Configuration

The Data Quality Agent can be configured through its web interface or using environment variables. This page provides details on how to use environment variables for configuration.

TIP

Configuration is typically done during deployment. See the Deployment Guide for basic setup instructions.

Environment Variables

Environment variables are the primary way to configure the Data Quality Agent, especially in containerized deployments (Docker). They allow you to modify the application's behavior without changing the code or rebuilding the image.

General Guidance

When deploying with Docker or Docker Compose, you can set environment variables in your compose.yaml file:

services:
  quality-agent:
    image: ghcr.io/bbmri-cz/data-quality-agent:latest
    environment:
      - ENV_VAR_NAME=value
      - ANOTHER_VAR=another_value

Configuration Overrides

The Data Quality Agent supports a flexible mechanism to override any application setting using environment variables. This is particularly useful for automated deployments or when you need to change settings that are not exposed through specific environment variables.

How It Works

Any setting available in the application configuration can be overridden by setting an environment variable with the prefix APP_SETTING_. The override system works as follows:

1. Prefix: Use APP_SETTING_ at the beginning of the environment variable name.
2. Normalization: The system normalizes both the environment variable name (after removing the prefix) and the internal setting names. Normalization involves:
   • Converting to lowercase.
   • Removing underscores (_), dots (.), and dashes (-).
3. Matching: If a normalized environment variable matches a normalized setting name, the setting's value is updated with the value from the environment variable.

Examples

Suppose you want to override the fhirUrl setting.

• Internal Setting Name: fhirUrl
• Allowed Environment Variable Formats:
  • APP_SETTING_FHIRURL=http://new-url.com
  • APP_SETTING_FHIR_URL=http://new-url.com
  • APP_SETTING_fhir_url=http://new-url.com

All of the above will successfully override the fhirUrl setting because they all normalize to fhirurl, which matches the normalized setting name.

The same logic applies to other settings like fhirUsername.

• Override fhirUsername: APP_SETTING_FHIR_USERNAME=admin

Secure Your Config

Be careful when using environment variables for sensitive information like passwords. Ensure your compose.yaml file is secure or use Docker secrets/env files where appropriate.

Specific Agent Configuration

The following are standard environment variables recognized by the Data Quality Agent:

Variable	Description	Default
REPORTING_SERVER_URL	URL of the central reporting server to send data to.	(Optional)
REPORTING_SERVER_NAME	Name of the reporting server for identification.	Central Data Quality Server of BBMRI
OTEL_METRICS_EXPORT_ENABLED	Enables OTLP metrics export (true/false).	false
OTEL_EXPORTER_OTLP_METRICS_ENDPOINT	OTLP HTTP metrics endpoint URL.	https://grafana.bbmri-eric.eu/otel/v1/metrics
OTEL_EXPORTER_OTLP_AUTHORIZATION	Optional Authorization header value (for example Bearer <token>) sent with OTLP metrics requests.	(Not set)
You can also define additional labels with MANAGEMENT_METRICS_TAGS_<LABEL_NAME>.

Additionally, as described above, you can override any internal setting using the APP_SETTING_ prefix. Common settings include:

• fhirUrl: The URL of the FHIR server to connect to.
• fhirUsername: Username for FHIR server authentication.
• fhirPassword: Password for FHIR server authentication (Base64 encoded).

By using environment variables, you can fully automate the configuration of your Data Quality Agent during deployment.