY:-} no_proxy: ""
CORS_ORIGIN: ${OVIS_CORS_ORIGIN:-*} CORS_ORIGIN: "*"
DB: ${DB:-onc_test} DB: onc_test
ADRESS: mongodb://mongo:27017 ADRESS: mongodb://mongo:27017
MONGO_VER: ${MONGO_VER:-latest} MONGO_VER: latest
OVIS_PREPROC_DECEASED_KEYWORDS: ${OVIS_PREPROC_DECEASED_KEYWORDS:-} OVIS_PREPROC_DECEASED_KEYWORDS: '["verstorben","dead","deceased","not alive","gestorben"]'
OVIS_PREPROC_REZIDIV_PREFIXES: ${OVIS_PREPROC_REZIDIV_PREFIXES:-} OVIS_PREPROC_REZIDIV_PREFIXES: '["Rezidiv"]'
OVIS_PREPROC_REZIDIV_CANONICAL: ${OVIS_PREPROC_REZIDIV_CANONICAL:-} OVIS_PREPROC_REZIDIV_CANONICAL: Rezidiv
OVIS_PREPROC_REZIDIV_LYMPH_STATES: ${OVIS_PREPROC_REZIDIV_LYMPH_STATES:-} OVIS_PREPROC_REZIDIV_LYMPH_STATES: '["Rezidiv","Neu"]'
OVIS_PREPROC_PROGRESS_LABELS: ${OVIS_PREPROC_PROGRESS_LABELS:-} OVIS_PREPROC_PROGRESS_LABELS: '["Progression","Divergentes Geschehen","Rezidiv"]'
OVIS_PREPROC_COMPLETE_REMISSION_LABELS: ${OVIS_PREPROC_COMPLETE_REMISSION_LABELS:-} OVIS_PREPROC_COMPLETE_REMISSION_LABELS: '["Vollremission / Tumorfrei (complete remission)"]'
OVIS_PREPROC_RCLASS_SUCCESS: ${OVIS_PREPROC_RCLASS_SUCCESS:-} OVIS_PREPROC_RCLASS_SUCCESS: '["R0"]'
OVIS_PREPROC_LOCAL_RSTATE_SUCCESS: ${OVIS_PREPROC_LOCAL_RSTATE_SUCCESS:-} OVIS_PREPROC_LOCAL_RSTATE_SUCCESS: '["R0"]'
OVIS_PREPROC_METASTASIS_PREFIXES: ${OVIS_PREPROC_METASTASIS_PREFIXES:-} OVIS_PREPROC_METASTASIS_PREFIXES: '["Rezidiv","Neu"]'
OVIS_PREPROC_METASTASIS_SPREAD_VALUES: ${OVIS_PREPROC_METASTASIS_SPREAD_VALUES:-} OVIS_PREPROC_METASTASIS_SPREAD_VALUES: '["Neu","Rezidiv","Tumornachweis"]'
OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON: ${OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON:-} OVIS_PREPROC_METASTASIS_STRAT_SYNCHRON: Synchrone Metastasierung
OVIS_PREPROC_METASTASIS_STRAT_NONE: ${OVIS_PREPROC_METASTASIS_STRAT_NONE:-} OVIS_PREPROC_METASTASIS_STRAT_NONE: keine synchrone Metastasierung
OVIS_PREPROC_NULL_STUDY_PHASES: ${OVIS_PREPROC_NULL_STUDY_PHASES:-} OVIS_PREPROC_NULL_STUDY_PHASES: '["NOPH","KA"]'
OVIS_PREPROC_PREV_THERAPY_SURGERY: ${OVIS_PREPROC_PREV_THERAPY_SURGERY:-} OVIS_PREPROC_PREV_THERAPY_SURGERY: '["operation"]'
OVIS_PREPROC_PREV_THERAPY_SYSTEMIC: ${OVIS_PREPROC_PREV_THERAPY_SYSTEMIC:-} OVIS_PREPROC_PREV_THERAPY_SYSTEMIC: '["systemic"]'
OVIS_PREPROC_PREV_THERAPY_RADIATION: ${OVIS_PREPROC_PREV_THERAPY_RADIATION:-} OVIS_PREPROC_PREV_THERAPY_RADIATION: '["radiation"]'
OVIS_PREPROC_PREV_CONSULTATION_NUTRITION: ${OVIS_PREPROC_PREV_CONSULTATION_NUTRITION:-} OVIS_PREPROC_PREV_CONSULTATION_NUTRITION: '["nutrition"]'
OVIS_PREPROC_PREV_CONSULTATION_SOCIAL: ${OVIS_PREPROC_PREV_CONSULTATION_SOCIAL:-} OVIS_PREPROC_PREV_CONSULTATION_SOCIAL: '["social"]'
OVIS_PREPROC_PREV_CONSULTATION_PSYCHO: ${OVIS_PREPROC_PREV_CONSULTATION_PSYCHO:-} OVIS_PREPROC_PREV_CONSULTATION_PSYCHO: '["psycho"]'
OVIS_PREPROC_PREV_CONSULTATION_GENETIC: ${OVIS_PREPROC_PREV_CONSULTATION_GENETIC:-} OVIS_PREPROC_PREV_CONSULTATION_GENETIC: '["genetic"]'
OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE: ${OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE:-} OVIS_PREPROC_TUMORBOARD_PATTERN_PRAE: prae|prä|pre
OVIS_PREPROC_TUMORBOARD_PATTERN_POST: ${OVIS_PREPROC_TUMORBOARD_PATTERN_POST:-} OVIS_PREPROC_TUMORBOARD_PATTERN_POST: post
