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Author SHA1 Message Date
Jan
b1f4bdb615 Test code owners changes 2025-02-20 17:22:25 +01:00
35 changed files with 132 additions and 343 deletions

2
.github/CODEOWNERS vendored
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@ -1 +1 @@
* @samply/bridgehead-developers @samply/bridgehead-developers

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@ -1,4 +1,4 @@
Apache License Apache License test
Version 2.0, January 2004 Version 2.0, January 2004
http://www.apache.org/licenses/ http://www.apache.org/licenses/

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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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@ -10,10 +10,6 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
export ERIC_BROKER_ID=broker.bbmri.samply.de export ERIC_BROKER_ID=broker.bbmri.samply.de
export ERIC_ROOT_CERT=eric export ERIC_ROOT_CERT=eric
;; ;;
"acceptance")
export ERIC_BROKER_ID=broker-acc.bbmri-acc.samply.de
export ERIC_ROOT_CERT=eric.acc
;;
"test") "test")
export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
export ERIC_ROOT_CERT=eric.test export ERIC_ROOT_CERT=eric.test

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@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

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@ -1,25 +1,3 @@
DEFAULT_LANGUAGE=EN
DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
BROKER_ID=broker-test.bbmri-test.samply.de
BROKER_URL=https://${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 # Makes sense for all European Biobanks
: ${ENABLE_ERIC:=true} : ${ENABLE_ERIC:=true}
@ -35,13 +13,6 @@ do
source $module source $module
done done
log DEBUG "sourcing ccp/modules/exporter-setup.sh"
source ccp/modules/exporter-setup.sh
log DEBUG "sourcing ccp/modules/teiler-setup.sh"
source ccp/modules/teiler-setup.sh
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}" BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"

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@ -69,7 +69,7 @@ loadVars() {
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
ENVIRONMENT="production" ENVIRONMENT="production"
else else
ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility ENVIRONMENT="test"
fi fi
fi fi
# Source the versions of the images components # Source the versions of the images components
@ -80,9 +80,6 @@ loadVars() {
"test") "test")
source ./versions/test source ./versions/test
;; ;;
"acceptance")
source ./versions/acceptance
;;
*) *)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!" report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
source ./versions/prod source ./versions/prod

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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:
exporter: exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-${PLATFORM}-exporter container_name: bridgehead-ccp-exporter
environment: environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO" LOG_LEVEL: "INFO"
@ -12,39 +12,39 @@ services:
EXPORTER_DB_USER: "exporter" EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter" EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/${PLATFORM}-exporter" HTTP_RELATIVE_PATH: "/ccp-exporter"
SITE: "${SITE_ID}" SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https" HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}" OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.exporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-exporter`)" - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
- "traefik.http.services.exporter_${PLATFORM}.loadbalancer.server.port=8092" - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_${PLATFORM}.tls=true" - "traefik.http.routers.exporter_ccp.tls=true"
- "traefik.http.middlewares.exporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-exporter" - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_${PLATFORM}.middlewares=exporter_${PLATFORM}_strip" - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
volumes: volumes:
- "/var/cache/bridgehead/${PLATFORM}/exporter-files:/app/exporter-files/output" - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
exporter-db: exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG} image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-${PLATFORM}-exporter-db container_name: bridgehead-ccp-exporter-db
environment: environment:
POSTGRES_USER: "exporter" POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter" POSTGRES_DB: "exporter"
volumes: volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer. # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/${PLATFORM}/exporter-db:/var/lib/postgresql/data" - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
reporter: reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-${PLATFORM}-reporter container_name: bridgehead-ccp-reporter
environment: environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO" LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}" CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/${PLATFORM}-reporter" HTTP_RELATIVE_PATH: "/ccp-reporter"
SITE: "${SITE_ID}" SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092" EXPORTER_URL: "http://exporter:8092"
@ -57,15 +57,14 @@ services:
# There is a risk that the bridgehead restarts, losing the already created export. # There is a risk that the bridgehead restarts, losing the already created export.
volumes: volumes:
- "/var/cache/bridgehead/${PLATFORM}/reporter-files:/app/reports" - "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.reporter_${PLATFORM}.rule=PathPrefix(`/${PLATFORM}-reporter`)" - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
- "traefik.http.services.reporter_${PLATFORM}.loadbalancer.server.port=8095" - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_${PLATFORM}.tls=true" - "traefik.http.routers.reporter_ccp.tls=true"
- "traefik.http.middlewares.reporter_${PLATFORM}_strip.stripprefix.prefixes=/${PLATFORM}-reporter" - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
- "traefik.http.routers.reporter_${PLATFORM}.middlewares=reporter_${PLATFORM}_strip" - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
focus: focus:
environment: environment:

