Fixed #622 Extension lost on ID datatype or extension of type primitive during parsing

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/IdDt.java

@@ -385,7 +385,7 @@ public class IdDt extends UriDt implements /*IPrimitiveDatatype<String>, */IIdTy
 
 	@Override
 	public boolean isEmpty() {
-		return isBlank(getValue());
+		return super.isBaseEmpty() && isBlank(getValue());
 	}
 
 	@Override

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

@@ -95,6 +95,8 @@ import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
 import ca.uhn.fhir.parser.json.JsonLikeWriter;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.util.ElementUtil;
+import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
+import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
 
 /**
  * This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use
@@ -869,9 +871,23 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		write(theEventWriter, "resourceType", resDef.getName());
     if (theResourceId != null && theResourceId.hasIdPart()) {
       write(theEventWriter, "id", theResourceId.getIdPart());
-			if (theResourceId.hasFormatComment()) {
+      final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
+      final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
+      // Undeclared extensions
+      extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
+      boolean haveExtension = false;
+      if (!extensions.isEmpty()) {
+        haveExtension = true;
+      }
+
+      if (theResourceId.hasFormatComment() || haveExtension) {
         beginObject(theEventWriter, "_id");
+        if (theResourceId.hasFormatComment()) {
           writeCommentsPreAndPost(theResourceId, theEventWriter);
+        }
+        if (haveExtension) {
+          writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+        }
         theEventWriter.endObject();
       }
     }
@@ -1429,6 +1445,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
   private void parseExtension(ParserState<?> theState, JsonLikeArray theValues, boolean theIsModifier) {
+    int allUnderscoreNames = 0;
+    int handledUnderscoreNames = 0;
+
     for (int i = 0; i < theValues.size(); i++) {
       JsonLikeObject nextExtObj = JsonLikeValue.asObject(theValues.get(i));
       JsonLikeValue jsonElement = nextExtObj.get("url");
@@ -1455,9 +1474,43 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
         } else if ("modifierExtension".equals(next)) {
           JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
           parseExtension(theState, jsonVal, true);
+        } else if (next.charAt(0) == '_') {
+          allUnderscoreNames++;
+          continue;
         } else {
           JsonLikeValue jsonVal = nextExtObj.get(next);
-					parseChildren(theState, next, jsonVal, null, null, false);
+          String alternateName = '_' + next;
+          JsonLikeValue alternateVal = nextExtObj.get(alternateName);
+          if (alternateVal != null) {
+            handledUnderscoreNames++;
+          }
+          parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
+        }
+      }
+      
+      /*
+       * This happens if an element has an extension but no actual value. I.e.
+		   * if a resource has a "_status" element but no corresponding "status"
+		   * element. This could be used to handle a null value with an extension
+		   * for example.
+		  */
+      if (allUnderscoreNames > handledUnderscoreNames) {
+        for (String alternateName : nextExtObj.keySet()) {
+          if (alternateName.startsWith("_") && alternateName.length() > 1) {
+            JsonLikeValue nextValue = nextExtObj.get(alternateName);
+            if (nextValue != null) {
+              if (nextValue.isObject()) {
+                String nextName = alternateName.substring(1);
+                if (nextExtObj.get(nextName) == null) {
+                  theState.enteringNewElement(null, nextName);
+                  parseAlternates(nextValue, theState, alternateName, alternateName);
+                  theState.endingElement();
+                }
+              } else {
+                getErrorHandler().incorrectJsonType(null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
+              }
+             }
+          }
         }
       }
       theState.endingElement();
@@ -1842,6 +1895,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				} else {
 					String childName = myDef.getChildNameByDatatype(myValue.getClass());
 					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, myParent, false);
+          managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
 				}
 
 				theEventWriter.endObject();
@@ -1897,6 +1951,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
 				}
 				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, myParent, false);
+        managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
 			}
 
