refactor: explicitly set logging - to squash

Feat/ccp ppi

.github/scripts/rename_inactive_branches.py

@@ -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()

.github/workflows/rename-inactive-branches.yml

@@ -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 }}

bbmri/docker-compose.yml

@@ -10,7 +10,8 @@ services:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"

bbmri/modules/eric-compose.yml

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

bbmri/modules/gbn-compose.yml

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

ccp/docker-compose.yml

@@ -8,8 +8,10 @@ services:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
+      LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
     volumes:
       - "blaze-data:/app/data"
     labels:
@@ -21,7 +23,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -32,6 +34,8 @@ services:
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+      RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
     volumes:
       - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
     depends_on:
@@ -49,6 +53,7 @@ services:
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
       ROOTCERT_FILE: /conf/root.crt.pem
+      RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
     secrets:
       - proxy.pem
     depends_on:
@@ -57,7 +62,6 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
-
 volumes:
   blaze-data:
 

ccp/modules/blaze-secondary-compose.yml

@@ -10,6 +10,7 @@ services:
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
       DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
+      LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
     volumes:
       - "blaze-secondary-data:/app/data"
     labels:

ccp/modules/datashield-compose.yml

@@ -10,6 +10,7 @@ services:
       DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
       HTTP_RELATIVE_PATH: "/rstudio"
       ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
+      LOG_LEVEL: ${LOG_LEVEL_RSTUDIO:-WARN}
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
@@ -54,6 +55,7 @@ services:
       BEAM_APP_ID: token-manager.${PROXY_ID}
       BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
       BEAM_DATASHIELD_PROXY: request-manager
+      LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
     volumes:
       - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
     secrets:
@@ -75,6 +77,8 @@ services:
     image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
     tmpfs:
       - /srv
+    environment:
+      LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
 
   beam-connect:
     image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
@@ -87,6 +91,7 @@ services:
       DISCOVERY_URL: "./map/central.json"
       LOCAL_TARGETS_FILE: "./map/local.json"
       NO_AUTH: "true"
+      RUST_LOG: ${LOG_LEVEL_BEAMCONNECT:-WARN}
     secrets:
       - opal-cert.pem
     depends_on:
@@ -151,7 +156,7 @@ services:
       --pass-access-token=false
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
+      - "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
       - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
       - "traefik.http.routers.oauth2_proxy.tls=true"
     environment:

ccp/modules/dnpm-compose.yml

@@ -17,7 +17,7 @@ services:
       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}
-      RUST_LOG: ${RUST_LOG:-info}
+      RUST_LOG: ${LOG_LEVEL_BEAMCONNECTDNPM:-WARN}
       NO_AUTH: "true"
       TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
     extra_hosts:

ccp/modules/exporter-compose.yml

@@ -6,7 +6,6 @@ services:
     container_name: bridgehead-ccp-exporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
       CROSS_ORIGINS: "https://${HOST}"
       EXPORTER_DB_USER: "exporter"
@@ -16,6 +15,7 @@ services:
       SITE: "${SITE_ID}"
       HTTP_SERVLET_REQUEST_SCHEME: "https"
       OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+      LOG_LEVEL: ${LOG_LEVEL_EXPORTER:-WARN}
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
@@ -42,7 +42,6 @@ services:
     container_name: bridgehead-ccp-reporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
       CROSS_ORIGINS: "https://${HOST}"
       HTTP_RELATIVE_PATH: "/ccp-reporter"
       SITE: "${SITE_ID}"
@@ -50,6 +49,7 @@ services:
       EXPORTER_URL: "http://exporter:8092"
       LOG_FHIR_VALIDATION: "false"
       HTTP_SERVLET_REQUEST_SCHEME: "https"
+      LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
 
