Additional tweaks for #4509 (#4510)

* Additional tweaks for #4509

* More teaks

* format imports

hapi-fhir-jpaserver-ips/src/main/java/ca/uhn/fhir/jpa/ips/generator/IpsGeneratorSvcImpl.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.ips.generator;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.fhirpath.IFhirPathEvaluationContext;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
@@ -32,6 +33,7 @@ import ca.uhn.fhir.jpa.ips.api.SectionRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.narrative.CustomThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -42,6 +44,10 @@ import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.util.CompositionBuilder;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import ca.uhn.fhir.util.ValidateUtil;
+import com.google.common.collect.BiMap;
+import com.google.common.collect.HashBiMap;
+import org.apache.commons.collections4.BidiMap;
+import org.apache.commons.collections4.bidimap.DualHashBidiMap;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
@@ -66,6 +72,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.jpa.term.api.ITermLoaderSvc.LOINC_URI;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -214,6 +221,8 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 
 							nextCandidate = previouslyExistingResource;
 							sectionResourcesToInclude.addResourceIfNotAlreadyPresent(nextCandidate, originalResourceId);
+						} else if (theGlobalResourcesToInclude.hasResourceWithReplacementId(originalResourceId)) {
+							sectionResourcesToInclude.addResourceIfNotAlreadyPresent(nextCandidate, originalResourceId);
 						} else {
 							IIdType id = myGenerationStrategy.massageResourceId(theIpsContext, nextCandidate);
 							nextCandidate.setId(id);
@@ -226,33 +235,6 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 
 			}
 
-			/*
-			 * Update any references within the added candidates - This is important
-			 * because we might be replacing resource IDs before including them in
-			 * the summary, so we need to also update the references to those
-			 * resources.
-			 */
-			for (IBaseResource nextResource : sectionResourcesToInclude.getResources()) {
-				List<ResourceReferenceInfo> references = myFhirContext.newTerser().getAllResourceReferences(nextResource);
-				for (ResourceReferenceInfo nextReference : references) {
-					String existingReference = nextReference.getResourceReference().getReferenceElement().getValue();
-					if (isNotBlank(existingReference)) {
-						existingReference = new IdType(existingReference).toUnqualifiedVersionless().getValue();
-						String replacement = theGlobalResourcesToInclude.getIdSubstitution(existingReference);
-						if (isNotBlank(replacement)) {
-							if (!replacement.equals(existingReference)) {
-								nextReference.getResourceReference().setReference(replacement);
-							}
-						} else if (theGlobalResourcesToInclude.getResourceById(existingReference) == null) {
-							// If this reference doesn't point to something we have actually
-							// included in the bundle, clear the reference.
-							nextReference.getResourceReference().setReference(null);
-							nextReference.getResourceReference().setResource(null);
-						}
-					}
-				}
-			}
-
 		}
 
 		if (sectionResourcesToInclude.isEmpty() && theSection.getNoInfoGenerator() != null) {
@@ -266,6 +248,33 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 			sectionResourcesToInclude.addResourceIfNotAlreadyPresent(noInfoResource, id);
 		}
 
+		/*
+		 * Update any references within the added candidates - This is important
+		 * because we might be replacing resource IDs before including them in
+		 * the summary, so we need to also update the references to those
+		 * resources.
+		 */
+		for (IBaseResource nextResource : sectionResourcesToInclude.getResources()) {
+			List<ResourceReferenceInfo> references = myFhirContext.newTerser().getAllResourceReferences(nextResource);
+			for (ResourceReferenceInfo nextReference : references) {
+				String existingReference = nextReference.getResourceReference().getReferenceElement().getValue();
+				if (isNotBlank(existingReference)) {
+					existingReference = new IdType(existingReference).toUnqualifiedVersionless().getValue();
+					String replacement = theGlobalResourcesToInclude.getIdSubstitution(existingReference);
+					if (isNotBlank(replacement)) {
+						if (!replacement.equals(existingReference)) {
+							nextReference.getResourceReference().setReference(replacement);
+						}
+					} else if (theGlobalResourcesToInclude.getResourceById(existingReference) == null) {
+						// If this reference doesn't point to something we have actually
+						// included in the bundle, clear the reference.
+						nextReference.getResourceReference().setReference(null);
+						nextReference.getResourceReference().setResource(null);
+					}
+				}
+			}
+		}
+
 		addSection(theSection, theCompositionBuilder, sectionResourcesToInclude, theGlobalResourcesToInclude);
 	}
 