 			// theEventWriter.name(myUndeclaredExtension.get);
@@ -1904,6 +1959,26 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			theEventWriter.endObject();
 		}
     
+    private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
+      if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
+        final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
+        final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
+        // Undeclared extensions
+        extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
+        // Declared extensions
+        if (def != null) {
+          extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
+        }
+        boolean haveContent = false;
+        if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
+          haveContent = true;
+        }
+        if (haveContent) {
+          beginObject(theEventWriter, '_' + childName);
+          writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+          theEventWriter.endObject();
+        }
+      }
+    }    
 	}  
-
 }

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

@@ -1473,6 +1473,7 @@ class ParserState<T> {
 				push(newState);
 				return;
 			}
+      case ID_DATATYPE:
 			case PRIMITIVE_DATATYPE: {
 				RuntimePrimitiveDatatypeDefinition primitiveTarget = (RuntimePrimitiveDatatypeDefinition) target;
 				IPrimitiveType<?> newChildInstance = primitiveTarget.newInstance(myDefinition.getInstanceConstructorArguments());
@@ -2264,10 +2265,16 @@ class ParserState<T> {
         // if (isNotBlank(entryBaseUrl)) {
         // nextResource.setId(new IdDt(entryBaseUrl, resourceName, bundleIdPart, version));
         // } else {
+        IdDt previousId = nextResource.getId();
         nextResource.setId(new IdDt(null, resourceName, bundleIdPart, version));
+        // Copy extensions
+        if (!previousId.getAllUndeclaredExtensions().isEmpty()) {
+          for (final ExtensionDt ext : previousId.getAllUndeclaredExtensions()) {
+            nextResource.getId().addUndeclaredExtension(ext);
+          }
+        }
        // }
 			}
-
 		}
 
 	}

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

@@ -509,10 +509,14 @@ public class XmlParser extends BaseParser /*implements IParser */{
 		case ID_DATATYPE: {
       IIdType value = IIdType.class.cast(theElement);
       String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue();
+      if (StringUtils.isNotBlank(encodedValue) || super.hasExtensions(value)) {
         theEventWriter.writeStartElement(childName);
+        if (StringUtils.isNotBlank(encodedValue)) {
           theEventWriter.writeAttribute("value", encodedValue);
+        }
         encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
         theEventWriter.writeEndElement();
+      }
       break;
 		}
 		case PRIMITIVE_DATATYPE: {
@@ -756,11 +760,13 @@ public class XmlParser extends BaseParser /*implements IParser */{
 		theEventWriter.writeDefaultNamespace(FHIR_NS);
 
 		if (theResource instanceof IAnyResource) {
-
 			// HL7.org Structures
      if (theResourceId != null) {
         writeCommentsPre(theEventWriter, theResourceId);
-				writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
+        theEventWriter.writeStartElement("id");
+        theEventWriter.writeAttribute("value", theResourceId.getIdPart());
+        encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false);
+        theEventWriter.writeEndElement();
         writeCommentsPost(theEventWriter, theResourceId);
       }
 
@@ -774,8 +780,13 @@ public class XmlParser extends BaseParser /*implements IParser */{
 
 				IResource resource = (IResource) theResource;
         if (theResourceId != null) {
-					writeCommentsPre(theEventWriter, theResourceId);
+          /*	writeCommentsPre(theEventWriter, theResourceId);
               writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
+					    writeCommentsPost(theEventWriter, theResourceId);*/
+          theEventWriter.writeStartElement("id");
+          theEventWriter.writeAttribute("value", theResourceId.getIdPart());
+          encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false);
+          theEventWriter.writeEndElement();
           writeCommentsPost(theEventWriter, theResourceId);
         }
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/ElementWithExtensionDstu2Test.java

@@ -1,14 +1,15 @@
 package ca.uhn.fhir.parser;
 
