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5 Commits
feature/qr
...
qr_bbmri
Author | SHA1 | Date | |
---|---|---|---|
502eef0cc8 | |||
c4b7620fd6 | |||
6a21a5b641 | |||
c04ffc5f33 | |||
b1bdf48e55 |
39
.github/scripts/rename_inactive_branches.py
vendored
39
.github/scripts/rename_inactive_branches.py
vendored
@ -1,39 +0,0 @@
|
||||
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()
|
27
.github/workflows/rename-inactive-branches.yml
vendored
27
.github/workflows/rename-inactive-branches.yml
vendored
@ -1,27 +0,0 @@
|
||||
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 }}
|
21
README.md
21
README.md
@ -34,7 +34,7 @@ This repository is the starting point for any information and tools you will nee
|
||||
|
||||
## Requirements
|
||||
|
||||
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:
|
||||
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:
|
||||
|
||||
- [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/)
|
||||
|
||||
@ -46,8 +46,6 @@ 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.
|
||||
@ -202,7 +200,7 @@ sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
|
||||
After starting the Bridgehead, you can watch the initialization process with the following command:
|
||||
|
||||
```shell
|
||||
/srv/docker/bridgehead/bridgehead logs <project> -f
|
||||
journalctl -u bridgehead@bbmri -f
|
||||
```
|
||||
|
||||
if this exits with something similar to the following:
|
||||
@ -222,9 +220,8 @@ docker ps
|
||||
There should be 6 - 10 Docker proceses. If there are fewer, then you know that something has gone wrong. To see what is going on, run:
|
||||
|
||||
```shell
|
||||
/srv/docker/bridgehead/bridgehead logs <Project> -f
|
||||
journalctl -u bridgehead@bbmri -f
|
||||
```
|
||||
This translates to a journalctl command so all the regular journalctl flags can be used.
|
||||
|
||||
Once the Bridgehead has passed these checks, take a look at the landing page:
|
||||
|
||||
@ -238,7 +235,7 @@ You can either do this in a browser or with curl. If you visit the URL in the br
|
||||
curl -k https://localhost
|
||||
```
|
||||
|
||||
Should the landing page not show anything, you can inspect the logs of the containers to determine what is going wrong. To do this you can use `./bridgehead docker-logs <Project> -f` to follow the logs of the container. This transaltes to a docker compose logs command meaning all the ususal docker logs flags work.
|
||||
If you get errors when you do this, you need to use ```docker logs``` to examine your landing page container in order to determine what is going wrong.
|
||||
|
||||
If you have chosen to take part in our monitoring program (by setting the ```MONITOR_APIKEY``` variable in the configuration), you will be informed by email when problems are detected in your Bridgehead.
|
||||
|
||||
@ -301,19 +298,19 @@ Once you have added your biobank to the Directory you got persistent identifier
|
||||
|
||||
The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature.
|
||||
|
||||
You should talk with your local data protection group regarding the information that is published by Directory sync.
|
||||
|
||||
Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
|
||||
|
||||
To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
|
||||
|
||||
```
|
||||
DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
|
||||
DS_DIRECTORY_USER_NAME=your_directory_username
|
||||
DS_DIRECTORY_USER_PASS=your_directory_password
|
||||
DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
|
||||
DS_TIMER_CRON="0 22 * * *"
|
||||
```
|
||||
Please contact your National Node to obtain this information.
|
||||
You must contact the Directory team for your national node to find the URL, and to register as a user.
|
||||
|
||||
Optionally, you **may** change when you want Directory sync to run by specifying a [cron](https://crontab.guru) expression, e.g. `DS_TIMER_CRON="0 22 * * *"` for 10 pm every evening.
|
||||
Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.
|
||||
|
||||
Once you edited the gitlab config, the bridgehead will autoupdate the config with the values and will sync the data.
|
||||
|
||||
|
@ -1,17 +1,16 @@
|
||||
version: "3.7"
|
||||
|
||||
# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see vars.
|
||||
# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see ccp vars.
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:latest
|
||||
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}
|
||||
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
volumes:
|
||||
- "blaze-data:/app/data"
|
||||
|
@ -4,13 +4,7 @@ services:
|
||||
directory_sync_service:
|
||||
image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
|
||||
environment:
|
||||
DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
|
||||
DS_DIRECTORY_URL: ${DS_DIRECTORY_URL}
|
||||
DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
|
||||
DS_DIRECTORY_USER_PASS: ${DS_DIRECTORY_USER_PASS}
|
||||
DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
|
||||
DS_DIRECTORY_ALLOW_STAR_MODEL: ${DS_DIRECTORY_ALLOW_STAR_MODEL:-true}
|
||||
DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK}
|
||||
DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID}
|
||||
DS_DIRECTORY_COUNTRY: ${DS_DIRECTORY_COUNTRY}
|
||||
depends_on:
|
||||
- "blaze"
|
||||
DS_DIRECTORY_PASS_CODE: ${DS_DIRECTORY_PASS_CODE}
|
||||
DS_TIMER_CRON: ${DS_TIMER_CRON}
|
||||
|
@ -16,7 +16,7 @@ services:
|
||||
- "blaze"
|
||||
|
||||
beam-proxy-eric:
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
|
||||
container_name: bridgehead-beam-proxy-eric
|
||||
environment:
|
||||
BROKER_URL: ${ERIC_BROKER_URL}
|
||||
|
@ -16,7 +16,7 @@ services:
|
||||
- "blaze"
|
||||
|
||||
beam-proxy-gbn:
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
|
||||
container_name: bridgehead-beam-proxy-gbn
|
||||
environment:
|
||||
BROKER_URL: ${GBN_BROKER_URL}
|
||||
|
81
bbmri/modules/teiler-compose.yml
Normal file
81
bbmri/modules/teiler-compose.yml
Normal file
@ -0,0 +1,81 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
|
||||
teiler-orchestrator:
|
||||
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
|
||||
container_name: bridgehead-teiler-orchestrator
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
|
||||
- "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
|
||||
- "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
|
||||
- "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
|
||||
- "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
|
||||
environment:
|
||||
TEILER_BACKEND_URL: "https://${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: "bbmri-qb"
|
||||
EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"
|
||||
|
||||
|
||||
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
|
33
bbmri/vars
33
bbmri/vars
@ -1,37 +1,30 @@
|
||||
BROKER_ID=broker-test.bbmri-test.samply.de
|
||||
BROKER_URL=https://${BROKER_ID}
|
||||
PROXY_ID=${SITE_ID}.${BROKER_ID}
|
||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||
|
||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
||||
|
||||
OIDC_USER_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})"
|
||||
