7860: Expand resource references in resources returned by export

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

@@ -37,7 +37,7 @@
 import ca.uhn.fhir.jpa.model.search.SearchBuilderLoadIncludesParameters;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.mdm.svc.MdmExpandersHolder;
+import ca.uhn.fhir.mdm.svc.IBulkExportMdmResourceExpander;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
@@ -56,6 +56,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -86,7 +87,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
 	private EntityManager myEntityManager;
 	private IHapiTransactionService myHapiTransactionService;
 	private ISearchParamRegistry mySearchParamRegistry;
-	private MdmExpandersHolder myMdmExpandersHolder;
+	private IBulkExportMdmResourceExpander myBulkExportMdmResourceExpander;
 
 	@Autowired
 	public JpaBulkExportProcessor(
@@ -99,7 +100,8 @@ public JpaBulkExportProcessor(
 			EntityManager theEntityManager,
 			IHapiTransactionService theHapiTransactionService,
 			ISearchParamRegistry theSearchParamRegistry,
-			MdmExpandersHolder theMdmExpandersHolder) {
+			@Qualifier("bulkExportMdmResourceExpander")
+					IBulkExportMdmResourceExpander theBulkExportMdmResourceExpander) {
 		myContext = theContext;
 		myBulkExportHelperSvc = theBulkExportHelperSvc;
 		myStorageSettings = theStorageSettings;
@@ -109,7 +111,7 @@ public JpaBulkExportProcessor(
 		myEntityManager = theEntityManager;
 		myHapiTransactionService = theHapiTransactionService;
 		mySearchParamRegistry = theSearchParamRegistry;
-		myMdmExpandersHolder = theMdmExpandersHolder;
+		myBulkExportMdmResourceExpander = theBulkExportMdmResourceExpander;
 	}
 
 	@Override
@@ -349,7 +351,7 @@ protected RuntimeSearchParam getPatientSearchParamForCurrentResourceType(String
 	public void expandMdmResources(List<IBaseResource> theResources) {
 		for (IBaseResource resource : theResources) {
 			if (!PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(resource.fhirType())) {
-				myMdmExpandersHolder.getBulkExportMDMResourceExpanderInstance().annotateResource(resource);
+				myBulkExportMdmResourceExpander.annotateResource(resource);
 			}
 		}
 	}
@@ -405,9 +407,8 @@ private LinkedHashSet<JpaPid> getExpandedPatientList(
 
 		if (theParameters.isExpandMdm()) {
 			RequestPartitionId partitionId = theParameters.getPartitionIdOrAllPartitions();
-			patientPidsToExport.addAll(myMdmExpandersHolder
-					.getBulkExportMDMResourceExpanderInstance()
-					.expandGroup(theParameters.getGroupId(), partitionId));
+			patientPidsToExport.addAll(
+					myBulkExportMdmResourceExpander.expandGroup(theParameters.getGroupId(), partitionId));
 		}
 		return patientPidsToExport;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaBulkExportConfig.java

@@ -29,7 +29,7 @@
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
-import ca.uhn.fhir.mdm.svc.MdmExpandersHolder;
+import ca.uhn.fhir.mdm.svc.IBulkExportMdmResourceExpander;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import jakarta.persistence.EntityManager;
 import org.springframework.context.annotation.Bean;
@@ -48,7 +48,7 @@ public IBulkExportProcessor<JpaPid> jpaBulkExportProcessor(
 			EntityManager theEntityManager,
 			IHapiTransactionService theHapiTransactionService,
 			ISearchParamRegistry theSearchParamRegistry,
-			MdmExpandersHolder theMdmExpandersHolder) {
+			IBulkExportMdmResourceExpander theBulkExportMdmResourceExpander) {
 		return new JpaBulkExportProcessor(
 				theFhirContext,
 				theBulkExportHelperService,
@@ -59,7 +59,7 @@ public IBulkExportProcessor<JpaPid> jpaBulkExportProcessor(
 				theEntityManager,
 				theHapiTransactionService,
 				theSearchParamRegistry,
-				theMdmExpandersHolder);
+				theBulkExportMdmResourceExpander);
 	}
 
