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Update ovis-compose.yml 

Please ignore the command in mongo :) It will be replaced soon with proper user authentication
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tm16-medma 2025-03-26 11:21:58 +01:00 committed by GitHub
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ccp/modules/ovis-compose.yml
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@ -1,4 +1,271 @@
version: '3.7'
services:
ovis-thing:
image: todo
traefik:
image: traefik:latest
restart: always
command:
- --entrypoints.web.address=:80
- --entrypoints.websecure.address=:443
- --providers.docker=true
- --providers.docker.exposedbydefault=false
- --accesslog=true
ports:
- "80:80"
- "443:443"
volumes:
- /var/run/docker.sock:/var/run/docker.sock:ro
networks:
- ovis-network
traefik-forward-auth:
image: quay.io/oauth2-proxy/oauth2-proxy:latest
environment:
- http_proxy=${http_proxy}
- https_proxy=${https_proxy}
- OAUTH2_PROXY_PROVIDER=oidc
- OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
- OAUTH2_PROXY_OIDC_ISSUER_URL=${OAUTH_ISSUER_URL}
- OAUTH2_PROXY_CLIENT_ID=${OAUTH_CLIENT_ID}
- OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
- OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
- OAUTH2_PROXY_COOKIE_DOMAINS=.${GUI_HOST:-localhost}
- OAUTH2_PROXY_COOKIE_REFRESH=4m
- OAUTH2_PROXY_COOKIE_EXPIRE=24h
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
- OAUTH2_PROXY_REVERSE_PROXY=true
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${GUI_HOST:-localhost}
- OAUTH2_PROXY_UPSTREAMS=static://202
- OAUTH2_PROXY_EMAIL_DOMAINS=*
- OAUTH2_PROXY_ALLOWED_GROUPS=app-ovis
- OAUTH2_PROXY_ERRORS_TO_INFO_LOG=true
- OAUTH2_PROXY_CODE_CHALLENGE_METHOD=S256
# For some reason, login.verbis.dkfz.de does not have a "groups" scope but this comes automatically through a
# scope called microprofile-jwt. Remove the following line once we have a "groups" scope.
- OAUTH2_PROXY_SCOPE=openid profile email
# Pass Authorization Header and some user information to spot
- OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
- OAUTH2_PROXY_SET_XAUTHREQUEST=true
labels:
- "traefik.enable=true"
- "traefik.http.middlewares.traefik-forward-auth.forwardauth.address=http://traefik-forward-auth:4180"
- "traefik.http.middlewares.traefik-forward-auth.forwardauth.authResponseHeaders=Authorization, X-Forwarded-User, X-Auth-Request-User, X-Auth-Request-Email"
- "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4180"
- "traefik.http.routers.oauth2.rule=Host(`${GUI_HOST:-localhost}`) && PathPrefix(`/oauth2/`)"
- "traefik.http.routers.oauth2.tls=true"
fhir-transformer:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-fhir-transformer:latest
restart: on-failure
network_mode: "host"
volumes:
- shared_data:/app/output
environment:
- FHIR_SERVER_URL=${FHIR_SERVER_URL:-http://localhost:8080/fhir}
- FHIR_USERNAME=${FHIR_USERNAME}
- FHIR_PASSWORD=${FHIR_PASSWORD}
command: >
sh -c "python main.py"
mongo:
image: mongo:${MONGO_VER:-latest}
restart: always
volumes:
- mongo_db:/data/db
- mongo_conf:/data/configdb
networks:
- ovis-network
command: |
bash -c '
cat > /docker-entrypoint-initdb.d/init.js << "EOFJS"
db = db.getSiblingDB("test_credos");
db.createCollection("user");
db.user.insertMany([{
"_id": "OVIS-Root",
"createdAt": new Date(),
"createdBy": "system",
"role": "super-admin",
"status": "active",
"pseudonymization": false,
"darkMode": false,
"colorTheme": "CCCMunich",
"language": "de",
}]);
db = db.getSiblingDB("onc_test");
db.createCollection("user");
db.user.insertMany([{
"_id": "OVIS-Root",
"createdAt": new Date(),
"createdBy": "system",
"role": "super-admin",
"status": "active",
"pseudonymization": false,
"darkMode": false,
"colorTheme": "CCCMunich",
"language": "de",
