5738: Skip alternate handling if already handled by previous step (#5971)

* 5738: Skip alternate handling if already handled by previous step

* Credit for #5738

---------

Co-authored-by: Stefan Lindström <stefan.lindstrom@ehalsomyndigheten.se>
Co-authored-by: James Agnew <jamesagnew@gmail.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -1359,9 +1359,17 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				String alternateName = keyIter.next();
 				if (alternateName.startsWith("_") && alternateName.length() > 1) {
 					BaseJsonLikeValue nextValue = theObject.get(alternateName);
+					String nextName = alternateName.substring(1);
+
 					if (nextValue != null) {
+						BaseJsonLikeValue nonAlternativeValue = theObject.get(nextName);
+
+						// Only alternate values with no corresponding "normal" value is unhandled from previous step.
+						if (nonAlternativeValue != null) {
+							continue;
+						}
+
 						if (nextValue.isObject()) {
-							String nextName = alternateName.substring(1);
 							if (theObject.get(nextName) == null) {
 								theState.enteringNewElement(null, nextName);
 								parseAlternates(nextValue, theState, alternateName, alternateName);

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5971-fix-json-parsing-alternate-names.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5971
+title: "The JSON Parser failed to parse alternate names (e.g. `_family`) containing extensions if the
+  corresponding regular named element (e.g. `family`) was not present. Thanks to Stefan Lindström for
+  the pull request!"

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java

@@ -46,6 +46,7 @@ import org.hl7.fhir.dstu2016may.model.Observation;
 import org.hl7.fhir.dstu2016may.model.Observation.ObservationStatus;
 import org.hl7.fhir.dstu2016may.model.Parameters;
 import org.hl7.fhir.dstu2016may.model.Patient;
+import org.hl7.fhir.dstu2016may.model.Practitioner;
 import org.hl7.fhir.dstu2016may.model.PrimitiveType;
 import org.hl7.fhir.dstu2016may.model.Quantity;
 import org.hl7.fhir.dstu2016may.model.QuestionnaireResponse;
@@ -55,6 +56,7 @@ import org.hl7.fhir.dstu2016may.model.SimpleQuantity;
 import org.hl7.fhir.dstu2016may.model.StringType;
 import org.hl7.fhir.dstu2016may.model.UriType;
 import org.hl7.fhir.dstu2016may.model.ValueSet;
+import org.hl7.fhir.dstu2016may.model.codesystems.DataAbsentReason;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
@@ -63,7 +65,6 @@ import org.junit.jupiter.api.Test;
 import org.mockito.ArgumentCaptor;
 
 import java.math.BigDecimal;
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -78,6 +79,7 @@ import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -1901,6 +1903,40 @@ public class JsonParserDstu2_1Test {
 		assertEquals(expectedJson, patientString);
 	}
 
+	@Test
+	public void testObjectWithBothPrimitiverAndArrayAlternatives() {
+		String resource = "{\n" +
+			"    \"resourceType\": \"Practitioner\",\n" +
+			"    \"id\": \"1\",\n" +
+			"    \"name\": [{\n" +
+			"            \"_family\": {\n" +
+			"                \"extension\": [{\n" +
+			"                        \"url\": \"http://hl7.org/fhir/StructureDefinition/data-absent-reason\",\n" +
+			"                        \"valueString\": \"masked\"\n" +
+			"                    }\n" +
+			"                ]\n" +
+			"            },\n" +
+			"            \"given\": [\n" +
+			"                null\n" +
+			"            ],\n" +
+			"            \"_given\": [{\n" +
+			"                    \"extension\": [{\n" +
+			"                            \"url\": \"http://hl7.org/fhir/StructureDefinition/data-absent-reason\",\n" +
+			"                            \"valueString\": \"masked\"\n" +
+			"                        }\n" +
+			"                    ]\n" +
+			"                }\n" +
+			"            ]\n" +
+			"        }\n" +
+			"    ]\n" +
+			"}\n";
+		Practitioner practitioner = assertDoesNotThrow(() -> ourCtx.newJsonParser().parseResource(Practitioner.class, resource));
+		HumanName humanName = practitioner.getName().get(0);
+		StringType given = humanName.getGiven().get(0);
+		assertTrue(given.getExtension().stream().allMatch(ext -> DataAbsentReason.MASKED.toCode().equals(ext.getValue().primitiveValue())));
+		assertTrue(humanName.getFamily().get(0).getExtension().stream().allMatch(ext -> DataAbsentReason.MASKED.toCode().equals(ext.getValue().primitiveValue())));
+	}
+
 	@AfterAll
 	public static void afterClassClearContext() {
 		TestUtil.randomizeLocaleAndTimezone();

