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| Author | SHA1 | Date | |
|---|---|---|---|
| 5fc9e01652 |
39
.github/scripts/rename_inactive_branches.py
vendored
39
.github/scripts/rename_inactive_branches.py
vendored
@ -1,39 +0,0 @@
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import os
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import requests
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from datetime import datetime, timedelta
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# Configuration
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GITHUB_TOKEN = os.getenv('GITHUB_TOKEN')
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REPO = 'samply/bridgehead'
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HEADERS = {'Authorization': f'token {GITHUB_TOKEN}', 'Accept': 'application/vnd.github.v3+json'}
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API_URL = f'https://api.github.com/repos/{REPO}/branches'
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INACTIVE_DAYS = 365
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CUTOFF_DATE = datetime.now() - timedelta(days=INACTIVE_DAYS)
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# Fetch all branches
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def get_branches():
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response = requests.get(API_URL, headers=HEADERS)
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response.raise_for_status()
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return response.json() if response.status_code == 200 else []
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# Rename inactive branches
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def rename_branch(old_name, new_name):
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rename_url = f'https://api.github.com/repos/{REPO}/branches/{old_name}/rename'
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response = requests.post(rename_url, json={'new_name': new_name}, headers=HEADERS)
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response.raise_for_status()
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print(f"Renamed branch {old_name} to {new_name}" if response.status_code == 201 else f"Failed to rename {old_name}: {response.status_code}")
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# Check if the branch is inactive
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def is_inactive(commit_url):
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last_commit_date = requests.get(commit_url, headers=HEADERS).json()['commit']['committer']['date']
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return datetime.strptime(last_commit_date, '%Y-%m-%dT%H:%M:%SZ') < CUTOFF_DATE
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# Rename inactive branches
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def main():
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for branch in get_branches():
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if is_inactive(branch['commit']['url']):
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#rename_branch(branch['name'], f"archived/{branch['name']}")
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print(f"[LOG] Branch '{branch['name']}' is inactive and would be renamed to 'archived/{branch['name']}'")
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if __name__ == "__main__":
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main()
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27
.github/workflows/rename-inactive-branches.yml
vendored
27
.github/workflows/rename-inactive-branches.yml
vendored
@ -1,27 +0,0 @@
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name: Cleanup - Rename Inactive Branches
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on:
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schedule:
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- cron: '0 0 * * 0' # Runs every Sunday at midnight
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jobs:
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archive-stale-branches:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Repository
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uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install Libraries
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run: pip install requests
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- name: Run Script to Rename Inactive Branches
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run: |
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python .github/scripts/rename_inactive_branches.py
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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@ -10,8 +10,7 @@ services:
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BASE_URL: "http://bridgehead-bbmri-blaze:8080"
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JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
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DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
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DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
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CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
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DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
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ENFORCE_REFERENTIAL_INTEGRITY: "false"
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volumes:
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- "blaze-data:/app/data"
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19
bbmri/vars
19
bbmri/vars
@ -1,21 +1,3 @@
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BROKER_ID=broker-test.bbmri-test.samply.de
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BROKER_URL=https://${BROKER_ID}
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PROXY_ID=${SITE_ID}.${BROKER_ID}
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PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
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BROKER_URL_FOR_PREREQ=$BROKER_URL
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OIDC_USER_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})"
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OIDC_ADMIN_GROUP="BBMRI_$(capitalize_first_letter ${SITE_ID})_Verwalter"
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OIDC_PUBLIC_CLIENT_ID="BBMRI_${SITE_ID}-public"
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# Use "test-realm-01" for testing
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OIDC_REALM="${OIDC_REALM:-test-realm-01}"
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OIDC_URL="https://login.verbis.dkfz.de"
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OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
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OIDC_GROUP_CLAIM="groups"
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POSTGRES_TAG=15.6-alpine
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# Makes sense for all European Biobanks
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: ${ENABLE_ERIC:=true}
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@ -31,7 +13,6 @@ do
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source $module
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done
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SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
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BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
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@ -38,12 +38,6 @@ case "$PROJECT" in
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itcc)
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#nothing extra to do
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;;
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kr)
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#nothing extra to do
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;;
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dhki)
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#nothing extra to do
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;;
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minimal)
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#nothing extra to do
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;;
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@ -106,8 +100,7 @@ case "$ACTION" in
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loadVars
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hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
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checkRequirements
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# NOTE: for testing only, we will need to properly setup secret sync if we want to use this code
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# sync_secrets
