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Author SHA1 Message Date
324c2b336d Merge pull request #287 from tm16-medma/patch-1
Update ovis-compose.yml
2025-04-14 08:19:20 +02:00
e8cb85eade adjusted traefik parameters 2025-04-09 14:00:39 +00:00
c59c425ad4 Merge branch 'patch-1' of https://github.com/tm16-medma/bridgehead into patch-1 2025-04-09 13:45:01 +00:00
e3f7f5d32b Refactor Docker Compose
- Replaced GUI_HOST with HOST
- Removed NODE_ENV
- Combine init_onco and backend service
- removed node_modules and .svelte-kit volumes
- removed mongodb volumes
- adjusted http_proxy and https_proxy
- adjusted path prefix from oaut2 to oauth2-ovis
- removed network-mode "host" in fhir-transformer service
2025-04-09 13:43:53 +00:00
1b01bd81ff Updated the fhir-transformer image and init_onco container to sleep after finishing 2025-04-03 15:04:01 +02:00
86a2b78d8f corrected a syntax error 2025-04-01 10:57:02 +00:00
cf1ba43d39 refactor: restructure ovis-compose.yml and added MongoDB initialization to sh
- Removed the traefik service and renamed traefik-forward-auth to ovis- with ovis-traefik-forward-auth the labels, however would need help there as i got no knowledge of how OAuth2 works (Torben initialized that container)
- Updated MongoDB service configuration to include a direct initialization script for user and operation collections in the sh instead of in the compose directly
- Adjusted volume paths to only use the /var/cache/bridgehead/ccp directory
- Adjusted frontend and backend service labels for Traefik routing to not use ports
- Cleaned up unnecessary network definitions and volumes.
- Renamed FHIR Server URL to bridgehead-ccp-blaze:8080/fhir
- Removed redundant entrypoint (python main.py) of fhir transformer
2025-04-01 10:46:48 +00:00
3b49faaeb4 Update ovis-compose.yml
Please ignore the command in mongo :) It will be replaced soon with proper user authentication
2025-03-26 11:21:58 +01:00
5ba9efe8d3 ovis wip 2025-02-12 10:45:48 +00:00
19 changed files with 276 additions and 103 deletions

1
.github/CODEOWNERS vendored
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@ -1 +0,0 @@
* @samply/bridgehead-developers

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@ -4,7 +4,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-bbmri-blaze container_name: bridgehead-bbmri-blaze
environment: environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080" BASE_URL: "http://bridgehead-bbmri-blaze:8080"

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@ -2,14 +2,13 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-cce-blaze container_name: bridgehead-cce-blaze
environment: environment:
BASE_URL: "http://bridgehead-cce-blaze:8080" BASE_URL: "http://bridgehead-cce-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m" JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000} DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP} DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false" ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes: volumes:
- "blaze-data:/app/data" - "blaze-data:/app/data"
@ -32,10 +31,6 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081 BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT} RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28 EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

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@ -1,2 +0,0 @@
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@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-ccp-blaze container_name: bridgehead-ccp-blaze
environment: environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080" BASE_URL: "http://bridgehead-ccp-blaze:8080"
@ -35,7 +35,7 @@ services:
QUERIES_TO_CACHE: '/queries_to_cache.conf' QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze} ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes: volumes:
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

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@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze-secondary: blaze-secondary:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-ccp-blaze-secondary container_name: bridgehead-ccp-blaze-secondary
environment: environment:
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080" BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

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@ -3,7 +3,7 @@ version: "3.7"
services: services:
obds2fhir-rest: obds2fhir-rest:
container_name: bridgehead-obds2fhir-rest container_name: bridgehead-obds2fhir-rest
image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
environment: environment:
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

