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55 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
967e45624e Add exporter configuration to focus (#249) 2024-11-05 15:46:00 +01:00
8cd5b93b95 Merge pull request #237 from samply/feat/ccp-ppi
Feat/ccp ppi
2024-11-05 13:59:01 +01:00
Jan
52c24ee6fa fix(fhir2sql): add the postgres connection string to focus (#245) 2024-11-05 13:34:36 +01:00
26712d3567 feat: add and set FOCUS_ENDPOINT_TYPE to support fhir2sql (#244)
* add and set FOCUS_ENDPOINT_TYPE

Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>

---------

Co-authored-by: davidmscholz <david.scholz@dkfz-heidelberg.de>
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
2024-10-30 15:21:15 +01:00
eea17c3478 fix: remove invalid beam-proxy tag and add it to focus instead (#242) 2024-10-22 16:48:48 +02:00
cf5230963c feat: add focus tags in ccp and bbmri (#240)
Co-authored-by: p.delpy@dkfz-heidelberg.de <p.delpy@dkfz-heidelberg.de>
2024-10-21 11:00:01 +02:00
7aaee5e7d5 feat: add auto archiving action (#238)
* feat: add auto archiving action

---------

Co-authored-by: p.delpy@dkfz-heidelberg.de <p.delpy@dkfz-heidelberg.de>
Co-authored-by: Martin Lablans <6804500+lablans@users.noreply.github.com>
2024-10-15 13:03:42 +02:00
3312ca8a64 feat: added blaze cql cache (#236) 2024-10-10 14:34:28 +02:00
23981062bb Move ppi to id-management 2024-10-10 13:27:24 +02:00
8e7fe6851e fix: use correct mainzelliste api key 2024-10-10 13:11:43 +02:00
760d599b7c Add CCP-PPI 2024-10-10 12:56:36 +02:00
072ee348fc fix: deactivate landingpage for KR project (#234)
fix: deactivate landingpage for KR project
2024-10-09 09:24:27 +02:00
f328e40963 Merge pull request #233 from samply/fix/id-management-redirection
Allow Usage of Centraxx Interface without login
2024-10-08 13:30:44 +02:00
599bcfcec4 Feature/send branch to healthchecks (#232)
feature: log git branches to healthchecks and code refactoring
2024-10-02 07:53:20 +02:00
eb2955872f fix: allow usage of centraxx interface without login
Before this change CentraXX was redirected to the
central login servers then interacting with the id-management
2024-10-01 13:30:23 +02:00
24da24d05e Traefik dashboard
Deactivate traefik dashboard by default. Add trailing slash to PathPrefix to clarify the URL the dashboard is available at.
2024-10-01 10:40:24 +02:00
65359c2ee6 Feature/pilot projects backup (#227)
add pilot projects
2024-09-12 10:04:53 +02:00
b1de62607f Merge pull request #223 from samply/feat/add-dkfz-hector-ki-project
Added DHKI project
2024-09-12 09:44:03 +02:00
969f1e7242 fix: remove accidental commit 2024-09-12 09:41:19 +02:00
77c870ab22 fix: fix bash path 2024-09-12 09:29:30 +02:00
f0bdb5c146 fix: re-add modules 2024-09-12 09:25:38 +02:00
735e064b03 Update queries_to_cache.conf 2024-09-12 09:19:21 +02:00
6465dcb0ad feat: added dhki project 2024-09-12 08:47:33 +02:00
c585322ee7 Merge pull request #226 from samply/main
Update Develop from Main
2024-09-12 08:22:17 +02:00
4568e32ffa readme: Data protection group --> officer 2024-09-04 09:26:37 +02:00
ed8dacaa59 Fix fhir2sql db pw generation (#219)
fix postgresql password generation so that the password does not contain problematic characters that mess with the connection string
2024-08-29 09:15:22 +02:00
Jan
3fe781255b feat: Configure beam-connect to trust ds-orchestrator beam proxy (#220) 2024-08-29 09:07:50 +02:00
775cef59d6 Merge pull request #199 from samply/feat/ds-orchestrator
Configure beam-connect to trust ds-orchestrator beam proxy
2024-08-01 10:16:41 +02:00
aca22fb3e3 Merge pull request #144 from samply/documentation/sharing_vm
Recommendation for standalone Bridgehead
2024-08-01 09:52:28 +02:00
33a2505517 Move down, rephrase 2024-08-01 09:51:49 +02:00
83b653e0c3 feat: Configure beam-connect to trust ds-orchestrator beam proxy 2024-07-31 07:18:30 +00:00
bc0f46ecc9 Merge pull request #197 from samply/beam-tag
In ENVIRONMENT=production, use main tag for Samply.Beam.
2024-07-29 15:16:53 +02:00
4ab10ff71d In ENVIRONMENT=production, use main tag for Samply.Beam. 2024-07-29 13:50:30 +02:00
cfa85067f0 initialize develop; add itcc and cce 2024-07-25 12:44:39 +02:00
e4bc34cce9 Amended following Tobias' comments 2024-02-21 10:08:54 +01:00
8fddb809a7 Recommendation for standalone Bridgehead
Requested by Zdenka
2024-01-25 13:49:46 +01:00
62 changed files with 1313 additions and 129 deletions