-import static org.junit.Assert.assertEquals;
-
-import org.junit.AfterClass;
-import org.junit.Ignore;
-import org.junit.Test;
-
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.util.TestUtil;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * Created by Sébastien Rivière 12/04/2017
@@ -16,7 +17,7 @@ import ca.uhn.fhir.util.TestUtil;
 public class ElementWithExtensionDstu2Test {
 
     private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ca.uhn.fhir.parser.ElementWithExtensionDstu2Test.class);
-	private static FhirContext ctx = FhirContext.forDstu2();
+    private final FhirContext ctx = FhirContext.forDstu2();
 
     @AfterClass
     public static void afterClassClearContext() {
@@ -24,13 +25,42 @@ public class ElementWithExtensionDstu2Test {
     }
 
     @Test
-	@Ignore
     public void testExtensionOnPrimitiveExtensionJson() throws Exception {
+        MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+        patient.setId("1");
+        final HumanNameDt name = patient.getNameFirstRep();
+        name.addFamily(new StringDt("family"));
+        name.getFamilyFirstRep().addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
+
+        final StringDt stringExt = new StringDt();
+        stringExt.setValue("myStringExt");
+        stringExt.addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
+        final ExtensionDt ext = new ExtensionDt();
+        ext.setValue(stringExt);
+        ext.setUrl("/myExt");
+        patient.addUndeclaredExtension(ext);
+
+
+        patient.setPetName(new StringDt("myPet"));
+        patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
+
+        final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
+        final String json = parser.encodeResourceToString(patient);
+
+        ourLog.info(json);
+
+        patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
+        assertEquals(1, patient.getName().get(0).getFamilyFirstRep().getUndeclaredExtensions().size());
+        assertEquals(1, ((StringDt) patient.getUndeclaredExtensionsByUrl("/myExt").get(0).getValue()).getUndeclaredExtensions().size());
+        assertEquals(1, patient.getPetName().getUndeclaredExtensions().size());
+    }
+
+    @Test
+    public void testExtensionOnPrimitiveExtensionWithNullValueJson() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
         patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
         final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
-		parser.setServerBaseUrl("http://foo");
         final String json = parser.encodeResourceToString(patient);
 
         ourLog.info(json);
@@ -39,13 +69,44 @@ public class ElementWithExtensionDstu2Test {
         assertEquals(1, patient.getPetName().getUndeclaredExtensions().size());
     }
 
+
     @Test
     public void testExtensionOnPrimitiveExtensionXml() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
+
+        final HumanNameDt name = patient.getNameFirstRep();
+        name.addFamily(new StringDt("family"));
+        name.getFamilyFirstRep().addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
+
+        final StringDt stringExt = new StringDt();
+        stringExt.setValue("myStringExt");
+        stringExt.addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
+        final ExtensionDt ext = new ExtensionDt();
+        ext.setValue(stringExt);
+        ext.setUrl("/myExt");
+        patient.addUndeclaredExtension(ext);
+
+
+        patient.setPetName(new StringDt("myPet"));
+        patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
+        final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
+        final String xml = parser.encodeResourceToString(patient);
+
+        ourLog.info(xml);
+
+        patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
+        assertEquals(1, patient.getName().get(0).getFamilyFirstRep().getUndeclaredExtensions().size());
+        assertEquals(1, ((StringDt) patient.getUndeclaredExtensionsByUrl("/myExt").get(0).getValue()).getUndeclaredExtensions().size());
+        assertEquals(1, patient.getPetName().getUndeclaredExtensions().size());
+    }
+
+    @Test
+    public void testExtensionOnPrimitiveExtensionWithNullValueXml() throws Exception {
+        MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+        patient.setId("1");
         patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
         final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
-		parser.setServerBaseUrl("http://foo");
         final String xml = parser.encodeResourceToString(patient);
 
         ourLog.info(xml);
@@ -55,13 +116,11 @@ public class ElementWithExtensionDstu2Test {
     }
 