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@ -0,0 +1,112 @@
version: '3.7'
services:
ovis-traefik-forward-auth:
image: quay.io/oauth2-proxy/oauth2-proxy:latest
environment:
- http_proxy=${http_proxy:-http://forward_proxy:3128}
- https_proxy=${https_proxy:-http://forward_proxy:3128}
- 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=.${HOST:-localhost}
- OAUTH2_PROXY_COOKIE_REFRESH=4m
- OAUTH2_PROXY_COOKIE_EXPIRE=24h
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
- OAUTH2_PROXY_REVERSE_PROXY=true
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${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.ovis-traefik-forward-auth.forwardauth.address=http://ovis-traefik-forward-auth:4180"
- "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.authResponseHeaders=Authorization, X-Forwarded-User, X-Auth-Request-User, X-Auth-Request-Email"
- "traefik.http.services.ovis-traefik-forward-auth.loadbalancer.server.port=4180"
- "traefik.http.routers.oauth2.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/oauth2-ovis/`)"
- "traefik.http.routers.oauth2.tls=true"
fhir-transformer:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-fhir-transformer:latest
restart: on-failure
environment:
- FHIR_SERVER_URL=${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:${MONGO_VER:-latest}
restart: always
command: mongod
- /var/cache/bridgehead/ccp/ovis/mongo/init/init.js:/docker-entrypoint-initdb.d/init.js
backend:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
restart: always
user: root
working_dir: /app
environment:
- APOLLO_PORT=${APOLLO_PORT:-4001}
- CREDOS_PORT=${CREDOS_PORT:-4000}
- MONGO_VER=latest
- CORS_ORIGIN=*
- DB=${DB:-onc_test}
- ADRESS=${ADRESS:-mongodb://mongo:27017}
depends_on:
- mongo
- fhir-transformer
healthcheck:
test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"]
interval: 5s
timeout: 3s
retries: 5
start_period: 10s
entrypoint: >
sh -c "
# First run the initialization process
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(`${HOST:-localhost}`) && PathPrefix(`/graphql`)"
- "traefik.http.routers.ovis-backend.tls=true"
- "traefik.http.services.ovis-backend.loadbalancer.server.port=${APOLLO_PORT:-4001}"
volumes:
- /var/cache/bridgehead/ccp/ovis/shared_data:/shared
frontend:
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest
restart: always
environment:
- PUBLIC_GRAPHQL_URL=https://${HOST:-localhost}/graphql
depends_on:
backend:
condition: service_healthy
working_dir: /app
labels:
- "traefik.enable=true"
- "traefik.http.routers.ovis-frontend.tls=true"
- "traefik.http.routers.ovis-frontend.rule=Host(`${HOST:-localhost}`)"
- "traefik.http.routers.ovis-frontend.middlewares=traefik-forward-auth"
- "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173"

108
ccp/modules/ovis-setup.sh Normal file
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@ -0,0 +1,108 @@
#!/bin/bash -e
if [ -n "$ENABLE_OVIS" ];then
# Setup MongoDB initialization directory if it doesn't exist
mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
# Generate MongoDB initialization script directly
cat > "/var/cache/bridgehead/ccp/ovis/mongo/init/init.js" << 'EOF'
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 "},
])
EOF
OVERRIDE+=" -f ./$PROJECT/modules/ovis-compose.yml"
fi

View File

@ -1,2 +1,2 @@
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View File

@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-dhki-blaze container_name: bridgehead-dhki-blaze
environment: environment:
BASE_URL: "http://bridgehead-dhki-blaze:8080" BASE_URL: "http://bridgehead-dhki-blaze:8080"
@ -33,7 +33,7 @@ services:
EPSILON: 0.28 EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf' QUERIES_TO_CACHE: '/queries_to_cache.conf'
volumes: volumes:
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -2,14 +2,13 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-itcc-blaze container_name: bridgehead-itcc-blaze
environment: environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080" BASE_URL: "http://bridgehead-itcc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m" JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000} DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP} DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false" ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes: volumes:
- "blaze-data:/app/data" - "blaze-data:/app/data"
@ -32,10 +31,6 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081 BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT} RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28 EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -1,2 +0,0 @@
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

