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https://github.com/samply/bridgehead.git
synced 2025-06-16 15:00:15 +02:00
Compare commits
25 Commits
refactor/d
...
bugfix/tes
Author | SHA1 | Date | |
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da069b7473 | |||
e3553370b6 | |||
1ad73d8f82 | |||
0b6fa439ba | |||
615990b92a | |||
db950d6d87 | |||
910289079b | |||
1003cd73cf | |||
3d1105b97c | |||
5c28e704d2 | |||
e3510363ad | |||
45aefd24e5 | |||
122ff16bb1 | |||
967e45624e | |||
8cd5b93b95 | |||
52c24ee6fa | |||
26712d3567 | |||
eea17c3478 | |||
cf5230963c | |||
7aaee5e7d5 | |||
3312ca8a64 | |||
23981062bb | |||
8e7fe6851e | |||
760d599b7c | |||
072ee348fc |
39
.github/scripts/rename_inactive_branches.py
vendored
Normal file
39
.github/scripts/rename_inactive_branches.py
vendored
Normal file
@ -0,0 +1,39 @@
|
|||||||
|
import os
|
||||||
|
import requests
|
||||||
|
from datetime import datetime, timedelta
|
||||||
|
|
||||||
|
# Configuration
|
||||||
|
GITHUB_TOKEN = os.getenv('GITHUB_TOKEN')
|
||||||
|
REPO = 'samply/bridgehead'
|
||||||
|
HEADERS = {'Authorization': f'token {GITHUB_TOKEN}', 'Accept': 'application/vnd.github.v3+json'}
|
||||||
|
API_URL = f'https://api.github.com/repos/{REPO}/branches'
|
||||||
|
INACTIVE_DAYS = 365
|
||||||
|
CUTOFF_DATE = datetime.now() - timedelta(days=INACTIVE_DAYS)
|
||||||
|
|
||||||
|
# Fetch all branches
|
||||||
|
def get_branches():
|
||||||
|
response = requests.get(API_URL, headers=HEADERS)
|
||||||
|
response.raise_for_status()
|
||||||
|
return response.json() if response.status_code == 200 else []
|
||||||
|
|
||||||
|
# Rename inactive branches
|
||||||
|
def rename_branch(old_name, new_name):
|
||||||
|
rename_url = f'https://api.github.com/repos/{REPO}/branches/{old_name}/rename'
|
||||||
|
response = requests.post(rename_url, json={'new_name': new_name}, headers=HEADERS)
|
||||||
|
response.raise_for_status()
|
||||||
|
print(f"Renamed branch {old_name} to {new_name}" if response.status_code == 201 else f"Failed to rename {old_name}: {response.status_code}")
|
||||||
|
|
||||||
|
# Check if the branch is inactive
|
||||||
|
def is_inactive(commit_url):
|
||||||
|
last_commit_date = requests.get(commit_url, headers=HEADERS).json()['commit']['committer']['date']
|
||||||
|
return datetime.strptime(last_commit_date, '%Y-%m-%dT%H:%M:%SZ') < CUTOFF_DATE
|
||||||
|
|
||||||
|
# Rename inactive branches
|
||||||
|
def main():
|
||||||
|
for branch in get_branches():
|
||||||
|
if is_inactive(branch['commit']['url']):
|
||||||
|
#rename_branch(branch['name'], f"archived/{branch['name']}")
|
||||||
|
print(f"[LOG] Branch '{branch['name']}' is inactive and would be renamed to 'archived/{branch['name']}'")
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
main()
|
27
.github/workflows/rename-inactive-branches.yml
vendored
Normal file
27
.github/workflows/rename-inactive-branches.yml
vendored
Normal file
@ -0,0 +1,27 @@
|
|||||||
|
name: Cleanup - Rename Inactive Branches
|
||||||
|
|
||||||
|
on:
|
||||||
|
schedule:
|
||||||
|
- cron: '0 0 * * 0' # Runs every Sunday at midnight
|
||||||
|
|
||||||
|
jobs:
|
||||||
|
archive-stale-branches:
|
||||||
|
runs-on: ubuntu-latest
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- name: Checkout Repository
|
||||||
|
uses: actions/checkout@v2
|
||||||
|
|
||||||
|
- name: Set up Python
|
||||||
|
uses: actions/setup-python@v2
|
||||||
|
with:
|
||||||
|
python-version: '3.x'
|
||||||
|
|
||||||
|
- name: Install Libraries
|
||||||
|
run: pip install requests
|
||||||
|
|
||||||
|
- name: Run Script to Rename Inactive Branches
|
||||||
|
run: |
|
||||||
|
python .github/scripts/rename_inactive_branches.py
|
||||||
|
env:
|
||||||
|
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
@ -76,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
|
|||||||
* git.verbis.dkfz.de
|
* git.verbis.dkfz.de
|
||||||
* To fetch docker images
|
* To fetch docker images
|
||||||
* docker.verbis.dkfz.de
|
* docker.verbis.dkfz.de
|
||||||
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
|
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
|
||||||
* hub.docker.com
|
* hub.docker.com
|
||||||
* registry-1.docker.io
|
* registry-1.docker.io
|
||||||
* production.cloudflare.docker.com
|
* production.cloudflare.docker.com
|
||||||
@ -254,6 +254,8 @@ sh bridgehead uninstall
|
|||||||
|
|
||||||
## Site-specific configuration
|
## Site-specific configuration
|
||||||
|
|
||||||
|
[How to Change Config Access Token](docs/update-access-token.md)