     @Test
-	@Ignore
     public void testExtensionOnIDDatatypeJson() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
         patient.getId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
         final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
-		parser.setServerBaseUrl("http://foo");
         final String json = parser.encodeResourceToString(patient);
 
         ourLog.info(json);
@@ -70,14 +129,14 @@ public class ElementWithExtensionDstu2Test {
         assertEquals(1, patient.getId().getUndeclaredExtensions().size());
     }
 
+
+
     @Test
-	@Ignore
     public void testExtensionOnIDDatatypeXml() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
         patient.getId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
         final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
-		parser.setServerBaseUrl("http://foo");
         final String xml = parser.encodeResourceToString(patient);
 
         ourLog.info(xml);
@@ -87,13 +146,26 @@ public class ElementWithExtensionDstu2Test {
     }
 
     @Test
-	@Ignore
     public void testExtensionOnIDDatatypeExtensionJson() throws Exception {
+        MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+        patient.setId("1");
+        patient.setCustomId(new IdDt("3"));
+        patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
+        final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
+        final String json = parser.encodeResourceToString(patient);
+
+        ourLog.info(json);
+
+        patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
+        assertEquals(1, patient.getCustomId().getUndeclaredExtensions().size());
+    }
+
+    @Test
+    public void testExtensionOnIDDatatypeExtensionNullValueJson() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
         patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
         final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
-		parser.setServerBaseUrl("http://foo");
         final String json = parser.encodeResourceToString(patient);
 
         ourLog.info(json);
@@ -103,13 +175,26 @@ public class ElementWithExtensionDstu2Test {
     }
 
     @Test
-	@Ignore
     public void testExtensionOnIDDatatypeExtensionXml() throws Exception {
+        MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+        patient.setId("1");
+        patient.setCustomId(new IdDt("4"));
+        patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
+        final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
+        final String xml = parser.encodeResourceToString(patient);
+
+        ourLog.info(xml);
+
+        patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
+        assertEquals(1, patient.getCustomId().getUndeclaredExtensions().size());
+    }
+
+    @Test
+    public void testExtensionOnIDDatatypeExtensionNullValueXml() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
         patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
         final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
-		parser.setServerBaseUrl("http://foo");
         final String xml = parser.encodeResourceToString(patient);
 
         ourLog.info(xml);

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/IdType.java

@@ -437,7 +437,7 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
 
   @Override
   public boolean isEmpty() {
-    return isBlank(getValue());
+    return super.isEmpty() && isBlank(getValue());
   }
 
   @Override

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/ElementWithExtensionDstu3Test.java

@@ -1,14 +1,15 @@
 package ca.uhn.fhir.parser;
 
-import static org.junit.Assert.assertEquals;
-
-import org.hl7.fhir.dstu3.model.StringType;
-import org.junit.AfterClass;
-import org.junit.Ignore;
-import org.junit.Test;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.dstu3.model.Extension;
+import org.hl7.fhir.dstu3.model.HumanName;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * Created by Sébastien Rivière 12/04/2017
@@ -16,7 +17,7 @@ import ca.uhn.fhir.util.TestUtil;
 public class ElementWithExtensionDstu3Test {
 
     private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ca.uhn.fhir.parser.ElementWithExtensionDstu3Test.class);
-  private static final FhirContext ctx = FhirContext.forDstu3();
+    private final FhirContext ctx = FhirContext.forDstu3();
 
     @AfterClass
     public static void afterClassClearContext() {
@@ -24,11 +25,43 @@ public class ElementWithExtensionDstu3Test {
     }
 