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@ -0,0 +1,39 @@
import os
import requests
from datetime import datetime, timedelta
# Configuration
GITHUB_TOKEN = os.getenv('GITHUB_TOKEN')
REPO = 'samply/bridgehead'
HEADERS = {'Authorization': f'token {GITHUB_TOKEN}', 'Accept': 'application/vnd.github.v3+json'}
API_URL = f'https://api.github.com/repos/{REPO}/branches'
INACTIVE_DAYS = 365
CUTOFF_DATE = datetime.now() - timedelta(days=INACTIVE_DAYS)
# Fetch all branches
def get_branches():
response = requests.get(API_URL, headers=HEADERS)
response.raise_for_status()
return response.json() if response.status_code == 200 else []
# Rename inactive branches
def rename_branch(old_name, new_name):
rename_url = f'https://api.github.com/repos/{REPO}/branches/{old_name}/rename'
response = requests.post(rename_url, json={'new_name': new_name}, headers=HEADERS)
response.raise_for_status()
print(f"Renamed branch {old_name} to {new_name}" if response.status_code == 201 else f"Failed to rename {old_name}: {response.status_code}")
# Check if the branch is inactive
def is_inactive(commit_url):
last_commit_date = requests.get(commit_url, headers=HEADERS).json()['commit']['committer']['date']
return datetime.strptime(last_commit_date, '%Y-%m-%dT%H:%M:%SZ') < CUTOFF_DATE
# Rename inactive branches
def main():
for branch in get_branches():
if is_inactive(branch['commit']['url']):
#rename_branch(branch['name'], f"archived/{branch['name']}")
print(f"[LOG] Branch '{branch['name']}' is inactive and would be renamed to 'archived/{branch['name']}'")
if __name__ == "__main__":
main()

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@ -0,0 +1,27 @@
name: Cleanup - Rename Inactive Branches
on:
schedule:
- cron: '0 0 * * 0' # Runs every Sunday at midnight
jobs:
archive-stale-branches:
runs-on: ubuntu-latest
steps:
- name: Checkout Repository
uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.x'
- name: Install Libraries
run: pip install requests
- name: Run Script to Rename Inactive Branches
run: |
python .github/scripts/rename_inactive_branches.py
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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@ -34,7 +34,7 @@ This repository is the starting point for any information and tools you will nee
## Requirements
The data protection group at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:
The data protection officer at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:
- [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/)
@ -46,6 +46,8 @@ Hardware requirements strongly depend on the specific use-cases of your network
- 32 GB RAM
- 160GB Hard Drive, SSD recommended
We recommend using a dedicated VM for the Bridgehead, with no other applications running on it. While the Bridgehead can, in principle, run on a shared VM, you might run into surprising problems such as resource conflicts (e.g., two apps using tcp port 443).
### Software
You are strongly recommended to install the Bridgehead under a Linux operating system (but see the section [Non-Linux OS](#non-linux-os)). You will need root (administrator) priveleges on this machine in order to perform the deployment. We recommend the newest Ubuntu LTS server release.
@ -252,6 +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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@ -4,13 +4,14 @@ 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"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
focus-eric:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
container_name: bridgehead-focus-eric
environment:
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
@ -16,7 +16,7 @@ services:
- "blaze"
beam-proxy-eric:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy-eric
environment:
BROKER_URL: ${ERIC_BROKER_URL}