OVIS_PREPROC_TUMORBOARD_PATTERN_MTB: ${OVIS_PREPROC_TUMORBOARD_PATTERN_MTB:-} OVIS_PREPROC_TUMORBOARD_PATTERN_MTB: mtb
OVIS_PREPROC_ECOG_PREFIX: ${OVIS_PREPROC_ECOG_PREFIX:-} OVIS_PREPROC_ECOG_PREFIX: ECOG
OVIS_PREPROC_DISTRESS_TYPE: ${OVIS_PREPROC_DISTRESS_TYPE:-} OVIS_PREPROC_DISTRESS_TYPE: distress
OVIS_PREPROC_DISTRESS_POSITIVE_VALUES: ${OVIS_PREPROC_DISTRESS_POSITIVE_VALUES:-} OVIS_PREPROC_DISTRESS_POSITIVE_VALUES: '["Positiv"]'
depends_on: depends_on:
- mongo - mongo
volumes: volumes:
@@ -67,7 +67,7 @@ services:
command: ["node", "./Preprocessing/catalogue-service.mjs"] command: ["node", "./Preprocessing/catalogue-service.mjs"]
ovis-backend-data-import: ovis-backend-data-import:
image: docker.verbis.dkfz.de/ovis/ovis-backend-data-import-${OVIS_IMPORT_MODE:-demo}:latest image: docker.verbis.dkfz.de/ovis/ovis-backend-data-import-demo:latest
container_name: bridgehead-ccp-ovis-import container_name: bridgehead-ccp-ovis-import
restart: on-failure restart: on-failure
depends_on: depends_on:
@@ -75,19 +75,19 @@ services:
condition: service_healthy condition: service_healthy
environment: environment:
# CCP mode: FHIR source configuration (ignored by DEMO image) # CCP mode: FHIR source configuration (ignored by DEMO image)
FHIR_SERVER_URL: ${FHIR_SERVER_URL:-http://bridgehead-ccp-blaze:8080/fhir} FHIR_SERVER_URL: http://bridgehead-ccp-blaze:8080/fhir
FHIR_USERNAME: ${FHIR_USERNAME:-} FHIR_USERNAME: your-fhir-username
FHIR_PASSWORD: ${FHIR_PASSWORD:-} FHIR_PASSWORD: your-fhir-password
ICD10_FILTER: ${ICD10_FILTER:-} ICD10_FILTER: ""
# Required for both CCP and DEMO: preprocessor upload endpoint # 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 # Proxy configuration
HTTP_PROXY: ${OVIS_HTTP_PROXY:-} HTTP_PROXY: ""
HTTPS_PROXY: ${OVIS_HTTPS_PROXY:-} HTTPS_PROXY: ""
NO_PROXY: ${OVIS_NO_PROXY:-} NO_PROXY: ""
http_proxy: ${OVIS_HTTP_PROXY:-} http_proxy: ""
https_proxy: ${OVIS_HTTPS_PROXY:-} https_proxy: ""
no_proxy: ${OVIS_NO_PROXY:-} no_proxy: ""
volumes: volumes:
- /var/cache/bridgehead/ccp/ovis/shared_data:/shared - /var/cache/bridgehead/ccp/ovis/shared_data:/shared
@@ -98,10 +98,10 @@ services:
user: root user: root
working_dir: /app working_dir: /app
environment: environment:
APOLLO_PORT: ${APOLLO_PORT:-4001} APOLLO_PORT: "4001"
CREDOS_PORT: ${CREDOS_PORT:-4000} CREDOS_PORT: "4000"
CORS_ORIGIN: ${OVIS_CORS_ORIGIN:-*} CORS_ORIGIN: "*"
DB: ${DB:-onc_test} DB: onc_test
ADRESS: mongodb://mongo:27017 ADRESS: mongodb://mongo:27017
depends_on: depends_on:
- mongo - mongo
@@ -114,33 +114,33 @@ services:
retries: 5 retries: 5
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.ovis-backend.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/graphql`)" - "traefik.http.routers.ovis-backend.rule=Host(`localhost`) && PathPrefix(`/graphql`)"
- "traefik.http.routers.ovis-backend.tls=true" - "traefik.http.routers.ovis-backend.tls=true"
- "traefik.http.routers.ovis-backend.middlewares=${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" - "traefik.http.routers.ovis-backend.middlewares=traefik-forward-auth"
- "traefik.http.routers.ovis-backend-ccp.rule=PathPrefix(`/ccp-ovis/graphql`)" - "traefik.http.routers.ovis-backend-ccp.rule=PathPrefix(`/ccp-ovis/graphql`)"
- "traefik.http.routers.ovis-backend-ccp.tls=true" - "traefik.http.routers.ovis-backend-ccp.tls=true"