}]);
db.ops.insertMany([
{"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an Nervensystem und endokrinen Organen "},
{"OPSC_4":"1-44","OPS_Gruppen_Text":"Biopsie ohne Inzision an den Verdauungsorganen"},
{"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an anderen Organen und Geweben"},
{"OPSC_4":"1-50","OPS_Gruppen_Text":"Biopsie an Haut, Mamma, Knochen und Muskeln durch Inzision"},
{"OPSC_4":"1-51","OPS_Gruppen_Text":"Biopsie an Nervengewebe, Hypophyse, Corpus pineale durch Inzision und Trepanation von Schädelknochen "},
{"OPSC_4":"1-55","OPS_Gruppen_Text":"Biopsie an anderen Verdauungsorganen, Zwerchfell und (Retro-)Peritoneum durch Inzision "},
{"OPSC_4":"1-56","OPS_Gruppen_Text":"Biopsie an Harnwegen und männlichen Geschlechtsorgannen durch Inzision"},
{"OPSC_4":"1-58","OPS_Gruppen_Text":"Biopsie an anderen Organen durch Inzision "},
{"OPSC_4":"1-63","OPS_Gruppen_Text":"Diagnostische Endoskopie des oberen Verdauungstraktes"},
{"OPSC_4":"1-65","OPS_Gruppen_Text":"Diagnostische Endoskopie des unteren Verdauungstraktes"},
{"OPSC_4":"1-69","OPS_Gruppen_Text":"Diagnostische Endoskopie durch Inzision und intraoperativ "},
{"OPSC_4":"5-01","OPS_Gruppen_Text":"Inzision (Trepanation) und Exzision an Schädel, Gehirn und Hirnhäuten"},
{"OPSC_4":"5-02","OPS_Gruppen_Text":"Andere Operationen an Schädel, Gehirn und Hirnhäuten"},
{"OPSC_4":"5-03","OPS_Gruppen_Text":"Operationen an Rückenmark, Rückenmarkhäuten und Spinalkanal"},
{"OPSC_4":"5-05","OPS_Gruppen_Text":"Andere Operationen an Nerven und Nervenganglien "},
{"OPSC_4":"5-06","OPS_Gruppen_Text":"Operationen an Schilddrüse und Nebenschilddrüse "},
{"OPSC_4":"5-07","OPS_Gruppen_Text":"Operationen an anderen endokrinen Drüsen "},
{"OPSC_4":"5-20","OPS_Gruppen_Text":"Andere Operationen an Mittel- und Innenohr "},
{"OPSC_4":"5-25","OPS_Gruppen_Text":"Operationen an der Zunge "},
{"OPSC_4":"5-31","OPS_Gruppen_Text":"Andere Larynxoperationen und Operationen an der Trachea "},
{"OPSC_4":"5-32","OPS_Gruppen_Text":"Exzision und Resektion an Lunge und Bronchus "},
{"OPSC_4":"5-33","OPS_Gruppen_Text":"Andere Operationen an Lunge und Bronchus"},
{"OPSC_4":"5-34","OPS_Gruppen_Text":"Operationen an Brustwand, Pleura, Mediastinum und Zwerchfell "},
{"OPSC_4":"5-37","OPS_Gruppen_Text":"Rhythmuschirurgie und andere Operationen an Herz und Perikard"},
{"OPSC_4":"5-38","OPS_Gruppen_Text":"Inzision, Exzision und Verschluß von Blutgefäßen "},
{"OPSC_4":"5-39","OPS_Gruppen_Text":"Andere Operationen an Blutgefäßen "},
{"OPSC_4":"5-40","OPS_Gruppen_Text":"Operationen am Lymphgewebe "},
{"OPSC_4":"5-41","OPS_Gruppen_Text":"Operationen an Milz und Knochenmark "},
{"OPSC_4":"5-42","OPS_Gruppen_Text":"Operationen am Ösophagus "},
{"OPSC_4":"5-43","OPS_Gruppen_Text":"Inzision, Exzision und Resektion am Magen "},
{"OPSC_4":"5-44","OPS_Gruppen_Text":"Erweiterte Magenresektion und andere Operationen am Magen "},
{"OPSC_4":"5-45","OPS_Gruppen_Text":"Inzision, Exzision, Resektion und Anastomose an Dünn- und Dickdarm "},
{"OPSC_4":"5-46","OPS_Gruppen_Text":"Andere Operationen an Dünn- und Dickdarm "},
{"OPSC_4":"5-47","OPS_Gruppen_Text":"Operationen an der Appendix "},
{"OPSC_4":"5-48","OPS_Gruppen_Text":"Operationen am Rektum "},
{"OPSC_4":"5-49","OPS_Gruppen_Text":"Operationen am Anus "},
{"OPSC_4":"5-50","OPS_Gruppen_Text":"Operationen an der Leber "},
{"OPSC_4":"5-51","OPS_Gruppen_Text":"Operationen an Gallenblase und Gallenwegen "},
{"OPSC_4":"5-52","OPS_Gruppen_Text":"Operationen am Pankreas "},
{"OPSC_4":"5-53","OPS_Gruppen_Text":"Verschluß abdominaler Hernien "},
{"OPSC_4":"5-54","OPS_Gruppen_Text":"Andere Operationen in der Bauchregion "},
{"OPSC_4":"5-55","OPS_Gruppen_Text":"Operationen an der Niere "},
{"OPSC_4":"5-56","OPS_Gruppen_Text":"Operationen am Ureter "},
