FHIR Resource Type Filter

[jawalonoski]

Requested Feature

Modify the FHIR exporters to only export specific resources, similar to how the CSV exporter can include/exclude specific files:

synthea/src/main/resources/synthea.properties

Lines 36 to 43 in c266ab6

	# included_files and excluded_files list out the files to include/exclude in the csv exporter
	# only one of these may be set at a time, if both are set then both will be ignored
	# if neither is set, then all files will be included
	# see list of files at: https://github.com/synthetichealth/synthea/wiki/CSV-File-Data-Dictionary
	# include filenames separated with a comma, ex: patients.csv,procedures.csv,medications.csv
	# NOTE: the csv exporter does not actively delete files, so if Run 1 you included a file, then Run 2 you exclude that file, the version from Run 1 will still be present
	exporter.csv.included_files =
	exporter.csv.excluded_files =

[willdalh]

Any update on this?

I have found that I can hack a solution for this by commenting out certain parts in org.mitre.synthea.export.FhirR4.java. In my case the lines for Claim and ExplanationOfBenefit.

synthea/src/main/java/org/mitre/synthea/export/FhirR4.java

Lines 267 to 337 in 5d90e08

	for (Encounter encounter : person.record.encounters) {
	BundleEntryComponent encounterEntry = encounter(person, personEntry, bundle, encounter);
	for (HealthRecord.Entry condition : encounter.conditions) {
	condition(person, personEntry, bundle, encounterEntry, condition);
	}
	for (HealthRecord.Allergy allergy : encounter.allergies) {
	allergy(person, personEntry, bundle, encounterEntry, allergy);
	}
	for (Observation observation : encounter.observations) {
	// If the Observation contains an attachment, use a Media resource, since
	// Observation resources in v4 don't support Attachments
	if (observation.value instanceof Attachment) {
	media(person, personEntry, bundle, encounterEntry, observation);
	} else {
	observation(person, personEntry, bundle, encounterEntry, observation);
	}
	}
	for (Procedure procedure : encounter.procedures) {
	procedure(person, personEntry, bundle, encounterEntry, procedure);
	}
	for (HealthRecord.Device device : encounter.devices) {
	device(person, personEntry, bundle, device);
	}
	for (HealthRecord.Supply supply : encounter.supplies) {
	supplyDelivery(person, personEntry, bundle, supply, encounter);
	}
	for (Medication medication : encounter.medications) {
	medicationRequest(person, personEntry, bundle, encounterEntry, encounter, medication);
	}
	for (HealthRecord.Entry immunization : encounter.immunizations) {
	immunization(person, personEntry, bundle, encounterEntry, immunization);
	}
	for (Report report : encounter.reports) {
	report(person, personEntry, bundle, encounterEntry, report);
	}
	for (CarePlan careplan : encounter.careplans) {
	BundleEntryComponent careTeamEntry =
	careTeam(person, personEntry, bundle, encounterEntry, careplan);
	carePlan(person, personEntry, bundle, encounterEntry, encounter.provider, careTeamEntry,
	careplan);
	}
	for (ImagingStudy imagingStudy : encounter.imagingStudies) {
	imagingStudy(person, personEntry, bundle, encounterEntry, imagingStudy);
	}
	if (USE_US_CORE_IG) {
	String clinicalNoteText = ClinicalNoteExporter.export(person, encounter);
	boolean lastNote =
	(encounter == person.record.encounters.get(person.record.encounters.size() - 1));
	clinicalNote(person, personEntry, bundle, encounterEntry, clinicalNoteText, lastNote);
	}
	// one claim per encounter
	BundleEntryComponent encounterClaim =
	encounterClaim(person, personEntry, bundle, encounterEntry, encounter);
	explanationOfBenefit(personEntry, bundle, encounterEntry, person,
	encounterClaim, encounter, encounter.claim);
	}

Would you recommend any other way? Ideally the resources I want to omit should not be generated at all, but I guess there are some dependencies between these.

[jawalonoski]

I don't believe anyone is actively working on this yet. If you are motivated enough to issue a Pull Request, we'd happily consider it.

The hack you are using is fine for a quick local change, but you are correct that there are dependencies... or at least, references between the resources. Ideally each time a reference is created, it would instead be conditionally created based on what resources are being included/exported. This would need some pretty good test cases though to validate the results (broken references would be invalid).

[dehall]

Implemented in #1178