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@ -2,7 +2,7 @@ version: "3.7"
services:
focus-gbn:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
container_name: bridgehead-focus-gbn
environment:
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
@ -16,7 +16,7 @@ services:
- "blaze"
beam-proxy-gbn:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy-gbn
environment:
BROKER_URL: ${GBN_BROKER_URL}

View File

@ -32,6 +32,18 @@ case "$PROJECT" in
bbmri)
#nothing extra to do
;;
cce)
#nothing extra to do
;;
itcc)
#nothing extra to do
;;
kr)
#nothing extra to do
;;
dhki)
#nothing extra to do
;;
minimal)
#nothing extra to do
;;
@ -75,13 +87,16 @@ loadVars() {
case "$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
}

63
cce/docker-compose.yml Normal file
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@ -0,0 +1,63 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-cce-blaze
environment:
BASE_URL: "http://bridgehead-cce-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_cce.rule=PathPrefix(`/cce-localdatamanagement`)"
- "traefik.http.middlewares.cce_b_strip.stripprefix.prefixes=/cce-localdatamanagement"
- "traefik.http.services.blaze_cce.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_cce.middlewares=cce_b_strip,auth"
- "traefik.http.routers.blaze_cce.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-cce-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@ -0,0 +1,33 @@
version: "3.7"
services:
landing:
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
spot:
image: docker.verbis.dkfz.de/ccp-private/central-spot
environment:
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "focus"
PROJECT_METADATA: "cce_supervisors"
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

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@ -0,0 +1,5 @@
#!/bin/bash
if [ -n "$ENABLE_LENS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
fi

20
cce/root.crt.pem Normal file
View File

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

14
cce/vars Normal file
View File

@ -0,0 +1,14 @@
BROKER_ID=test-no-real-data.broker.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done

View File

@ -2,13 +2,14 @@ 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"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
@ -21,7 +22,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -32,6 +33,7 @@ services:
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
depends_on:
@ -39,7 +41,7 @@ services:
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
@ -57,7 +59,6 @@ services:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:

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"

View File

@ -151,7 +151,7 @@ services:
--pass-access-token=false
labels:
- "traefik.enable=true"
- "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
- "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
- "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
- "traefik.http.routers.oauth2_proxy.tls=true"
environment:

View File

@ -33,7 +33,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
echo "$sites" | docker_jq -n --args '[{
"external": "'"$SITE_ID"':443",
"internal": "opal:8443",
"allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
"allowed": input | map("\(.).'"$BROKER_ID"'")
}]' >/tmp/bridgehead/opal-map/local.json
if [ "$USER" == "root" ]; then
chown -R bridgehead:docker /tmp/bridgehead

View File

@ -10,5 +10,6 @@
"essen",
"dktk-datashield-test",
"dktk-test",
"mannheim"
"mannheim",
"central-ds-orchestrator"
]

View File

@ -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
- /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

@ -65,3 +65,8 @@ services:
- "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}"

View File

@ -23,3 +23,7 @@ services:
POSTGRES_DB: "dashboard"
volumes:
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
focus:
environment:
POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"

View File

@ -3,5 +3,6 @@
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="$(echo \"This is a salt string to generate one consistent password for the Dashboard database. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
FOCUS_ENDPOINT_TYPE="blaze-and-sql"
fi

View File

@ -19,10 +19,18 @@ services:
- traefik-forward-auth
labels:
- "traefik.enable=true"
# Router with Authentication
- "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
- "traefik.http.services.id-manager.loadbalancer.server.port=8080"
- "traefik.http.routers.id-manager.tls=true"
- "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
- "traefik.http.routers.id-manager.service=id-manager-service"
# Router without Authentication
- "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
- "traefik.http.routers.id-manager-compatibility.tls=true"
- "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
# Definition of Service
- "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
- "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
patientlist:
image: docker.verbis.dkfz.de/bridgehead/mainzelliste
@ -57,7 +65,7 @@ services:
- "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
traefik-forward-auth:
image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
environment:
- http_proxy=http://forward_proxy:3128
- https_proxy=http://forward_proxy:3128
@ -67,6 +75,7 @@ services:
- OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
- OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
- OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
- OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
- OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
- OAUTH2_PROXY_REVERSE_PROXY=true
@ -92,5 +101,12 @@ 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