@@ -278,6 +287,9 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 		sectionBuilder.addCodeCoding(LOINC_URI, theSection.getSectionCode(), theSection.getSectionDisplay());
 
 		for (IBaseResource next : theResourcesToInclude.getResources()) {
+			if (ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next) == BundleEntrySearchModeEnum.INCLUDE) {
+				continue;
+			}
 
 			IBaseExtension<?, ?> narrativeLink = ((IBaseHasExtensions) next).addExtension();
 			narrativeLink.setUrl("http://hl7.org/fhir/StructureDefinition/narrativeLink");
@@ -314,7 +326,18 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 
 	private String determinePatientCompartmentSearchParameterName(String theResourceType) {
 		RuntimeResourceDefinition resourceDef = myFhirContext.getResourceDefinition(theResourceType);
-		return resourceDef.getSearchParamsForCompartmentName("Patient").get(0).getName();
+		Set<String> searchParams = resourceDef.getSearchParamsForCompartmentName("Patient")
+			.stream()
+			.map(RuntimeSearchParam::getName)
+			.collect(Collectors.toSet());
+		// Prefer "patient", then "subject" then anything else
+		if (searchParams.contains(Observation.SP_PATIENT)) {
+			return Observation.SP_PATIENT;
+		}
+		if (searchParams.contains(Observation.SP_SUBJECT)) {
+			return Observation.SP_SUBJECT;
+		}
+		return searchParams.iterator().next();
 	}
 
 	private void massageResourceId(IpsContext theIpsContext, IBaseResource theResource) {
@@ -519,7 +542,7 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 
 		private final List<IBaseResource> myResources = new ArrayList<>();
 		private final Map<String, IBaseResource> myIdToResource = new HashMap<>();
-		private final Map<String, String> myOriginalIdToNewId = new HashMap<>();
+		private final BiMap<String, String> myOriginalIdToNewId = HashBiMap.create();
 
 		public List<IBaseResource> getResources() {
 			return myResources;
@@ -549,6 +572,10 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
 			return getResourceById(theReference.toUnqualifiedVersionless().getValue());
 		}
 
+		public boolean hasResourceWithReplacementId(String theReplacementId) {
+			return myOriginalIdToNewId.containsValue(theReplacementId);
+		}
+
 		public IBaseResource getResourceById(String theReference) {
 			return myIdToResource.get(theReference);
 		}

hapi-fhir-jpaserver-ips/src/test/java/ca/uhn/fhir/jpa/ips/generator/IpsGenerationTest.java

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.ips.generator;
 
-import ca.uhn.fhir.batch2.jobs.models.BatchResourceId;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
@@ -9,11 +9,16 @@ import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
 import ca.uhn.fhir.util.ClasspathUtil;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ValidationResult;
+import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.MedicationStatement;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Resource;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -22,10 +27,13 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.test.context.ContextConfiguration;
 
+import java.util.List;
+
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.matchesPattern;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 @ContextConfiguration(classes = {IpsGenerationTest.IpsConfig.class})
 public class IpsGenerationTest extends BaseResourceProviderR4Test {
@@ -41,6 +49,7 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
 	@AfterEach
 	public void afterEach() {
 		myServer.withServer(t -> t.unregisterProvider(myIpsOperationProvider));
+		myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC);
 	}
 
