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@ -23,7 +23,6 @@ This repository is the starting point for any information and tools you will nee
- [File structure](#file-structure)
- [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
- [Loading data](#loading-data)
- [Metadata feedback](#metadata-feedback)
4. [Things you should know](#things-you-should-know)
- [Auto-Updates](#auto-updates)
- [Auto-Backups](#auto-backups)
@ -77,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
* git.verbis.dkfz.de
* To fetch docker images
* docker.verbis.dkfz.de
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
* hub.docker.com
* registry-1.docker.io
* production.cloudflare.docker.com
@ -156,7 +155,6 @@ Clone the bridgehead repository:
```shell
sudo mkdir -p /srv/docker/
sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
sudo git checkout metadata_fb # Only needed if you want to use metadata feedback
```
Then, run the installation script:
@ -256,8 +254,6 @@ sh bridgehead uninstall
## Site-specific configuration
[How to Change Config Access Token](docs/update-access-token.md)
### HTTPS Access
Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).
@ -349,26 +345,6 @@ Normally, you will need to build your own ETL to feed the Bridgehead. However, t
You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
### Metadata feedback
The Bridgehead comes with a tool that allows you to associate metadata with samples. Multiple arbitrary text strings are allowed. A typical use case would be publications based on research using a sample. Here, one could lay down the DOI of the publication in the sample.
Full details of the system can be found [here](https://github.com/samply/feedback-deployment). To avail yourself of this feature, you need to
- Use the bbmri project.
- work with the ```metadata_fb``` branch of the Bridgehead repository.
- Build the feedback-agent Docker container (more details [here](https://github.com/samply/feedback-agent/)).
- Build the feedback-agent-ui Docker container (more details [here](https://github.com/samply/feedback-agent-ui/)).
The following extra environment variables need to be added to your ```/etc/bridgehead/bbmri.conf``` file:
``` code
ENABLE_EXPORTER=true
ENABLE_FEEDBACK_AGENT=true
FEEDBACK_HUB_URL=<URL for central feedback hub backend API>
FOCUS_RETRY_COUNT=256
```
## Things you should know
### Auto-Updates

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@ -4,7 +4,7 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-bbmri-blaze
environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080"

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@ -2,7 +2,7 @@ version: "3.7"
services:
focus-eric:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus-eric
environment:
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
@ -22,7 +22,6 @@ services:
BROKER_URL: ${ERIC_BROKER_URL}
PROXY_ID: ${ERIC_PROXY_ID}
APP_focus_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
APP_feedback-agent_KEY: ${FEEDBACK_AGENT_BEAM_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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@ -1,67 +0,0 @@
version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-ccp-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
CROSS_ORIGINS: "https://${HOST}"
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}"
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_ccp.tls=true"
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
volumes:
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-ccp-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}"
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-ccp-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
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/ccp/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "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"

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@ -1,9 +0,0 @@
#!/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)"
POSTGRES_TAG=15.6-alpine
fi

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@ -1,15 +0,0 @@
# Exporter and Reporter
## Exporter
The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
## Exporter-DB
It is a database to save queries for its execution in the exporter.
The exporter manages also the different executions of the same query in through the database.
## Reporter
This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
It is compatible with different template engines as Groovy, Thymeleaf,...
It is perfect to generate a document as our traditional CCP quality report.

