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19 Commits

Author SHA1 Message Date
e7e38cd57c Whitespace formatting 2025-02-04 13:02:44 +01:00
eb8cb669a6 fix authup redirect (#262)
When a OIDC provider is configured, you'll get redirected to authup by Keycloak which redirects you to the DNPM:DIP. 

Currently the url looks like this: https://myserver/authup//someurl
and produces an error. Manually removing the additional / fixes the issue.
2025-01-27 10:34:50 +01:00
0eff362690 dnpm: Secure endpoints for ETL and p2p communications (#254) 2025-01-21 12:39:57 +00:00
4e8eb6218a chore: pin mysql 2025-01-21 12:39:57 +00:00
5807a3c260 chore: change dnpm images 2025-01-21 12:39:57 +00:00
7acf7b06c3 dnpm: replace named volumes with fs volumes 2025-01-21 12:39:57 +00:00
af88abfae2 dnpm: add uksh to central targets 2025-01-21 12:39:57 +00:00
2a11b6cab1 dnpm: add goettingen to central targets 2025-01-21 12:39:57 +00:00
6ed1cd402b host central targets in git 2025-01-21 12:39:57 +00:00
eed1fe79bf use SITE_NAME for dnpm LOCAL_SITE 2025-01-21 12:39:57 +00:00
839207702b hardcode dnpm connector type to broker 2025-01-21 12:39:57 +00:00
a4039672a5 feat: migrate to new dnpm:dip node 2025-01-21 12:39:57 +00:00
910289079b docs: documentation for changing your configuration repository access token (#256) 2025-01-21 09:35:25 +01:00
1003cd73cf fix: changed ccp_ppi to use IDMANAGEMENT_FRIENDLY_ID instead of SITE_NAME (#259) 2025-01-21 09:30:20 +01:00
3d1105b97c Update: Blaze to version 0.31 (#260) 2025-01-21 09:28:47 +01:00
Jan
5c28e704d2 fix: remove restart: always in compose files (#261) 2025-01-21 09:27:27 +01:00
e3510363ad fix: remove credentials from git remote, if update fails (#253)
Signed-off-by: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
2024-12-10 17:18:07 +01:00
45aefd24e5 renamed exporter API key to EXPORTER_API_KEY (#252) 2024-12-06 11:27:38 +01:00
122ff16bb1 fix: use verbis cache image instead of docker-hub (#250) 2024-11-12 09:58:17 +01:00
27 changed files with 397 additions and 125 deletions

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@ -254,6 +254,8 @@ 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).

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@ -4,7 +4,7 @@ version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
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:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
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:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-ccp-blaze
environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080"
@ -11,7 +11,6 @@ services:
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
volumes:
- "blaze-data:/app/data"
labels:
@ -35,7 +34,6 @@ services:
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
volumes:
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
depends_on:
@ -53,7 +51,6 @@ services:
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
secrets:
- proxy.pem
depends_on:

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
blaze-secondary:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-ccp-blaze-secondary
environment:
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
@ -10,7 +10,6 @@ services:
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
ENFORCE_REFERENTIAL_INTEGRITY: "false"
LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
volumes:
- "blaze-secondary-data:/app/data"
labels:

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@ -10,7 +10,6 @@ services:
DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
HTTP_RELATIVE_PATH: "/rstudio"
ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
LOG_LEVEL: ${LOG_LEVEL_RSTUDIO:-WARN}
labels:
- "traefik.enable=true"
- "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
@ -55,7 +54,6 @@ services:
BEAM_APP_ID: token-manager.${PROXY_ID}
BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
BEAM_DATASHIELD_PROXY: request-manager
LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
volumes:
- "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
secrets:
@ -77,8 +75,6 @@ services:
image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
tmpfs:
- /srv
environment:
LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
beam-connect:
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
@ -91,7 +87,6 @@ services:
DISCOVERY_URL: "./map/central.json"
LOCAL_TARGETS_FILE: "./map/local.json"
NO_AUTH: "true"
RUST_LOG: ${LOG_LEVEL_BEAMCONNECT:-WARN}
secrets:
- opal-cert.pem
depends_on:

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@ -13,11 +13,11 @@ 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}
RUST_LOG: ${LOG_LEVEL_BEAMCONNECTDNPM:-WARN}
RUST_LOG: ${RUST_LOG:-info}
NO_AUTH: "true"
TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
extra_hosts:
@ -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
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

View File

@ -1,34 +1,99 @@
version: "3.7"
services:
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
dnpm-mysql:
image: mysql:9
healthcheck:
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
interval: 3s
timeout: 5s
retries: 5
environment:
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
MYSQL_ROOT_HOST: "%"
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
dnpm-authup:
image: authup/authup:latest
container_name: bridgehead-dnpm-authup
volumes:
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
command: server/core start
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
- 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.routers.bwhc-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
- "traefik.http.routers.bwhc-frontend.tls=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:
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
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
depends_on:
dnpm-authup:
condition: service_healthy
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"
landing:
labels:
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"