 	@Bean

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/MdmJpaConfig.java

@@ -30,15 +30,18 @@
 import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.mdm.api.IMdmLinkExpandSvc;
+import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.api.MdmModeEnum;
 import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
 import ca.uhn.fhir.mdm.dao.IMdmLinkImplFactory;
 import ca.uhn.fhir.mdm.svc.BulkExportMdmEidMatchOnlyResourceExpander;
 import ca.uhn.fhir.mdm.svc.BulkExportMdmResourceExpander;
+import ca.uhn.fhir.mdm.svc.IBulkExportMdmResourceExpander;
 import ca.uhn.fhir.mdm.svc.MdmEidMatchOnlyExpandSvc;
-import ca.uhn.fhir.mdm.svc.MdmExpandersHolder;
 import ca.uhn.fhir.mdm.svc.MdmExpansionCacheSvc;
 import ca.uhn.fhir.mdm.svc.MdmLinkExpandSvc;
 import ca.uhn.fhir.mdm.svc.MdmSearchExpansionSvc;
+import ca.uhn.fhir.mdm.util.EIDHelper;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
@@ -47,29 +50,45 @@
 public class MdmJpaConfig {
 
 	@Bean
-	public MdmExpandersHolder mdmLinkExpandSvcHolder(
-			FhirContext theFhirContext,
-			IMdmLinkExpandSvc theMdmLinkExpandSvc,
-			MdmEidMatchOnlyExpandSvc theMdmEidMatchOnlyLinkExpandSvc,
-			BulkExportMdmEidMatchOnlyResourceExpander theBulkExportMdmEidMatchOnlyResourceExpander,
-			BulkExportMdmResourceExpander theBulkExportMdmResourceExpander) {
-		return new MdmExpandersHolder(
-				theFhirContext,
-				theMdmLinkExpandSvc,
-				theMdmEidMatchOnlyLinkExpandSvc,
-				theBulkExportMdmResourceExpander,
-				theBulkExportMdmEidMatchOnlyResourceExpander);
+	public MdmEidMatchOnlyExpandSvc mdmEidMatchOnlyLinkExpandSvc(
+			IMdmSettings theMdmSettings, DaoRegistry theDaoRegistry, FhirContext theFhirContext) {
+		MdmEidMatchOnlyExpandSvc mdmEidMatchOnlyExpandSvc = new MdmEidMatchOnlyExpandSvc(theDaoRegistry);
+		mdmEidMatchOnlyExpandSvc.setMyEidHelper(new EIDHelper(theFhirContext, theMdmSettings));
+		return mdmEidMatchOnlyExpandSvc;
 	}
 
 	@Bean
-	public MdmEidMatchOnlyExpandSvc mdmEidMatchOnlyLinkExpandSvc(DaoRegistry theDaoRegistry) {
-		return new MdmEidMatchOnlyExpandSvc(theDaoRegistry);
+	@Primary
+	public IMdmLinkExpandSvc mdmLinkExpandSvc(
+			IMdmSettings theMdmSettings, DaoRegistry theDaoRegistry, FhirContext theFhirContext) {
+		IMdmLinkExpandSvc res;
+		if (isEidMatchOnly(theMdmSettings)) {
+			res = mdmEidMatchOnlyLinkExpandSvc(theMdmSettings, theDaoRegistry, theFhirContext);
+		} else {
+			res = new MdmLinkExpandSvc();
+		}
+		return res;
 	}
 
 	@Bean
-	@Primary
-	public IMdmLinkExpandSvc mdmLinkExpandSvc() {
-		return new MdmLinkExpandSvc();
+	public IBulkExportMdmResourceExpander bulkExportMdmResourceExpander(
+			MdmExpansionCacheSvc theMdmExpansionCacheSvc,
+			IMdmLinkDao theMdmLinkDao,
+			IIdHelperService<JpaPid> theIdHelperService,
+			DaoRegistry theDaoRegistry,
+			FhirContext theFhirContext,
+			MdmEidMatchOnlyExpandSvc theMdmEidMatchOnlyLinkExpandSvc,
+			IMdmSettings theMdmSettings) {
+
+		IBulkExportMdmResourceExpander res;
+		if (isEidMatchOnly(theMdmSettings)) {
+			res = new BulkExportMdmEidMatchOnlyResourceExpander(
+					theDaoRegistry, theMdmEidMatchOnlyLinkExpandSvc, theFhirContext, theIdHelperService);
+		} else {
+			res = new BulkExportMdmResourceExpander(
+					theMdmExpansionCacheSvc, theMdmLinkDao, theIdHelperService, theDaoRegistry, theFhirContext);
+		}
+		return res;
 	}
 