     @Test
-  @Ignore
     public void testNullFlavorPrimitiveExtensionJson() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
+        final HumanName name = patient.getNameFirstRep();
+        name.setFamily("family");
+        name.getFamilyElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
+        patient.setPetName(new StringType("myPet"));
+        patient.getExtensionsByUrl("/petname");
         patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
+        final StringType stringExt = new StringType();
+        stringExt.setValue("myStringExt");
+        stringExt.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+        final Extension ext = new Extension();
+        ext.setValue(stringExt);
+        ext.setUrl("/myExt");
+        patient.addExtension(ext);
+
+        final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
+        final String json = parser.encodeResourceToString(patient);
+
+        ourLog.info(json);
+
+        patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
+        assertEquals(1, patient.getName().get(0).getFamilyElement().getExtension().size());
+        assertEquals(1, patient.getExtensionsByUrl("/myExt").get(0).getValue().getExtension().size());
+        assertEquals(1, patient.getPetName().getExtension().size());
+    }
+
+    @Test
+    public void testNullFlavorPrimitiveExtensionNullValueJson() throws Exception {
+        MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+        patient.setId("1");
+        patient.getExtensionsByUrl("/petname");
+        patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
         final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
         final String json = parser.encodeResourceToString(patient);
 
@@ -39,11 +72,45 @@ public class ElementWithExtensionDstu3Test {
     }
 
     @Test
-  @Ignore
     public void testNullFlavorPrimitiveExtensionXml() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
+        final HumanName name = patient.getNameFirstRep();
+        name.setFamily("family");
+        name.getFamilyElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
+        patient.setPetName(new StringType("myPet"));
+        patient.getExtensionsByUrl("/petname");
         patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
+        final StringType stringExt = new StringType();
+        stringExt.setValue("myStringExt");
+        stringExt.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+        final Extension ext = new Extension();
+        ext.setValue(stringExt);
+        ext.setUrl("/myExt");
+        patient.addExtension(ext);
+
+        final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
+        final String xml = parser.encodeResourceToString(patient);
+
+        ourLog.info(xml);
+
+        patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
+        assertEquals(1, patient.getName().get(0).getFamilyElement().getExtension().size());
+        assertEquals(1, patient.getExtensionsByUrl("/myExt").get(0).getValue().getExtension().size());
+        assertEquals(1, patient.getPetName().getExtension().size());
+    }
+
+
+    @Test
+    public void testNullFlavorPrimitiveExtensionNullValueXml() throws Exception {
+        MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+        patient.setId("1");
+
+        patient.getExtensionsByUrl("/petname");
+        patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
         final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
         final String xml = parser.encodeResourceToString(patient);
 
@@ -53,8 +120,8 @@ public class ElementWithExtensionDstu3Test {
         assertEquals(1, patient.getPetName().getExtension().size());
     }
 
+
     @Test
-  @Ignore
     public void testNullFlavorIDDatatypeJson() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
@@ -69,7 +136,6 @@ public class ElementWithExtensionDstu3Test {
     }
 
     @Test
-  @Ignore
     public void testNullFlavorIDDatatypeXml() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
@@ -84,10 +150,10 @@ public class ElementWithExtensionDstu3Test {
     }
 
     @Test
-  @Ignore
     public void testNullFlavorExtensionIDDatatypeJson() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
+        patient.setCustomId(new IdType(("4")));
         patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
         final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
         final String json = parser.encodeResourceToString(patient);
@@ -99,12 +165,13 @@ public class ElementWithExtensionDstu3Test {
     }
 
     @Test
-  @Ignore
     public void testNullFlavorExtensionIDDatatypeXml() throws Exception {
         MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
         patient.setId("1");
-    patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
         final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
+        patient.setCustomId(new IdType(("4")));
+        patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
+
         final String xml = parser.encodeResourceToString(patient);
 
         ourLog.info(xml);

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

@@ -36,7 +36,7 @@ public class MyPatientWithCustomUrlExtension extends Patient {
 
     @Override
     public boolean isEmpty() {
-    return super.isEmpty() && myPetName.isEmpty();
+        return super.isEmpty() && getCustomId().isEmpty() && getPetName().isEmpty();
     }
 
     public IdType getCustomId() {