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@ -2,7 +2,7 @@
if [ "$ENABLE_EXPORTER" == true ]; then if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service." 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/${SITE_ID}.priv.pem | base64 | head -c 30)" EXPORTER_DB_PASSWORD="$(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/${SITE_ID}.priv.pem | base64 | head -c 64)" EXPORTER_API_KEY="$(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 fi

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

View File

@ -2,6 +2,8 @@
if [ "$ENABLE_TEILER" == true ];then if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services." 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/*" add_public_oidc_redirect_url "/ccp-teiler/*"
fi fi

View File

@ -1,2 +1,2 @@
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 bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwoKY29kZXN5c3RlbSBsb2luYzogJ2h0dHA6Ly9sb2luYy5vcmcnCgpjb250ZXh0IFBhdGllbnQKCgpES1RLX1NUUkFUX0dFTkRFUl9TVFJBVElGSUVSCgpES1RLX1NUUkFUX1BSSU1BUllfRElBR05PU0lTX05PX1NPUlRfU1RSQVRJRklFUgpES1RLX1NUUkFUX0FHRV9DTEFTU19TVFJBVElGSUVSCgpES1RLX1NUUkFUX0RFQ0VBU0VEX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfRElBR05PU0lTX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfU1BFQ0lNRU5fU1RSQVRJRklFUgoKREtUS19TVFJBVF9QUk9DRURVUkVfU1RSQVRJRklFUgoKREtUS19TVFJBVF9NRURJQ0FUSU9OX1NUUkFUSUZJRVIKCiAgREtUS19TVFJBVF9ISVNUT0xPR1lfU1RSQVRJRklFUgpES1RLX1NUUkFUX0RFRl9JTl9JTklUSUFMX1BPUFVMQVRJT04KdHJ1ZQ==
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View File

@ -1,6 +1,3 @@
DEFAULT_LANGUAGE=EN
DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
BROKER_ID=broker.ccp-it.dktk.dkfz.de BROKER_ID=broker.ccp-it.dktk.dkfz.de
BROKER_URL=https://${BROKER_ID} BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID} PROXY_ID=${SITE_ID}.${BROKER_ID}
@ -8,7 +5,6 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64} FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
PLATFORM=bbmri
BROKER_URL_FOR_PREREQ=$BROKER_URL BROKER_URL_FOR_PREREQ=$BROKER_URL
@ -33,12 +29,4 @@ done
idManagementSetup idManagementSetup
mtbaSetup mtbaSetup
obds2fhirRestSetup obds2fhirRestSetup
blazeSecondarySetup blazeSecondarySetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

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

@ -15,7 +15,7 @@ services:
environment: environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard" TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE_LOWER_CASE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler" HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard: teiler-dashboard:
@ -29,9 +29,8 @@ services:
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard" - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip" - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
environment: environment:
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}" OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}" OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -42,6 +41,7 @@ services:
TEILER_PROJECT: "${PROJECT}" TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${OIDC_USER_GROUP}" TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@ -63,12 +63,13 @@ services:
LOG_LEVEL: "INFO" LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085" APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}" APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf" CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de" TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en" TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
CENTRAX_URL: "${CENTRAXX_URL}"
HTTP_PROXY: "http://forward_proxy:3128" HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}" ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}" ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"

