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4 Commits

Author SHA1 Message Date
5f5e626501 minor fix 2024-10-15 12:29:41 +02:00
2b391a5156 minor fix 2024-10-15 11:54:26 +02:00
022d6e9a72 to squash 2024-10-15 10:44:14 +02:00
4446f9b9ac feat: use project overarching vars 2024-10-15 10:29:13 +02:00
62 changed files with 204 additions and 881 deletions

1
.github/CODEOWNERS vendored
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@ -1 +0,0 @@
* @samply/bridgehead-developers

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@ -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()

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@ -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 }}

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@ -76,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
* git.verbis.dkfz.de
* To fetch docker images
* docker.verbis.dkfz.de
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
* hub.docker.com
* registry-1.docker.io
* production.cloudflare.docker.com
@ -154,7 +154,7 @@ Pay special attention to:
Clone the bridgehead repository:
```shell
sudo mkdir -p /srv/docker/
sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
```
Then, run the installation script:
@ -254,8 +254,6 @@ sh bridgehead uninstall
## Site-specific configuration
[How to Change Config Access Token](docs/update-access-token.md)
### HTTPS Access
Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).

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

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

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

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

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@ -7,6 +7,7 @@
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
source versions
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"

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@ -53,48 +53,18 @@ case "$PROJECT" in
;;
esac
# Loads config variables and runs the projects setup script
loadVars() {
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
set -a
# Source the project specific config file
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
# Source the project specific local config file if present
# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
fi
# Set execution environment on main default to prod else test
if [[ -z "${ENVIRONMENT+x}" ]]; then
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
ENVIRONMENT="production"
else
ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility
fi
fi
# Source the versions of the images components
case "$ENVIRONMENT" in
"production")
source ./versions/prod
;;
"test")
source ./versions/test
;;
"acceptance")
source ./versions/acceptance
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
source ./versions/prod
;;
esac
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
setHostname
optimizeBlazeMemoryUsage
# Run project specific setup if it exists
# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
# This is also where projects specify which modules to load
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
[ -e ./$PROJECT/vars ] && source ./versions ./$PROJECT/vars
set +a
OVERRIDE=${OVERRIDE:=""}
@ -109,6 +79,26 @@ loadVars() {
fi
detectCompose
setupProxy
# Set some project-independent default values
: ${ENVIRONMENT:=production}
export ENVIRONMENT
case "$ENVIRONMENT" in
"production")
export FOCUS_TAG=main
export BEAM_TAG=main
;;
"test")
export FOCUS_TAG=develop
export BEAM_TAG=develop
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
export FOCUS_TAG=main
export BEAM_TAG=main
;;
esac
}
case "$ACTION" in

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@ -8,8 +8,7 @@ services:
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}
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"
@ -32,10 +31,6 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081
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/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"

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@ -1,2 +0,0 @@
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@ -7,6 +7,7 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
source versions
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"

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@ -22,7 +22,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -33,9 +33,8 @@ 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:ro
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
depends_on:
- "beam-proxy"
- "blaze"
@ -59,6 +58,7 @@ services:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:

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@ -8,7 +8,8 @@ services:
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
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-secondary-data:/app/data"

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

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

View File

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

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:test
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-ccp-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
@ -65,8 +65,3 @@ 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

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

View File

@ -4,5 +4,4 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
FOCUS_ENDPOINT_TYPE="blaze-and-sql"
fi

View File

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

View File

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

View File

@ -3,13 +3,14 @@ version: "3.7"
services:
obds2fhir-rest:
container_name: bridgehead-obds2fhir-rest
image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
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`)"

View File

@ -19,8 +19,7 @@ services:
HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard:
#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
@ -32,7 +31,6 @@ services:
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -43,6 +41,7 @@ services:
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: "${OIDC_ADMIN_GROUP}"
@ -70,10 +69,10 @@ services:
TEILER_ORCHESTRATOR_URL: "https://${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: "${ENABLE_DATASHIELD}"
IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active
secrets:
- ccp.conf

View File

@ -1,2 +1,2 @@
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

View File

@ -18,8 +18,7 @@ OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups"
POSTGRES_TAG=15.6-alpine
source versions
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
@ -30,11 +29,3 @@ idManagementSetup
mtbaSetup
obds2fhirRestSetup
blazeSecondarySetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

View File

@ -33,13 +33,13 @@ services:
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
volumes:
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
depends_on:
- "beam-proxy"
- "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}