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sync_secrets
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hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
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exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
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;;
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@ -3,11 +3,6 @@ services:
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landing:
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container_name: lens_federated-search
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image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
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- "traefik.http.services.landing.loadbalancer.server.port=80"
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- "traefik.http.routers.landing.tls=true"
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spot:
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image: docker.verbis.dkfz.de/ccp-private/central-spot
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@ -3,3 +3,4 @@
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if [ -n "$ENABLE_LENS" ];then
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OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
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fi
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}
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2
cce/vars
2
cce/vars
@ -3,7 +3,7 @@ BROKER_URL=https://${BROKER_ID}
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PROXY_ID=${SITE_ID}.${BROKER_ID}
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FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
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FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
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SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
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SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
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PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
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BROKER_URL_FOR_PREREQ=$BROKER_URL
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@ -8,8 +8,7 @@ services:
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BASE_URL: "http://bridgehead-ccp-blaze:8080"
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JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
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DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
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DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
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CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
|
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DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
|
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ENFORCE_REFERENTIAL_INTEGRITY: "false"
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volumes:
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- "blaze-data:/app/data"
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@ -151,7 +151,7 @@ services:
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--pass-access-token=false
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
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- "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
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- "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
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- "traefik.http.routers.oauth2_proxy.tls=true"
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environment:
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@ -19,18 +19,10 @@ services:
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- traefik-forward-auth
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labels:
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- "traefik.enable=true"
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# Router with Authentication
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- "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
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- "traefik.http.services.id-manager.loadbalancer.server.port=8080"
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- "traefik.http.routers.id-manager.tls=true"
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- "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
|
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- "traefik.http.routers.id-manager.service=id-manager-service"
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# Router without Authentication
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- "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
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||||
- "traefik.http.routers.id-manager-compatibility.tls=true"
|
||||
- "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
|
||||
# Definition of Service
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- "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
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- "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
|
||||
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patientlist:
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image: docker.verbis.dkfz.de/bridgehead/mainzelliste
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@ -65,7 +57,7 @@ services:
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||||
- "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
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||||
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||||
traefik-forward-auth:
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image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
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||||
image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
|
||||
environment:
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||||
- http_proxy=http://forward_proxy:3128
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||||
- https_proxy=http://forward_proxy:3128
|
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@ -75,7 +67,6 @@ services:
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||||
- 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
|
||||
|
||||
@ -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)"
|
||||
|
||||
@ -7,7 +7,7 @@ function obds2fhirRestSetup() {
|
||||
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
|
||||
PATIENTLIST_URL=" "
|
||||
fi
|
||||
OVERRIDE+=" -f ./ccp/modules/obds2fhir-rest-compose.yml"
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml"
|
||||
LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
fi
|
||||
}
|
||||
|
||||
1
ccp/vars
1
ccp/vars
@ -5,7 +5,6 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
|
||||
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
|
||||
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
|
||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||
PLATFORM=ccp
|
||||
|
||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
||||
|
||||
|
||||
@ -1,66 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-dhki-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${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 $module
|
||||
done
|
||||
|
||||
idManagementSetup
|
||||
obds2fhirRestSetup
|
||||
@ -3,11 +3,6 @@ services:
|
||||
landing:
|
||||
container_name: lens_federated-search
|
||||
image: docker.verbis.dkfz.de/ccp/lens:${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
|
||||
|
||||
@ -3,7 +3,7 @@ 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=${FOCUS_RETRY_COUNT:-64}
|
||||
SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
|
||||
SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
|
||||
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
|
||||
BROKER_URL_FOR_PREREQ=$BROKER_URL
|
||||
|
||||
|
||||
@ -1,67 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
landing:
|
||||
deploy:
|
||||
replicas: 0 #deactivate landing page
|
||||
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-kr-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${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
|
||||
@ -54,7 +54,7 @@ checkOwner(){
|
||||
|
||||
printUsage() {
|
||||
echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
|
||||
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
|
||||
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc"
|
||||
}
|
||||
|
||||
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
|
||||
}
|
||||
|
||||
@ -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)"
|
||||
|
||||
@ -57,15 +57,6 @@ case "$PROJECT" in
|
||||
;;
|
||||
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 $(git branch --show-current)")"
|
||||
done
|
||||
|
||||
log INFO "Success - all prerequisites are met!"