|
||||||
|
|
||||||
### HTTPS Access
|
### 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).
|
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).
|
||||||
|
@ -4,13 +4,14 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||||
container_name: bridgehead-bbmri-blaze
|
container_name: bridgehead-bbmri-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
|
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
|
||||||
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
||||||
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
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: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||||
volumes:
|
volumes:
|
||||||
- "blaze-data:/app/data"
|
- "blaze-data:/app/data"
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
focus-eric:
|
focus-eric:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
|
||||||
container_name: bridgehead-focus-eric
|
container_name: bridgehead-focus-eric
|
||||||
environment:
|
environment:
|
||||||
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
|
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
focus-gbn:
|
focus-gbn:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
|
||||||
container_name: bridgehead-focus-gbn
|
container_name: bridgehead-focus-gbn
|
||||||
environment:
|
environment:
|
||||||
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
|
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
|
||||||
|
49
bridgehead
49
bridgehead
@ -53,17 +53,44 @@ case "$PROJECT" in
|
|||||||
;;
|
;;
|
||||||
esac
|
esac
|
||||||
|
|
||||||
|
# Loads config variables and runs the projects setup script
|
||||||
loadVars() {
|
loadVars() {
|
||||||
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
|
|
||||||
set -a
|
set -a
|
||||||
|
# Source the project specific config file
|
||||||
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
|
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/$PROJECT.local.conf ]; then
|
if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
|
||||||
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
|
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
|
||||||
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
|
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
|
||||||
fi
|
fi
|
||||||
|
# Set execution environment on main default to prod else test
|
||||||
|
if [[ -z "${ENVIRONMENT+x}" ]]; then
|
||||||
|
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
|
||||||
|
ENVIRONMENT="production"
|
||||||
|
else
|
||||||
|
ENVIRONMENT="test"
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
# Source the versions of the images components
|
||||||
|
case "$ENVIRONMENT" in
|
||||||
|
"production")
|
||||||
|
source ./versions/prod
|
||||||
|
;;
|
||||||
|
"test")
|
||||||
|
source ./versions/test
|
||||||
|
;;
|
||||||
|
*)
|
||||||
|
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
|
||||||
|
source ./versions/prod
|
||||||
|
;;
|
||||||
|
esac
|
||||||
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
|
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
|
||||||
setHostname
|
setHostname
|
||||||
optimizeBlazeMemoryUsage
|
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 ./$PROJECT/vars ] && source ./$PROJECT/vars
|
||||||
set +a
|
set +a
|
||||||
|
|
||||||
@ -79,26 +106,6 @@ loadVars() {
|
|||||||
fi
|
fi
|
||||||
detectCompose
|
detectCompose
|
||||||
setupProxy
|
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
|
case "$ACTION" in
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||||
container_name: bridgehead-cce-blaze
|
container_name: bridgehead-cce-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-cce-blaze:8080"
|
BASE_URL: "http://bridgehead-cce-blaze:8080"
|
||||||
|
@ -8,7 +8,8 @@ services:
|
|||||||
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
||||||
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
||||||
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
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: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||||
volumes:
|
volumes:
|
||||||
- "blaze-data:/app/data"
|
- "blaze-data:/app/data"
|
||||||
@ -21,7 +22,7 @@ services:
|
|||||||
- "traefik.http.routers.blaze_ccp.tls=true"
|
- "traefik.http.routers.blaze_ccp.tls=true"
|
||||||
|
|
||||||
focus:
|
focus:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
|
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