 
@@ -65,26 +74,52 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
 		ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
 
 		// Verify
-
+		validateDocument(outcome);
-		assertEquals(37, output.getEntry().size());
+		assertEquals(117, output.getEntry().size());
-		String patientId = findFirstEntryResource(output, Patient.class).getId();
+		String patientId = findFirstEntryResource(output, Patient.class, 1).getId();
 		assertThat(patientId, matchesPattern("urn:uuid:.*"));
-		MedicationStatement medicationStatement = findFirstEntryResource(output, MedicationStatement.class);
+		MedicationStatement medicationStatement = findFirstEntryResource(output, MedicationStatement.class, 2);
 		assertEquals(patientId, medicationStatement.getSubject().getReference());
 		assertNull(medicationStatement.getInformationSource().getReference());
 	}
 
-	@SuppressWarnings("unchecked")
+	@Test
-	private <T extends IBaseResource> T findFirstEntryResource(Bundle theBundle, Class<T> theType) {
+	public void testGenerateTinyPatientSummary() {
-		return (T) theBundle
+		myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ANY);
-			.getEntry()
+
-			.stream()
+		Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/tiny-patient-everything.json.gz");
-			.filter(t -> theType.isAssignableFrom(t.getResource().getClass()))
+		sourceData.setType(Bundle.BundleType.TRANSACTION);
-			.findFirst()
+		for (Bundle.BundleEntryComponent nextEntry : sourceData.getEntry()) {
-			.orElseThrow()
+			nextEntry.getRequest().setMethod(Bundle.HTTPVerb.PUT);
-			.getResource();
+			nextEntry.getRequest().setUrl(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
+		}
+		Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
+		ourLog.info("Created {} resources", outcome.getEntry().size());
+
+		Bundle output = myClient
+			.operation()
+			.onInstance("Patient/5342998")
+			.named(JpaConstants.OPERATION_SUMMARY)
+			.withNoParameters(Parameters.class)
+			.returnResourceType(Bundle.class)
+			.execute();
+		ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+		// Verify
+		validateDocument(outcome);
+		assertEquals(7, output.getEntry().size());
+		String patientId = findFirstEntryResource(output, Patient.class, 1).getId();
+		assertThat(patientId, matchesPattern("urn:uuid:.*"));
+		assertEquals(patientId, findEntryResource(output, Condition.class, 0, 2).getSubject().getReference());
+		assertEquals(patientId, findEntryResource(output, Condition.class, 1, 2).getSubject().getReference());
 	}
 
+	private void validateDocument(Bundle theOutcome) {
+		FhirValidator validator = myFhirContext.newValidator();
+		validator.registerValidatorModule(new FhirInstanceValidator(myFhirContext));
+		ValidationResult validation = validator.validateWithResult(theOutcome);
+		assertTrue(validation.isSuccessful(), () -> myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(validation.toOperationOutcome()));
+	}
 
 	@Configuration
 	public static class IpsConfig {
@@ -107,5 +142,21 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
 
 	}
 
+	@SuppressWarnings("unchecked")
+	private static <T extends IBaseResource> T findFirstEntryResource(Bundle theBundle, Class<T> theType, int theExpectedCount) {
+		return findEntryResource(theBundle, theType, 0, theExpectedCount);
+	}
+
+	@SuppressWarnings("unchecked")
+	static <T extends IBaseResource> T findEntryResource(Bundle theBundle, Class<T> theType, int index, int theExpectedCount) {
+		List<Resource> resources = theBundle
+			.getEntry()
+			.stream()
+			.map(Bundle.BundleEntryComponent::getResource)
+			.filter(r -> theType.isAssignableFrom(r.getClass()))
+			.toList();
+		assertEquals(theExpectedCount, resources.size());
+		return (T) resources.get(index);
+	}
 
 }

hapi-fhir-jpaserver-ips/src/test/java/ca/uhn/fhir/jpa/ips/generator/IpsGeneratorSvcImplTest.java