{"OPSC_4":"5-57","OPS_Gruppen_Text":"Operationen an der Harnblase "},
{"OPSC_4":"5-59","OPS_Gruppen_Text":"Andere Operationen an den Harnorganen "},
{"OPSC_4":"5-60","OPS_Gruppen_Text":"Operationen an Prostata und Vesiculae seminales "},
{"OPSC_4":"5-61","OPS_Gruppen_Text":"Operationen an Skrotum und Tunica vaginalis testis"},
{"OPSC_4":"5-62","OPS_Gruppen_Text":"Operationen am Hoden "},
{"OPSC_4":"5-65","OPS_Gruppen_Text":"Operationen am Ovar "},
{"OPSC_4":"5-68","OPS_Gruppen_Text":"Inzision, Exzision und Exstirpation des Uterus "},
{"OPSC_4":"5-70","OPS_Gruppen_Text":"Operationen an Vagina und Douglasraum "},
{"OPSC_4":"5-71","OPS_Gruppen_Text":"Operationen an der Vulva "},
{"OPSC_4":"5-85","OPS_Gruppen_Text":"Operationen an Muskeln, Sehnen, Faszien und Schleimbeuteln"},
{"OPSC_4":"5-87","OPS_Gruppen_Text":"Exzision und Resektion der Mamma "},
{"OPSC_4":"5-89","OPS_Gruppen_Text":"Operationen an Haut und Unterhaut "},
{"OPSC_4":"5-90","OPS_Gruppen_Text":"Operative Wiederherstellung und Rekonstruktion von Haut und Unterhaut"},
{"OPSC_4":"5-91","OPS_Gruppen_Text":"Andere Operationen an Haut und Unterhaut "},
{"OPSC_4":"5-93","OPS_Gruppen_Text":"Angaben zum Transplantat und zu verwendeten Materialien"},
{"OPSC_4":"5-98","OPS_Gruppen_Text":"Spezielle Operationstechniken und Operationen bei speziellen Versorgungssituationen "},
{"OPSC_4":"8-13","OPS_Gruppen_Text":"Manipulation am Harntrakt"},
{"OPSC_4":"8-14","OPS_Gruppen_Text":"Therapeutische Kathedirisierung, Aspiration, Punktion und Spülung "},
{"OPSC_4":"8-15","OPS_Gruppen_Text":"Therapeutische Aspiration und Entleerung durch Punktion "},
{"OPSC_4":"8-17","OPS_Gruppen_Text":"Spülung (Lavage) "},
{"OPSC_4":"8-19","OPS_Gruppen_Text":"Verbände "},
{"OPSC_4":"8-77","OPS_Gruppen_Text":"Maßnahmen im Rahmen der Reanimation "},
{"OPSC_4":"8-92","OPS_Gruppen_Text":"Neurologisches Monitoring "},
])
EOFJS
exec docker-entrypoint.sh mongod'
init_onco:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
restart: on-failure
working_dir: /app
user: root
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';"
volumes:
- shared_data:/shared
- nodemodules:/app/node_modules
depends_on:
- mongo
- fhir-transformer
environment:
- APOLLO_PORT=${APOLLO_PORT:-4001}
- CREDOS_PORT=${CREDOS_PORT:-4000}
- MONGO_VER=latest
- DB=${DB:-onc_test}
- ADRESS=${ADRESS:-mongodb://mongo:27017}
networks:
- ovis-network
backend:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
restart: always
working_dir: /app
environment:
- APOLLO_PORT=${APOLLO_PORT:-4001}
- CREDOS_PORT=${CREDOS_PORT:-4000}
- MONGO_VER=latest
- NODE_ENV=development
- CORS_ORIGIN=*
- DB=${DB:-onc_test}
- ADRESS=${ADRESS:-mongodb://mongo:27017}
ports:
- "${APOLLO_PORT:-4001}:${APOLLO_PORT:-4001}"
depends_on:
- mongo
- init_onco
networks:
- ovis-network
healthcheck:
test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"]
interval: 5s
timeout: 3s
retries: 5
start_period: 10s
entrypoint: ["node", "--watch", "index.js"]
frontend:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest
restart: always
ports:
- "${FRONTEND_PORT:-5173}:5173"
environment:
- NODE_ENV=development
- VITE_GRAPHQL_URL=http://localhost:${APOLLO_PORT:-4001}/graphql
depends_on:
backend:
condition: service_healthy
networks:
- ovis-network
volumes:
- /app/.svelte-kit
working_dir: /app
labels:
- "traefik.enable=true"
- "traefik.http.routers.lens.tls=true"
- "traefik.http.routers.lens.rule=Host(`${GUI_HOST:-localhost}`)"
# - "traefik.http.routers.lens.middlewares=traefik-forward-auth"
- "traefik.http.services.frontend.loadbalancer.server.port=5173"
networks:
ovis-network:
driver: bridge
volumes:
shared_data:
mongo_db:
name: ovis_repo_mongo_db
mongo_conf:
name: ovis_repo_mongo_conf
nodemodules:
name: ovis_repo_node_modules