Hi Stephen,
To confirm, does the clinical system expect the response data to be a FHIR resource (Patient resource in this case)?
I ask because the HTTP GET request format you specified (http://server/getpatientbyid?pid=M1234567) does not conform to FHIR's RESTful Search specification; it appears to be a custom REST call, which may have a different set of expectations in terms what response data/format is required, etc. Based on your description, it sounds like you are seeking to implement a message transformation interface that enables a PDQ (Patient Demographics Query)-type transaction.
For message conversion and processing, I think you should take a look at our existing support for IHE PDQ (v2) and PDQm (FHIR-based) profiles and see what existing components and internal calls may be used to achieve the data transformation required by your specific scenario. If the client system could be made to conform to the FHIR RESTful Search standard, then it may be easier to make direct use of our existing PDQm capabilities.
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