View File

@ -8,8 +8,7 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
POSTGRES_TAG=15.6-alpine
source versions
for module in ccp/modules/*.sh
do
log DEBUG "sourcing $module"
@ -18,11 +17,3 @@ done
idManagementSetup
obds2fhirRestSetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

View File

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

View File

@ -8,8 +8,7 @@ services:
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}
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"
@ -32,10 +31,6 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081
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/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"

View File

@ -1,2 +0,0 @@
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
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

View File

@ -7,6 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
source versions
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"

View File

@ -40,7 +40,7 @@ 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}

View File

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

View File

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

View File

@ -31,7 +31,6 @@ services:
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
@ -42,6 +41,7 @@ services:
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: "${OIDC_ADMIN_GROUP}"
@ -69,6 +69,7 @@ services:
TEILER_ORCHESTRATOR_URL: "https://${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}"

View File

@ -1,19 +0,0 @@
# 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.

View File

@ -7,6 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
source versions
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"

View File

@ -116,7 +116,7 @@ assertVarsNotEmpty() {
MISSING_VARS=""
for VAR in $@; do
if [ -z "${!VAR}" ]; then
if [ -z "${!VAR}" ]; then
MISSING_VARS+="$VAR "
fi
done
@ -170,11 +170,11 @@ optimizeBlazeMemoryUsage() {
available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
if [ $available_system_memory_chunks -eq 0 ]; then
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
export BLAZE_RESOURCE_CACHE_CAP=128000;
export BLAZE_CQL_CACHE_CAP=32;
export BLAZE_RESOURCE_CACHE_CAP=128000
export BLAZE_CQL_CACHE_CAP=32
else
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16))
fi
fi
}
@ -313,82 +313,15 @@ function sync_secrets() {
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \
-e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
-e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
set -a # Export variables as environment variables
source /var/cache/bridgehead/secrets/oidc
source /var/cache/bridgehead/secrets/*
set +a # Export variables in the regular way
}
function secret_sync_gitlab_token() {
# Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
local gitlab
case "$(git -C /etc/bridgehead remote get-url origin)" in
*git.verbis.dkfz.de*) gitlab=verbis;;
*gitlab.bbmri-eric.eu*) gitlab=bbmri;;
*)
log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
return
;;
esac
if [ "$PROJECT" == "bbmri" ]; then
# If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
proxy_id=$ERIC_PROXY_ID
broker_url=$ERIC_BROKER_URL
broker_id=$ERIC_BROKER_ID
root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
else
proxy_id=$PROXY_ID
broker_url=$BROKER_URL
broker_id=$BROKER_ID
root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
fi
# Create a temporary directory for Secret Sync that is valid per boot
secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
mkdir -p $secret_sync_tempdir
# Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
# The git credential helper reads the token from the file during git pull.
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
docker run --rm \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-v $secret_sync_tempdir:/secret-sync/ \
-e CACHE_PATH=/secret-sync/gitlab-token \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$proxy_id \
-e BROKER_URL=$broker_url \
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
if [ $? -eq 0 ]; then
log "INFO" "Secret Sync was successful"
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
# Set the git credential helper
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
else
log "WARN" "Secret Sync failed"
# Remove the git credential helper
git -C /etc/bridgehead config --unset credential.helper
fi
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
# believe that it was removed on all/most production servers.
git -C /srv/docker/bridgehead config --unset credential.helper
}
capitalize_first_letter() {
input="$1"
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"

View File

@ -1,11 +0,0 @@
#!/bin/bash
[ "$1" = "get" ] || exit
source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
# Any non-empty username works, only the token matters
cat << EOF
username=bk
password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
EOF

41
lib/gitpassword.sh Executable file
View File

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

View File

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

View File

@ -57,9 +57,9 @@ case "$PROJECT" in
;;
itcc)
site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
;;
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
kr)
site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"

View File

@ -67,7 +67,7 @@ fi
log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
source "${CONFIG_DIR}${PROJECT}".conf
source ${PROJECT}/vars
source ${PROJECT}/vars vars
if [ "${PROJECT}" != "minimal" ]; then
set +e

View File

@ -19,7 +19,7 @@ fi
hc_send log "Checking for bridgehead updates ..."
CONFFILE=/etc/bridgehead/$PROJECT.conf
CONFFILE=/etc/bridgehead/$1.conf
if [ ! -e $CONFFILE ]; then
fail_and_report 1 "Configuration file $CONFFILE not found."
@ -33,7 +33,7 @@ export SITE_ID
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
secret_sync_gitlab_token
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
CHANGES=""
@ -45,6 +45,10 @@ for DIR in /etc/bridgehead $(pwd); do
if [ -n "$OUT" ]; then
report_error log "The working directory $DIR is modified. Changed files: $OUT"
fi
if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
log "INFO" "Configuring repo to use bridgehead git credential helper."
git -C $DIR config credential.helper "$CREDHELPER"
fi
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
log "INFO" "Git is using no proxy!"
@ -54,8 +58,7 @@ for DIR in /etc/bridgehead $(pwd); do
OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
fi
if [ $? -ne 0 ]; then
OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
report_error log "Unable to update git $DIR: $OUT_SAN"
report_error log "Unable to update git $DIR: $OUT"
fi
new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"