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@ -1,59 +0,0 @@
version: "3.7"
services:
feedback-agent-ui:
image: "samply/feedback-agent-ui"
environment:
- VUE_APP_EXPORTER_URL=https://localhost/ccp-exporter
- VUE_APP_FB_BACKEND_URL=http://localhost:8072
labels:
- traefik.enable=true
# HTTPS
- traefik.http.routers.feedback_agent_ui_ccp_https.rule=PathPrefix(`/ccp-feedback-agent-ui`)
- traefik.http.services.feedback_agent_ui_ccp_https.loadbalancer.server.port=8096
- traefik.http.routers.feedback_agent_ui_ccp_https.entrypoints=websecure
- traefik.http.routers.feedback_agent_ui_ccp_https.tls=true
feedback-agent:
image: "samply/feedback-agent"
environment:
- SPRING_DATASOURCE_URL=jdbc:postgresql://feedback-agent-db:5432/compose-postgres
- SPRING_DATASOURCE_USERNAME=compose-postgres
- SPRING_DATASOURCE_PASSWORD=${FEEDBACK_AGENT_DB_PASSWORD}
- SPRING_JPA_HIBERNATE_DDL_AUTO=update
- BEAM_PROXY_URI=http://beam-proxy-eric:8081
- FEEDBACK_HUB_URL=${FEEDBACK_HUB_URL}
- BLAZE_BASE_URL=http://blaze:8080/fhir
- FEEDBACK_AGENT_SECRET=${FEEDBACK_AGENT_BEAM_SECRET}
- FEEDBACK_AGENT_BEAM_ID=feedback-agent.${ERIC_PROXY_ID}
- FEEDBACK_HUB_BEAM_ID=feedback-hub.feedback-central.${ERIC_BROKER_ID}
- EXPORTER_API_KEY=${EXPORTER_API_KEY}
- CORS_ALLOWED_ORIGINS="https://${HOST}
networks:
# Only needed for local testing.
- feedback
- default
labels:
- traefik.enable=true
# HTTPS
- traefik.http.routers.feedback_agent_ccp_https.rule=PathPrefix(`/ccp-feedback-agent`)
- traefik.http.services.feedback_agent_ccp_https.loadbalancer.server.port=8072
- traefik.http.routers.feedback_agent_ccp_https.entrypoints=websecure
- traefik.http.middlewares.feedback_agent_ccp_https_strip.stripprefix.prefixes=/ccp-feedback-agent
- traefik.http.routers.feedback_agent_ccp_https.middlewares=feedback_agent_ccp_https_strip
- traefik.http.routers.feedback_agent_ccp_https.tls=true
feedback-agent-db:
image: 'postgres:13.1-alpine'
container_name: feedback-agent-db
environment:
- POSTGRES_USER=compose-postgres
- POSTGRES_PASSWORD=${FEEDBACK_AGENT_DB_PASSWORD}
# This is needed when you run both agent and hub locally in a test
# environment. Not necessary in production, though it probably won't
# cause any problems.
networks:
# Network to connect agent and hub.
feedback:
name: feedback
driver: bridge

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@ -1,8 +0,0 @@
#!/bin/bash
if [ "$ENABLE_FEEDBACK_AGENT" == true ]; then
OVERRIDE+=" -f ./$PROJECT/modules/feedback-agent-compose.yml"
FEEDBACK_AGENT_BEAM_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FEEDBACK_AGENT_DB_PASSWORD="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
fi

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@ -1,6 +0,0 @@
# Metadata feedback agent
This component can be used to choose the sample to be associated
with a given piece of metadata (generally the ID of a publication
relating to research done with the sample).

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

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@ -1,3 +1,22 @@
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}
@ -13,6 +32,13 @@ 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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@ -53,44 +53,17 @@ case "$PROJECT" in
;;
esac
# Loads config variables and runs the projects setup script
loadVars() {
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
set -a
# Source the project specific config file
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
# Source the project specific local config file if present
# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
fi
# Set execution environment on main default to prod else test
if [[ -z "${ENVIRONMENT+x}" ]]; then
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
ENVIRONMENT="production"
else
ENVIRONMENT="test"
fi
fi
# Source the versions of the images components
case "$ENVIRONMENT" in
"production")
source ./versions/prod
;;
"test")
source ./versions/test
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
source ./versions/prod
;;
esac
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
setHostname
optimizeBlazeMemoryUsage
# Run project specific setup if it exists
# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
# This is also where projects specify which modules to load
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
set +a
@ -106,6 +79,26 @@ loadVars() {
fi
detectCompose
setupProxy
# Set some project-independent default values
: ${ENVIRONMENT:=production}
export ENVIRONMENT
case "$ENVIRONMENT" in
"production")
export FOCUS_TAG=main
export BEAM_TAG=main
;;
"test")
export FOCUS_TAG=develop
export BEAM_TAG=develop
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
export FOCUS_TAG=main
export BEAM_TAG=main
;;
esac
}
case "$ACTION" in
@ -113,7 +106,8 @@ case "$ACTION" in
loadVars
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
checkRequirements
sync_secrets
# NOTE: for testing only, we will need to properly setup secret sync if we want to use this code
# 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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@ -2,7 +2,7 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-cce-blaze
environment:
BASE_URL: "http://bridgehead-cce-blaze:8080"

