Merge pull request #379 from samply/develop

* feat: add Data Quality Agent configuration and setup

* fix: correct environment variable name in Data Quality Agent configuration

* feat: update Data Quality Agent configuration and setup instructions

* feat: update Data Quality Agent setup and documentation

* feat: add volume configuration for agent data in Data Quality Agent compose file

* feat: update volume configuration for Data Quality Agent in compose file

* Update README.md

Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>

---------

Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>

README.md

@@ -27,6 +27,7 @@ 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)
@@ -424,6 +425,32 @@ 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

@@ -0,0 +1,23 @@
+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

@@ -0,0 +1,7 @@
+#!/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
+

lib/functions.sh

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

minimal/docker-compose.yml

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

versions/acceptance

@@ -3,4 +3,5 @@ BEAM_TAG=develop
 BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
-MTBA_TAG=develop
+MTBA_TAG=develop
+DATA_QUALITY_AGENT_TAG=latest

versions/prod

@@ -3,4 +3,5 @@ BEAM_TAG=main
 BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=main
-MTBA_TAG=main
+MTBA_TAG=main
+DATA_QUALITY_AGENT_TAG=0.1

versions/test

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