     # 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
@@ -65,3 +65,8 @@ services:
       - "traefik.http.routers.reporter_ccp.tls=true"
       - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
       - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
+
+  focus:
+    environment:
+      EXPORTER_URL: "http://exporter:8092"
+      AUTH_HEADER: "${EXPORTER_API_KEY}"

ccp/modules/fhir2sql-compose.yml

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

ccp/modules/fhir2sql-setup.sh

@@ -4,4 +4,5 @@ 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

ccp/modules/id-management-compose.yml

@@ -14,15 +14,24 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
+      ML_LOG_LEVEL: ${LOG_LEVEL_IDMANAGER:-WARN}
     depends_on:
       - patientlist
       - traefik-forward-auth
     labels:
       - "traefik.enable=true"
+      # Router with Authentication
       - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
-      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
       - "traefik.http.routers.id-manager.tls=true"
       - "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
+      - "traefik.http.routers.id-manager.service=id-manager-service"
+      # Router without Authentication
+      - "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
+      - "traefik.http.routers.id-manager-compatibility.tls=true"
+      - "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
+      # Definition of Service
+      - "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
+      - "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
 
   patientlist:
     image: docker.verbis.dkfz.de/bridgehead/mainzelliste
@@ -36,6 +45,8 @@ services:
       - ML_UPLOAD_API_KEY=${IDMANAGER_UPLOAD_APIKEY}
       # Add Variables from /etc/patientlist-id-generators.env
       - PATIENTLIST_SEEDS_TRANSFORMED
+      - ML_LOG_LEVEL=${LOG_LEVEL_PATIENTLIST:-WARN}
+      #TODO confirm LOG_LEVEL
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
@@ -57,7 +68,7 @@ services:
       - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
 
   traefik-forward-auth:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
+    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
     environment:
       - http_proxy=http://forward_proxy:3128
       - https_proxy=http://forward_proxy:3128
@@ -67,6 +78,7 @@ services:
       - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
       - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
       - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
+      - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
       - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
       - OAUTH2_PROXY_HTTP_ADDRESS=:4180
       - OAUTH2_PROXY_REVERSE_PROXY=true
@@ -92,5 +104,12 @@ services:
       forward_proxy:
         condition: service_healthy
 
+  ccp-patient-project-identificator:
+    image: samply/ccp-patient-project-identificator
+    container_name: bridgehead-ccp-patient-project-identificator
+    environment:
+      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      SITE_NAME: ${SITE_NAME}
+
 volumes:
   patientlist-db-data:

ccp/modules/mtba-compose.yml

@@ -25,6 +25,7 @@ services:
       OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
       OIDC_REALM: "${OIDC_REALM}"
       OIDC_URL: "${OIDC_URL}"
+      LOG_LEVEL: ${LOG_LEVEL_MTBA:-WARN}
 
     labels:
       - "traefik.enable=true"

ccp/modules/nngm-compose.yml

@@ -12,6 +12,7 @@ services:
       CTS_API_KEY: ${NNGM_CTS_APIKEY}
       CRYPT_KEY: ${NNGM_CRYPTKEY}
       #CTS_MAGICPL_SITE: ${SITE_ID}TODO
+      LOG_LEVEL: ${LOG_LEVEL_NNGM:-WARN}
     restart: always
     labels:
       - "traefik.enable=true"

ccp/modules/obds2fhir-rest-compose.yml

@@ -10,6 +10,7 @@ services:
       SALT: ${LOCAL_SALT}
       KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
       MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
+      LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
     restart: always
     labels:
       - "traefik.enable=true"

ccp/modules/teiler-compose.yml

@@ -17,6 +17,7 @@ services:
       TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/ccp-teiler"
+      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
 
   teiler-dashboard:
     image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
@@ -47,6 +48,7 @@ services:
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
       REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
       EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
+      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
 
 
   teiler-backend:
@@ -60,7 +62,6 @@ services:
       - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
       - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
     environment:
-      LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
       APPLICATION_ADDRESS: "${HOST}"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
@@ -73,6 +74,7 @@ services:
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
     secrets:
       - ccp.conf
 