 	@Bean
@@ -82,27 +101,6 @@ public IMdmLinkDao<JpaPid, MdmLink> mdmLinkDao() {
 		return new MdmLinkDaoJpaImpl();
 	}
 
-	@Bean
-	public BulkExportMdmResourceExpander bulkExportMDMResourceExpander(
-			MdmExpansionCacheSvc theMdmExpansionCacheSvc,
-			IMdmLinkDao theMdmLinkDao,
-			IIdHelperService<JpaPid> theIdHelperService,
-			DaoRegistry theDaoRegistry,
-			FhirContext theFhirContext) {
-		return new BulkExportMdmResourceExpander(
-				theMdmExpansionCacheSvc, theMdmLinkDao, theIdHelperService, theDaoRegistry, theFhirContext);
-	}
-
-	@Bean
-	public BulkExportMdmEidMatchOnlyResourceExpander bulkExportMDMEidMatchOnlyResourceExpander(
-			DaoRegistry theDaoRegistry,
-			MdmEidMatchOnlyExpandSvc theMdmEidMatchOnlyLinkExpandSvc,
-			FhirContext theFhirContext,
-			IIdHelperService<JpaPid> theIdHelperService) {
-		return new BulkExportMdmEidMatchOnlyResourceExpander(
-				theDaoRegistry, theMdmEidMatchOnlyLinkExpandSvc, theFhirContext, theIdHelperService);
-	}
-
 	@Bean
 	public IMdmLinkImplFactory<MdmLink> mdmLinkImplFactory() {
 		return new JpaMdmLinkImplFactory();
@@ -112,4 +110,11 @@ public IMdmLinkImplFactory<MdmLink> mdmLinkImplFactory() {
 	public IMdmClearHelperSvc<JpaPid> helperSvc(IDeleteExpungeSvc<JpaPid> theDeleteExpungeSvc) {
 		return new MdmClearHelperSvcImpl(theDeleteExpungeSvc);
 	}
+
+	private boolean isEidMatchOnly(IMdmSettings theMdmSettings) {
+		return theMdmSettings.getMode() == MdmModeEnum.MATCH_ONLY
+				&& theMdmSettings.getMdmRules() != null
+				&& theMdmSettings.getMdmRules().getEnterpriseEIDSystems() != null
+				&& !theMdmSettings.getMdmRules().getEnterpriseEIDSystems().isEmpty();
+	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessorTest.java

@@ -19,7 +19,6 @@
 import ca.uhn.fhir.jpa.model.search.SearchBuilderLoadIncludesParameters;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.mdm.svc.MdmExpandersHolder;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -130,9 +129,6 @@ public JpaPid next() {
 	@Mock
 	private IIdHelperService<JpaPid> myIdHelperService;
 
-	@Mock
-	private MdmExpandersHolder myMdmExpandersHolder;
-
 	@Mock
 	private IBulkExportMdmResourceExpander myBulkExportMDMResourceExpander;
 
@@ -298,8 +294,6 @@ public void getResourcePidIterator_groupExportStyleWithPatientResource_returnsIt
 		// mdm expansion stuff
 		final JpaPid mdmExpandedPatientId = JpaPid.fromId(4567L);
 		if (theMdm) {
-
-			when(myMdmExpandersHolder.getBulkExportMDMResourceExpanderInstance()).thenReturn(myBulkExportMDMResourceExpander);
 			// mock the call to expandGroup method of the expander
 			when(myBulkExportMDMResourceExpander.expandGroup(parameters.getGroupId(), getPartitionIdFromParams(thePartitioned)))
 				.thenReturn(Set.of(mdmExpandedPatientId));
@@ -395,7 +389,6 @@ public void getResourcePidIterator_groupExportStyleWithNonPatientResource_return
 			.thenReturn(observationResultsIterator);
 
 		if (theMdm) {
-			when(myMdmExpandersHolder.getBulkExportMDMResourceExpanderInstance()).thenReturn(myBulkExportMDMResourceExpander);
 			// mock the call to expandGroup method of the expander
 			when(myBulkExportMDMResourceExpander.expandGroup(parameters.getGroupId(), getPartitionIdFromParams(thePartitioned)))
 				.thenReturn(Collections.emptySet());