View File

@ -6,7 +6,7 @@ services:
replicas: 0 #deactivate landing page replicas: 0 #deactivate landing page
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-kr-blaze container_name: bridgehead-kr-blaze
environment: environment:
BASE_URL: "http://bridgehead-kr-blaze:8080" BASE_URL: "http://bridgehead-kr-blaze:8080"

View File

@ -313,7 +313,7 @@ function sync_secrets() {
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \ -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \ -e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \ -e BROKER_URL=$BROKER_URL \
-e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \ -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-e SECRET_DEFINITIONS=$secret_sync_args \ -e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
@ -322,70 +322,6 @@ function sync_secrets() {
set +a # Export variables in the regular way set +a # Export variables in the regular way
} }
function secret_sync_gitlab_token() {
# Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
local gitlab
case "$(git -C /etc/bridgehead remote get-url origin)" in
*git.verbis.dkfz.de*) gitlab=verbis;;
*gitlab.bbmri-eric.eu*) gitlab=bbmri;;
*)
log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
return
;;
esac
if [ "$PROJECT" == "bbmri" ]; then
# If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
proxy_id=$ERIC_PROXY_ID
broker_url=$ERIC_BROKER_URL
broker_id=$ERIC_BROKER_ID
root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
else
proxy_id=$PROXY_ID
broker_url=$BROKER_URL
broker_id=$BROKER_ID
root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
fi
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull.
mkdir -p /var/cache/bridgehead/secrets
touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \
-v /var/cache/bridgehead/secrets/gitlab_token:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$proxy_id \
-e BROKER_URL=$broker_url \
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
if [ $? -eq 0 ]; then
log "INFO" "Secret Sync was successful"
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
# Set the git credential helper
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
else
log "WARN" "Secret Sync failed"
# Remove the git credential helper
git -C /etc/bridgehead config --unset credential.helper
fi
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
# believe that it was removed on all/most production servers.
git -C /srv/docker/bridgehead config --unset credential.helper
}
capitalize_first_letter() { capitalize_first_letter() {
input="$1" input="$1"
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}" capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"

View File

@ -33,7 +33,43 @@ export SITE_ID
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead" checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead" checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
secret_sync_gitlab_token # Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull.
mkdir -p /var/cache/bridgehead/secrets
touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
log "INFO" "Running Secret Sync for the GitLab token"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \
-v /var/cache/bridgehead/secrets/gitlab_token:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN: \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
if [ $? -eq 0 ]; then
log "INFO" "Secret Sync was successful"
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
# Set the git credential helper
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
else
log "WARN" "Secret Sync failed"
# Remove the git credential helper
git -C /etc/bridgehead config --unset credential.helper
fi
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
# believe that it was removed on all/most production servers.
git -C /srv/docker/bridgehead config --unset credential.helper
CHANGES="" CHANGES=""

View File

@ -17,13 +17,11 @@ services:
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID} - EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc - DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
- RUST_LOG=${RUST_LOG:-info} - RUST_LOG=${RUST_LOG:-info}
- TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
volumes: volumes:
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
transfair-input-blaze: transfair-input-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-transfair-input-blaze container_name: bridgehead-transfair-input-blaze
environment: environment:
BASE_URL: "http://bridgehead-transfair-input-blaze:8080" BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
@ -36,7 +34,7 @@ services:
profiles: ["transfair-input-blaze"] profiles: ["transfair-input-blaze"]
transfair-request-blaze: transfair-request-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-transfair-requests-blaze container_name: bridgehead-transfair-requests-blaze
environment: environment:
BASE_URL: "http://bridgehead-transfair-requests-blaze:8080" BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"

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@ -1,3 +1,2 @@
FOCUS_TAG=main FOCUS_TAG=main
BEAM_TAG=main BEAM_TAG=main
BLAZE_TAG=0.32

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@ -1,3 +1,2 @@
FOCUS_TAG=develop FOCUS_TAG=develop
BEAM_TAG=develop BEAM_TAG=develop
BLAZE_TAG=main