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@ -2,7 +2,7 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-ccp-blaze
environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080"
@ -22,7 +22,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -33,7 +33,6 @@ 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:
@ -59,6 +58,7 @@ 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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@ -2,7 +2,7 @@ version: "3.7"
services:
blaze-secondary:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-ccp-blaze-secondary
environment:
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

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@ -13,7 +13,7 @@ services:
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
APP_ID: dnpm-connect.${PROXY_ID}
DISCOVERY_URL: "./conf/central_targets.json"
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
HTTP_PROXY: "http://forward_proxy:3128"
HTTPS_PROXY: "http://forward_proxy:3128"
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@ -25,7 +25,7 @@ services:
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

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@ -1,99 +1,34 @@
version: "3.7"
services:
dnpm-mysql:
image: mysql:9
healthcheck:
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
interval: 3s
timeout: 5s
retries: 5
environment:
MYSQL_ROOT_HOST: "%"
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes:
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
dnpm-authup:
image: authup/authup:latest
container_name: bridgehead-dnpm-authup
volumes:
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
command: server/core start
environment:
- PUBLIC_URL=https://${HOST}/auth/
- AUTHORIZE_REDIRECT_URL=https://${HOST}
- ROBOT_ADMIN_ENABLED=true
- ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
- ROBOT_ADMIN_SECRET_RESET=true
- DB_TYPE=mysql
- DB_HOST=dnpm-mysql
- DB_USERNAME=root
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
- DB_DATABASE=auth
labels:
- "traefik.enable=true"
- "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
- "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
- "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
- "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
- "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest
container_name: bridgehead-dnpm-portal
environment:
- NUXT_API_URL=http://dnpm-backend:9000/
- NUXT_PUBLIC_API_URL=https://${HOST}/api/
- NUXT_AUTHUP_URL=http://dnpm-authup:3000/
- NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
- "traefik.http.routers.dnpm-frontend.tls=true"
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
image: ghcr.io/dnpm-dip/backend:latest
environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
- MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
- HATEOAS_HOST=https://${HOST}
- CONNECTOR_TYPE=broker
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
depends_on:
dnpm-authup:
condition: service_healthy
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
# expose everything
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
- "traefik.http.routers.dnpm-backend.tls=true"
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
# except ETL
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
- "traefik.http.routers.dnpm-backend-etl.tls=true"
- "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
# this needs an ETL processor with support for basic auth
- "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
# except peer-to-peer
- "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
- "traefik.http.routers.dnpm-backend-peer.tls=true"
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
# this effectively denies all requests
# this is okay, because requests from peers don't go through Traefik
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
landing:
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
labels:
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
- "traefik.enable=true"
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
- "traefik.http.routers.bwhc-frontend.tls=true"

View File

@ -1,16 +1,28 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected -- will start DNPM:DIP node."
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
if [ -z "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1
fi
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
if [ -z "${DNPM_DATA_DIR+x}" ]; then
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
exit 1
fi
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
fi

View File

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

View File

@ -2,7 +2,7 @@
if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service."
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
OVERRIDE+=" -f ./ccp/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

View File

@ -23,7 +23,3 @@ 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"

View File

@ -4,5 +4,4 @@ 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

View File

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

View File

@ -12,6 +12,7 @@ services:
CTS_API_KEY: ${NNGM_CTS_APIKEY}
CRYPT_KEY: ${NNGM_CRYPTKEY}
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"

