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4 Commits

Author SHA1 Message Date
David Juarez
529f894dae fix: add nngm to prepare-system script 2025-09-12 15:09:02 +02:00
David Juarez
30648a8fd6 fix: add nngm to bridgehead script 2025-09-12 15:06:46 +02:00
David Juarez
1a37930ec9 feat: nngm broker id and url 2025-09-12 14:51:55 +02:00
David Juarez
d643888157 feat: nNGM project 2025-09-12 14:32:45 +02:00
16 changed files with 293 additions and 60 deletions

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@@ -44,6 +44,9 @@ case "$PROJECT" in
dhki)
#nothing extra to do
;;
nngm)
#nothing extra to do
;;
minimal)
#nothing extra to do
;;
@@ -176,13 +179,6 @@ case "$ACTION" in
;;
postRun | postUpdate)
;;
send-file)
loadVars
log "WARNING" "Your are about to send a file to another bridgehead in your network!"
read -p "Please name the bridgehead you want to send the file to (proxy-id): " RECEIVER_PROXY_ID
read -p "Continue? (Y/N): " confirm && [[ $confirm == [yY] || $confirm == [yY][eE][sS] ]] || exit 1
exec $COMPOSE -p $PROJECT -f ./modules/beam-file-compose.yml --profile beam-file-sender run beam-file-sender send --to beamfile.$RECEIVER_PROXY_ID /data/outfile
;;
*)
printUsage
exit 1

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@@ -45,7 +45,6 @@ services:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
APP_beamfilesend_KEY: ${BEAM_FILE_SEND_SECRET}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs

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@@ -5,7 +5,6 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BEAM_FILE_SEND_SECRET="$(echo \"beam-file-send-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
BROKER_URL_FOR_PREREQ=$BROKER_URL
@@ -25,5 +24,4 @@ do
done
transfairSetup
scoutSetup
beamFileSetup
scoutSetup

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@@ -54,7 +54,7 @@ checkOwner(){
printUsage() {
echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki|nngm"
}
checkRequirements() {

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@@ -67,6 +67,9 @@ case "$PROJECT" in
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
nngm)
site_configuration_repository_middle="git.verbis.dkfz.de/nngm/"
;;
minimal)
site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
;;

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@@ -1,35 +0,0 @@
# NOTE: Current implementation is restricted to a bridgehead only being able to either upload or download data
services:
beam-file-sender:
image: samply/beam-file:${BEAM_FILE_TAG}
container_name: bridgehead-beam-file-sender
environment:
- BEAM_ID=beamfilesend.${PROXY_ID}
- BEAM_SECRET=${BEAM_FILE_SEND_SECRET}
- BEAM_URL=http://beam-proxy:8081
- BIND_ADDR=0.0.0.0:8085
- API_KEY=${BEAM_FILE_API_KEY}
# Only uncomment if your are sure what to do
# ports:
# - 8085:8085
volumes:
- /var/cache/bridgehead/beam-file-out/:/data
profiles: ["beam-file-sender"]
beam-file-receiver:
image: samply/beam-file:${BEAM_FILE_TAG}
container_name: bridgehead-beam-file-receiver
environment:
- BEAM_ID=beamfile.${PROXY_ID}
- BEAM_SECRET=${BEAM_FILE_SECRET}
- BEAM_URL=http://beam-proxy:8081
- API_KEY=${BEAM_FILE_API_KEY}
command: ["receive", "save", "--outdir", "/data"]
volumes:
- /var/cache/bridgehead/beam-file/:/data
profiles: ["beam-file-receiver"]
beam-proxy:
environment:
APP_beamfile_KEY: ${BEAM_FILE_SECRET}
profiles: ["beam-file-receiver"]

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@@ -1,11 +0,0 @@
#!/bin/bash -e
function beamFileSetup() {
if [ -n "$ENABLE_BEAM_FILE_RECEIVER" ]; then
echo "Starting beam file in receiver mode"
OVERRIDE+=" -f ./modules/beam-file-compose.yml --profile beam-file-receiver"
BEAM_FILE_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
BEAM_FILE_API_KEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
log INFO "Beam File in Receiver Mode available uses ApiKey ${BEAM_FILE_API_KEY}"
fi
}