OIDC_ADMIN_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})_Verwalter"
|
||||
OIDC_PUBLIC_CLIENT_ID="BBMRI_${SITE_ID}-public"
|
||||
# Use "test-realm-01" for testing
|
||||
OIDC_REALM="${OIDC_REALM:-test-realm-01}"
|
||||
OIDC_URL="https://login.verbis.dkfz.de"
|
||||
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
|
||||
OIDC_GROUP_CLAIM="groups"
|
||||
|
||||
POSTGRES_TAG=15.6-alpine
|
||||
|
||||
# Makes sense for all European Biobanks
|
||||
: ${ENABLE_ERIC:=true}
|
||||
|
||||
# Makes only sense for German Biobanks
|
||||
: ${ENABLE_GBN:=false}
|
||||
|
||||
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
|
||||
FOCUS_RETRY_COUNT=32
|
||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||
|
||||
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
|
||||
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
|
||||
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
|
||||
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
|
||||
# Use "test-realm-01" for testing
|
||||
OIDC_REALM="${OIDC_REALM:-master}"
|
||||
OIDC_URL="https://login.verbis.dkfz.de"
|
||||
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
|
||||
OIDC_GROUP_CLAIM="groups"
|
||||
|
||||
POSTGRES_TAG=15.6-alpine
|
||||
|
||||
for module in $PROJECT/modules/*.sh
|
||||
do
|
||||
log DEBUG "sourcing $module"
|
||||
source $module
|
||||
done
|
||||
|
||||
|
||||
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
|
||||
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
|
||||
|
||||
|
24
bridgehead
24
bridgehead
@ -32,18 +32,6 @@ 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
|
||||
;;
|
||||
@ -82,21 +70,17 @@ loadVars() {
|
||||
|
||||
# Set some project-independent default values
|
||||
: ${ENVIRONMENT:=production}
|
||||
export ENVIRONMENT
|
||||
|
||||
case "$ENVIRONMENT" in
|
||||
"production")
|
||||
export FOCUS_TAG=main
|
||||
export BEAM_TAG=main
|
||||
;;
|
||||
"test")
|
||||
export FOCUS_TAG=develop
|
||||
export BEAM_TAG=develop
|
||||
;;
|
||||
*)
|
||||
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
|
||||
export FOCUS_TAG=main
|
||||
export BEAM_TAG=main
|
||||
;;
|
||||
esac
|
||||
}
|
||||
@ -106,8 +90,7 @@ case "$ACTION" in
|
||||
loadVars
|
||||
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
|
||||
checkRequirements
|
||||
# NOTE: for testing only, we will need to properly setup secret sync if we want to use this code
|
||||
# sync_secrets
|
||||
sync_secrets
|
||||
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
|
||||
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
|
||||
;;
|
||||
@ -124,11 +107,6 @@ case "$ACTION" in
|
||||
exit $?
|
||||
;;
|
||||
logs)
|
||||
loadVars
|
||||
shift 2
|
||||
exec journalctl -u bridgehead@$PROJECT -u bridgehead-update@$PROJECT -a $@
|
||||
;;
|
||||
docker-logs)
|
||||
loadVars
|
||||
shift 2
|
||||
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@
|
||||
|
@ -1,63 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-cce-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-cce-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${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
|
@ -1,33 +0,0 @@
|
||||
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(`${HOST}`) && PathPrefix(`/backend`)"
|
||||
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
|
||||
- "traefik.http.routers.spot.tls=true"
|
||||
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
|
@ -1,5 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "$ENABLE_LENS" ];then
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
|
||||
fi
|
@ -1,20 +0,0 @@
|
||||
-----BEGIN CERTIFICATE-----
|
||||
MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
|
||||
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
|
||||
MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
|
||||
AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
|
||||
TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
|
||||
OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
|
||||
XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
|
||||
pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
|
||||
K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
|
||||
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
|
||||
poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
|
||||
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
|
||||
AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
|
||||
fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
|
||||
3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
|
||||
n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
|
||||
7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
|
||||
Rtup0MTxSJtN
|
||||
-----END CERTIFICATE-----
|
14
cce/vars
14
cce/vars
@ -1,14 +0,0 @@
|
||||
BROKER_ID=test-no-real-data.broker.samply.de
|
||||
BROKER_URL=https://${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 $module
|
||||
done
|
@ -2,14 +2,13 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:latest
|
||||
container_name: bridgehead-ccp-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
||||
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
||||
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
|
||||
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
volumes:
|
||||
- "blaze-data:/app/data"
|
||||
@ -22,7 +21,7 @@ services:
|
||||
- "traefik.http.routers.blaze_ccp.tls=true"
|
||||
|
||||
focus:
|
||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
|
||||
container_name: bridgehead-focus
|
||||
environment:
|
||||
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
|
||||
@ -32,15 +31,12 @@ services:
|
||||
BEAM_PROXY_URL: http://beam-proxy:8081
|
||||
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
||||
EPSILON: 0.28
|
||||
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
||||
beam-proxy:
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
|
||||
container_name: bridgehead-beam-proxy
|
||||
environment:
|
||||
BROKER_URL: ${BROKER_URL}
|
||||
|
18
ccp/modules/adt2fhir-rest-compose.yml
Normal file
18
ccp/modules/adt2fhir-rest-compose.yml
Normal file
@ -0,0 +1,18 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
adt2fhir-rest:
|
||||
container_name: bridgehead-adt2fhir-rest
|
||||
image: docker.verbis.dkfz.de/ccp/adt2fhir-rest:main
|
||||
environment:
|
||||
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
|
||||
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||
SALT: ${LOCAL_SALT}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.adt2fhir-rest.rule=PathPrefix(`/adt2fhir-rest`)"
|
||||
- "traefik.http.middlewares.adt2fhir-rest_strip.stripprefix.prefixes=/adt2fhir-rest"
|
||||
- "traefik.http.services.adt2fhir-rest.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.adt2fhir-rest.tls=true"
|
||||
- "traefik.http.routers.adt2fhir-rest.middlewares=adt2fhir-rest_strip,auth"
|
13
ccp/modules/adt2fhir-rest-setup.sh
Normal file
13
ccp/modules/adt2fhir-rest-setup.sh
Normal file
@ -0,0 +1,13 @@
|
||||
#!/bin/bash
|
||||
|
||||
function adt2fhirRestSetup() {
|
||||
if [ -n "$ENABLE_ADT2FHIR_REST" ]; then
|
||||
log INFO "ADT2FHIR-REST setup detected -- will start adt2fhir-rest API."