View File

@ -10,6 +10,7 @@ services:
SALT: ${LOCAL_SALT}
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"

View File

@ -7,30 +7,31 @@ services:
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "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"
- "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"
environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/${PLATFORM}-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/ccp/samply/teiler-dashboard:bbmri
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "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"
- "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"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_BACKEND_URL: "https://${HOST}/${PLATFORM}-teiler-backend"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -40,42 +41,42 @@ services:
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PLATFORM}-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PLATFORM}-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
REPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "${PLATFORM}"
teiler-backend:
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
image: docker.verbis.dkfz.de/ccp/${PROJECT}-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "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"
- "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"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
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://${HOST}/ccp-teiler-dashboard/en"
CONFIG_ENV_VAR_PATH: "/run/secrets/project-conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${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"
CENTRAX_URL: "${CENTRAXX_URL}"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
secrets:
- ccp.conf
- project-conf
secrets:
ccp.conf:
file: /etc/bridgehead/ccp.conf
project-conf:
file: "/etc/bridgehead/${PROJECT}.conf"

View File

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

View File

@ -5,6 +5,7 @@ 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

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-dhki-blaze
environment:
BASE_URL: "http://bridgehead-dhki-blaze:8080"

View File

@ -1,42 +0,0 @@
## How to Change Config Access Token
### 1. Generate a New Access Token
1. Go to your Git configuration repository provider, it might be either [git.verbis.dkfz.de](https://git.verbis.dkfz.de) or [gitlab.bbmri-eric.eu](https://gitlab.bbmri-eric.eu).
2. Navigate to the configuration repository for your site.
3. Go to **Settings → Access Tokens** to check if your Access Token is valid or expired.
- **If expired**, create a new Access Token.
4. Configure the new Access Token with the following settings:
- **Expiration date**: One year from today, minus one day.
- **Role**: Developer.
- **Scope**: Only `read_repository`.
5. Save the newly generated Access Token in a secure location.
---
### 2. Replace the Old Access Token
1. Navigate to `/etc/bridgehead` in your system.
2. Run the following command to retrieve the current Git remote URL:
```bash
git remote get-url origin
```
Example output:
```
https://name40dkfz-heidelberg.de:<old_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
```
3. Replace `<old_access_token>` with your new Access Token in the URL.
4. Set the updated URL using the following command:
```bash
git remote set-url origin https://name40dkfz-heidelberg.de:<new_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
```
5. Start the Bridgehead update service by running:
```bash
systemctl start bridgehead-update@<project>
```
6. View the output to ensure the update process is successful:
```bash
journalctl -u bridgehead-update@<project> -f
```

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-itcc-blaze
environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080"

View File

@ -6,7 +6,7 @@ services:
replicas: 0 #deactivate landing page
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
container_name: bridgehead-kr-blaze
environment:
BASE_URL: "http://bridgehead-kr-blaze:8080"

View File

@ -10,6 +10,7 @@ services:
SALT: ${LOCAL_SALT}
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"

View File

@ -116,7 +116,7 @@ assertVarsNotEmpty() {
MISSING_VARS=""
for VAR in $@; do
if [ -z "${!VAR}" ]; then
if [ -z "${!VAR}" ]; then
MISSING_VARS+="$VAR "
fi
done
@ -318,7 +318,7 @@ function sync_secrets() {
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
set -a # Export variables as environment variables
source /var/cache/bridgehead/secrets/oidc
source /var/cache/bridgehead/secrets/*
set +a # Export variables in the regular way
}

View File

@ -1,11 +0,0 @@
#!/bin/bash
[ "$1" = "get" ] || exit
source /var/cache/bridgehead/secrets/gitlab_token
# Any non-empty username works, only the token matters
cat << EOF
username=bk
password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
EOF