@@ -33,6 +33,7 @@ import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Device;
 import org.hl7.fhir.r4.model.DeviceUseStatement;
 import org.hl7.fhir.r4.model.DiagnosticReport;
+import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Immunization;
 import org.hl7.fhir.r4.model.Medication;
@@ -60,12 +61,15 @@ import java.util.Collections;
 import java.util.List;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.jpa.ips.generator.IpsGenerationTest.findEntryResource;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
@@ -74,6 +78,8 @@ public class IpsGeneratorSvcImplTest {
 	public static final String MEDICATION_ID = "Medication/tyl";
 	public static final String MEDICATION_STATEMENT_ID = "MedicationStatement/meds";
 	public static final String MEDICATION_STATEMENT_ID2 = "MedicationStatement/meds2";
+	public static final String PATIENT_ID = "Patient/123";
+	public static final String ENCOUNTER_ID = "Encounter/encounter";
 	private static final List<Class<? extends IBaseResource>> RESOURCE_TYPES = Lists.newArrayList(
 		AllergyIntolerance.class,
 		CarePlan.class,
@@ -157,7 +163,7 @@ public class IpsGeneratorSvcImplTest {
 		registerRemainingResourceDaos();
 
 		// Test
-		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
 
 		// Verify Bundle Contents
 		List<String> contentResourceTypes = toEntryResourceTypeStrings(outcome);
@@ -170,12 +176,7 @@ public class IpsGeneratorSvcImplTest {
 
 		// Verify
 		Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
-		Composition.SectionComponent section = compositions
+		Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.MEDICATION_SUMMARY);
-			.getSection()
-			.stream()
-			.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.MEDICATION_SUMMARY).getTitle()))
-			.findFirst()
-			.orElseThrow();
 
 		HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
 		ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
@@ -191,6 +192,17 @@ public class IpsGeneratorSvcImplTest {
 		assertThat(row.getCell(4).asNormalizedText(), containsString("2023"));
 	}
 
+	@Nonnull
+	private Composition.SectionComponent findSection(Composition compositions, IpsSectionEnum sectionEnum) {
+		Composition.SectionComponent section = compositions
+			.getSection()
+			.stream()
+			.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(sectionEnum).getTitle()))
+			.findFirst()
+			.orElseThrow();
+		return section;
+	}
+
 	@Test
 	public void testMedicationSummary_DuplicateSecondaryResources() {
 		myStrategy.setSectionRegistry(new SectionRegistry().addGlobalCustomizer(t -> t.withNoInfoGenerator(null)));
@@ -209,7 +221,7 @@ public class IpsGeneratorSvcImplTest {
 		registerRemainingResourceDaos();
 
 		// Test
-		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
 
 		// Verify Bundle Contents
 		List<String> contentResourceTypes = toEntryResourceTypeStrings(outcome);
@@ -248,7 +260,7 @@ public class IpsGeneratorSvcImplTest {
 		registerRemainingResourceDaos();
 
 		// Test
-		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
 
 		// Verify Bundle Contents
 		List<String> contentResourceTypes = toEntryResourceTypeStrings(outcome);
@@ -263,12 +275,7 @@ public class IpsGeneratorSvcImplTest {
 
 		// Verify narrative - should have 2 rows (one for each primary MedicationStatement)
 		Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
-		Composition.SectionComponent section = compositions
+		Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.MEDICATION_SUMMARY);
-			.getSection()
-			.stream()
-			.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.MEDICATION_SUMMARY).getTitle()))
-			.findFirst()
-			.orElseThrow();
 
 		HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
 		ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
@@ -304,16 +311,11 @@ public class IpsGeneratorSvcImplTest {
 		registerRemainingResourceDaos();
 
 		// Test
-		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
 
 		// Verify
 		Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
-		Composition.SectionComponent section = compositions
+		Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.MEDICAL_DEVICES);
-			.getSection()
-			.stream()
-			.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.MEDICAL_DEVICES).getTitle()))
-			.findFirst()
-			.orElseThrow();
 