View File

@ -3,5 +3,7 @@
if [ "$ENABLE_TEILER" == true ];then if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services." log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml" OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
TEILER_DEFAULT_LANGUAGE=DE
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
add_public_oidc_redirect_url "/ccp-teiler/*" add_public_oidc_redirect_url "/ccp-teiler/*"
fi fi

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
@ -322,73 +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
# Create a temporary directory for Secret Sync that is valid per boot
secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
mkdir -p $secret_sync_tempdir
# Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull.
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \
-v $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 \
-v $secret_sync_tempdir:/secret-sync/ \
-e CACHE_PATH=/secret-sync/gitlab-token \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$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

@ -2,7 +2,7 @@
[ "$1" = "get" ] || exit [ "$1" = "get" ] || exit
source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token" source /var/cache/bridgehead/secrets/gitlab_token
# Any non-empty username works, only the token matters # Any non-empty username works, only the token matters
cat << EOF cat << EOF

View File

@ -41,14 +41,6 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
fi fi
if [ -z "$TRANSFAIR_AUTH" ]; then
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
log "INFO" "Now generating basic auth user for transfair API (see adduser in bridgehead for more information). "
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
add_basic_auth_user "transfair" $generated_passwd "TRANSFAIR_AUTH" $PROJECT
fi
fi
log "INFO" "Registering system units for bridgehead and bridgehead-update" log "INFO" "Registering system units for bridgehead and bridgehead-update"
cp -v \ cp -v \
lib/systemd/bridgehead\@.service \ lib/systemd/bridgehead\@.service \

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

@ -1,17 +0,0 @@
version: "3.7"
services:
ssh-tunnel:
image: docker.verbis.dkfz.de/cache/samply/ssh-tunnel
container_name: bridgehead-ccp-ssh-tunnel
environment:
SSH_TUNNEL_USERNAME: "${SSH_TUNNEL_USERNAME}"
SSH_TUNNEL_HOST: "${SSH_TUNNEL_HOST}"
SSH_TUNNEL_PORT: "${SSH_TUNNEL_PORT:-22}"
volumes:
- "/etc/bridgehead/ssh-tunnel.conf:/ssh-tunnel.conf:ro"
secrets:
- privkey
secrets:
privkey:
file: /etc/bridgehead/pki/ssh-tunnel.priv.pem

View File

@ -1,6 +0,0 @@
#!/bin/bash
if [ -n "$ENABLE_SSH_TUNNEL" ]; then
log INFO "SSH Tunnel setup detected -- will start SSH Tunnel."
OVERRIDE+=" -f ./modules/ssh-tunnel-compose.yml"
fi

View File

@ -1,19 +0,0 @@
# SSH Tunnel Module
This module enables SSH tunneling capabilities for the Bridgehead installation.
The primary use case for this is to connect bridgehead components that are hosted externally due to security concerns.
To connect the new components to the locally running bridgehead infra one is supposed to write a docker-compose.override.yml changing the urls to point to the corresponding forwarded port of the ssh-tunnel container.
## Configuration Variables
- `ENABLE_SSH_TUNNEL`: Required to enable the module
- `SSH_TUNNEL_USERNAME`: Username for SSH connection
- `SSH_TUNNEL_HOST`: Target host for SSH tunnel
- `SSH_TUNNEL_PORT`: SSH port (defaults to 22)
## Configuration Files
The module requires the following files to be present:
- `/etc/bridgehead/ssh-tunnel.conf`: SSH tunnel configuration file. Detailed information can be found [here](https://github.com/samply/ssh-tunnel?tab=readme-ov-file#configuration).
- `/etc/bridgehead/pki/ssh-tunnel.priv.pem`: The SSH private key used to connect to the `SSH_TUNNEL_HOST`. **Passphrases for the key are not supported!**