|
||||||
container_name: bridgehead-focus
|
container_name: bridgehead-focus
|
||||||
environment:
|
environment:
|
||||||
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
|
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
|
||||||
@ -32,6 +33,7 @@ services:
|
|||||||
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
||||||
EPSILON: 0.28
|
EPSILON: 0.28
|
||||||
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
||||||
|
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||||
volumes:
|
volumes:
|
||||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
||||||
depends_on:
|
depends_on:
|
||||||
@ -57,7 +59,6 @@ services:
|
|||||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||||
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
|
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
|
||||||
|
|
||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
blaze-data:
|
blaze-data:
|
||||||
|
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze-secondary:
|
blaze-secondary:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||||
container_name: bridgehead-ccp-blaze-secondary
|
container_name: bridgehead-ccp-blaze-secondary
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
||||||
|
@ -65,3 +65,8 @@ services:
|
|||||||
- "traefik.http.routers.reporter_ccp.tls=true"
|
- "traefik.http.routers.reporter_ccp.tls=true"
|
||||||
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
|
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
|
||||||
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
|
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
|
||||||
|
|
||||||
|
focus:
|
||||||
|
environment:
|
||||||
|
EXPORTER_URL: "http://exporter:8092"
|
||||||
|
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
||||||
|
@ -23,3 +23,7 @@ services:
|
|||||||
POSTGRES_DB: "dashboard"
|
POSTGRES_DB: "dashboard"
|
||||||
volumes:
|
volumes:
|
||||||
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
|
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
|
||||||
|
|
||||||
|
focus:
|
||||||
|
environment:
|
||||||
|
POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"
|
@ -4,4 +4,5 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then
|
|||||||
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
|
log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
|
||||||
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
|
OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
|
||||||
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
|
DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
|
||||||
|
FOCUS_ENDPOINT_TYPE="blaze-and-sql"
|
||||||
fi
|
fi
|
||||||
|
@ -101,5 +101,12 @@ services:
|
|||||||
forward_proxy:
|
forward_proxy:
|
||||||
condition: service_healthy
|
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:
|
volumes:
|
||||||
patientlist-db-data:
|
patientlist-db-data:
|
||||||
|
@ -12,7 +12,6 @@ services:
|
|||||||
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
||||||
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
||||||
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
||||||
restart: always
|
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
||||||
|
@ -10,7 +10,6 @@ services:
|
|||||||
SALT: ${LOCAL_SALT}
|
SALT: ${LOCAL_SALT}
|
||||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||||
restart: always
|
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||||
container_name: bridgehead-dhki-blaze
|
container_name: bridgehead-dhki-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
||||||
|
42
docs/update-access-token.md
Normal file
42
docs/update-access-token.md
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
## How to Change Config Access Token
|
||||||
|
|
||||||
|
### 1. Generate a New Access Token
|
||||||
|
|
||||||
|
1. Go to your Git configuration repository provider, it might be either [git.verbis.dkfz.de](https://git.verbis.dkfz.de) or [gitlab.bbmri-eric.eu](https://gitlab.bbmri-eric.eu).
|
||||||
|
2. Navigate to the configuration repository for your site.
|
||||||
|
3. Go to **Settings → Access Tokens** to check if your Access Token is valid or expired.
|
||||||
|
- **If expired**, create a new Access Token.
|
||||||
|
4. Configure the new Access Token with the following settings:
|
||||||
|
- **Expiration date**: One year from today, minus one day.
|
||||||
|
- **Role**: Developer.
|
||||||
|
- **Scope**: Only `read_repository`.