- "traefik.http.middlewares.ovis-backend-ccp-strip.stripprefix.prefixes=/ccp-ovis" - "traefik.http.middlewares.ovis-backend-ccp-strip.stripprefix.prefixes=/ccp-ovis"
- "traefik.http.routers.ovis-backend-ccp.middlewares=ovis-backend-ccp-strip,${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" - "traefik.http.routers.ovis-backend-ccp.middlewares=ovis-backend-ccp-strip,traefik-forward-auth"
- "traefik.http.services.ovis-backend.loadbalancer.server.port=${APOLLO_PORT:-4001}" - "traefik.http.services.ovis-backend.loadbalancer.server.port=4001"
frontend: frontend:
image: docker.verbis.dkfz.de/ovis/ovis-frontend:latest image: docker.verbis.dkfz.de/ovis/ovis-frontend:latest
container_name: bridgehead-ccp-ovis-frontend container_name: bridgehead-ccp-ovis-frontend
restart: always restart: always
environment: environment:
PUBLIC_GRAPHQL_URL: https://${HOST:-localhost}/ccp-ovis/graphql PUBLIC_GRAPHQL_URL: https://localhost/ccp-ovis/graphql
PUBLIC_LOGIN_ENABLED: ${PUBLIC_LOGIN_ENABLED:-false} PUBLIC_LOGIN_ENABLED: "false"
PUBLIC_OVIS_IMPORT: ${OVIS_IMPORT_MODE:-demo} PUBLIC_OVIS_IMPORT: demo
OVIS_CATALOGUE_UPSTREAM_URL: ${OVIS_CATALOGUE_UPSTREAM_URL:-http://ovis-backend-data-preprocessing:9000/catalogue} OVIS_CATALOGUE_UPSTREAM_URL: http://ovis-backend-data-preprocessing:9000/catalogue
EXPRESS_AUTH_URL: ${EXPRESS_AUTH_URL:-http://express-auth:5000} EXPRESS_AUTH_URL: http://express-auth:5000
EXPRESS_AUTH_USERNAME: ${EXPRESS_AUTH_USERNAME:-admin} EXPRESS_AUTH_USERNAME: your-express-username
EXPRESS_AUTH_PASSWORD: ${EXPRESS_AUTH_PASSWORD:-admin} EXPRESS_AUTH_PASSWORD: your-express-password
HTTP_PROXY: ${OVIS_HTTP_PROXY:-} HTTP_PROXY: ""
HTTPS_PROXY: ${OVIS_HTTPS_PROXY:-} HTTPS_PROXY: ""
NO_PROXY: ${OVIS_NO_PROXY:-} NO_PROXY: ""
http_proxy: ${OVIS_HTTP_PROXY:-} http_proxy: ""
https_proxy: ${OVIS_HTTPS_PROXY:-} https_proxy: ""
no_proxy: ${OVIS_NO_PROXY:-} no_proxy: ""
depends_on: depends_on:
backend: backend:
condition: service_healthy condition: service_healthy
@@ -150,10 +150,10 @@ services:
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.ovis-frontend.tls=true" - "traefik.http.routers.ovis-frontend.tls=true"
- "traefik.http.routers.ovis-frontend.rule=Host(`${HOST:-localhost}`)" - "traefik.http.routers.ovis-frontend.rule=Host(`localhost`)"
- "traefik.http.routers.ovis-frontend.middlewares=${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" - "traefik.http.routers.ovis-frontend.middlewares=traefik-forward-auth"
- "traefik.http.routers.ovis-frontend-ccp.rule=PathPrefix(`/ccp-ovis`)" - "traefik.http.routers.ovis-frontend-ccp.rule=PathPrefix(`/ccp-ovis`)"
- "traefik.http.routers.ovis-frontend-ccp.tls=true" - "traefik.http.routers.ovis-frontend-ccp.tls=true"
- "traefik.http.middlewares.ovis-frontend-ccp-strip.stripprefix.prefixes=/ccp-ovis" - "traefik.http.middlewares.ovis-frontend-ccp-strip.stripprefix.prefixes=/ccp-ovis"
- "traefik.http.routers.ovis-frontend-ccp.middlewares=ovis-frontend-ccp-strip,${OVIS_AUTH_MIDDLEWARE:-traefik-forward-auth}" - "traefik.http.routers.ovis-frontend-ccp.middlewares=ovis-frontend-ccp-strip,traefik-forward-auth"
- "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173" - "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173"