|
||||
if [ ! -n "$IDMANAGER_LOCAL_PATIENTLIST_APIKEY" ]; then
|
||||
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
|
||||
exit 1;
|
||||
fi
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/adt2fhir-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
|
||||
}
|
@ -1,32 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
blaze-secondary:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-ccp-blaze-secondary
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
||||
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-secondary-data:/app/data"
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.blaze-secondary_ccp.rule=PathPrefix(`/ccp-localdatamanagement-secondary`)"
|
||||
- "traefik.http.middlewares.ccp_b-secondary_strip.stripprefix.prefixes=/ccp-localdatamanagement-secondary"
|
||||
- "traefik.http.services.blaze-secondary_ccp.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.blaze-secondary_ccp.middlewares=ccp_b-secondary_strip,auth"
|
||||
- "traefik.http.routers.blaze-secondary_ccp.tls=true"
|
||||
|
||||
obds2fhir-rest:
|
||||
environment:
|
||||
STORE_PATH: ${STORE_PATH:-http://blaze:8080/fhir}
|
||||
|
||||
exporter:
|
||||
environment:
|
||||
BLAZE_HOST: "blaze-secondary"
|
||||
|
||||
volumes:
|
||||
blaze-secondary-data:
|
@ -1,11 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
function blazeSecondarySetup() {
|
||||
if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
|
||||
log INFO "Secondary Blaze setup detected -- will start second blaze."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml"
|
||||
#make oBDS2FHIR ignore ID-Management and replace target Blaze
|
||||
PATIENTLIST_URL=" "
|
||||
STORE_PATH="http://blaze-secondary:8080/fhir"
|
||||
fi
|
||||
}
|
@ -151,7 +151,7 @@ services:
|
||||
--pass-access-token=false
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
|
||||
- "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`, `/oauth2/callback`)"
|
||||
- "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
|
||||
- "traefik.http.routers.oauth2_proxy.tls=true"
|
||||
environment:
|
||||
|
@ -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("\(.).'"$BROKER_ID"'")
|
||||
"allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
|
||||
}]' >/tmp/bridgehead/opal-map/local.json
|
||||
if [ "$USER" == "root" ]; then
|
||||
chown -R bridgehead:docker /tmp/bridgehead
|
||||
|
@ -10,6 +10,5 @@
|
||||
"essen",
|
||||
"dktk-datashield-test",
|
||||
"dktk-test",
|
||||
"mannheim",
|
||||
"central-ds-orchestrator"
|
||||
"mannheim"
|
||||
]
|
||||
|
@ -1,5 +1,5 @@
|
||||
# DataSHIELD
|
||||
This module constitutes the infrastructure to run DataSHIELD within the bridgehead.
|
||||
This module constitutes the infrastructure to run DataSHIELD within the bridghead.
|
||||
For more information about DataSHIELD, please visit https://www.datashield.org/
|
||||
|
||||
## R-Studio
|
||||
|
@ -3,7 +3,7 @@ version: "3.7"
|
||||
services:
|
||||
exporter:
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
|
||||
container_name: bridgehead-${PROJECT}-exporter
|
||||
container_name: bridgehead-ccp-exporter
|
||||
environment:
|
||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||
LOG_LEVEL: "INFO"
|
||||
@ -12,41 +12,39 @@ services:
|
||||
EXPORTER_DB_USER: "exporter"
|
||||
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
||||
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
|
||||
HTTP_RELATIVE_PATH: "/${PROJECT}-exporter"
|
||||
HTTP_RELATIVE_PATH: "/ccp-exporter"
|
||||
SITE: "${SITE_ID}"
|
||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
||||
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.exporter_${PROJECT}.rule=PathPrefix(`/${PROJECT}-exporter`)"
|
||||
- "traefik.http.services.exporter_${PROJECT}.loadbalancer.server.port=8092"
|
||||
- "traefik.http.routers.exporter_${PROJECT}.tls=true"
|
||||
- "traefik.http.middlewares.exporter_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-exporter"
|
||||
- "traefik.http.routers.exporter_${PROJECT}.middlewares=exporter_${PROJECT}_strip"
|
||||
- "traefik.http.routers.connector.middlewares=connector_strip,auth-qr"
|
||||
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
|
||||
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
|
||||
- "traefik.http.routers.exporter_ccp.tls=true"
|
||||
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
|
||||
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
|
||||
volumes:
|
||||
- "/var/cache/bridgehead/${PROJECT}/exporter-files:/app/exporter-files/output"
|
||||
|
||||
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
|
||||
|
||||
exporter-db:
|
||||
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
||||
container_name: bridgehead-${PROJECT}-exporter-db
|
||||
container_name: bridgehead-ccp-exporter-db
|
||||
environment:
|
||||
POSTGRES_USER: "exporter"
|
||||
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
||||
POSTGRES_DB: "exporter"
|
||||
volumes:
|
||||
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
|
||||
- "/var/cache/bridgehead/${PROJECT}/exporter-db:/var/lib/postgresql/data"
|
||||
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
|
||||
|
||||
reporter:
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
|
||||
container_name: bridgehead-${PROJECT}-reporter
|
||||
container_name: bridgehead-ccp-reporter
|
||||
environment:
|
||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||
LOG_LEVEL: "INFO"
|
||||
CROSS_ORIGINS: "https://${HOST}"
|
||||
HTTP_RELATIVE_PATH: "/${PROJECT}-reporter"
|
||||
HTTP_RELATIVE_PATH: "/ccp-reporter"
|
||||
SITE: "${SITE_ID}"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
||||
EXPORTER_URL: "http://exporter:8092"
|
||||
@ -59,15 +57,11 @@ services:
