secure db and ml

README.md

@@ -27,7 +27,6 @@ This repository is the starting point for any information and tools you will nee
     - [Teiler (Frontend)](#teiler-frontend)
     - [Data Exporter Service](#data-exporter-service)
       - [Data Quality Report](#data-quality-report)
-    - [Data Quality Agent](#data-quality-agent)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -425,32 +424,6 @@ ENABLE_EXPORTER=true
 ```
 [For further information](docs/exporter.md)  
 
-### Data Quality Agent
-
-The Data Quality Agent is an optional module that periodically evaluates the quality of FHIR data stored in Blaze. It generates local data quality reports accessible via the Bridgehead web interface.
-
-To enable the service, set the following variable in your `<PROJECT>.conf` file:
-
-```bash
-ENABLE_DATA_QUALITY_AGENT=true
-```
-
-#### Sharing Data Quality Reports (recommended)
-
-We encourage sharing your data quality reports with the central BBMRI-ERIC quality dashboard. The reports contain only aggregated, non-patient-identifiable statistics and help the network to monitor and improve overall data quality. However, quality reporting is completely optional and opt-in.
-
-To opt in, additionally set the following variables in your `<PROJECT>.conf` file:
-
-```bash
-DATA_QUALITY_SERVER_URL=https://quality-dashboard.bbmri-eric.eu
-DATA_QUALITY_SERVER_NAME=Central Data Quality Server of BBMRI
-```
-
-If these variables are not set, the Data Quality Agent will still run and generate local reports, but no data will be shared externally.
-
-Reports are accessible at `https://<your-host>/bbmri-data-quality-agent` (default credentials are admin:admin, please change it after first login!!).
-
-[Official documentation](https://fdqf.bbmri-eric.eu/user/deployment.html)
 ## Things you should know
 
 ### Auto-Updates

bbmri/modules/data-quality-agent-compose.yml

@@ -1,23 +0,0 @@
-version: "3.7"
-
-services:
-  data-quality-agent:
-    image: ghcr.io/bbmri-cz/data-quality-server:${DATA_QUALITY_AGENT_TAG}
-    container_name: bridgehead-bbmri-data-quality-agent
-    environment:
-      APP_SETTING_FHIR_URL: http://bridgehead-bbmri-blaze:8080/fhir
-      REPORTING_SERVER_URL: ${DATA_QUALITY_SERVER_URL}
-      REPORTING_SERVER_NAME: ${DATA_QUALITY_SERVER_NAME}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.data_quality_agent_bbmri.rule=PathPrefix(`/bbmri-data-quality-agent`)"
-      - "traefik.http.services.data_quality_agent_bbmri.loadbalancer.server.port=8082"
-      - "traefik.http.routers.data_quality_agent_bbmri.tls=true"
-      - "traefik.http.middlewares.data_quality_agent_bbmri_strip.stripprefix.prefixes=/bbmri-data-quality-agent"
-      - "traefik.http.routers.data_quality_agent_bbmri.middlewares=data_quality_agent_bbmri_strip,auth"
-    depends_on:
-      - "blaze"
-    volumes:
-      - /var/cache/bridgehead/bbmri/agent-db:/app/data
-      - /etc/localtime:/etc/localtime:ro
-      - /etc/timezone:/etc/timezone:ro

bbmri/modules/data-quality-agent-setup.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-
-if [ "$ENABLE_DATA_QUALITY_AGENT" == "true" ]; then
-    log INFO "Data Quality Agent setup detected -- will start data-quality-agent service."
-    OVERRIDE+=" -f ./$PROJECT/modules/data-quality-agent-compose.yml"
-fi
-

bbmri/modules/directory-sync.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ -n "${DS_DIRECTORY_USER_NAME}" ] || [ -n "${DS_DIRECTORY_USER_TOKEN}" ]; then
+if [ -n "${DS_DIRECTORY_USER_NAME}" ]; then
 	log INFO "Directory sync setup detected -- will start directory sync service."
 	OVERRIDE+=" -f ./$PROJECT/modules/directory-sync-compose.yml"
 fi

cce/modules/osiris2fhir-setup.sh

@@ -1,6 +0,0 @@
-#!/bin/bash
-if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
-  log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module."
