Refactor to support all new tests

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java

@@ -33,17 +33,20 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
+import ca.uhn.fhir.mdm.util.CanonicalIdentifier;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.HapiExtensions;
+import ca.uhn.fhir.util.TerserUtil;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -122,11 +125,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 			@SuppressWarnings("unchecked")
 			T newResource = (T) missingResourceDef.newInstance();
 
-			if (newResource instanceof IBaseHasExtensions) {
+			tryToAddPlaceholderExtensionToResource(newResource);
-				IBaseExtension<?, ?> extension = ((IBaseHasExtensions) newResource).addExtension();
-				extension.setUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
-				extension.setValue(myContext.getPrimitiveBoolean(true));
-			}
 
 			IFhirResourceDao<T> placeholderResourceDao = myDaoRegistry.getResourceDao(theType);
 			ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
@@ -146,9 +145,34 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 		return Optional.ofNullable(valueOf);
 	}
 
+	private <T extends IBaseResource> void tryToAddPlaceholderExtensionToResource(T newResource) {
+		if (newResource instanceof IBaseHasExtensions) {
+			IBaseExtension<?, ?> extension = ((IBaseHasExtensions) newResource).addExtension();
+			extension.setUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
+			extension.setValue(myContext.getPrimitiveBoolean(true));
+		}
+	}
+
 	private <T extends IBaseResource> void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
-		boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
+//		boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
-		if (referenceHasIdentifier) {
+		CanonicalIdentifier referenceMatchUrlIdentifier = extractIdentifierFromUrl(theSourceReference.getReferenceElement().getValue());
+		CanonicalIdentifier referenceIdentifier = extractIdentifierReference(theSourceReference);
+
+		if (referenceIdentifier == null && referenceMatchUrlIdentifier != null) {
+			addMatchUrlIdentifierToTargetResource(theTargetResourceDef, theTargetResource, referenceMatchUrlIdentifier);
+		} else if (referenceIdentifier!= null && referenceMatchUrlIdentifier == null) {
+			addSubjectIdentifierToTargetResource(theSourceReference, theTargetResourceDef, theTargetResource);
+		} else if (referenceIdentifier != null && referenceMatchUrlIdentifier != null) {
+			if (referenceIdentifier.equals(referenceMatchUrlIdentifier)) {
+				addSubjectIdentifierToTargetResource(theSourceReference, theTargetResourceDef, theTargetResource);
+			} else {
+				addSubjectIdentifierToTargetResource(theSourceReference, theTargetResourceDef, theTargetResource);
+				addMatchUrlIdentifierToTargetResource(theTargetResourceDef, theTargetResource, referenceMatchUrlIdentifier);
+			}
+		}
+	}
+
+	private <T extends IBaseResource> void addSubjectIdentifierToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
 		BaseRuntimeChildDefinition targetIdentifier = theTargetResourceDef.getChildByName("identifier");
 		if (targetIdentifier != null) {
 			BaseRuntimeElementDefinition<?> identifierElement = targetIdentifier.getChildByName("identifier");
@@ -160,10 +184,57 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 				BaseRuntimeChildDefinition referenceIdentifierChild = referenceElement.getChildByName("identifier");
 				Optional<IBase> identifierOpt = referenceIdentifierChild.getAccessor().getFirstValueOrNull(theSourceReference);
 				identifierOpt.ifPresent(theIBase -> targetIdentifier.getMutator().addValue(theTargetResource, theIBase));
+			}
+		}
+	}
 