67
nngm/docker-compose.yml Normal file
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@@ -0,0 +1,67 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-nngm-blaze
environment:
BASE_URL: "http://bridgehead-nngm-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${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: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_nngm.rule=PathPrefix(`/nngm-localdatamanagement`)"
- "traefik.http.middlewares.nngm_b_strip.stripprefix.prefixes=/nngm-localdatamanagement"
- "traefik.http.services.blaze_nngm.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_nngm.middlewares=nngm_b_strip,auth"
- "traefik.http.routers.blaze_nngm.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-nngm-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/nngm/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/nngm/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@@ -0,0 +1,72 @@
version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-nngm-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
CROSS_ORIGINS: "https://${HOST}"
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/nngm-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_nngm.rule=PathPrefix(`/nngm-exporter`)"
- "traefik.http.services.exporter_nngm.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_nngm.tls=true"
- "traefik.http.middlewares.exporter_nngm_strip.stripprefix.prefixes=/nngm-exporter"
- "traefik.http.routers.exporter_nngm.middlewares=exporter_nngm_strip"
volumes:
- "/var/cache/bridgehead/nngm/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-nngm-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/nngm/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-nngm-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/nngm-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092"
LOG_FHIR_VALIDATION: "false"
HTTP_SERVLET_REQUEST_SCHEME: "https"
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
# a process that can take several hours, because it depends on the exporter.
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/nngm/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_nngm.rule=PathPrefix(`/nngm-reporter`)"
- "traefik.http.services.reporter_nngm.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_nngm.tls=true"
- "traefik.http.middlewares.reporter_nngm_strip.stripprefix.prefixes=/nngm-reporter"
- "traefik.http.routers.reporter_nngm.middlewares=reporter_nngm_strip"
focus:
environment:
EXPORTER_URL: "http://exporter:8092"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

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@@ -0,0 +1,8 @@
#!/bin/bash -e
if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service."
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
fi

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@@ -0,0 +1,73 @@
version: "3.7"
services:
teiler-orchestrator:
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_orchestrator_nngm.rule=PathPrefix(`/nngm-teiler`)"
- "traefik.http.services.teiler_orchestrator_nngm.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_nngm.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_nngm_strip.stripprefix.prefixes=/nngm-teiler"
- "traefik.http.routers.teiler_orchestrator_nngm.middlewares=teiler_orchestrator_nngm_strip"
environment:
TEILER_BACKEND_URL: "/nngm-teiler-backend"
TEILER_DASHBOARD_URL: "/nngm-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/nngm-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_nngm.rule=PathPrefix(`/nngm-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_nngm.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_nngm.tls=true"
- "traefik.http.middlewares.teiler_dashboard_nngm_strip.stripprefix.prefixes=/nngm-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_nngm.middlewares=teiler_dashboard_nngm_strip"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "/nngm-teiler-backend"
TEILER_DASHBOARD_URL: "/nngm-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "/nngm-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/nngm-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
# TODO: Replace dktk-teiler-backend with nngm-teiler-backend
teiler-backend:
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_backend_nngm.rule=PathPrefix(`/nngm-teiler-backend`)"
- "traefik.http.services.teiler_backend_nngm.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_nngm.tls=true"
- "traefik.http.middlewares.teiler_backend_nngm_strip.stripprefix.prefixes=/nngm-teiler-backend"
- "traefik.http.routers.teiler_backend_nngm.middlewares=teiler_backend_nngm_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/nngm-teiler"
TEILER_ORCHESTRATOR_URL: "/nngm-teiler"
TEILER_DASHBOARD_DE_URL: "/nngm-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "/nngm-teiler-dashboard/en"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active

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@@ -0,0 +1,8 @@
#!/bin/bash -e
if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
TEILER_DEFAULT_LANGUAGE=DE
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
fi

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20
nngm/root.crt.pem Normal file
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@@ -0,0 +1,20 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

36
nngm/vars Normal file
View File

@@ -0,0 +1,36 @@
# TODO: Replace after getting FQDN from ITCF
# BROKER_ID=broker.nngm.dktk.dkfz.de
# BROKER_URL=https://${BROKER_ID}
BROKER_ID=e260-nngm-lens.inet.dkfz-heidelberg.de
BROKER_URL=http://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
# TODO: Add real nNGM-Support email
SUPPORT_EMAIL=support-nngm@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
# TODO: Replace with nNGM OIDC Server
OIDC_USER_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PSP_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})_PSP"
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
OIDC_GROUP_CLAIM="groups"
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done

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@@ -3,5 +3,4 @@ BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine
TEILER_DASHBOARD_TAG=develop
MTBA_TAG=develop
BEAM_FILE_TAG=task-based-files
MTBA_TAG=develop