|
||||||
|
5. Save the newly generated Access Token in a secure location.
|
||||||
|
|
||||||
|
---
|
||||||
|
|
||||||
|
### 2. Replace the Old Access Token
|
||||||
|
|
||||||
|
1. Navigate to `/etc/bridgehead` in your system.
|
||||||
|
2. Run the following command to retrieve the current Git remote URL:
|
||||||
|
```bash
|
||||||
|
git remote get-url origin
|
||||||
|
```
|
||||||
|
Example output:
|
||||||
|
```
|
||||||
|
https://name40dkfz-heidelberg.de:<old_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
|
||||||
|
```
|
||||||
|
3. Replace `<old_access_token>` with your new Access Token in the URL.
|
||||||
|
4. Set the updated URL using the following command:
|
||||||
|
```bash
|
||||||
|
git remote set-url origin https://name40dkfz-heidelberg.de:<new_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
|
||||||
|
|
||||||
|
```
|
||||||
|
|
||||||
|
5. Start the Bridgehead update service by running:
|
||||||
|
```bash
|
||||||
|
systemctl start bridgehead-update@<project>
|
||||||
|
```
|
||||||
|
6. View the output to ensure the update process is successful:
|
||||||
|
```bash
|
||||||
|
journalctl -u bridgehead-update@<project> -f
|
||||||
|
```
|
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||||
container_name: bridgehead-itcc-blaze
|
container_name: bridgehead-itcc-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
||||||
|
@ -1,8 +1,12 @@
|
|||||||
version: "3.7"
|
version: "3.7"
|
||||||
|
|
||||||
services:
|
services:
|
||||||
|
landing:
|
||||||
|
deploy:
|
||||||
|
replicas: 0 #deactivate landing page
|
||||||
|
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||||
container_name: bridgehead-kr-blaze
|
container_name: bridgehead-kr-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
||||||
|
@ -1,6 +1,8 @@
|
|||||||
version: "3.7"
|
version: "3.7"
|
||||||
services:
|
services:
|
||||||
landing:
|
landing:
|
||||||
|
deploy:
|
||||||
|
replicas: 1 #reactivate if lens is in use
|
||||||
container_name: lens_federated-search
|
container_name: lens_federated-search
|
||||||
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
|
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
|
||||||
labels:
|
labels:
|
||||||
|
@ -10,7 +10,6 @@ services:
|
|||||||
SALT: ${LOCAL_SALT}
|
SALT: ${LOCAL_SALT}
|
||||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||||
restart: always
|
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||||
|
@ -116,7 +116,7 @@ assertVarsNotEmpty() {
|
|||||||
MISSING_VARS=""
|
MISSING_VARS=""
|
||||||
|
|
||||||
for VAR in $@; do
|
for VAR in $@; do
|
||||||
if [ -z "${!VAR}" ]; then
|
if [ -z "${!VAR}" ]; then
|
||||||
MISSING_VARS+="$VAR "
|
MISSING_VARS+="$VAR "
|
||||||
fi
|
fi
|
||||||
done
|
done
|
||||||
@ -171,8 +171,10 @@ optimizeBlazeMemoryUsage() {
|
|||||||
if [ $available_system_memory_chunks -eq 0 ]; then
|
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."
|
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
|
||||||
export BLAZE_RESOURCE_CACHE_CAP=128000;
|
export BLAZE_RESOURCE_CACHE_CAP=128000;
|
||||||
|
export BLAZE_CQL_CACHE_CAP=32;
|
||||||
else
|
else
|
||||||
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
|
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
|
||||||
|
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
|
||||||
fi
|
fi
|
||||||
fi
|
fi
|
||||||
}
|
}
|
||||||
@ -316,7 +318,7 @@ function sync_secrets() {
|
|||||||
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
||||||
|
|
||||||
set -a # Export variables as environment variables
|
set -a # Export variables as environment variables
|
||||||
source /var/cache/bridgehead/secrets/*
|
source /var/cache/bridgehead/secrets/oidc
|
||||||
set +a # Export variables in the regular way
|
set +a # Export variables in the regular way
|
||||||
}
|
}
|
||||||
|
|
||||||
|
11
lib/gitlab-token-helper.sh
Executable file
11
lib/gitlab-token-helper.sh
Executable file
@ -0,0 +1,11 @@
|
|||||||
|
#!/bin/bash
|
||||||
|
|
||||||
|
[ "$1" = "get" ] || exit
|
||||||
|
|
||||||
|
source /var/cache/bridgehead/secrets/gitlab_token
|
||||||
|
|
||||||
|
# Any non-empty username works, only the token matters
|
||||||
|
cat << EOF
|
||||||
|
username=bk
|
||||||
|
password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
|
||||||
|
EOF
|
@ -1,41 +0,0 @@
|
|||||||
#!/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
|
|
@ -19,7 +19,7 @@ fi
|
|||||||
|
|
||||||
hc_send log "Checking for bridgehead updates ..."