|
||||
# There is a risk that the bridgehead restarts, losing the already created export.
|
||||
|
||||
volumes:
|
||||
- "/var/cache/bridgehead/${PROJECT}/reporter-files:/app/reports"
|
||||
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.reporter_${PROJECT}.rule=PathPrefix(`/${PROJECT}-reporter`)"
|
||||
- "traefik.http.services.reporter_${PROJECT}.loadbalancer.server.port=8095"
|
||||
- "traefik.http.routers.reporter_${PROJECT}.tls=true"
|
||||
- "traefik.http.middlewares.reporter_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-reporter"
|
||||
- "traefik.http.routers.reporter_${PROJECT}.middlewares=reporter_${PROJECT}_strip"
|
||||
|
||||
traefik:
|
||||
labels:
|
||||
- "traefik.http.middlewares.auth-qr.basicauth.users=${QR_AUTH}"
|
||||
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
|
||||
- "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
|
||||
- "traefik.http.routers.reporter_ccp.tls=true"
|
||||
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
|
||||
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
|
@ -1,25 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
fhir2sql:
|
||||
depends_on:
|
||||
- "dashboard-db"
|
||||
- "blaze"
|
||||
image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
|
||||
container_name: bridgehead-ccp-dashboard-fhir2sql
|
||||
environment:
|
||||
BLAZE_BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
||||
PG_HOST: "dashboard-db"
|
||||
PG_USERNAME: "dashboard"
|
||||
PG_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
|
||||
PG_DBNAME: "dashboard"
|
||||
|
||||
dashboard-db:
|
||||
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
||||
container_name: bridgehead-ccp-dashboard-db
|
||||
environment:
|
||||
POSTGRES_USER: "dashboard"
|
||||
POSTGRES_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
|
||||
POSTGRES_DB: "dashboard"
|
||||
volumes:
|
||||
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
|
@ -1,7 +0,0 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
if [ "$ENABLE_FHIR2SQL" == true ]; then
|
||||
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
|
||||
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
|
||||
fi
|
@ -1,36 +0,0 @@
|
||||
# fhir2sql
|
||||
fhir2sql connects to Blaze, retrieves data, and syncs it with a PostgreSQL database. The application is designed to run continuously, syncing data at regular intervals.
|
||||
The Dashboard module is a optional component of the Bridgehead CCP setup. When enabled, it starts two Docker services: **fhir2sql** and **dashboard-db**. Data held in PostgreSQL is only stored temporarily and Blaze is considered to be the 'leading system' or 'source of truth'.
|
||||
|
||||
## Services
|
||||
### fhir2sql
|
||||
* Image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
|
||||
* Container name: bridgehead-ccp-dashboard-fhir2sql
|
||||
* Depends on: dashboard-db
|
||||
* Environment variables:
|
||||
- BLAZE_BASE_URL: The base URL of the Blaze FHIR server (set to http://blaze:8080/fhir/)
|
||||
- PG_HOST: The hostname of the PostgreSQL database (set to dashboard-db)
|
||||
- PG_USERNAME: The username for the PostgreSQL database (set to dashboard)
|
||||
- PG_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
|
||||
- PG_DBNAME: The name of the PostgreSQL database (set to dashboard)
|
||||
|
||||
### dashboard-db
|
||||
|
||||
* Image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
||||
* Container name: bridgehead-ccp-dashboard-db
|
||||
* Environment variables:
|
||||
- POSTGRES_USER: The username for the PostgreSQL database (set to dashboard)
|
||||
- POSTGRES_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
|
||||
- POSTGRES_DB: The name of the PostgreSQL database (set to dashboard)
|
||||
* Volumes:
|
||||
- /var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data
|
||||
|
||||
The volume used by dashboard-db can be removed safely and should be restored to a working order by re-importing data from Blaze.
|
||||
|
||||
### Environment Variables
|
||||
* DASHBOARD_DB_PASSWORD: A generated password for the PostgreSQL database, created using a salt string and the SHA1 hash function.
|
||||
* POSTGRES_TAG: The tag of the PostgreSQL image to use (not set in this module, but required by the dashboard-db service).
|
||||
|
||||
|
||||
### Setup
|
||||
To enable the Dashboard module, set the ENABLE_FHIR2SQL environment variable to true. The dashboard-setup.sh script will then start the fhir2sql and dashboard-db services, using the environment variables and volumes defined above.