kr/docker-compose.yml

@@ -1,6 +1,10 @@
 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

kr/modules/lens-compose.yml

@@ -1,6 +1,8 @@
 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:

lib/functions.sh

@@ -171,8 +171,10 @@ optimizeBlazeMemoryUsage() {
 		if [ $available_system_memory_chunks -eq 0 ]; then
 			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
 			export BLAZE_RESOURCE_CACHE_CAP=128000;
+			export BLAZE_CQL_CACHE_CAP=32;
 		else
 			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
+			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
 		fi
 	fi
 }

minimal/modules/onko.root.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUcGXxIZMxUOoI2kf8FArsOvQfvwwwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQxMDMxMDkxOTUwWhcNMzQx
-MDI5MDkyMDIwWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBALX+8X4r2mWki4HLs2E5dXR9oGL+8Zos1s9Rmeaz
-FgxnpKf6wlop4ZlJd01Pgi3HNFo7XPFi76zalRsHS+rWN3tOy6r5KIjCYiqPb3AY
-luZuy7jAQOBGHKODVfJH1QCRqsvEwRbOU6nNFAkMcjSxt5+PmwB1U7+Kvmly4sYI
-i4t/gyVvcfEsiZ5LYQ7IpEf+or2Ugpb6j4KlTn+gKFzSfgl+yRhE0bnFEf0eBa+r
-HLLpq4hL16+pb6/WZ4DfM9QDioX6Tj2Hje9Va4RJ2dROENuq5sJugdE28hH9qEwE
-2bmKh6qvblgwkI3rJFkYH+scBtLEUH0KJY+SZ1iYHkoEaCkCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFOe/txl3B7Sd
-NFE+615Z3rfzqBR4MB8GA1UdIwQYMBaAFOe/txl3B7SdNFE+615Z3rfzqBR4MBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQA3kVJlBOHn
-Tscsk1FKLYNWE/fr3oUNPUYzXi4lln+UNdRHSdXUPzBp4B5oIi3uymdYg2Rzq9Su
-/xjE7++thgQJ37l/DpCm/TUmUFfH5ZqcaMPA+L21mw9G129teCP1nVuXjtYhwnBk
-fRiz1tzpO1rZCxC+vxIhcPeYSKbaAQTywtJu0MpduGFrfIwLtrxa4GLRQFD06KPx
-Ijq6Pt6kC2abcYtKCMCWmpzttQAq4csWbmWINKkD6GMkuJVpzEx3csg8rCyPCaX0
-HedLiKRqaSOzDRnIWfD2CQX6qMg8TNtnxFnZTlc9honxnwcGaeLZKNEg+1oPA40V
-NOffBIMF4DAV
------END CERTIFICATE-----