-  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
-  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-fi

itcc/docker-compose.yml

@@ -32,7 +32,7 @@ services:
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
-      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      QUERIES_TO_CACHE: "/queries_to_cache.conf"
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
       - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
@@ -41,12 +41,13 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop-sockets
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
       PROXY_ID: ${PROXY_ID}
       APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      APP_omics-endpoint_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
@@ -59,7 +60,6 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
 
-
 volumes:
   blaze-data:
 

itcc/modules/itcc-omics-ingest.sh

@@ -3,4 +3,5 @@
 if [ -n "$ENABLE_OMICS" ];then
   OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml"
   GENERATE_API_KEY="$(generate_simple_password 'omics')"
+  PATIENTLIST_POSTGRES_PASSWORD=="$(generate_simple_password 'mainzelliste')"
 fi

itcc/modules/itcc-omics-ingest.yaml

@@ -1,8 +1,20 @@
 services:
   omics-endpoint:
-    image: ghcr.io/samply/itcc-omics-ingest:main
+    image: ghcr.io/samply/itcc-omics-ingest:fix-task
     environment:
-      - API_KEY=${GENERATE_API_KEY}
+      API_KEY: ${GENERATE_API_KEY}
+      RUST_LOG: debug
+      BEAM_ID: "omics-endpoint.${PROXY_ID}"
+      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
+      BEAM_URL: http://beam-proxy:8081
+      ML_URL: http://mainzelliste:8080
+      BLAZE_URL: http://bridgehead-itcc-blaze:8080/fhir/
+      DWH_SOCKET_ID: "${DWH_SOCKET_ID}"
+      DWH_TASK_ID: "${DWH_TASK_ID}"
+      ENABLE_SOCKETS: true
+      PARTNER_ID: itcc-inform
+      ML_API_KEY: ${GENERATE_API_KEY}
+
     volumes:
       - /var/cache/bridgehead/omics/data:/data/uploads
     labels:
@@ -12,3 +24,58 @@ services:
       - "traefik.http.routers.omics.tls=true"
       - "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api"
       - "traefik.http.routers.omics.middlewares=omics-stripprefix"
+
+  db:
+    image: postgres:15
+    container_name: db
+    restart: unless-stopped
+    environment:
+      POSTGRES_DB: mainzelliste
+      POSTGRES_USER: ${ML_DB_USER}
+      POSTGRES_PASSWORD: ${PATIENTLIST_POSTGRES_PASSWORD}
+    ports:
+      - "5432:5432"
+    volumes:
+      - db_data:/var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U ${ML_DB_USER} -d mainzelliste"]
+      interval: 5s
+      timeout: 5s
+      retries: 10
+      start_period: 10s
+
+  mainzelliste:
+    image: medicalinformatics/mainzelliste:latest
+    container_name: mainzelliste
+    restart: unless-stopped
+    depends_on:
+      db:
+        condition: service_healthy
+    ports:
+      - 7887:8080
+
+    environment:
+      ML_API_KEY: ${GENERATE_API_KEY}
+      ML_DB_HOST: db
+      ML_DB_PORT: "5432"
+      ML_DB_NAME: mainzelliste
+      ML_DB_USER: ${ML_DB_USER}
+      ML_DB_PASS: ${PATIENTLIST_POSTGRES_PASSWORD}
+      ML_DB_DRIVER: org.postgresql.Driver
+      ML_DB_TYPE: postgresql
+      ML_LOG_LEVEL: INFO
+      ML_ALLOWEDREMOTEADDRESSES: "127.0.0.1,::1,172.16.0.0/12"
+
+    secrets:
+      - mainzelliste.docker.conf
+      - source: symmetric_key
+        target: /etc/resources/keys/symmetric_key.der
+
+volumes:
+  db_data:
+secrets:
+  mainzelliste.docker.conf:
+    file: /etc/bridgehead/mainzelliste/mainzelliste.docker.conf
+
+  symmetric_key:
+    file: /etc/bridgehead/mainzelliste/keyset_siv.json

itcc/vars

@@ -7,6 +7,9 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 PUBLIC_ENVIRONMENT=prod
+DWH_SOCKET_ID=socket.itcc-datalake.${BROKER_ID}
+DWH_TASK_ID=task.itcc-datalake.${BROKER_ID}
+ML_DB_USER=mainzelliste
 
 for module in $PROJECT/modules/*.sh
 do

kr/docker-compose.yml

@@ -12,8 +12,7 @@ services:
       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}
+      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"