 		HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
 		ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
@@ -356,16 +358,11 @@ public class IpsGeneratorSvcImplTest {
 		registerRemainingResourceDaos();
 
 		// Test
-		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
 
 		// Verify
 		Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
-		Composition.SectionComponent section = compositions
+		Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.IMMUNIZATIONS);
-			.getSection()
-			.stream()
-			.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.IMMUNIZATIONS).getTitle()))
-			.findFirst()
-			.orElseThrow();
 
 		HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
 		ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
@@ -383,10 +380,82 @@ public class IpsGeneratorSvcImplTest {
 		assertThat(row.getCell(6).asNormalizedText(), containsString("2023"));
 	}
 
+
+	@Test
+	public void testReferencesUpdatedInSecondaryInclusions() {
+		// Setup Patient
+		registerPatientDaoWithRead();
+
+		// Setup Medication + MedicationStatement
+		Encounter encounter = new Encounter();
+		encounter.setId(new IdType(ENCOUNTER_ID));
+		encounter.setSubject(new Reference(PATIENT_ID));
+		ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(encounter, BundleEntrySearchModeEnum.INCLUDE);
+
+		Condition conditionActive = new Condition();
+		conditionActive.setId("Condition/conditionActive");
+		conditionActive.getClinicalStatus().addCoding()
+			.setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical")
+			.setCode("active");
+		conditionActive.setSubject(new Reference(PATIENT_ID));
+		conditionActive.setEncounter(new Reference(ENCOUNTER_ID));
+		ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(conditionActive, BundleEntrySearchModeEnum.MATCH);
+
+		Condition conditionResolved = new Condition();
+		conditionResolved.setId("Condition/conditionResolved");
+		conditionResolved.getClinicalStatus().addCoding()
+			.setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical")
+			.setCode("resolved");
+		conditionResolved.setSubject(new Reference(PATIENT_ID));
+		conditionResolved.setEncounter(new Reference(ENCOUNTER_ID));
+		ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(conditionResolved, BundleEntrySearchModeEnum.MATCH);
+
+		// Conditions will be loaded from two sections (problem list and illness history) so
+		// we return an active condition the first time and a resolved one the second
+		IFhirResourceDao<Condition> conditionDao = registerResourceDaoWithNoData(Condition.class);
+		when(conditionDao.search(any(), any())).thenReturn(
+			new SimpleBundleProvider(Lists.newArrayList(conditionActive, encounter)),
+			new SimpleBundleProvider(Lists.newArrayList(conditionResolved, encounter))
+		);
+
+		registerRemainingResourceDaos();
+
+		// Test
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
+
+		// Verify cross-references
+		Patient addedPatient = findEntryResource(outcome, Patient.class, 0, 1);
+		assertThat(addedPatient.getId(), startsWith("urn:uuid:"));
+		Condition addedCondition = findEntryResource(outcome, Condition.class, 0, 2);
+		assertThat(addedCondition.getId(), startsWith("urn:uuid:"));
+		Condition addedCondition2 = findEntryResource(outcome, Condition.class, 1, 2);
+		assertThat(addedCondition2.getId(), startsWith("urn:uuid:"));
+		Encounter addedEncounter = findEntryResource(outcome, Encounter.class, 0, 1);
+		assertThat(addedEncounter.getId(), startsWith("urn:uuid:"));
+		MedicationStatement addedMedicationStatement = findEntryResource(outcome, MedicationStatement.class, 0, 1);
+		assertThat(addedMedicationStatement.getId(), startsWith("urn:uuid:"));
+		assertEquals("no-medication-info", addedMedicationStatement.getMedicationCodeableConcept().getCodingFirstRep().getCode());
+		assertEquals(addedPatient.getId(), addedCondition.getSubject().getReference());
+		assertEquals(addedEncounter.getId(), addedCondition.getEncounter().getReference());
+		assertEquals(addedPatient.getId(), addedEncounter.getSubject().getReference());
+		assertEquals(addedPatient.getId(), addedMedicationStatement.getSubject().getReference());
+
+		// Verify sections
+		ourLog.info("Resource: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
+		verify(conditionDao, times(2)).search(any(), any());
+		Composition composition = (Composition) outcome.getEntry().get(0).getResource();
+		Composition.SectionComponent problemListSection = findSection(composition, IpsSectionEnum.PROBLEM_LIST);
+		assertEquals(addedCondition.getId(), problemListSection.getEntry().get(0).getReference());
+		assertEquals(1, problemListSection.getEntry().size());
+		Composition.SectionComponent illnessHistorySection = findSection(composition, IpsSectionEnum.ILLNESS_HISTORY);
+		assertEquals(addedCondition2.getId(), illnessHistorySection.getEntry().get(0).getReference());
+		assertEquals(1, illnessHistorySection.getEntry().size());
+	}
+
 	private void registerPatientDaoWithRead() {
 		IFhirResourceDao<Patient> patientDao = registerResourceDaoWithNoData(Patient.class);
 		Patient patient = new Patient();
-		patient.setId("Patient/123");
+		patient.setId(PATIENT_ID);
 		when(patientDao.read(any(), any())).thenReturn(patient);
 	}
 