|
@ -14,23 +14,15 @@ services:
|
||||
MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
|
||||
MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
|
||||
MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
|
||||
MAGICPL_OIDC_CLIENT_ID: ${IDMANAGER_AUTH_CLIENT_ID}
|
||||
MAGICPL_OIDC_CLIENT_SECRET: ${IDMANAGER_AUTH_CLIENT_SECRET}
|
||||
depends_on:
|
||||
- patientlist
|
||||
- traefik-forward-auth
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
# Router with Authentication
|
||||
- "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
|
||||
- "traefik.http.services.id-manager.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.id-manager.tls=true"
|
||||
- "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
|
||||
- "traefik.http.routers.id-manager.service=id-manager-service"
|
||||
# Router without Authentication
|
||||
- "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
|
||||
- "traefik.http.routers.id-manager-compatibility.tls=true"
|
||||
- "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
|
||||
# Definition of Service
|
||||
- "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
|
||||
- "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
|
||||
|
||||
patientlist:
|
||||
image: docker.verbis.dkfz.de/bridgehead/mainzelliste
|
||||
@ -64,42 +56,5 @@ services:
|
||||
# NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
|
||||
- "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
|
||||
|
||||
traefik-forward-auth:
|
||||
image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
|
||||
environment:
|
||||
- http_proxy=http://forward_proxy:3128
|
||||
- https_proxy=http://forward_proxy:3128
|
||||
- OAUTH2_PROXY_PROVIDER=oidc
|
||||
- OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
|
||||
- OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master
|
||||
- OAUTH2_PROXY_CLIENT_ID=bridgehead-${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=.${HOST}
|
||||
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
|
||||
- OAUTH2_PROXY_REVERSE_PROXY=true
|
||||
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
|
||||
- OAUTH2_PROXY_UPSTREAMS=static://202
|
||||
- OAUTH2_PROXY_EMAIL_DOMAINS=*
|
||||
- OAUTH2_PROXY_SCOPE=openid profile email
|
||||
# Pass Authorization Header and some user information to backend services
|
||||
- OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
|
||||
- OAUTH2_PROXY_SET_XAUTHREQUEST=true
|
||||
# Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
|
||||
- OAUTH2_PROXY_COOKIE_REFRESH=60s
|
||||
- OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
|
||||
- OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4180"
|
||||
- "traefik.http.routers.traefik-forward-auth.rule=Host(`${HOST}`) && PathPrefix(`/oauth2-idm`)"
|
||||
- "traefik.http.routers.traefik-forward-auth.tls=true"
|
||||
- "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.address=http://traefik-forward-auth:4180"
|
||||
- "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.authResponseHeaders=Authorization"
|
||||
depends_on:
|
||||
forward_proxy:
|
||||
condition: service_healthy
|
||||
|
||||
volumes:
|
||||
patientlist-db-data:
|
||||
|
@ -3,7 +3,7 @@
|
||||
function idManagementSetup() {
|
||||
if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
|
||||
log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
|
||||
OVERRIDE+=" -f ./ccp/modules/id-management-compose.yml"
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
|
||||
|
||||
# Auto Generate local Passwords
|
||||
PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
|
@ -5,6 +5,7 @@ function mtbaSetup() {
|
||||
log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
|
||||
if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
|
||||
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
|
||||
exit 1;
|
||||
fi
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
|
||||
add_private_oidc_redirect_url "/mtba/*"
|
||||
|
@ -1,20 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
obds2fhir-rest:
|
||||
container_name: bridgehead-obds2fhir-rest
|
||||
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
|
||||
environment:
|
||||
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
|
||||
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||
SALT: ${LOCAL_SALT}
|
||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||
- "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
|
||||
- "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.obds2fhir-rest.tls=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"
|
@ -1,13 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
function obds2fhirRestSetup() {
|
||||
if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
|
||||
log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
|
||||
if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
|
||||
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
|
||||
PATIENTLIST_URL=" "
|
||||
fi
|
||||
OVERRIDE+=" -f ./ccp/modules/obds2fhir-rest-compose.yml"
|
||||
LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
fi
|
||||
}
|
@ -5,5 +5,5 @@ if [ "$ENABLE_TEILER" == true ];then
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
|
||||
TEILER_DEFAULT_LANGUAGE=DE
|
||||
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
|
||||
add_public_oidc_redirect_url "/${PROJECT}-teiler/*"
|
||||
add_public_oidc_redirect_url "/ccp-teiler/*"
|
||||
fi
|
@ -1,2 +0,0 @@
|
||||
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
|
||||
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
|
6
ccp/vars
6
ccp/vars
@ -2,10 +2,9 @@ BROKER_ID=broker.ccp-it.dktk.dkfz.de
|
||||
BROKER_URL=https://${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}
|
||||
FOCUS_RETRY_COUNT=32
|
||||
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
|
||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||
PLATFORM=ccp
|
||||
|
||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
||||
|
||||
@ -29,5 +28,4 @@ done
|
||||
|
||||
idManagementSetup
|
||||
mtbaSetup
|
||||
obds2fhirRestSetup
|
||||
blazeSecondarySetup
|
||||
adt2fhirRestSetup
|
||||
|
@ -1,66 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
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
|
@ -1,2 +0,0 @@
|
||||
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
|
||||
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
|
@ -1,20 +0,0 @@
|
||||
-----BEGIN CERTIFICATE-----
|
||||
MIIDNTCCAh2gAwIBAgIUSWUPebUMNfJvPKMjdgX+WiH+OXgwDQYJKoZIhvcNAQEL
|
||||
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTA1MDg1NTM4WhcNMzQw
|
||||
MTAyMDg1NjA4WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
|
||||
AQEBBQADggEPADCCAQoCggEBAL/nvo9Bn1/6Z/K4BKoLM6/mVziM4cmXTVx4npVz
|
||||
pnptwPPFU4rz47akRZ6ZMD5MO0bsyvaxG1nwVrW3aAGC42JIGTdZHKwMKrd35sxw
|
||||
k3YlGJagGUs+bKHUCL55OcSmyDWlh/UhA8+eeJWjOt9u0nYXv+vi+N4JSHA0oC9D
|
||||
bTF1v+7blrTQagf7PTPSF3pe22iXOjJYdOkZMWoMoNAjn6F958fkLNLY3csOZwvP
|
||||
/3eyNNawyAEPWeIm33Zk630NS8YHggz6WCqwXvuaKb6910mRP8jgauaYsqgsOyDt
|
||||
pbWuvk//aZWdGeN9RNsAA8eGppygiwm/m9eRC6I0shDwv6ECAwEAAaN7MHkwDgYD
|
||||
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFFn/dbW1J3ry
|
||||
7TBzbKo3H4vJr2MiMB8GA1UdIwQYMBaAFFn/dbW1J3ry7TBzbKo3H4vJr2MiMBYG
|
||||
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCa2V8B8aad
|
||||
XNDS1EUIi9oMdvGvkolcdFwx9fI++qu9xSIaZs5GETHck3oYKZF0CFP5ESnKDn5w
|
||||
enWgm5M0y+hVZppzB163WmET1efBXwrdyn8j4336NjX352h63JGWCaI2CfZ1qG1p
|
||||
kf5W9CVXllSFaJe5r994ovgyHvK2ucWwe8l8iMJbQhH79oKi/9uJMCD6aUXnpg1K
|
||||
nPHW1lsVx6foqYWijdBdtFU2i7LSH2OYo0nb1PgRnY/SABV63JHfJnqW9dZy4f7G
|
||||
rpsvvrmFrKmEnCZH0n6qveY3Z5bMD94Yx0ebkCTYEqAw3pV65gwxrzBTpEg6dgF0
|
||||
eG0eKFUS0REJ
|
||||
-----END CERTIFICATE-----
|
20
dhki/vars
20
dhki/vars
@ -1,20 +0,0 @@
|
||||
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 $module
|
||||
done
|
||||
|
||||
idManagementSetup
|
||||
obds2fhirRestSetup
|
