applying Taha Attari's fix on branch merging to rel_7_4 (#6177)

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

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

@@ -101,7 +101,7 @@ public class FhirTerser {
 		return newList;
 	}
 
-	private ExtensionDt createEmptyExtensionDt(IBaseExtension theBaseExtension, String theUrl) {
+	private ExtensionDt createEmptyExtensionDt(IBaseExtension<?, ?> theBaseExtension, String theUrl) {
 		return createEmptyExtensionDt(theBaseExtension, false, theUrl);
 	}
 
@@ -122,13 +122,13 @@ public class FhirTerser {
 		return theSupportsUndeclaredExtensions.addUndeclaredExtension(theIsModifier, theUrl);
 	}
 
-	private IBaseExtension createEmptyExtension(IBaseHasExtensions theBaseHasExtensions, String theUrl) {
-		return (IBaseExtension) theBaseHasExtensions.addExtension().setUrl(theUrl);
+	private IBaseExtension<?, ?> createEmptyExtension(IBaseHasExtensions theBaseHasExtensions, String theUrl) {
+		return (IBaseExtension<?, ?>) theBaseHasExtensions.addExtension().setUrl(theUrl);
 	}
 
-	private IBaseExtension createEmptyModifierExtension(
+	private IBaseExtension<?, ?> createEmptyModifierExtension(
 			IBaseHasModifierExtensions theBaseHasModifierExtensions, String theUrl) {
-		return (IBaseExtension)
+		return (IBaseExtension<?, ?>)
 				theBaseHasModifierExtensions.addModifierExtension().setUrl(theUrl);
 	}
 
@@ -407,7 +407,7 @@ public class FhirTerser {
 
 	public String getSinglePrimitiveValueOrNull(IBase theTarget, String thePath) {
 		return getSingleValue(theTarget, thePath, IPrimitiveType.class)
-				.map(t -> t.getValueAsString())
+				.map(IPrimitiveType::getValueAsString)
 				.orElse(null);
 	}
 
@@ -487,7 +487,7 @@ public class FhirTerser {
 			} else {
 				// DSTU3+
 				final String extensionUrlForLambda = extensionUrl;
-				List<IBaseExtension> extensions = Collections.emptyList();
+				List<IBaseExtension<?, ?>> extensions = Collections.emptyList();
 				if (theCurrentObj instanceof IBaseHasExtensions) {
 					extensions = ((IBaseHasExtensions) theCurrentObj)
 							.getExtension().stream()
@@ -505,7 +505,7 @@ public class FhirTerser {
 					}
 				}
 
-				for (IBaseExtension next : extensions) {
+				for (IBaseExtension<?, ?> next : extensions) {
 					if (theWantedClass.isAssignableFrom(next.getClass())) {
 						retVal.add((T) next);
 					}
@@ -581,7 +581,7 @@ public class FhirTerser {
 			} else {
 				// DSTU3+
 				final String extensionUrlForLambda = extensionUrl;
-				List<IBaseExtension> extensions = Collections.emptyList();
+				List<IBaseExtension<?, ?>> extensions = Collections.emptyList();
 
 				if (theCurrentObj instanceof IBaseHasModifierExtensions) {
 					extensions = ((IBaseHasModifierExtensions) theCurrentObj)
@@ -602,7 +602,7 @@ public class FhirTerser {
 					}
 				}
 
-				for (IBaseExtension next : extensions) {
+				for (IBaseExtension<?, ?> next : extensions) {
 					if (theWantedClass.isAssignableFrom(next.getClass())) {
 						retVal.add((T) next);
 					}
@@ -1203,7 +1203,6 @@ public class FhirTerser {
 	public void visit(IBase theElement, IModelVisitor2 theVisitor) {
 		BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
 		if (def instanceof BaseRuntimeElementCompositeDefinition) {
-			BaseRuntimeElementCompositeDefinition<?> defComposite = (BaseRuntimeElementCompositeDefinition<?>) def;
 			visit(theElement, null, def, theVisitor, new ArrayList<>(), new ArrayList<>(), new ArrayList<>());
 		} else if (theElement instanceof IBaseExtension) {
 			theVisitor.acceptUndeclaredExtension(
@@ -1562,7 +1561,7 @@ public class FhirTerser {
 				throw new DataFormatException(Msg.code(1796) + "Invalid path " + thePath + ": Element of type "
 						+ def.getName() + " has no child named " + nextPart + ". Valid names: "
 						+ def.getChildrenAndExtension().stream()
-								.map(t -> t.getElementName())
+								.map(BaseRuntimeChildDefinition::getElementName)
 								.sorted()
 								.collect(Collectors.joining(", ")));
 			}
@@ -1817,7 +1816,18 @@ public class FhirTerser {
 			if (getResourceToIdMap() == null) {
 				return null;
 			}
-			return getResourceToIdMap().get(theNext);
+
+			var idFromMap = getResourceToIdMap().get(theNext);
+			if (idFromMap != null) {
+				return idFromMap;
+			} else if (theNext.getIdElement().getIdPart() != null) {
+				return getResourceToIdMap().values().stream()
+						.filter(id -> theNext.getIdElement().getIdPart().equals(id.getIdPart()))
+						.findAny()
+						.orElse(null);
+			} else {
+				return null;
+			}
 		}
 
 		private List<IBaseResource> getOrCreateResourceList() {

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/4837-fix-stringify-parse-copy-contained-duplicate-bug.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4837
+title: "In the case where a resource was serialized, deserialized, copied and reserialized it resulted in duplication of
+ contained resources. This has been corrected."

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/FhirTerserR4Test.java

@@ -21,6 +21,7 @@ import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Identifier;
+import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.MarkdownType;
 import org.hl7.fhir.r4.model.Medication;
 import org.hl7.fhir.r4.model.MedicationAdministration;
@@ -28,6 +29,7 @@ import org.hl7.fhir.r4.model.MedicationRequest;
 import org.hl7.fhir.r4.model.Money;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Patient.LinkType;
 import org.hl7.fhir.r4.model.Practitioner;
@@ -1528,6 +1530,27 @@ public class FhirTerserR4Test {
 		return retVal;
 	}
 
+	@Test
+	void copyingAndParsingCreatesDuplicateContainedResources() {
+		var input = new Library();
+		var params = new Parameters();
+		var id = "#expansion-parameters-ecr";
+		params.setId(id);
+		params.addParameter("system-version", new StringType("test2"));
+		var paramsExt = new Extension();
+		paramsExt.setUrl("test").setValue(new Reference(id));
+		input.addContained(params);
+		input.addExtension(paramsExt);
+		final var parser = FhirContext.forR4Cached().newJsonParser();
+		var stringified = parser.encodeResourceToString(input);
+		var parsed = parser.parseResource(stringified);
+		var copy = ((Library) parsed).copy();
+		assertEquals(1, copy.getContained().size());
+		var stringifiedCopy = parser.encodeResourceToString(copy);
+		var parsedCopy = parser.parseResource(stringifiedCopy);
+		assertEquals(1, ((Library) parsedCopy).getContained().size());
+	}
+
 	/**
 	 * See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
 	 */