@ -3,7 +3,7 @@
function idManagementSetup() {
if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
OVERRIDE+=" -f ./ccp/modules/id-management-compose.yml"
# Auto Generate local Passwords
PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

View File

@ -12,7 +12,6 @@ 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`)"

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

@ -7,7 +7,7 @@ function obds2fhirRestSetup() {
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
PATIENTLIST_URL=" "
fi
OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml"
OVERRIDE+=" -f ./ccp/modules/obds2fhir-rest-compose.yml"
LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
fi
}

66
dhki/docker-compose.yml Normal file
View File

@ -0,0 +1,66 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-dhki-blaze
environment:
BASE_URL: "http://bridgehead-dhki-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_dhki.rule=PathPrefix(`/dhki-localdatamanagement`)"
- "traefik.http.middlewares.dhki_b_strip.stripprefix.prefixes=/dhki-localdatamanagement"
- "traefik.http.services.blaze_dhki.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_dhki.middlewares=dhki_b_strip,auth"
- "traefik.http.routers.blaze_dhki.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-dhki-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
volumes:
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@ -0,0 +1,2 @@
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

20
dhki/root.crt.pem Normal file
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@ -0,0 +1,20 @@
-----BEGIN CERTIFICATE-----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enWgm5M0y+hVZppzB163WmET1efBXwrdyn8j4336NjX352h63JGWCaI2CfZ1qG1p
kf5W9CVXllSFaJe5r994ovgyHvK2ucWwe8l8iMJbQhH79oKi/9uJMCD6aUXnpg1K
nPHW1lsVx6foqYWijdBdtFU2i7LSH2OYo0nb1PgRnY/SABV63JHfJnqW9dZy4f7G
rpsvvrmFrKmEnCZH0n6qveY3Z5bMD94Yx0ebkCTYEqAw3pV65gwxrzBTpEg6dgF0
eG0eKFUS0REJ
-----END CERTIFICATE-----

20
dhki/vars Normal file
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@ -0,0 +1,20 @@
BROKER_ID=broker.hector.dkfz.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
POSTGRES_TAG=15.6-alpine
for module in ccp/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
idManagementSetup
obds2fhirRestSetup