kr/modules/export-and-qb.curl-templates

@@ -0,0 +1,6 @@
+# Full Excel Export
+curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
+--header 'x-api-key: ${EXPORT_API_KEY}'
+
+# QB
+curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

kr/modules/lens-compose.yml

@@ -4,41 +4,32 @@ services:
     deploy:
       replicas: 1 #reactivate if lens is in use
     container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/kr-explorer:main
+    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    environment:
-      PUBLIC_SPOT_URL: https://${HOST}/prod
     labels:
-      - "traefik.http.services.lens.loadbalancer.server.port=3000"
       - "traefik.enable=true"
-      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.routers.lens.tls=true"
+      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.landing.tls=true"
 
   spot:
-    image: samply/rustyspot:latest
+    image: docker.verbis.dkfz.de/ccp-private/central-spot
     environment:
       BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_PROXY_URL: http://beam-proxy:8081
+      BEAM_URL: http://beam-proxy:8081
-      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
+      BEAM_PROXY_ID: ${SITE_ID}
-      CORS_ORIGIN: "https://${HOST}"
+      BEAM_BROKER_ID: ${BROKER_ID}
-      SITES: ${SITES}
+      BEAM_APP_ID: "focus"
-      TRANSFORM: LENS
+      PROJECT_METADATA: "kr_supervisors"
-      PROJECT: kr
-      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8055"
+      - "traefik.http.services.spot.loadbalancer.server.port=8080"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
       - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
-
-  beam-proxy:
-    environment:
-      APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}

kr/modules/obds2fhir-rest-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
   obds2fhir-rest:
     container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
+    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
     environment:
       IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
       MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

kr/vars

@@ -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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=p.delpy@dkfz-heidelberg.de
+SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 

lib/functions.sh

@@ -337,7 +337,7 @@ function sync_secrets() {
 }
 
 function secret_sync_gitlab_token() {
-    if [[ "$PROJECT" != "ccp" && "$PROJECT" != "bbmri" ]]; then
+    if [[ "$PROJECT" != "dktk" && "$PROJECT" != "bbmri" ]]; then
         log "INFO" "Not running Secret Sync for project minimal"
         return
     fi

pscc/modules/osiris2fhir-compose.yml

@@ -1,15 +0,0 @@
-services:
-  osiris2fhir:
-    container_name: bridgehead-osiris2fhir
-    image: docker.verbis.dkfz.de/ccp/osiris2fhir
-    environment:
-      FHIR_PROFILE: ${PROJECT:-pscc}
-      LOG_LEVEL: ${LOG_LEVEL:-INFO}
-      SALT: ${LOCAL_SALT}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.osiris2fhir.rule=PathPrefix(`/osiris2fhir`)"
-      - "traefik.http.middlewares.osiris2fhir_strip.stripprefix.prefixes=/osiris2fhir"
-      - "traefik.http.services.osiris2fhir.loadbalancer.server.port=8080"
-      - "traefik.http.routers.osiris2fhir.tls=true"
-      - "traefik.http.routers.osiris2fhir.middlewares=osiris2fhir_strip,auth"

pscc/modules/osiris2fhir-setup.sh

@@ -1,6 +0,0 @@
-#!/bin/bash
-if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
-  log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module."
-  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
-  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-fi

versions/acceptance

@@ -4,4 +4,3 @@ BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
 MTBA_TAG=develop
-DATA_QUALITY_AGENT_TAG=latest

versions/prod

@@ -4,4 +4,3 @@ BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=main
 MTBA_TAG=main
-DATA_QUALITY_AGENT_TAG=0.1

versions/test

@@ -4,4 +4,3 @@ BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
 MTBA_TAG=develop
-DATA_QUALITY_AGENT_TAG=latest