View File

@ -5,13 +5,8 @@ services:
container_name: bridgehead-transfair container_name: bridgehead-transfair
environment: environment:
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values # NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
- TTP_URL - INSTITUTE_TTP_URL
- TTP_ML_API_KEY - INSTITUTE_TTP_API_KEY
- TTP_GW_SOURCE
- TTP_GW_EPIX_DOMAIN
- TTP_GW_GPAS_DOMAIN
- TTP_TYPE
- TTP_AUTH
- PROJECT_ID_SYSTEM - PROJECT_ID_SYSTEM
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL} - FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
- FHIR_INPUT_URL=${FHIR_INPUT_URL} - FHIR_INPUT_URL=${FHIR_INPUT_URL}
@ -22,27 +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
- TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
- NO_PROXY=${TRANSFAIR_NO_PROXIES}
- ALL_PROXY=http://forward_proxy:3128
volumes: volumes:
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
labels:
- "traefik.enable=true"
- "traefik.http.middlewares.transfair-strip.stripprefix.prefixes=/transfair"
- "traefik.http.routers.transfair.middlewares=transfair-strip,transfair-auth"
- "traefik.http.routers.transfair.rule=PathPrefix(`/transfair`)"
- "traefik.http.services.transfair.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair.tls=true"
traefik:
labels:
- "traefik.http.middlewares.transfair-auth.basicauth.users=${TRANSFAIR_AUTH}"
transfair-input-blaze: transfair-input-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${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"
@ -53,19 +32,12 @@ services:
volumes: volumes:
- "transfair-input-blaze-data:/app/data" - "transfair-input-blaze-data:/app/data"
profiles: ["transfair-input-blaze"] profiles: ["transfair-input-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
- "traefik.http.routers.transfair-input-blaze.tls=true"
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-request-blaze container_name: bridgehead-transfair-requests-blaze
environment: environment:
BASE_URL: "http://bridgehead-transfair-request-blaze:8080" BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m" JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024 DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8 CQL_EXPR_CACHE_SIZE: 8
@ -73,13 +45,6 @@ services:
volumes: volumes:
- "transfair-request-blaze-data:/app/data" - "transfair-request-blaze-data:/app/data"
profiles: ["transfair-request-blaze"] profiles: ["transfair-request-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-request-blaze.rule=PathPrefix(`/data-requests`)"
- "traefik.http.middlewares.transfair-request-strip.stripprefix.prefixes=/data-requests"
- "traefik.http.services.transfair-request-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-request-blaze.middlewares=transfair-request-strip,transfair-auth"
- "traefik.http.routers.transfair-request-blaze.tls=true"
volumes: volumes:
transfair-input-blaze-data: transfair-input-blaze-data:

View File

@ -1,7 +1,7 @@
#!/bin/bash -e #!/bin/bash -e
function transfairSetup() { function transfairSetup() {
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then if [[ -n "$INSTITUTE_TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
echo "Starting transfair." echo "Starting transfair."
OVERRIDE+=" -f ./modules/transfair-compose.yml" OVERRIDE+=" -f ./modules/transfair-compose.yml"
if [ -n "$FHIR_INPUT_URL" ]; then if [ -n "$FHIR_INPUT_URL" ]; then
@ -15,21 +15,8 @@ function transfairSetup() {
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL" log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
else else
log INFO "TransFAIR request fhir store not set writing to internal blaze" log INFO "TransFAIR request fhir store not set writing to internal blaze"
FHIR_REQUEST_URL="http://transfair-request-blaze:8080" FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
OVERRIDE+=" --profile transfair-request-blaze" OVERRIDE+=" --profile transfair-request-blaze"
fi fi
if [ -n "$TTP_GW_SOURCE" ]; then
log INFO "TransFAIR configured with greifswald as ttp"
TTP_TYPE="greifswald"
elif [ -n "$TTP_ML_API_KEY" ]; then
log INFO "TransFAIR configured with mainzelliste as ttp"
TTP_TYPE="mainzelliste"
else
log INFO "TransFAIR configured without ttp"
fi
TRANSFAIR_NO_PROXIES="transfair-input-blaze,blaze,transfair-requests-blaze"
if [ -n "${TRANSFAIR_NO_PROXY}" ]; then
TRANSFAIR_NO_PROXIES+=",${TRANSFAIR_NO_PROXY}"
fi
fi fi
} }

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@ -1,3 +0,0 @@
FOCUS_TAG=develop
BEAM_TAG=develop
BLAZE_TAG=main

View File

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

View File

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