41
lib/gitpassword.sh Executable file
View File

@ -0,0 +1,41 @@
#!/bin/bash
if [ "$1" != "get" ]; then
echo "Usage: $0 get"
exit 1
fi
baseDir() {
# see https://stackoverflow.com/questions/59895
SOURCE=${BASH_SOURCE[0]}
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
SOURCE=$(readlink "$SOURCE")
[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
echo $DIR
}
BASE=$(baseDir)
cd $BASE
source lib/functions.sh
assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
PARAMS="$(cat)"
GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
fetchVarsFromVault GIT_PASSWORD
if [ -z "${GIT_PASSWORD}" ]; then
fail_and_report 1 "gitpassword.sh failed: Git password not found."
fi
cat <<EOF
protocol=https
host=$GITHOST
username=bk-${SITE_ID}
password=${GIT_PASSWORD}
EOF

View File

@ -19,7 +19,7 @@ fi
hc_send log "Checking for bridgehead updates ..."
CONFFILE=/etc/bridgehead/$PROJECT.conf
CONFFILE=/etc/bridgehead/$1.conf
if [ ! -e $CONFFILE ]; then
fail_and_report 1 "Configuration file $CONFFILE not found."
@ -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 /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.
# 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
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
CHANGES=""
@ -81,6 +45,10 @@ for DIR in /etc/bridgehead $(pwd); do
if [ -n "$OUT" ]; then
report_error log "The working directory $DIR is modified. Changed files: $OUT"
fi
if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
log "INFO" "Configuring repo to use bridgehead git credential helper."
git -C $DIR config credential.helper "$CREDHELPER"
fi
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
log "INFO" "Git is using no proxy!"
@ -90,8 +58,7 @@ for DIR in /etc/bridgehead $(pwd); do
OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
fi
if [ $? -ne 0 ]; then
OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
report_error log "Unable to update git $DIR: $OUT_SAN"
report_error log "Unable to update git $DIR: $OUT"
fi
new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"

View File

@ -16,7 +16,7 @@ services:
- --entrypoints.web.http.redirections.entrypoint.scheme=https
labels:
- "traefik.enable=true"
- "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
- "traefik.http.routers.dashboard.entrypoints=websecure"
- "traefik.http.routers.dashboard.service=api@internal"
- "traefik.http.routers.dashboard.tls=true"

View File

@ -1,142 +0,0 @@
{
"sites": [
{
"id": "UKFR",
"name": "Freiburg",
"virtualhost": "ukfr.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKHD",
"name": "Heidelberg",
"virtualhost": "ukhd.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKT",
"name": "Tübingen",
"virtualhost": "ukt.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKU",
"name": "Ulm",
"virtualhost": "uku.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UM",
"name": "Mainz",
"virtualhost": "um.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKMR",
"name": "Marburg",
"virtualhost": "ukmr.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKE",
"name": "Hamburg",
"virtualhost": "uke.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKA",
"name": "Aachen",
"virtualhost": "uka.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "Charite",
"name": "Berlin",
"virtualhost": "charite.dnpm.de",
"beamconnect": "dnpm-connect.berlin-test.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "MRI",
"name": "Muenchen-tum",
"virtualhost": "mri.dnpm.de",
"beamconnect": "dnpm-connect.muenchen-tum.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "KUM",
"name": "Muenchen-lmu",
"virtualhost": "kum.dnpm.de",
"beamconnect": "dnpm-connect.muenchen-lmu.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "MHH",
"name": "Hannover",
"virtualhost": "mhh.dnpm.de",
"beamconnect": "dnpm-connect.hannover.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKDD",
"name": "dresden-dnpm",
"virtualhost": "ukdd.dnpm.de",
"beamconnect": "dnpm-connect.dresden-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKB",
"name": "Bonn",
"virtualhost": "ukb.dnpm.de",
"beamconnect": "dnpm-connect.bonn-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKD",
"name": "Duesseldorf",
"virtualhost": "ukd.dnpm.de",
"beamconnect": "dnpm-connect.duesseldorf-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKK",
"name": "Koeln",
"virtualhost": "ukk.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UME",
"name": "Essen",
"virtualhost": "ume.dnpm.de",
"beamconnect": "dnpm-connect.essen.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKM",
"name": "Muenster",
"virtualhost": "ukm.dnpm.de",
"beamconnect": "dnpm-connect.muenster-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKF",
"name": "Frankfurt",
"virtualhost": "ukf.dnpm.de",
"beamconnect": "dnpm-connect.frankfurt.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UMG",
"name": "Goettingen",
"virtualhost": "umg.dnpm.de",
"beamconnect": "dnpm-connect.goettingen.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKW",
"name": "Würzburg",
"virtualhost": "ukw.dnpm.de",
"beamconnect": "dnpm-connect.wuerzburg-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKSH",
"name": "Schleswig-Holstein",
"virtualhost": "uksh.dnpm.de",
"beamconnect": "dnpm-connect.uksh-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "TKT",
"name": "Test",
"virtualhost": "tkt.dnpm.de",
"beamconnect": "dnpm-connect.tobias-develop.broker.ccp-it.dktk.dkfz.de"
}
]
}