View File

@ -1,28 +1,16 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
log INFO "DNPM setup detected -- will start DNPM:DIP node."
OVERRIDE+=" -f ./$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 "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1
fi
if [ -z "${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
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')"
fi

View File

@ -6,6 +6,7 @@ services:
container_name: bridgehead-ccp-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
CROSS_ORIGINS: "https://${HOST}"
EXPORTER_DB_USER: "exporter"
@ -15,7 +16,6 @@ services:
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
LOG_LEVEL: ${LOG_LEVEL_EXPORTER:-WARN}
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
@ -42,6 +42,7 @@ services:
container_name: bridgehead-ccp-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter"
SITE: "${SITE_ID}"
@ -49,7 +50,6 @@ services:
EXPORTER_URL: "http://exporter:8092"
LOG_FHIR_VALIDATION: "false"
HTTP_SERVLET_REQUEST_SCHEME: "https"
LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
@ -69,4 +69,4 @@ services:
focus:
environment:
EXPORTER_URL: "http://exporter:8092"
AUTH_HEADER: "${EXPORTER_API_KEY}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

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@ -14,7 +14,6 @@ services:
MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
ML_LOG_LEVEL: ${LOG_LEVEL_IDMANAGER:-WARN}
depends_on:
- patientlist
- traefik-forward-auth
@ -45,8 +44,6 @@ services:
- ML_UPLOAD_API_KEY=${IDMANAGER_UPLOAD_APIKEY}
# Add Variables from /etc/patientlist-id-generators.env
- PATIENTLIST_SEEDS_TRANSFORMED
- ML_LOG_LEVEL=${LOG_LEVEL_PATIENTLIST:-WARN}
#TODO confirm LOG_LEVEL
labels:
- "traefik.enable=true"
- "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
@ -105,11 +102,11 @@ services:
condition: service_healthy
ccp-patient-project-identificator:
image: samply/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: ${SITE_NAME}
SITE_NAME: ${IDMANAGEMENT_FRIENDLY_ID}
volumes:
patientlist-db-data:

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@ -25,7 +25,6 @@ services:
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_URL: "${OIDC_URL}"
LOG_LEVEL: ${LOG_LEVEL_MTBA:-WARN}
labels:
- "traefik.enable=true"

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@ -12,8 +12,6 @@ services:
CTS_API_KEY: ${NNGM_CTS_APIKEY}
CRYPT_KEY: ${NNGM_CRYPTKEY}
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
LOG_LEVEL: ${LOG_LEVEL_NNGM:-WARN}
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"

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@ -10,8 +10,6 @@ services:
SALT: ${LOCAL_SALT}
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"

View File

@ -17,7 +17,6 @@ services:
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
@ -48,7 +47,6 @@ services:
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
teiler-backend:
@ -62,6 +60,7 @@ services:
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
@ -74,7 +73,6 @@ services:
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
secrets:
- ccp.conf

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

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@ -0,0 +1,42 @@
## 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
```

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

View File

@ -10,7 +10,6 @@ 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

@ -58,7 +58,8 @@ 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
report_error log "Unable to update git $DIR: $OUT"
OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
report_error log "Unable to update git $DIR: $OUT_SAN"
fi
new_git_hash="$(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(`/api`) || PathPrefix(`/dashboard/`)"
- "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
- "traefik.http.routers.dashboard.entrypoints=websecure"
- "traefik.http.routers.dashboard.service=api@internal"
- "traefik.http.routers.dashboard.tls=true"

View File

@ -0,0 +1,142 @@
{
"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
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

View File

@ -1,34 +1,99 @@
version: "3.7"
services:
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
dnpm-mysql:
image: mysql:9
healthcheck:
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
interval: 3s
timeout: 5s
retries: 5
environment:
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
MYSQL_ROOT_HOST: "%"
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
dnpm-authup:
image: authup/authup:latest
container_name: bridgehead-dnpm-authup
volumes:
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
command: server/core start
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
- 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.routers.bwhc-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
- "traefik.http.routers.bwhc-frontend.tls=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:
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
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
depends_on:
dnpm-authup:
condition: service_healthy
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"
landing:
labels:
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"

View File

@ -1,28 +1,16 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
log INFO "DNPM setup detected -- will start DNPM:DIP node."
OVERRIDE+=" -f ./$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 "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1
fi
if [ -z "${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
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')"
fi

View File

@ -11,7 +11,6 @@ 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`)"