View File

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

View File

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

View File

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

View File

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

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

View File

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

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@ -1,3 +1,5 @@
source versions
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"

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

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

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

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@ -1,86 +0,0 @@
services:
transfair:
image: docker.verbis.dkfz.de/cache/samply/transfair:latest
container_name: bridgehead-transfair
environment:
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
- TTP_URL
- TTP_ML_API_KEY
- TTP_GW_SOURCE
- TTP_GW_EPIX_DOMAIN
- TTP_GW_GPAS_DOMAIN
- TTP_TYPE
- TTP_AUTH
- PROJECT_ID_SYSTEM
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
- FHIR_INPUT_URL=${FHIR_INPUT_URL}
- FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
- FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
- FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
- FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
- RUST_LOG=${RUST_LOG:-info}
- TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
- TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
- NO_PROXY=${TRANSFAIR_NO_PROXIES}
- ALL_PROXY=http://forward_proxy:3128
volumes:
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
labels:
- "traefik.enable=true"
- "traefik.http.middlewares.transfair-strip.stripprefix.prefixes=/transfair"
- "traefik.http.routers.transfair.middlewares=transfair-strip,transfair-auth"
- "traefik.http.routers.transfair.rule=PathPrefix(`/transfair`)"
- "traefik.http.services.transfair.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair.tls=true"
traefik:
labels:
- "traefik.http.middlewares.transfair-auth.basicauth.users=${TRANSFAIR_AUTH}"
transfair-input-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-input-blaze
environment:
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-input-blaze-data:/app/data"
profiles: ["transfair-input-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
- "traefik.http.routers.transfair-input-blaze.tls=true"
transfair-request-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-request-blaze
environment:
BASE_URL: "http://bridgehead-transfair-request-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-request-blaze-data:/app/data"
profiles: ["transfair-request-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-request-blaze.rule=PathPrefix(`/data-requests`)"
- "traefik.http.middlewares.transfair-request-strip.stripprefix.prefixes=/data-requests"
- "traefik.http.services.transfair-request-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-request-blaze.middlewares=transfair-request-strip,transfair-auth"
- "traefik.http.routers.transfair-request-blaze.tls=true"
volumes:
transfair-input-blaze-data:
transfair-request-blaze-data:

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@ -1,35 +0,0 @@
#!/bin/bash -e
function transfairSetup() {
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
echo "Starting transfair."
OVERRIDE+=" -f ./modules/transfair-compose.yml"
if [ -n "$FHIR_INPUT_URL" ]; then
log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
else
log INFO "TransFAIR input fhir store not set writing to internal blaze"
FHIR_INPUT_URL="http://transfair-input-blaze:8080"
OVERRIDE+=" --profile transfair-input-blaze"
fi
if [ -n "$FHIR_REQUEST_URL" ]; then
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
else
log INFO "TransFAIR request fhir store not set writing to internal blaze"
FHIR_REQUEST_URL="http://transfair-request-blaze:8080"
OVERRIDE+=" --profile transfair-request-blaze"
fi
if [ -n "$TTP_GW_SOURCE" ]; then
log INFO "TransFAIR configured with greifswald as ttp"
TTP_TYPE="greifswald"
elif [ -n "$TTP_ML_API_KEY" ]; then
log INFO "TransFAIR configured with mainzelliste as ttp"
TTP_TYPE="mainzelliste"
else
log INFO "TransFAIR configured without ttp"
fi
TRANSFAIR_NO_PROXIES="transfair-input-blaze,blaze,transfair-requests-blaze"
if [ -n "${TRANSFAIR_NO_PROXY}" ]; then
TRANSFAIR_NO_PROXIES+=",${TRANSFAIR_NO_PROXY}"
fi
fi
}

2
versions Normal file
View File

@ -0,0 +1,2 @@
BLAZE_TAG=0.28
POSTGRES_TAG=15.6-alpine

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

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@ -1,3 +0,0 @@
FOCUS_TAG=main
BEAM_TAG=main
BLAZE_TAG=0.32

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