View File

@ -29,7 +29,7 @@ services:
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
APP_ID: dnpm-connect.${DNPM_PROXY_ID}
DISCOVERY_URL: "./conf/central_targets.json"
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
HTTP_PROXY: http://forward_proxy:3128
HTTPS_PROXY: http://forward_proxy:3128
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@ -41,7 +41,7 @@ services:
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

View File

@ -1,99 +1,34 @@
version: "3.7"
services:
dnpm-mysql:
image: mysql:9
healthcheck:
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
interval: 3s
timeout: 5s
retries: 5
environment:
MYSQL_ROOT_HOST: "%"
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes:
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
dnpm-authup:
image: authup/authup:latest
container_name: bridgehead-dnpm-authup
volumes:
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
command: server/core start
environment:
- PUBLIC_URL=https://${HOST}/auth/
- AUTHORIZE_REDIRECT_URL=https://${HOST}
- ROBOT_ADMIN_ENABLED=true
- ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
- ROBOT_ADMIN_SECRET_RESET=true
- DB_TYPE=mysql
- DB_HOST=dnpm-mysql
- DB_USERNAME=root
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
- DB_DATABASE=auth
labels:
- "traefik.enable=true"
- "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth/"
- "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
- "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
- "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
- "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest
container_name: bridgehead-dnpm-portal
environment:
- NUXT_API_URL=http://dnpm-backend:9000/
- NUXT_PUBLIC_API_URL=https://${HOST}/api/
- NUXT_AUTHUP_URL=http://dnpm-authup:3000/
- NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
- "traefik.http.routers.dnpm-frontend.tls=true"
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
image: ghcr.io/dnpm-dip/backend:latest
environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
- MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
- HATEOAS_HOST=https://${HOST}
- CONNECTOR_TYPE=broker
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
depends_on:
dnpm-authup:
condition: service_healthy
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
# expose everything
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
- "traefik.http.routers.dnpm-backend.tls=true"
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
# except ETL
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
- "traefik.http.routers.dnpm-backend-etl.tls=true"
- "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
# this needs an ETL processor with support for basic auth
- "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
# except peer-to-peer
- "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
- "traefik.http.routers.dnpm-backend-peer.tls=true"
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
# this effectively denies all requests
# this is okay, because requests from peers don't go through Traefik
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
landing:
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
labels:
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
- "traefik.enable=true"
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
- "traefik.http.routers.bwhc-frontend.tls=true"

View File

@ -1,16 +1,28 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected -- will start DNPM:DIP node."
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
if [ -z "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1
fi
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
if [ -z "${DNPM_DATA_DIR+x}" ]; then
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
exit 1
fi
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
fi

View File

@ -11,6 +11,7 @@ services:
CTS_API_KEY: ${NNGM_CTS_APIKEY}
CRYPT_KEY: ${NNGM_CRYPTKEY}
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"

View File

@ -1,2 +0,0 @@
FOCUS_TAG=main
BEAM_TAG=main

View File

@ -1,2 +0,0 @@
FOCUS_TAG=develop
BEAM_TAG=develop