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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
```

63
itcc/docker-compose.yml Normal file
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@ -0,0 +1,63 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-itcc-blaze
environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
- "traefik.http.middlewares.itcc_b_strip.stripprefix.prefixes=/itcc-localdatamanagement"
- "traefik.http.services.blaze_itcc.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_itcc.middlewares=itcc_b_strip,auth"
- "traefik.http.routers.blaze_itcc.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-itcc-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@ -0,0 +1,33 @@
version: "3.7"
services:
landing:
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
spot:
image: docker.verbis.dkfz.de/ccp-private/central-spot
environment:
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "focus"
PROJECT_METADATA: "dktk_supervisors"
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

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@ -0,0 +1,5 @@
#!/bin/bash
if [ -n "$ENABLE_LENS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
fi

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

14
itcc/vars Normal file
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@ -0,0 +1,14 @@
BROKER_ID=test-no-real-data.broker.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done

67
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version: "3.7"
services:
landing:
deploy:
replicas: 0 #deactivate landing page
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
container_name: bridgehead-kr-blaze
environment:
BASE_URL: "http://bridgehead-kr-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_kr.rule=PathPrefix(`/kr-localdatamanagement`)"
- "traefik.http.middlewares.kr_b_strip.stripprefix.prefixes=/kr-localdatamanagement"
- "traefik.http.services.blaze_kr.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_kr.middlewares=kr_b_strip,auth"
- "traefik.http.routers.blaze_kr.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-kr-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@ -0,0 +1,6 @@
# Full Excel Export
curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
--header 'x-api-key: ${EXPORT_API_KEY}'
# QB
curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

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@ -0,0 +1,67 @@
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: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
CROSS_ORIGINS: "https://${HOST}"
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter"
SITE: "${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: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-ccp-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092"
LOG_FHIR_VALIDATION: "false"
HTTP_SERVLET_REQUEST_SCHEME: "https"
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
# a process that can take several hours, because it depends on the exporter.
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/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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@ -0,0 +1,8 @@
#!/bin/bash -e
if [ "$ENABLE_EXPORTER" == true ]; then
log INFO "Exporter setup detected -- will start Exporter service."
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
fi

15
kr/modules/exporter.md Normal file
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@ -0,0 +1,15 @@
# 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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@ -0,0 +1,35 @@
version: "3.7"
services:
landing:
deploy:
replicas: 1 #reactivate if lens is in use
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
spot:
image: docker.verbis.dkfz.de/ccp-private/central-spot
environment:
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "focus"
PROJECT_METADATA: "kr_supervisors"
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

5
kr/modules/lens-setup.sh Normal file
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@ -0,0 +1,5 @@
#!/bin/bash
if [ -n "$ENABLE_LENS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
fi

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@ -0,0 +1,19 @@
version: "3.7"
services:
obds2fhir-rest:
container_name: bridgehead-obds2fhir-rest
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
environment:
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
SALT: ${LOCAL_SALT}
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
labels:
- "traefik.enable=true"
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
- "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
- "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
- "traefik.http.routers.obds2fhir-rest.tls=true"
- "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"

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@ -0,0 +1,13 @@
#!/bin/bash
function obds2fhirRestSetup() {
if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
PATIENTLIST_URL=" "
fi
OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml"
LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
fi
}

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@ -0,0 +1,81 @@
version: "3.7"
services:
teiler-orchestrator:
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
- "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
- "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
teiler-backend:
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
- "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_ccp.tls=true"
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
CENTRAX_URL: "${CENTRAXX_URL}"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
secrets:
- ccp.conf
secrets:
ccp.conf:
file: /etc/bridgehead/ccp.conf

View File

@ -0,0 +1,9 @@
#!/bin/bash -e
if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
TEILER_DEFAULT_LANGUAGE=DE
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
add_public_oidc_redirect_url "/ccp-teiler/*"
fi

19
kr/modules/teiler.md Normal file
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@ -0,0 +1,19 @@