|
hc_send log "Checking for bridgehead updates ..."
|
||||||
|
|
||||||
CONFFILE=/etc/bridgehead/$1.conf
|
CONFFILE=/etc/bridgehead/$PROJECT.conf
|
||||||
|
|
||||||
if [ ! -e $CONFFILE ]; then
|
if [ ! -e $CONFFILE ]; then
|
||||||
fail_and_report 1 "Configuration file $CONFFILE not found."
|
fail_and_report 1 "Configuration file $CONFFILE not found."
|
||||||
@ -33,7 +33,43 @@ export SITE_ID
|
|||||||
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
|
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"
|
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
|
||||||
|
|
||||||
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
|
# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
|
||||||
|
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
|
||||||
|
# The git credential helper reads the token from the file during git pull.
|
||||||
|
mkdir -p /var/cache/bridgehead/secrets
|
||||||
|
touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
|
||||||
|
log "INFO" "Running Secret Sync for the GitLab token"
|
||||||
|
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
|
||||||
|
docker run --rm \
|
||||||
|
-v /var/cache/bridgehead/secrets/gitlab_token:/usr/local/cache \
|
||||||
|
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
||||||
|
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
|
||||||
|
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
||||||
|
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
||||||
|
-e NO_PROXY=localhost,127.0.0.1 \
|
||||||
|
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
||||||
|
-e PROXY_ID=$PROXY_ID \
|
||||||
|
-e BROKER_URL=$BROKER_URL \
|
||||||
|
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
|
||||||
|
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN: \
|
||||||
|
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
||||||
|
if [ $? -eq 0 ]; then
|
||||||
|
log "INFO" "Secret Sync was successful"
|
||||||
|
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
|
||||||
|
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
|
||||||
|
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
|
||||||
|
# Set the git credential helper
|
||||||
|
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
|
||||||
|
else
|
||||||
|
log "WARN" "Secret Sync failed"
|
||||||
|
# Remove the git credential helper
|
||||||
|
git -C /etc/bridgehead config --unset credential.helper
|
||||||
|
fi
|
||||||
|
|
||||||
|
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
|
||||||
|
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
|
||||||
|
# believe that it was removed on all/most production servers.
|
||||||
|
git -C /srv/docker/bridgehead config --unset credential.helper
|
||||||
|
|
||||||
CHANGES=""
|
CHANGES=""
|
||||||
|
|
||||||
@ -45,10 +81,6 @@ for DIR in /etc/bridgehead $(pwd); do
|
|||||||
if [ -n "$OUT" ]; then
|
if [ -n "$OUT" ]; then
|
||||||
report_error log "The working directory $DIR is modified. Changed files: $OUT"
|
report_error log "The working directory $DIR is modified. Changed files: $OUT"
|
||||||
fi
|
fi
|
||||||
if [ "$(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 $DIR rev-parse --verify HEAD)"
|
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
|
||||||
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
|
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
|
||||||
log "INFO" "Git is using no proxy!"
|
log "INFO" "Git is using no proxy!"
|
||||||
@ -58,7 +90,8 @@ for DIR in /etc/bridgehead $(pwd); do
|
|||||||
OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
|
OUT=$(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
|
fi
|
||||||
if [ $? -ne 0 ]; then
|
if [ $? -ne 0 ]; then
|
||||||
report_error log "Unable to update git $DIR: $OUT"
|
OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
|
||||||
|
report_error log "Unable to update git $DIR: $OUT_SAN"
|
||||||
fi
|
fi
|
||||||
|
|
||||||
new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
|
new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
|
||||||
|
@ -11,7 +11,6 @@ services:
|
|||||||
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
||||||
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
||||||
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
||||||
restart: always
|
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
||||||
|
2
versions/prod
Normal file
2
versions/prod
Normal file
@ -0,0 +1,2 @@
|
|||||||
|
FOCUS_TAG=main
|
||||||
|
BEAM_TAG=main
|
2
versions/test
Normal file
2
versions/test
Normal file
@ -0,0 +1,2 @@
|
|||||||
|
FOCUS_TAG=develop
|
||||||
|
BEAM_TAG=develop
|
Reference in New Issue
Block a user