@phb that sounds great!
Will the LIS initiate the request for data from the lab instruments? The OpenHIM facilitates this, as well as periodic polling for data from systems.
For your data exchange from your tabular data or LIS2 connection format to FHIR that could be managed by the mapping mediator - translating data from a custom format into FHIR is a common use case. The mapping mediator currently supports JSON and XML messages. The actual conversion to FHIR is up to someone with the whole message flow context. As an example, we have a BAHMNI Patient message that we convert to a FHIR Patient resource using the mapping mediator.
We have documentation on this mediator here as well as a setup tutorial video.
Hope this helps.