# Teiler
This module orchestrates the different microfrontends of the bridgehead as a single page application.
## Teiler Orchestrator
Single SPA component that consists on the root HTML site of the single page application and a javascript code that
gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly.
The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
## Teiler Dashboard
It consists on the main dashboard and a set of embedded services.
### Login
user and password in ccp.local.conf
## Teiler Backend
In this component, the microfrontends are configured.

20
kr/root.crt.pem Normal file
View File

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

16
kr/vars Normal file
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@ -0,0 +1,16 @@
BROKER_ID=test-no-real-data.broker.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
obds2fhirRestSetup

View File

@ -54,7 +54,7 @@ checkOwner(){
printUsage() {
echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri"
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
}
checkRequirements() {
@ -171,8 +171,10 @@ optimizeBlazeMemoryUsage() {
if [ $available_system_memory_chunks -eq 0 ]; then
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
export BLAZE_RESOURCE_CACHE_CAP=128000;
export BLAZE_CQL_CACHE_CAP=32;
else
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
fi
fi
}

View File

@ -52,6 +52,21 @@ case "$PROJECT" in
bbmri)
site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
;;
cce)
site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
;;
itcc)
site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
;;
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
kr)
site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"
;;
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
minimal)
site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
;;

View File

@ -3,14 +3,16 @@
source lib/functions.sh
detectCompose
CONFIG_DIR="/etc/bridgehead/"
COMPONENT_DIR="/srv/docker/bridgehead/"
if ! id "bridgehead" &>/dev/null; then
log ERROR "User bridgehead does not exist. Please run bridgehead install $PROJECT"
exit 1
fi
checkOwner /srv/docker/bridgehead bridgehead || exit 1
checkOwner /etc/bridgehead bridgehead || exit 1
checkOwner "${CONFIG_DIR}" bridgehead || exit 1
checkOwner "${COMPONENT_DIR}" bridgehead || exit 1
## Check if user is a su
log INFO "Checking if all prerequisites are met ..."
@ -32,31 +34,31 @@ fi
log INFO "Checking configuration ..."
## Download submodule
if [ ! -d "/etc/bridgehead/" ]; then
fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
if [ ! -d "${CONFIG_DIR}" ]; then
fail_and_report 1 "Please set up the config folder at ${CONFIG_DIR}. Instruction are in the readme."
fi
# TODO: Check all required variables here in a generic loop
#check if project env is present
if [ -d "/etc/bridgehead/${PROJECT}.conf" ]; then
fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under /etc/bridgehead-config/${PROJECT}.conf."
if [ -d "${CONFIG_DIR}${PROJECT}.conf" ]; then
fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under ${CONFIG_DIR}${PROJECT}.conf."
fi
# TODO: Make sure you're in the right directory, or, even better, be independent from the working directory.
log INFO "Checking ssl cert for accessing bridgehead via https"
if [ ! -d "/etc/bridgehead/traefik-tls" ]; then
if [ ! -d "${CONFIG_DIR}traefik-tls" ]; then
log WARN "TLS certs for accessing bridgehead via https missing, we'll now create a self-signed one. Please consider getting an officially signed one (e.g. via Let's Encrypt ...) and put into /etc/bridgehead/traefik-tls"
mkdir -p /etc/bridgehead/traefik-tls
fi
if [ ! -e "/etc/bridgehead/traefik-tls/fullchain.pem" ]; then
if [ ! -e "${CONFIG_DIR}traefik-tls/fullchain.pem" ]; then
openssl req -x509 -newkey rsa:4096 -nodes -keyout /etc/bridgehead/traefik-tls/privkey.pem -out /etc/bridgehead/traefik-tls/fullchain.pem -days 3650 -subj "/CN=$HOST"
fi
if [ -e /etc/bridgehead/vault.conf ]; then
if [ -e "${CONFIG_DIR}"vault.conf ]; then
if [ "$(stat -c "%a %U" /etc/bridgehead/vault.conf)" != "600 bridgehead" ]; then
fail_and_report 1 "/etc/bridgehead/vault.conf has wrong owner/permissions. To correct this issue, run chmod 600 /etc/bridgehead/vault.conf && chown bridgehead /etc/bridgehead/vault.conf."
fi
@ -64,7 +66,7 @@ fi
log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
source /etc/bridgehead/${PROJECT}.conf
source "${CONFIG_DIR}${PROJECT}".conf
source ${PROJECT}/vars
if [ "${PROJECT}" != "minimal" ]; then
@ -92,10 +94,10 @@ if [ "${PROJECT}" != "minimal" ]; then
fi
fi
checkPrivKey() {
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
if [ -e "${CONFIG_DIR}pki/${SITE_ID}.priv.pem" ]; then
log INFO "Success - private key found."
else
log ERROR "Unable to find private key at /etc/bridgehead/pki/${SITE_ID}.priv.pem. To fix, please run\n bridgehead enroll ${PROJECT}\nand follow the instructions."
log ERROR "Unable to find private key at ${CONFIG_DIR}pki/${SITE_ID}.priv.pem. To fix, please run\n bridgehead enroll ${PROJECT}\nand follow the instructions."
return 1
fi
return 0
@ -107,6 +109,11 @@ else
checkPrivKey || exit 1
fi
for dir in "${CONFIG_DIR}" "${COMPONENT_DIR}"; do
log INFO "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
hc_send log "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
done
log INFO "Success - all prerequisites are met!"
hc_send log "Success - all prerequisites are met!"

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

@ -10,13 +10,13 @@ services:
- --providers.docker=true
- --providers.docker.exposedbydefault=false
- --providers.file.directory=/configuration/
- --api.dashboard=true
- --api.dashboard=false
- --accesslog=true
- --entrypoints.web.http.redirections.entrypoint.to=websecure
- --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

@ -2,7 +2,7 @@ version: "3.7"
services:
dnpm-beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-dnpm-beam-proxy
environment:
BROKER_URL: ${DNPM_BROKER_URL}
@ -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`)"