@@ -432,12 +501,11 @@ public class IpsGeneratorSvcImplTest {
 
 	@Nonnull
 	private static List<String> toEntryResourceTypeStrings(Bundle outcome) {
-		List<String> contentResourceTypes = outcome
+		return outcome
 			.getEntry()
 			.stream()
 			.map(t -> t.getResource().getResourceType().name())
 			.collect(Collectors.toList());
-		return contentResourceTypes;
 	}
 
 	@Nonnull

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -1,5 +1,5 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -48,11 +48,16 @@
 			<version>${project.version}</version>
 			<classifier>classes</classifier>
 		</dependency>
-        <dependency>
+		<dependency>
-            <groupId>ca.uhn.hapi.fhir</groupId>
+			<groupId>ca.uhn.hapi.fhir</groupId>
-            <artifactId>hapi-fhir-server-openapi</artifactId>
+			<artifactId>hapi-fhir-server-openapi</artifactId>
-            <version>${project.version}</version>
+			<version>${project.version}</version>
-        </dependency>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-ips</artifactId>
+			<version>${project.version}</version>
+		</dependency>
 
 		<dependency>
 			<groupId>com.helger</groupId>

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
+import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
 import ca.uhn.fhir.jpa.provider.DiffProvider;
 import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
@@ -152,6 +153,7 @@ public class TestRestfulServer extends RestfulServer {
 				setServerConformanceProvider(confProvider);
 				providers.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
 				providers.add(myAppCtx.getBean(GraphQLProvider.class));
+				providers.add(myAppCtx.getBean(IpsOperationProvider.class));
 				break;
 			}
 			case "R4B": {

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -2,9 +2,15 @@ package ca.uhn.fhirtest.config;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.config.HapiJpaConfig;
 import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
+import ca.uhn.fhir.jpa.ips.generator.IIpsGeneratorSvc;
+import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
+import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
+import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@@ -196,5 +202,19 @@ public class TestR4Config {
 		return new PropertySourcesPlaceholderConfigurer();
 	}
 
+	@Bean
+	public IIpsGenerationStrategy ipsGenerationStrategy() {
+		return new DefaultIpsGenerationStrategy();
+	}
+
+	@Bean
+	public IIpsGeneratorSvc ipsGeneratorSvc(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry) {
+		return new IpsGeneratorSvcImpl(theFhirContext, theGenerationStrategy, theDaoRegistry);
+	}
+
+	@Bean
+	public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc) {
+		return new IpsOperationProvider(theIpsGeneratorSvc);
+	}
 
 }