+	private <T extends IBaseResource> void addMatchUrlIdentifierToTargetResource(RuntimeResourceDefinition theTargetResourceDef, T theTargetResource, CanonicalIdentifier referenceMatchUrlIdentifier) {
+		BaseRuntimeChildDefinition identifierDefinition = theTargetResourceDef.getChildByName("identifier");
+		IBase identifierIBase = identifierDefinition.getChildByName("identifier").newInstance(identifierDefinition.getInstanceConstructorArguments());
+		IBase systemIBase = TerserUtil.newElement(myContext, "uri", referenceMatchUrlIdentifier.getSystemElement().getValueAsString());
+		IBase valueIBase = TerserUtil.newElement(myContext, "string", referenceMatchUrlIdentifier.getValueElement().getValueAsString());
+		//Set system in the IBase Identifier
+
+		BaseRuntimeElementDefinition<?> elementDefinition = myContext.getElementDefinition(identifierIBase.getClass());
+
+		BaseRuntimeChildDefinition systemDefinition = elementDefinition.getChildByName("system");
+		systemDefinition.getMutator().setValue(identifierIBase, systemIBase);
+
+		BaseRuntimeChildDefinition valueDefinition = elementDefinition.getChildByName("value");
+		valueDefinition.getMutator().setValue(identifierIBase, valueIBase);
+
+		//Set Value in the IBase identifier
+		identifierDefinition.getMutator().addValue(theTargetResource, identifierIBase);
+	}
+
+	private CanonicalIdentifier extractIdentifierReference(IBaseReference theSourceReference) {
+		Optional<IBase> identifier = myContext.newFhirPath().evaluateFirst(theSourceReference, "identifier", IBase.class);
+		if (!identifier.isPresent()) {
+			return null;
+		} else {
+			CanonicalIdentifier canonicalIdentifier = new CanonicalIdentifier();
+			Optional<IPrimitiveType> system = myContext.newFhirPath().evaluateFirst(identifier.get(), "system", IPrimitiveType.class);
+			Optional<IPrimitiveType> value = myContext.newFhirPath().evaluateFirst(identifier.get(), "value", IPrimitiveType.class);
+
+			system.ifPresent(theIPrimitiveType -> canonicalIdentifier.setSystem(theIPrimitiveType.getValueAsString()));
+			value.ifPresent(theIPrimitiveType -> canonicalIdentifier.setValue(theIPrimitiveType.getValueAsString()));
+			return canonicalIdentifier;
 		}
 	}
+
+	private CanonicalIdentifier extractIdentifierFromUrl(String theValue) {
+		if (!theValue.contains("identifier=")) {
+			return null;
 		}
+		CanonicalIdentifier identifier = new CanonicalIdentifier();
+		String identifierString = theValue.substring(theValue.indexOf("=") + 1);
+		String[] split = identifierString.split("\\|");
+		if (split.length != 2) {
+			throw new IllegalArgumentException("Can't create a placeholder reference with identifier " + theValue + ". It is not a valid identifier");
+		}
+		identifier.setSystem(split[0]);
+		identifier.setValue(split[1]);
+		return identifier;
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java

@@ -276,6 +276,7 @@ public class SearchParamWithInlineReferencesExtractor {
 					throw new InvalidRequestException(msg);
 				}
 				Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
+				//Attempt to find the target reference before creating a placeholder
 				Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest);
 
 				ResourcePersistentId match;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java

@@ -423,13 +423,13 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		List<Identifier> identifiers = placeholderPat.getIdentifier();
 
 		//inline match-url identifier
-		assertThat(identifiers.get(0).getSystem(), is(equalTo("http://foo")));
-		assertThat(identifiers.get(0).getValue(), is(equalTo("123")));
-
-		//subject identifier
 		assertThat(identifiers.get(1).getSystem(), is(equalTo("http://foo")));
 		assertThat(identifiers.get(1).getValue(), is(equalTo("123")));
 
+		//subject identifier
+		assertThat(identifiers.get(0).getSystem(), is(equalTo("http://bar")));
+		assertThat(identifiers.get(0).getValue(), is(equalTo("321")));
+
 
 		// Conditionally update a Patient with the same identifier
 		Patient patToConditionalUpdate = new Patient();

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/IdentifierUtil.java

@@ -49,6 +49,8 @@ public final class IdentifierUtil {
 		return retval;
 	}
 
+
+
 	/**
 	 * Retrieves appropriate FHIR Identifier model instance based on the context version
 	 *