4360 bulk export questionnaireresponses should get picked when author is not empty (#4361)

* added failing test

* implemented solution

* added more tests

* added changelog

* changed the implementation, now extended to get all the patient based search params for a given resource instead of 2 in a fixed list of resources

* added test for patient bulk export for resources not in patient compartment, fixed implementation to pass test

Co-authored-by: Steven Li <steven@smilecdr.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SearchParameterUtil.java

@@ -59,7 +59,7 @@ public class SearchParameterUtil {
 	 * Given the resource type, fetch its patient-based search parameter name
 	 * 1. Attempt to find one called 'patient'
 	 * 2. If that fails, find one called 'subject'
-	 * 3. If that fails, find find by Patient Compartment.
+	 * 3. If that fails, find one by Patient Compartment.
 	 * 3.1 If that returns >1 result, throw an error
 	 * 3.2 If that returns 1 result, return it
 	 */
@@ -76,6 +76,29 @@ public class SearchParameterUtil {
 		return Optional.ofNullable(myPatientSearchParam);
 	}
 
+	/**
+	 * Given the resource type, fetch all its patient-based search parameter name that's available
+	 */
+	public static Set<String> getPatientSearchParamsForResourceType(FhirContext theFhirContext, String theResourceType) {
+		RuntimeResourceDefinition runtimeResourceDefinition = theFhirContext.getResourceDefinition(theResourceType);
+
+		List<RuntimeSearchParam> searchParams = new ArrayList<>(runtimeResourceDefinition.getSearchParamsForCompartmentName("Patient"));
+		// add patient search parameter for resources that's not in the compartment
+		RuntimeSearchParam myPatientSearchParam = runtimeResourceDefinition.getSearchParam("patient");
+		if (myPatientSearchParam != null) {
+			searchParams.add(myPatientSearchParam);
+		}
+		RuntimeSearchParam mySubjectSearchParam = runtimeResourceDefinition.getSearchParam("subject");
+		if (mySubjectSearchParam != null) {
+			searchParams.add(mySubjectSearchParam);
+		}
+		if (searchParams == null || searchParams.size() == 0) {
+			String errorMessage = String.format("Resource type [%s] is not eligible for this type of export, as it contains no Patient compartment, and no `patient` or `subject` search parameter", runtimeResourceDefinition.getId());
+			throw new IllegalArgumentException(Msg.code(2222) + errorMessage);
+		}
+		// deduplicate list of searchParams and get their names
+		return searchParams.stream().map(RuntimeSearchParam::getName).collect(Collectors.toSet());
+	}
 
 	/**
 	 * Search the resource definition for a compartment named 'patient' and return its related Search Parameter.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4360-bulk-export-questionnaireresponses-should-get-picked-when-author-is-not-empty.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4360
+title: "Previously, Patient Bulk Export on certain resources with reference to patient only in author or performer did not get exported.
+This has been fixed."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java

@@ -146,9 +146,10 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
 			throw new IllegalStateException(Msg.code(797) + errorMessage);
 		}
 
-		List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParams);
+		Set<String> patientSearchParams = SearchParameterUtil.getPatientSearchParamsForResourceType(myContext, theParams.getResourceType());
-		String patientSearchParam = getPatientSearchParamForCurrentResourceType(theParams.getResourceType()).getName();
 
+		for (String patientSearchParam : patientSearchParams) {
+			List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParams);
 			for (SearchParameterMap map : maps) {
 				//Ensure users did not monkey with the patient compartment search parameter.
 				validateSearchParametersForPatient(map, theParams);
@@ -163,6 +164,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
 					pids.add(resultIterator.next());
 				}
 			}
+		}
 		return pids;
 	}
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportTest.java

@@ -13,19 +13,25 @@ import com.google.common.collect.Sets;
 import org.apache.commons.io.LineIterator;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Basic;
 import org.hl7.fhir.r4.model.Binary;
+import org.hl7.fhir.r4.model.CarePlan;
 import org.hl7.fhir.r4.model.Device;
+import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Group;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Location;
+import org.hl7.fhir.r4.model.MedicationAdministration;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.Provenance;
+import org.hl7.fhir.r4.model.QuestionnaireResponse;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.ServiceRequest;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
@@ -460,6 +466,113 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
 		verifyBulkExportResults(options, List.of("Patient/P1", obsId, provId, devId, devId2), List.of("Patient/P2", provId2, devId3));
 	}
 