@ -1,63 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-itcc-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${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
|
@ -1,33 +0,0 @@
|
||||
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(`${HOST}`) && PathPrefix(`/backend`)"
|
||||
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
|
||||
- "traefik.http.routers.spot.tls=true"
|
||||
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
|
@ -1,5 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "$ENABLE_LENS" ];then
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
|
||||
fi
|
@ -1,20 +0,0 @@
|
||||
-----BEGIN CERTIFICATE-----
|
||||
MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
|
||||
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
|
||||
MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
|
||||
AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
|
||||
TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
|
||||
OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
|
||||
XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
|
||||
pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
|
||||
K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
|
||||
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
|
||||
poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
|
||||
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
|
||||
AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
|
||||
fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
|
||||
3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
|
||||
n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
|
||||
7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
|
||||
Rtup0MTxSJtN
|
||||
-----END CERTIFICATE-----
|
14
itcc/vars
14
itcc/vars
@ -1,14 +0,0 @@
|
||||
BROKER_ID=test-no-real-data.broker.samply.de
|
||||
BROKER_URL=https://${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 $module
|
||||
done
|
@ -1,67 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
landing:
|
||||
deploy:
|
||||
replicas: 0 #deactivate landing page
|
||||
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-kr-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${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
|
@ -1,35 +0,0 @@
|
||||
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(`${HOST}`) && PathPrefix(`/backend`)"
|
||||
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
|
||||
- "traefik.http.routers.spot.tls=true"
|
||||
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
|
@ -1,5 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "$ENABLE_LENS" ];then
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
|
||||
fi
|
@ -1,20 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
obds2fhir-rest:
|
||||
container_name: bridgehead-obds2fhir-rest
|
||||
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
|
||||
environment:
|
||||
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
|
||||
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||
SALT: ${LOCAL_SALT}
|
||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||
- "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
|
||||
- "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.obds2fhir-rest.tls=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"
|
@ -1,13 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
function obds2fhirRestSetup() {
|
||||
if [ -n "$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
|
||||
}
|
@ -1,20 +0,0 @@
|
||||
-----BEGIN CERTIFICATE-----
|
||||
MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
|
||||
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
|
||||
MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
|
||||
AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
|
||||
TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
|
||||
OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
|
||||
XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
|
||||
pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
|
||||
K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
|
||||
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
|
||||
poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
|
||||
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
|
||||
AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
|
||||
fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
|
||||
3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
|
||||
n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
|
||||
7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
|
||||
Rtup0MTxSJtN
|
||||
-----END CERTIFICATE-----
|
16
kr/vars
16
kr/vars
@ -1,16 +0,0 @@
|
||||
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
|
@ -53,8 +53,8 @@ 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|cce|itcc|kr|dhki"
|
||||
echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
|
||||
echo "PROJECTNAME should be one of ccp|bbmri"
|
||||
}
|
||||
|
||||
checkRequirements() {
|
||||
@ -171,10 +171,8 @@ 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
|
||||
}
|
||||
@ -301,18 +299,33 @@ function sync_secrets() {
|
||||
if [[ $secret_sync_args == "" ]]; then
|
||||
return
|
||||
fi
|
||||
|
||||
if [ "${ENABLE_ERIC}" == "true" ]; then
|
||||
BROKER_ROOT_CERT=/srv/docker/bridgehead/bbmri/$ERIC_ROOT_CERT.crt.pem
|
||||
PROXY_ID=$ERIC_PROXY_ID
|
||||
BROKER_ID=$ERIC_BROKER_ID
|
||||
elif [ "${ENABLE_GBN}" == "true" ]; then
|
||||
BROKER_ROOT_CERT=/srv/docker/bridgehead/bbmri/$GBN_ROOT_CERT.crt.pem
|
||||
PROXY_ID=$GBN_PROXY_ID
|
||||
BROKER_ID=$GBN_BROKER_ID
|
||||
elif [ "${PROJECT}" == "ccp"]; then
|
||||
BROKER_ROOT_CERT=/srv/docker/bridgehead/ccp/root.crt.pem
|
||||
else
|
||||
fail_and_report 1 "Could not start secret sync as the configuration does not seem to use beam"
|
||||
fi
|
||||
local broker_url="https://$BROKER_ID"
|
||||
mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
|
||||
touch /var/cache/bridgehead/secrets/oidc
|
||||
docker run --rm \
|
||||
-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
|
||||
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
||||
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
|
||||
-v $BROKER_ROOT_CERT:/run/secrets/root.crt.pem:ro \
|
||||
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
||||
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
||||
-e NO_PROXY=localhost,127.0.0.1 \
|
||||
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
||||
-e PROXY_ID=$PROXY_ID \
|
||||
-e BROKER_URL=$BROKER_URL \
|
||||
-e BROKER_URL=$broker_url \
|
||||
-e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
|
||||
-e SECRET_DEFINITIONS=$secret_sync_args \
|
||||
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
||||
|
@ -35,12 +35,6 @@ if [ -z "$LDM_AUTH" ]; then
|
||||
add_basic_auth_user $PROJECT $generated_passwd "LDM_AUTH" $PROJECT
|
||||
fi
|
||||
|
||||
if [ "$ENABLE_EXPORTER" == true ]; then
|
||||
log "INFO" "Now generating basic auth for the quality reports. "
|
||||
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
||||
add_basic_auth_user $PROJECT $generated_passwd "QR_AUTH" $PROJECT
|
||||
fi
|
||||
|
||||
if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
|
||||
log "INFO" "Now generating basic auth for nNGM upload API (see adduser in bridgehead for more information). "
|
||||
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
||||
|
@ -52,21 +52,6 @@ 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/"
|
||||
;;
|
||||
|
@ -3,16 +3,14 @@
|
||||
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 $PROJECT"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
checkOwner "${CONFIG_DIR}" bridgehead || exit 1
|
||||
checkOwner "${COMPONENT_DIR}" bridgehead || exit 1
|
||||
checkOwner /srv/docker/bridgehead bridgehead || exit 1
|
||||
checkOwner /etc/bridgehead bridgehead || exit 1
|
||||
|
||||
## Check if user is a su
|
||||
log INFO "Checking if all prerequisites are met ..."
