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14 changed files with 78 additions and 90 deletions

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@ -2,7 +2,7 @@ version: "3.7"
services:
focus-eric:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
container_name: bridgehead-focus-eric
environment:
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}

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@ -2,7 +2,7 @@ version: "3.7"
services:
focus-gbn:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
container_name: bridgehead-focus-gbn
environment:
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}

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@ -1,22 +1,3 @@
BROKER_ID=broker-test.bbmri-test.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
PLATFORM=bbmri
BROKER_URL_FOR_PREREQ=$BROKER_URL
OIDC_USER_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PUBLIC_CLIENT_ID="BBMRI_${SITE_ID}-public"
# Use "test-realm-01" for testing
OIDC_REALM="${OIDC_REALM:-test-realm-01}"
OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups"
POSTGRES_TAG=15.6-alpine
# Makes sense for all European Biobanks
: ${ENABLE_ERIC:=true}
@ -32,13 +13,6 @@ do
source $module
done
log DEBUG "sourcing ccp/modules/exporter-setup.sh"
source ccp/modules/exporter-setup.sh
log DEBUG "sourcing ccp/modules/teiler-setup.sh"
source ccp/modules/teiler-setup.sh
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"

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@ -106,8 +106,7 @@ case "$ACTION" in
loadVars
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
checkRequirements
# NOTE: for testing only, we will need to properly setup secret sync if we want to use this code
# sync_secrets
sync_secrets
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
;;

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@ -22,7 +22,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -33,6 +33,7 @@ services:
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/ccp/queries_to_cache.conf:/queries_to_cache.conf
depends_on:
@ -58,7 +59,6 @@ services:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:

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@ -22,7 +22,7 @@ services:
opal:
container_name: bridgehead-opal
image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
image: docker.verbis.dkfz.de/ccp/dktk-opal:test
labels:
- "traefik.enable=true"
- "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"

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@ -3,7 +3,7 @@ version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-${PLATFORM}-exporter
container_name: bridgehead-ccp-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
@ -12,39 +12,39 @@ services:
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/${PLATFORM}-exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-exporter`)"
- "traefik.http.services.exporter_${PLATFORM}.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_${PLATFORM}.tls=true"
- "traefik.http.middlewares.exporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-exporter"
- "traefik.http.routers.exporter_${PLATFORM}.middlewares=exporter_${PLATFORM}_strip"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_ccp.tls=true"
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
volumes:
- "/var/cache/bridgehead/${PLATFORM}/exporter-files:/app/exporter-files/output"
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-${PLATFORM}-exporter-db
container_name: bridgehead-ccp-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/${PLATFORM}/exporter-db:/var/lib/postgresql/data"
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-${PLATFORM}-reporter
container_name: bridgehead-ccp-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/${PLATFORM}-reporter"
HTTP_RELATIVE_PATH: "/ccp-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092"
@ -57,11 +57,16 @@ services:
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/${PLATFORM}/reporter-files:/app/reports"
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-reporter`)"
- "traefik.http.services.reporter_${PLATFORM}.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_${PLATFORM}.tls=true"
- "traefik.http.middlewares.reporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-reporter"
- "traefik.http.routers.reporter_${PLATFORM}.middlewares=reporter_${PLATFORM}_strip"
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
- "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_ccp.tls=true"
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
focus:
environment:
EXPORTER_URL: "http://exporter:8092"
AUTH_HEADER: "${EXPORTER_API_KEY}"

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@ -2,7 +2,7 @@
if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service."
OVERRIDE+=" -f ./ccp/modules/exporter-compose.yml"
OVERRIDE+=" -f ./$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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@ -23,3 +23,7 @@ services:
POSTGRES_DB: "dashboard"
volumes:
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
focus:
environment:
POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"

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@ -4,4 +4,5 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
FOCUS_ENDPOINT_TYPE="blaze-and-sql"
fi

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@ -101,5 +101,12 @@ services:
forward_proxy:
condition: service_healthy
ccp-patient-project-identificator:
image: samply/ccp-patient-project-identificator
container_name: bridgehead-ccp-patient-project-identificator
environment:
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
SITE_NAME: ${SITE_NAME}
volumes:
patientlist-db-data:

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@ -7,31 +7,30 @@ services:
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler`)"
- "traefik.http.services.teiler_orchestrator_${PLATFORM}.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler"
- "traefik.http.routers.teiler_orchestrator_${PLATFORM}.middlewares=teiler_orchestrator_${PLATFORM}_strip"
- "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
- "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
- "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
environment:
TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard:
#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/ccp/samply/teiler-dashboard:bbmri
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_${PLATFORM}.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_${PLATFORM}.tls=true"
- "traefik.http.middlewares.teiler_dashboard_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_${PLATFORM}.middlewares=teiler_dashboard_${PLATFORM}_strip"
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -41,42 +40,42 @@ services:
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PLATFORM}-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
teiler-backend:
image: docker.verbis.dkfz.de/ccp/${PROJECT}-teiler-backend:latest
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_backend_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-teiler-backend`)"
- "traefik.http.services.teiler_backend_${PLATFORM}.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_${PLATFORM}.tls=true"
- "traefik.http.middlewares.teiler_backend_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-teiler-backend"
- "traefik.http.routers.teiler_backend_${PLATFORM}.middlewares=teiler_backend_${PLATFORM}_strip"
- "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
- "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_ccp.tls=true"
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/project-conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PLATFORM}-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard/en"
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
CENTRAX_URL: "${CENTRAXX_URL}"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
secrets:
- project-conf
- ccp.conf
secrets:
project-conf:
file: "/etc/bridgehead/${PROJECT}.conf"
ccp.conf:
file: /etc/bridgehead/ccp.conf

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@ -2,7 +2,7 @@
if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./ccp/modules/teiler-compose.yml"
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
TEILER_DEFAULT_LANGUAGE=DE
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
add_public_oidc_redirect_url "/ccp-teiler/*"

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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/${SITE_ID}.priv.pem
PLATFORM=ccp
BROKER_URL_FOR_PREREQ=$BROKER_URL
@ -30,4 +29,4 @@ done
idManagementSetup
mtbaSetup
obds2fhirRestSetup
blazeSecondarySetup
blazeSecondarySetup