|
||||
hc_send log "Success - all prerequisites are met!"
|
||||
|
||||
|
||||
@ -10,17 +10,18 @@ services:
|
||||
- --providers.docker=true
|
||||
- --providers.docker.exposedbydefault=false
|
||||
- --providers.file.directory=/configuration/
|
||||
- --api.dashboard=false
|
||||
- --api.dashboard=true
|
||||
- --accesslog=true
|
||||
- --entrypoints.web.http.redirections.entrypoint.to=websecure
|
||||
- --entrypoints.web.http.redirections.entrypoint.scheme=https
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
|
||||
- "traefik.http.routers.dashboard.entrypoints=websecure"
|
||||
- "traefik.http.routers.dashboard.service=api@internal"
|
||||
- "traefik.http.routers.dashboard.tls=true"
|
||||
- "traefik.http.routers.dashboard.middlewares=auth"
|
||||
- "traefik.http.middlewares.auth.basicauth.users=${LDM_AUTH}"
|
||||
ports:
|
||||
- 80:80
|
||||
- 443:443
|
||||
|
||||
@ -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}'
|
||||
@ -1,73 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
exporter:
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
|
||||
container_name: bridgehead-${PROJECT}-exporter
|
||||
environment:
|
||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||
LOG_LEVEL: "INFO"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
||||
CROSS_ORIGINS: "https://${HOST}"
|
||||
EXPORTER_DB_USER: "exporter"
|
||||
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
|
||||
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
|
||||
HTTP_RELATIVE_PATH: "/${PROJECT}-exporter"
|
||||
SITE: "${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_${PROJECT}_strip"
|
||||
- "traefik.http.routers.connector.middlewares=connector_strip,auth-qr"
|
||||
volumes:
|
||||
- "/var/cache/bridgehead/${PROJECT}/exporter-files:/app/exporter-files/output"
|
||||
|
||||
|
||||
exporter-db:
|
||||
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
|
||||
container_name: bridgehead-${PROJECT}-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"
|
||||
|
||||
reporter:
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
|
||||
container_name: bridgehead-${PROJECT}-reporter
|
||||
environment:
|
||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||
LOG_LEVEL: "INFO"
|
||||
CROSS_ORIGINS: "https://${HOST}"
|
||||
HTTP_RELATIVE_PATH: "/${PROJECT}-reporter"
|
||||
SITE: "${SITE_ID}"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
||||
EXPORTER_URL: "http://exporter:8092"
|
||||
LOG_FHIR_VALIDATION: "false"
|
||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
||||
|
||||
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
|
||||
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
|
||||
# a process that can take several hours, because it depends on the exporter.
|
||||
# There is a risk that the bridgehead restarts, losing the already created export.
|
||||
|
||||
volumes:
|
||||
- "/var/cache/bridgehead/${PROJECT}/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=${QR_AUTH}"
|
||||
@ -1,8 +0,0 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
if [ "$ENABLE_EXPORTER" == true ]; then
|
||||
log INFO "Exporter setup detected -- will start Exporter service."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
|
||||
EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
|
||||
fi
|
||||
@ -1,15 +0,0 @@
|
||||
# Exporter and Reporter
|
||||
|
||||
|
||||
## Exporter
|
||||
The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
|
||||
It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
|
||||
|
||||
## Exporter-DB
|
||||
It is a database to save queries for its execution in the exporter.
|
||||
The exporter manages also the different executions of the same query in through the database.
|
||||
|
||||
## Reporter
|
||||
This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
|
||||
It is compatible with different template engines as Groovy, Thymeleaf,...
|
||||
It is perfect to generate a document as our traditional CCP quality report.
|
||||
@ -1,82 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
|
||||
teiler-orchestrator:
|
||||
image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
|
||||
container_name: bridgehead-teiler-orchestrator
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.teiler_orchestrator_${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/${PROJECT}.conf"
|
||||
@ -1,9 +0,0 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
if [ "$ENABLE_TEILER" == true ];then
|
||||
log INFO "Teiler setup detected -- will start Teiler services."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
|
||||
TEILER_DEFAULT_LANGUAGE=DE
|
||||
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
|
||||
add_public_oidc_redirect_url "/${PROJECT}-teiler/*"
|
||||
fi
|
||||
@ -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.
|
||||
Reference in New Issue
Block a user