|
||||
@ -34,31 +32,31 @@ fi
|
||||
log INFO "Checking configuration ..."
|
||||
|
||||
## Download submodule
|
||||
if [ ! -d "${CONFIG_DIR}" ]; then
|
||||
fail_and_report 1 "Please set up the config folder at ${CONFIG_DIR}. Instruction are in the readme."
|
||||
if [ ! -d "/etc/bridgehead/" ]; then
|
||||
fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
|
||||
fi
|
||||
|
||||
# TODO: Check all required variables here in a generic loop
|
||||
|
||||
#check if project env is present
|
||||
if [ -d "${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."
|
||||
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."
|
||||
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 "${CONFIG_DIR}traefik-tls" ]; then
|
||||
if [ ! -d "/etc/bridgehead/traefik-tls" ]; then
|
||||
log WARN "TLS certs for accessing bridgehead via https missing, we'll now create a self-signed one. Please consider getting an officially signed one (e.g. via Let's Encrypt ...) and put into /etc/bridgehead/traefik-tls"
|
||||
mkdir -p /etc/bridgehead/traefik-tls
|
||||
fi
|
||||
|
||||
if [ ! -e "${CONFIG_DIR}traefik-tls/fullchain.pem" ]; then
|
||||
if [ ! -e "/etc/bridgehead/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=$HOST"
|
||||
fi
|
||||
|
||||
if [ -e "${CONFIG_DIR}"vault.conf ]; then
|
||||
if [ -e /etc/bridgehead/vault.conf ]; then
|
||||
if [ "$(stat -c "%a %U" /etc/bridgehead/vault.conf)" != "600 bridgehead" ]; then
|
||||
fail_and_report 1 "/etc/bridgehead/vault.conf has wrong owner/permissions. To correct this issue, run chmod 600 /etc/bridgehead/vault.conf && chown bridgehead /etc/bridgehead/vault.conf."
|
||||
fi
|
||||
@ -66,7 +64,7 @@ fi
|
||||
|
||||
log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
|
||||
|
||||
source "${CONFIG_DIR}${PROJECT}".conf
|
||||
source /etc/bridgehead/${PROJECT}.conf
|
||||
source ${PROJECT}/vars
|
||||
|
||||
if [ "${PROJECT}" != "minimal" ]; then
|
||||
@ -94,10 +92,10 @@ if [ "${PROJECT}" != "minimal" ]; then
|
||||
fi
|
||||
fi
|
||||
checkPrivKey() {
|
||||
if [ -e "${CONFIG_DIR}pki/${SITE_ID}.priv.pem" ]; then
|
||||
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
|
||||
log INFO "Success - private key found."
|
||||
else
|
||||
log ERROR "Unable to find private key at ${CONFIG_DIR}pki/${SITE_ID}.priv.pem. To fix, please run\n bridgehead enroll ${PROJECT}\nand follow the instructions."
|
||||
log ERROR "Unable to find private key at /etc/bridgehead/pki/${SITE_ID}.priv.pem. To fix, please run\n bridgehead enroll ${PROJECT}\nand follow the instructions."
|
||||
return 1
|
||||
fi
|
||||
return 0
|
||||
@ -109,11 +107,6 @@ else
|
||||
checkPrivKey || exit 1
|
||||
fi
|
||||
|
||||
for dir in "${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 $(git branch --show-current)")"
|
||||
done
|
||||
|
||||
log INFO "Success - all prerequisites are met!"
|
||||
hc_send log "Success - all prerequisites are met!"
