features/stateful emitter

[bwalsh]

This PR:

• has a small enhancement to LocalFHIRDatabase, on insert the records will be merged instead of replaced
• an experimental test tests/unit/dataframer which contains a hopefully more readable version of the the dataframer. That specifically addresses "Observations on a DocumentReference that focuses on a Specimen"

[bwalsh]

Note: body_temperature and heart_rate are contrived (silly) example observations for a document reference :-)

Should produce:

identifier	resourceType	id	status	docStatus	date	description	type	patient_identifier	patient_id	patient_gender	patient_birthDate	specimen_identifier	specimen_id	specimen_type	body_temperature	heart_rate
	DocumentReference	document-reference	current	preliminary	2024-08-14	Laboratory report for specimen analysis	Laboratory report		patient	male	1980-05-15		specimen	Blood specimen	36.6 Cel	72 beats/minute

Where:

Source	Fields ...
From DocumentReference:	identifier	resourceType	id	status	docStatus	date	description	type
From subject (Patient)	patient_identifier	patient_id	patient_gender	patient_birthDate
From focus(Specimen)	specimen_identifier	specimen_id	specimen_type
From Observation	body_temperature	heart_rate

[bwalsh]

@teslajoy See deepmerge: is this still useful? https://github.com/ACED-IDP/gen3_util/pull/87/commits/eb5289d856d6fa192a74ac54ed99d9f5d7aad607

[bwalsh]

Note: this branch and PR should probably be separated between the "stateful emitter" and dataframer use cases. For now, let's review and see if it is useful, I can separate later.

[teslajoy]

@teslajoy See deepmerge: is this still useful? eb5289d

It will be super useful if updating data was not handled by the etl process ex. data attributes exists across different views/tables where it wasn't merged downstream or normalized after FHIRization.