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Author SHA1 Message Date
82841a6f04 Fix airgapped-blaze-compose.yml file.
- BASE_URL & traefik settings
2025-03-25 15:23:16 +01:00
ba6f2c3b11 Modify container name (as it was a duplicate). 2025-03-24 09:50:06 +01:00
39a4231c1f Add airgapped-blaze-{compose,setup} files in cce modules.
- for testing out airgapped-blaze at VHIO
2025-03-21 15:15:03 +01:00
6f3aba1eaa feat: support self-signed cert on ttp (#283) 2025-03-12 15:45:55 +01:00
Jan
82ced89b33 chore: unify blaze versioning and upgrade to 0.32 (#277) 2025-03-12 12:52:00 +01:00
5d94bac0e2 Mount queries_to_cache.conf readonly (#282) 2025-03-10 16:03:05 +01:00
83555540f5 chore: update central Secret Sync proxy ID (#280) 2025-03-10 12:08:19 +01:00
e396e00178 Fix/ccp cql cache (#279)
* fix: adapt focus caching to new cql and add focus caching for cce and itcc

---------

Co-authored-by: p.delpy@dkfz-heidelberg.de <p.delpy@dkfz-heidelberg.de>
2025-03-07 12:20:38 +01:00
ecb29830e4 Send the origin of /etc/bridgehead repo to Secret Sync
This is to anticipate an upcoming change in Secret Sync that will allow it to support multiple GitLab servers, e.g. verbis GitLab and BBMRI GitLab.
2025-03-05 11:04:22 +01:00
98121c17e8 Make Codeowners Rule apply to all Files in Repo 2025-02-20 17:28:38 +01:00
e38511e118 Add Codeowners File 2025-02-20 17:20:54 +01:00
8334fac84d fix: use correct obds2fhir-rest image
---------

Co-authored-by: Pierre Delpy <p.delpy@dkfz-heidelberg.de>
2025-02-20 13:48:10 +01:00
21 changed files with 118 additions and 276 deletions

1
.github/CODEOWNERS vendored Normal file
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@ -0,0 +1 @@
* @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:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
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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@ -2,13 +2,14 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-cce-blaze container_name: bridgehead-cce-blaze
environment: environment:
BASE_URL: "http://bridgehead-cce-blaze:8080" BASE_URL: "http://bridgehead-cce-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${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"
@ -31,6 +32,10 @@ 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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@ -0,0 +1,25 @@
version: "3.7"
services:
blaze-airgapped:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-cce-blaze-airgapped
environment:
BASE_URL: "http://bridgehead-cce-blaze-airgapped:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-airgapped-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze-airgapped_cce.rule=PathPrefix(`/cce-localdatamanagement-airgapped`)"
- "traefik.http.middlewares.cce_b-a_strip.stripprefix.prefixes=/cce-localdatamanagement-airgapped"
- "traefik.http.services.blaze-airgapped_cce.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze-airgapped_cce.middlewares=cce_b-a_strip,auth"
- "traefik.http.routers.blaze-airgapped_cce.tls=true"
volumes:
blaze-airgapped-data:

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@ -0,0 +1,3 @@
#!/bin/bash
OVERRIDE+=" -f ./$PROJECT/modules/airgapped-blaze-compose.yml"

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@ -0,0 +1,2 @@
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@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
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 - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
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:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
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/ccp/obds2fhir-rest:main image: docker.verbis.dkfz.de/samply/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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@ -1,112 +0,0 @@
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"

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@ -1,108 +0,0 @@
#!/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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 bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwoKY29kZXN5c3RlbSBsb2luYzogJ2h0dHA6Ly9sb2luYy5vcmcnCmNvZGVzeXN0ZW0gaWNkMTA6ICdodHRwOi8vZmhpci5kZS9Db2RlU3lzdGVtL2JmYXJtL2ljZC0xMC1nbScKY29kZXN5c3RlbSBtb3JwaDogJ3VybjpvaWQ6Mi4xNi44NDAuMS4xMTM4ODMuNi40My4xJwoKY29udGV4dCBQYXRpZW50CgoKREtUS19TVFJBVF9HRU5ERVJfU1RSQVRJRklFUgoKREtUS19TVFJBVF9QUklNQVJZX0RJQUdOT1NJU19OT19TT1JUX1NUUkFUSUZJRVIKREtUS19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgoKREtUS19TVFJBVF9ERUNFQVNFRF9TVFJBVElGSUVSCgpES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCgpES1RLX1JFUExBQ0VfU1BFQ0lNRU5fU1RSQVRJRklFUmlmIEluSW5pdGlhbFBvcHVsYXRpb24gdGhlbiBbU3BlY2ltZW5dIGVsc2Uge30gYXMgTGlzdDxTcGVjaW1lbj4KREtUS19TVFJBVF9QUk9DRURVUkVfU1RSQVRJRklFUgoKREtUS19TVFJBVF9NRURJQ0FUSU9OX1NUUkFUSUZJRVIKCiAgREtUS19SRVBMQUNFX0hJU1RPTE9HWV9TVFJBVElGSUVSCiBpZiBoaXN0by5jb2RlLmNvZGluZy53aGVyZShjb2RlID0gJzU5ODQ3LTQnKS5jb2RlLmZpcnN0KCkgaXMgbnVsbCB0aGVuIDAgZWxzZSAxCkRLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTihleGlzdHMgW0NvbmRpdGlvbjogQ29kZSAnQzYxJyBmcm9tIGljZDEwXSkgYW5kIAooKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MTQwLzMnKSBvciAKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MTQ3LzMnKSBvciAKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4NDgwLzMnKSBvciAKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4NTAwLzMnKSk=

View File

@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
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 - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -2,13 +2,14 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-itcc-blaze container_name: bridgehead-itcc-blaze
environment: environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080" BASE_URL: "http://bridgehead-itcc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${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"
@ -31,6 +32,10 @@ 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

@ -0,0 +1,2 @@
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
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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:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
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.oidc-client-enrollment.$BROKER_ID \ -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$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
@ -322,6 +322,57 @@ 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 "$(git -C /etc/bridgehead remote get-url origin)" in
*git.verbis.dkfz.de*) gitlab=verbis;;
*gitlab.bbmri-eric.eu*) gitlab=bbmri;;
*)
log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
return
;;
esac
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull.
mkdir -p /var/cache/bridgehead/secrets
touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$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 $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v /srv/docker/bridgehead/$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=$BROKER_URL \
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$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

@ -33,43 +33,7 @@ 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"
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token. secret_sync_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

@ -17,11 +17,13 @@ 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:0.28 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-input-blaze container_name: bridgehead-transfair-input-blaze
environment: environment:
BASE_URL: "http://bridgehead-transfair-input-blaze:8080" BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
@ -34,7 +36,7 @@ services:
profiles: ["transfair-input-blaze"] profiles: ["transfair-input-blaze"]
transfair-request-blaze: transfair-request-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
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"

View File

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

View File

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