|
||||
|
||||
|
@ -1,9 +1,8 @@
|
||||
[Unit]
|
||||
Description=Daily Updates at 6am of Bridgehead (%i)
|
||||
Description=Hourly Updates of Bridgehead (%i)
|
||||
|
||||
[Timer]
|
||||
OnCalendar=*-*-* 06:00:00
|
||||
Persistent=true
|
||||
OnCalendar=*-*-* *:00:00
|
||||
|
||||
[Install]
|
||||
WantedBy=basic.target
|
||||
|
@ -10,17 +10,18 @@ services:
|
||||
- --providers.docker=true
|
||||
- --providers.docker.exposedbydefault=false
|
||||
- --providers.file.directory=/configuration/
|
||||
- --api.dashboard=false
|
||||
- --api.dashboard=true
|
||||
- --accesslog=true
|
||||
- --entrypoints.web.http.redirections.entrypoint.to=websecure
|
||||
- --entrypoints.web.http.redirections.entrypoint.scheme=https
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
|
||||
- "traefik.http.routers.dashboard.entrypoints=websecure"
|
||||
- "traefik.http.routers.dashboard.service=api@internal"
|
||||
- "traefik.http.routers.dashboard.tls=true"
|
||||
- "traefik.http.routers.dashboard.middlewares=auth"
|
||||
- "traefik.http.middlewares.auth.basicauth.users=${LDM_AUTH}"
|
||||
ports:
|
||||
- 80:80
|
||||
- 443:443
|
||||
@ -57,4 +58,3 @@ services:
|
||||
HOST: ${HOST}
|
||||
PROJECT: ${PROJECT}
|
||||
SITE_NAME: ${SITE_NAME}
|
||||
ENVIRONMENT: ${ENVIRONMENT}
|
||||
|
2
minimal/modules/bbmri vars
Normal file
2
minimal/modules/bbmri vars
Normal file
@ -0,0 +1,2 @@
|
||||
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
|
||||
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
|
7
minimal/modules/ccp vars
Normal file
7
minimal/modules/ccp vars
Normal file
@ -0,0 +1,7 @@
|
||||
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
|
||||
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
|
||||
# Use "test-realm-01" for testing
|
||||
OIDC_REALM="${OIDC_REALM:-master}"
|
||||
OIDC_URL="https://login.verbis.dkfz.de"
|
||||
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
|
||||
OIDC_GROUP_CLAIM="groups"
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
dnpm-beam-proxy:
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
|
||||
container_name: bridgehead-dnpm-beam-proxy
|
||||
environment:
|
||||
BROKER_URL: ${DNPM_BROKER_URL}
|
||||
|
@ -1,6 +0,0 @@
|
||||
# Full Excel Export
|
||||
curl --location --request POST 'https://${HOST}/${PROJECT}-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=${PROJECT}&output-format=EXCEL' \
|
||||
--header 'x-api-key: ${EXPORT_API_KEY}'
|
||||
|
||||
# QB
|
||||
curl --location --request POST 'https://${HOST}/${PROJECT}-reporter/generate?template-id=${PROJECT}'
|
@ -1,82 +0,0 @@
|
||||
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_${PROJECT}.rule=PathPrefix(`/${PROJECT}-teiler`)"
|
||||
- "traefik.http.services.teiler_orchestrator_${PROJECT}.loadbalancer.server.port=9000"
|
||||
- "traefik.http.routers.teiler_orchestrator_${PROJECT}.tls=true"
|
||||
- "traefik.http.middlewares.teiler_orchestrator_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-teiler"
|
||||
- "traefik.http.routers.teiler_orchestrator_${PROJECT}.middlewares=teiler_orchestrator_${PROJECT}_strip"
|
||||
environment:
|
||||
TEILER_BACKEND_URL: "https://${HOST}/${PROJECT}-teiler-backend"
|
||||
TEILER_DASHBOARD_URL: "https://${HOST}/${PROJECT}-teiler-dashboard"
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
|
||||
HTTP_RELATIVE_PATH: "/${PROJECT}-teiler"
|
||||
|
||||
teiler-dashboard:
|
||||
#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
|
||||
image: docker.verbis.dkfz.de/ccp/samply/teiler-dashboard:bbmri
|
||||
container_name: bridgehead-teiler-dashboard
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.teiler_dashboard_${PROJECT}.rule=PathPrefix(`/${PROJECT}-teiler-dashboard`)"
|
||||
- "traefik.http.services.teiler_dashboard_${PROJECT}.loadbalancer.server.port=80"
|
||||
- "traefik.http.routers.teiler_dashboard_${PROJECT}.tls=true"
|
||||
- "traefik.http.middlewares.teiler_dashboard_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-teiler-dashboard"
|
||||
- "traefik.http.routers.teiler_dashboard_${PROJECT}.middlewares=teiler_dashboard_${PROJECT}_strip"
|
||||
environment:
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||
TEILER_BACKEND_URL: "https://${HOST}/${PROJECT}-teiler-backend"
|
||||
OIDC_URL: "${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}/${PROJECT}-teiler"
|
||||
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/${PROJECT}-teiler-dashboard"
|
||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PROJECT}-teiler"
|
||||
TEILER_USER: "${OIDC_USER_GROUP}"
|
||||
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
|
||||
REPORTER_DEFAULT_TEMPLATE_ID: "${PROJECT}-qb"
|
||||
EXPORTER_DEFAULT_TEMPLATE_ID: "${PROJECT}"
|
||||
|
||||
|
||||
teiler-backend:
|
||||
image: docker.verbis.dkfz.de/ccp/${PROJECT}-teiler-backend:latest
|
||||
container_name: bridgehead-teiler-backend
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.teiler_backend_${PROJECT}.rule=PathPrefix(`/${PROJECT}-teiler-backend`)"
|
||||
- "traefik.http.services.teiler_backend_${PROJECT}.loadbalancer.server.port=8085"
|
||||
- "traefik.http.routers.teiler_backend_${PROJECT}.tls=true"
|
||||
- "traefik.http.middlewares.teiler_backend_${PROJECT}_strip.stripprefix.prefixes=/${PROJECT}-teiler-backend"
|
||||
- "traefik.http.routers.teiler_backend_${PROJECT}.middlewares=teiler_backend_${PROJECT}_strip"
|
||||
environment:
|
||||
LOG_LEVEL: "INFO"
|
||||
APPLICATION_PORT: "8085"
|
||||
APPLICATION_ADDRESS: "${HOST}"
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||
CONFIG_ENV_VAR_PATH: "/run/secrets/project-conf"
|
||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/${PROJECT}-teiler"
|
||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/${PROJECT}-teiler"
|
||||
TEILER_DASHBOARD_DE_URL: "https://${HOST}/${PROJECT}-teiler-dashboard/de"
|
||||
TEILER_DASHBOARD_EN_URL: "https://${HOST}/${PROJECT}-teiler-dashboard/en"
|
||||
CENTRAX_URL: "${CENTRAXX_URL}"
|
||||
HTTP_PROXY: "http://forward_proxy:3128"
|
||||
ENABLE_MTBA: "${ENABLE_MTBA}"
|
||||
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
|
||||
secrets:
|
||||
- project-conf
|
||||
|
||||
secrets:
|
||||
project-conf:
|
||||
file: "/etc/bridgehead/${PROJECT}.conf"
|
Reference in New Issue
Block a user