+	@Test
+	public void testPatientBulkExportWithReferenceToAuthor_ShouldShowUp() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		// Create some resources
+		Patient patient = new Patient();
+		patient.setId("P1");
+		patient.setActive(true);
+		myClient.update().resource(patient).execute();
+
+		Basic basic = new Basic();
+		basic.setAuthor(new Reference("Patient/P1"));
+		String basicId = myClient.create().resource(basic).execute().getId().toUnqualifiedVersionless().getValue();
+
+		DocumentReference documentReference = new DocumentReference();
+		documentReference.setStatus(Enumerations.DocumentReferenceStatus.CURRENT);
+		documentReference.addAuthor(new Reference("Patient/P1"));
+		String docRefId = myClient.create().resource(documentReference).execute().getId().toUnqualifiedVersionless().getValue();
+
+		QuestionnaireResponse questionnaireResponseSub = new QuestionnaireResponse();
+		questionnaireResponseSub.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		questionnaireResponseSub.setSubject(new Reference("Patient/P1"));
+		String questRespSubId = myClient.create().resource(questionnaireResponseSub).execute().getId().toUnqualifiedVersionless().getValue();
+
+		QuestionnaireResponse questionnaireResponseAuth = new QuestionnaireResponse();
+		questionnaireResponseAuth.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		questionnaireResponseAuth.setAuthor(new Reference("Patient/P1"));
+		String questRespAuthId = myClient.create().resource(questionnaireResponseAuth).execute().getId().toUnqualifiedVersionless().getValue();
+
+		// set the export options
+		BulkDataExportOptions options = new BulkDataExportOptions();
+		options.setResourceTypes(Sets.newHashSet("Patient", "Basic", "DocumentReference", "QuestionnaireResponse"));
+		options.setExportStyle(BulkDataExportOptions.ExportStyle.PATIENT);
+		options.setOutputFormat(Constants.CT_FHIR_NDJSON);
+		verifyBulkExportResults(options, List.of("Patient/P1", basicId, docRefId, questRespAuthId, questRespSubId), Collections.emptyList());
+	}
+
+	@Test
+	public void testPatientBulkExportWithReferenceToPerformer_ShouldShowUp() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		// Create some resources
+		Patient patient = new Patient();
+		patient.setId("P1");
+		patient.setActive(true);
+		myClient.update().resource(patient).execute();
+
+		CarePlan carePlan = new CarePlan();
+		carePlan.setStatus(CarePlan.CarePlanStatus.COMPLETED);
+		CarePlan.CarePlanActivityComponent carePlanActivityComponent = new CarePlan.CarePlanActivityComponent();
+		CarePlan.CarePlanActivityDetailComponent carePlanActivityDetailComponent = new CarePlan.CarePlanActivityDetailComponent();
+		carePlanActivityDetailComponent.addPerformer(new Reference("Patient/P1"));
+		carePlanActivityComponent.setDetail(carePlanActivityDetailComponent);
+		carePlan.addActivity(carePlanActivityComponent);
+		String carePlanId = myClient.create().resource(carePlan).execute().getId().toUnqualifiedVersionless().getValue();
+
+		MedicationAdministration medicationAdministration = new MedicationAdministration();
+		medicationAdministration.setStatus(MedicationAdministration.MedicationAdministrationStatus.COMPLETED);
+		MedicationAdministration.MedicationAdministrationPerformerComponent medicationAdministrationPerformerComponent = new MedicationAdministration.MedicationAdministrationPerformerComponent();
+		medicationAdministrationPerformerComponent.setActor(new Reference("Patient/P1"));
+		medicationAdministration.addPerformer(medicationAdministrationPerformerComponent);
+		String medAdminId = myClient.create().resource(medicationAdministration).execute().getId().toUnqualifiedVersionless().getValue();
+
+		ServiceRequest serviceRequest = new ServiceRequest();
+		serviceRequest.setStatus(ServiceRequest.ServiceRequestStatus.COMPLETED);
+		serviceRequest.addPerformer(new Reference("Patient/P1"));
+		String sevReqId = myClient.create().resource(serviceRequest).execute().getId().toUnqualifiedVersionless().getValue();
+
+		Observation observationSub = new Observation();
+		observationSub.setStatus(Observation.ObservationStatus.AMENDED);
+		observationSub.setSubject(new Reference("Patient/P1"));
+		String obsSubId = myClient.create().resource(observationSub).execute().getId().toUnqualifiedVersionless().getValue();
+
+		Observation observationPer = new Observation();
+		observationPer.setStatus(Observation.ObservationStatus.AMENDED);
+		observationPer.addPerformer(new Reference("Patient/P1"));
+		String obsPerId = myClient.create().resource(observationPer).execute().getId().toUnqualifiedVersionless().getValue();
+
+		// set the export options
+		BulkDataExportOptions options = new BulkDataExportOptions();
+		options.setResourceTypes(Sets.newHashSet("Patient", "Observation", "CarePlan", "MedicationAdministration", "ServiceRequest"));
+		options.setExportStyle(BulkDataExportOptions.ExportStyle.PATIENT);
+		options.setOutputFormat(Constants.CT_FHIR_NDJSON);
+		verifyBulkExportResults(options, List.of("Patient/P1", carePlanId, medAdminId, sevReqId, obsSubId, obsPerId), Collections.emptyList());
+	}
+
+	@Test
+	public void testPatientBulkExportWithResourceNotInCompartment_ShouldShowUp() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		// Create some resources
+		Patient patient = new Patient();
+		patient.setId("P1");
+		patient.setActive(true);
+		myClient.update().resource(patient).execute();
+
+		Device device = new Device();
+		device.setStatus(Device.FHIRDeviceStatus.ACTIVE);
+		device.setPatient(new Reference("Patient/P1"));
+		String deviceId = myClient.create().resource(device).execute().getId().toUnqualifiedVersionless().getValue();
+
+
+		// set the export options
+		BulkDataExportOptions options = new BulkDataExportOptions();
+		options.setResourceTypes(Sets.newHashSet("Patient", "Device"));
+		options.setExportStyle(BulkDataExportOptions.ExportStyle.PATIENT);
+		options.setOutputFormat(Constants.CT_FHIR_NDJSON);
+		verifyBulkExportResults(options, List.of("Patient/P1", deviceId), Collections.emptyList());
+	}
+
 	private void verifyBulkExportResults(BulkDataExportOptions theOptions, List<String> theContainedList, List<String> theExcludedList) {
 		Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(theOptions));