Nexus-Patho-to-Fhir

Kafka processor transforms Nexus pathology report data to FHIR resources meeting MII pathology profiling

Details about applied MII FHIR profiles can be reviewed Medizininformatik Initiative - Modul Pathologie

Configuration

We provide default code mapping, which is located at resources/mappings folder. Mapping information is provided via CSV files, expected columns and order is localCode, localShortName, snomedCode, snomedDisplayName.

You may provide your own mappings:

Key	Content
mapping.location.specimenType	extracted specimen with extraction method
mapping.location.specimenExtractionMethod	extraction method

Workflow (TODO)

• explain expected input
• explain created topics and their purpose

processor overview (wip)

This is how components will be organized:

Requirements

• Kafka 3.0+

Deployment (TODO)

• Kafka connect
• sample environment variable file
• expected topic configuration

Build

You may build a docker image `nexus-patho-to-fhir:latest' via

./gradlew bootBuildImage

Development (TODO)

• explain environment variables