minimal/modules/onkofdz-compose.yml

@@ -1,91 +0,0 @@
-version: "3.7"
-
-services:
-  beam-proxy:
-    image: samply/beam-proxy:develop-sockets
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      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
-      APP_beamsel_KEY: ${BEAMSEL_SECRET}
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/minimal/modules/onko.root.pem:/conf/root.crt.pem:ro
-  postgres:
-    image: postgres:9.5-alpine
-    container_name: bridgehead-onkofdz-postgres
-    environment:
-      POSTGRES_DB: mainzelliste-sel
-      POSTGRES_USER: mainzelliste-sel
-      POSTGRES_PASSWORD: ${MAINZELLISTE_DB_PASSWORD}
-    volumes:
-      # - ./postgres-logs:/var/log/postgresql
-      - ml-data:/var/lib/postgresql/data
-    depends_on:
-      - secureepilinker
-  mainzelliste:
-    image: medicalinformatics/mainzelliste:secureepilinker-alpha
-    container_name: bridgehead-onkofdz-mainzelliste
-    environment:
-      ML_API_KEY: ${LOCAL_SEL_API_KEY}
-      ML_DB_HOST: postgres
-      ML_DB_PORT: 5432
-      ML_DB_USER: mainzelliste-sel
-      ML_DB_NAME: mainzelliste-sel
-      ML_DB_PASS: ${MAINZELLISTE_DB_PASSWORD}
-      ML_LOCAL_ID: ${SITE_ID}
-      ML_LOCAL_SEL_URL: http://secureepilinker:8161
-      ML_LOCAL_CALLBACK_LINK_URL: http://mainzelliste:8080/Communicator/linkCallback
-      ML_LOCAL_CALLBACK_MATCH_URL: http://mainzelliste:8080/Communicator/matchCallback/${REMOTE_SEL_SITE}
-      ML_LOCAL_DATA_SERVICE_URL: http://mainzelliste:8080/Communicator/getAllRecords
-      ML_LOCAL_AUTHENTICATION_TYPE: apiKey
-      ML_LOCAL_API_KEY: ${LOCAL_SEL_API_KEY}
-      ML_SERVER_0_REMOTEID: ${REMOTE_SEL_SITE}
-      ML_SERVER_0_IDTYPE: link-${SITE_ID}-${REMOTE_SEL_SITE}
-      ML_SERVER_0_REMOTE_SEL_URL: http://beamsel:8080
-      ML_SERVER_0_APIKEY: ${REMOTE_SEL_API_KEY}
-      ### Linkage Service not used for matching
-      ML_SERVER_0_LINKAGE_SERVICE_BASE_URL: ${LS_SEL_URL}
-      ML_SERVER_0_LINKAGE_SERVICE_AUTH_TYPE: apiKey
-      ML_SERVER_0_LINKAGE_SERVICE_SHARED_KEY: ${LS_SEL_SHARED_KEY}
-      ML_LOG_MODE: stdout #stdout=stdout everything else =logging in mainzelliste.log
-      ML_LOG_LEVEL: INFO
-      no_proxy: "localhost,secureepilinker"
-    volumes:
-      # - ./logs:/usr/local/tomcat/logs/
-      - /etc/bridgehead/onkofdz/config/mainzelliste.conf.docker:/run/secrets/mainzelliste.docker.conf
-      - /etc/bridgehead/onkofdz/config/sel.conf.docker:/run/secrets/sel.docker.conf
-    depends_on:
-      - postgres
-      - secureepilinker
-  secureepilinker:
-    image: docker.verbis.dkfz.de/onkofdz/secureepilinker:beamsel
-    container_name: bridgehead-onkofdz-secureepilinker
-    environment:
-      no_proxy: "mainzelliste,beamsel"
-    volumes:
-      - "/etc/bridgehead/onkofdz/config/epilinker.serverconf.json:/data/serverconf.json"
-    command: '-vvvv'
-  beamsel:
-    image: docker.verbis.dkfz.de/onkofdz/beam-sel
-    container_name: bridgehead-onkofdz-beamsel
-    environment:
-      BEAM_URL: "http://beam-proxy:8081"
-      BEAM_SECRET: ${BEAMSEL_SECRET}
-      BEAM_ID: beamsel.${PROXY_ID}
-      SEL_ADDR: "secureepilinker:8161"
-    depends_on:
-      - secureepilinker
-volumes:
-  ml-data:
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

minimal/modules/onkofdz-setup.sh

@@ -1,15 +0,0 @@
-#!/bin/bash
-
-if [ -n "${ENABLE_ONKOFDZ}" ]; then
-  BROKER_ID=test.broker.onkofdz.samply.de
-  BROKER_URL=https://${BROKER_ID}
-  PROXY_ID=${SITE_ID}.${BROKER_ID}
-  BEAMSEL_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-  SUPPORT_EMAIL=tobias.kussel@dkfz-heidelberg.de
-  PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-
-  BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-  log INFO "Loading OnkoFDZ module"
-  OVERRIDE+=" -f ./$PROJECT/modules/onkofdz-compose.yml"
-fi