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -63,6 +63,7 @@ import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
 import org.hl7.fhir.dstu3.model.Organization;
 import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Practitioner;
 import org.hl7.fhir.dstu3.model.PrimitiveType;
 import org.hl7.fhir.dstu3.model.Quantity;
 import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
@@ -74,6 +75,7 @@ import org.hl7.fhir.dstu3.model.SimpleQuantity;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.dstu3.model.codesystems.DataAbsentReason;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
@@ -101,6 +103,7 @@ import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -2548,6 +2551,41 @@ public class JsonParserDstu3Test {
 		assertThat(patientString, is(not(containsString("fhir_comment"))));
 	}
 
+		@Test
+	public void testObjectWithBothPrimitiverAndArrayAlternatives() {
+		String resource = "{\n" +
+			"    \"resourceType\": \"Practitioner\",\n" +
+			"    \"id\": \"1\",\n" +
+			"    \"name\": [{\n" +
+			"            \"_family\": {\n" +
+			"                \"extension\": [{\n" +
+			"                        \"url\": \"http://hl7.org/fhir/StructureDefinition/data-absent-reason\",\n" +
+			"                        \"valueString\": \"masked\"\n" +
+			"                    }\n" +
+			"                ]\n" +
+			"            },\n" +
+			"            \"given\": [\n" +
+			"                null\n" +
+			"            ],\n" +
+			"            \"_given\": [{\n" +
+			"                    \"extension\": [{\n" +
+			"                            \"url\": \"http://hl7.org/fhir/StructureDefinition/data-absent-reason\",\n" +
+			"                            \"valueString\": \"masked\"\n" +
+			"                        }\n" +
+			"                    ]\n" +
+			"                }\n" +
+			"            ]\n" +
+			"        }\n" +
+			"    ]\n" +
+			"}\n";
+		Practitioner practitioner = assertDoesNotThrow(() -> ourCtx.newJsonParser().parseResource(Practitioner.class, resource));
+		HumanName humanName = practitioner.getName().get(0);
+		StringType given = humanName.getGiven().get(0);
+		assertTrue(given.getExtension().stream().allMatch(ext -> DataAbsentReason.MASKED.toCode().equals(ext.getValue().primitiveValue())));
+		assertTrue(humanName.getFamilyElement().getExtension().stream().allMatch(ext -> DataAbsentReason.MASKED.toCode().equals(ext.getValue().primitiveValue())));
+	}
+
+
 	@AfterAll
 	public static void afterClassClearContext() {
 		TestUtil.randomizeLocaleAndTimezone();

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

@@ -45,6 +45,7 @@ import org.hl7.fhir.r4.model.QuestionnaireResponse;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Type;
+import org.hl7.fhir.r4.model.codesystems.DataAbsentReason;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
@@ -73,6 +74,7 @@ import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.notNullValue;
 import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.hamcrest.core.IsNot.not;
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
@@ -1190,6 +1192,40 @@ public class JsonParserR4Test extends BaseTest {
 		assertEquals(expected, actual);
 	}
 
+	@Test
+	public void testObjectWithBothPrimitiverAndArrayAlternatives() {
+		String resource = "{\n" +
+			"    \"resourceType\": \"Practitioner\",\n" +
+			"    \"id\": \"1\",\n" +
+			"    \"name\": [{\n" +
+			"            \"_family\": {\n" +
+			"                \"extension\": [{\n" +
+			"                        \"url\": \"http://hl7.org/fhir/StructureDefinition/data-absent-reason\",\n" +
+			"                        \"valueString\": \"masked\"\n" +
+			"                    }\n" +
+			"                ]\n" +
+			"            },\n" +
+			"            \"given\": [\n" +
+			"                null\n" +
+			"            ],\n" +
+			"            \"_given\": [{\n" +
+			"                    \"extension\": [{\n" +
+			"                            \"url\": \"http://hl7.org/fhir/StructureDefinition/data-absent-reason\",\n" +
+			"                            \"valueString\": \"masked\"\n" +
+			"                        }\n" +
+			"                    ]\n" +
+			"                }\n" +
+			"            ]\n" +
+			"        }\n" +
+			"    ]\n" +
+			"}\n";
+		Practitioner practitioner = assertDoesNotThrow(() -> ourCtx.newJsonParser().parseResource(Practitioner.class, resource));
+		HumanName humanName = practitioner.getNameFirstRep();
+		StringType given = humanName.getGiven().get(0);
+		assertTrue(given.getExtension().stream().allMatch(ext -> DataAbsentReason.MASKED.toCode().equals(ext.getValue().primitiveValue())));
+		assertTrue(humanName.getFamilyElement().getExtension().stream().allMatch(ext -> DataAbsentReason.MASKED.toCode().equals(ext.getValue().primitiveValue())));
+	}
+
 	@Test
 	public void testEncodeToString_GeneralPurposeDataType() {
 		HumanName name = new HumanName();

pom.xml

@@ -917,6 +917,11 @@
 			<id>subigre</id>
 			<name>Renaud Subiger</name>
 		</developer>
+		<developer>
+			<id>stefan-lindstrom</id>
+			<name>Stefan Lindström</name>
+			<organization>Softhouse AB</organization>
+		</developer>
 	</developers>
 
 	<licenses>