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/MdmHelperConfig.java

@@ -1,8 +1,12 @@
 package ca.uhn.fhir.jpa.mdm.helper;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.mdm.api.IMdmLinkExpandSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
+import ca.uhn.fhir.mdm.svc.MdmLinkExpandSvc;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.springframework.beans.factory.annotation.Value;
@@ -39,4 +43,10 @@ IMdmSettings mdmSettings(MdmRuleValidator theMdmRuleValidator) throws IOExceptio
 			.setPreventEidUpdates(myPreventEidUpdates)
 			.setPreventMultipleEids(myPreventMultipleEids);
 	}
+
+	@Bean
+	@Primary
+	public IMdmLinkExpandSvc mdmLinkExpandSvc() {
+		return new MdmLinkExpandSvc();
+	}
 }

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmReadVirtualizationInterceptorTest.java

@@ -9,9 +9,7 @@
 import ca.uhn.fhir.jpa.mdm.helper.testmodels.MDMState;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.interceptor.MdmReadVirtualizationInterceptor;
-import ca.uhn.fhir.mdm.svc.MdmExpandersHolder;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
@@ -129,7 +127,7 @@ public void testRead_ObservationReferencingSourcePatient(boolean theUseClientAss
 		Observation obs = myObservationDao.read(myObservationReferencingSourcePatientA0Id, mySrd);
 
 		// Verify
-		assertEquals(mySourcePatientA0Id.getValue(), obs.getSubject().getReference());
+		assertEquals(myGoldenResourcePatientAId.getValue(), obs.getSubject().getReference());
 	}
 
 	/**

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

@@ -24,7 +24,6 @@
 import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
 import ca.uhn.fhir.mdm.rules.json.MdmRulesJson;
-import ca.uhn.fhir.mdm.svc.MdmExpandersHolder;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -75,6 +74,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -102,11 +102,11 @@
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
-
+@ContextConfiguration(classes = {BulkExportUseCaseTestConfig.class})
 public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(BulkExportUseCaseTest.class);
 
-	private static final  String TEST_PATIENT_EID_SYS = "http://patient-eid-sys";
+	static final  String TEST_PATIENT_EID_SYS = "http://patient-eid-sys";
 	@Autowired
 	private IJobCoordinator myJobCoordinator;
 
@@ -120,10 +120,7 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
 	private IBatch2WorkChunkRepository myWorkChunkRepository;
 	@Autowired
 	private IInterceptorService myInterceptorService;
-	@Autowired
-	private MdmRuleValidator myMdmRulesValidator;
-	@Autowired
-	private MdmExpandersHolder myMdmExpandersHolder;
+
 
 	@BeforeEach
 	public void beforeEach() {
@@ -685,12 +682,6 @@ public void testExportEmptyResult() {
 
 	@Nested
 	public class GroupBulkExportTests {
-
-		@AfterEach
-		void tearDown() {
-			restoreMdmSettingsToDefault();
-		}
-
 		@Test
 		public void testGroupExportSuccessfulyExportsPatientForwardReferences() {
 			BundleBuilder bb = new BundleBuilder(myFhirContext);
@@ -1865,8 +1856,6 @@ private IIdType createPatient() {
 
 	@Test
 	void testGroupExportWithMdmEnabled_EidMatchOnly() {
-
-		createAndSetMdmSettingsForEidMatchOnly();
 		BundleBuilder bb = new BundleBuilder(myFhirContext);
 
 		//In this test, we create two patients with the same Eid value for the eid system specified in mdm rules
@@ -1918,23 +1907,6 @@ void testGroupExportWithMdmEnabled_EidMatchOnly() {
 
 	}
 
-
-	private void createAndSetMdmSettingsForEidMatchOnly() {
-		MdmSettings mdmSettings = new MdmSettings(myMdmRulesValidator);
-		mdmSettings.setEnabled(true);
-		mdmSettings.setMdmMode(MdmModeEnum.MATCH_ONLY);
-		MdmRulesJson rules = new MdmRulesJson();
-		rules.setMdmTypes(List.of("Patient"));
-		rules.addEnterpriseEIDSystem("Patient", TEST_PATIENT_EID_SYS);
-		mdmSettings.setMdmRules(rules);
-
-		myMdmExpandersHolder.setMdmSettings(mdmSettings);
-	}
-
-	private void restoreMdmSettingsToDefault() {
-		myMdmExpandersHolder.setMdmSettings(new MdmSettings(myMdmRulesValidator));
-	}
-
 	private static void assertResourcesIds(List<IBaseResource> theResources, String... theExpectedResourceIds) {
 		assertThat(theResources).hasSize(theExpectedResourceIds.length);
 		assertThat(theResources)