Goal

Convert discrete genomic results in JSONs from VarSeq VSClinical to HL7v2 messages compatible with EPIC's DiscreteGenomicResults interface.

Scope

• Host a REST API to receive VSClinical JSONs containing discrete data on variants.
• Maintain a custom VSClinical report script (report_cancer.js) that enables VarSeq to send this JSON to the API.
• Map discrete variant data from the VSClinical JSON to LOINC codes supported by EPIC.
• Use the JSON and this mapping to construct and send an HL7v2 message to a pre-configured EPIC interface.

Usage

Launch the Flask server which hosts the REST API:

python3 varseq_hl7.py

When this server receives a POST request with a VSClinical JSON, it will send an HL7v2 message representing the JSON's data to the HOSTNAME and PORT variables set in varseq_hl7.py

Custom Report Script

To automate sending a JSON to this server from VSClinical, we use a customized report script.

This GoldenHelix blog post contains a tutorial on creating a custom report script.

report_cancer.js is an example custom report script. When a report is rendered in VarSeq using this script, it sends its JSON to the Flask server (by default assumed to be hosted at http://localhost:5000/)