Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java

@@ -605,4 +605,29 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
 	}
 
+	public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
+		public ExtensionResourceMetadataKey(String url) {
+			super(url);
+		}
+
+		@Override
+		public ExtensionDt get(IResource theResource) {
+			Object retValObj = theResource.getResourceMetadata().get(this);
+			if (retValObj == null) {
+				return null;
+			} else if (retValObj instanceof ExtensionDt) {
+				return (ExtensionDt) retValObj;
+			}
+			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
+				+ "' in resource metadata for key " + this.name() + " - Expected "
+				+ ExtensionDt.class.getCanonicalName());
+		}
+
+		@Override
+		public void put(IResource theResource, ExtensionDt theObject) {
+			theResource.getResourceMetadata().put(this, theObject);
+		}
+	}
+
+	
 }

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

@@ -918,6 +918,18 @@ public abstract class BaseParser implements IParser {
 		throw new DataFormatException(nextChild + " has no child of type " + theType);
 	}
 
+	protected List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> getExtensionMetadataKeys(IResource resource) {
+		List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys = new ArrayList<Map.Entry<ResourceMetadataKeyEnum<?>, Object>>();
+		for (Map.Entry<ResourceMetadataKeyEnum<?>, Object> entry : resource.getResourceMetadata().entrySet()) {
+			if (entry.getKey() instanceof ResourceMetadataKeyEnum.ExtensionResourceMetadataKey) {
+				extensionMetadataKeys.add(entry);
+			}
+		}
+
+		return extensionMetadataKeys;
+	}
+
+
 	protected static <T> List<T> extractMetadataListNotNull(IResource resource, ResourceMetadataKeyEnum<List<T>> key) {
 		List<? extends T> securityLabels = key.get(resource);
 		if (securityLabels == null) {

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

@@ -45,10 +45,7 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Writer;
 import java.math.BigDecimal;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
 
 import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
 import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
@@ -654,8 +651,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			if (isBlank(versionIdPart)) {
 				versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
 			}
+			List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys = getExtensionMetadataKeys(resource);
 
-			if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
+			if (super.shouldEncodeResourceMeta(resource) && (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) || !extensionMetadataKeys.isEmpty()) {
 				beginObject(theEventWriter, "meta");
 				writeOptionalTagWithTextNode(theEventWriter, "versionId", versionIdPart);
 				writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", updated);
@@ -695,6 +693,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					theEventWriter.endArray();
 				}
 
+				addExtensionMetadata(theResDef, theResource, theContainedResource, theSubResource, extensionMetadataKeys, resDef, theEventWriter);
+
 				theEventWriter.endObject(); // end meta
 			}
 		}
@@ -704,6 +704,23 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		theEventWriter.endObject();
 	}
 
+
+	private void addExtensionMetadata(RuntimeResourceDefinition theResDef, IBaseResource theResource,
+												 boolean theContainedResource, boolean theSubResource,
+												 List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys,
+												 RuntimeResourceDefinition resDef,
+												 JsonLikeWriter theEventWriter) throws IOException {
+		if (extensionMetadataKeys.isEmpty()) {
+			return;
+		}
+
+		ExtensionDt metaResource = new ExtensionDt();
+		for (Map.Entry<ResourceMetadataKeyEnum<?>, Object> entry : extensionMetadataKeys) {
+			metaResource.addUndeclaredExtension((ExtensionDt) entry.getValue());
+		}
+		encodeCompositeElementToStreamWriter(theResDef, theResource, metaResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
+	}
+
 	/**
 	 * This is useful only for the two cases where extensions are encoded as direct children (e.g. not in some object
 	 * called _name): resource extensions, and extension extensions

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

@@ -841,6 +841,25 @@ class ParserState<T> {
 			}
 		}
 
+		@Override
+		public void enteringNewElementExtension(StartElement theElem, String theUrlAttr, boolean theIsModifier, final String baseServerUrl) {
+			ResourceMetadataKeyEnum.ExtensionResourceMetadataKey resourceMetadataKeyEnum = new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(theUrlAttr);
+			Object metadataValue = myMap.get(resourceMetadataKeyEnum);
+			ExtensionDt newExtension;
+			if (metadataValue == null) {
+				newExtension = new ExtensionDt(theIsModifier);
+			} else if (metadataValue instanceof ExtensionDt) {
+				newExtension = (ExtensionDt) metadataValue;
+			} else {
+				throw new IllegalStateException("Expected ExtensionDt as custom resource metadata type, got: " + metadataValue.getClass().getSimpleName());
+			}
+			newExtension.setUrl(theUrlAttr);
+			myMap.put(resourceMetadataKeyEnum, newExtension);
+
+			ExtensionState newState = new ExtensionState(getPreResourceState(), newExtension);
+			push(newState);
+		}
+
 	}
 
 	private class MetaVersionElementState extends BaseState {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java

@@ -104,26 +104,35 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
 	void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
 		String q = theQualifier;
 		String resourceType = null;
+		boolean skipSetValue = false;
 		if (isNotBlank(q)) {
 			if (q.startsWith(":")) {
 				int nextIdx = q.indexOf('.');
 				if (nextIdx != -1) {
 					resourceType = q.substring(1, nextIdx);
 					myChain = q.substring(nextIdx + 1);
+					// type is explicitly defined so use it
+					myId.setParts(null, resourceType, theValue, null);
+					skipSetValue = true;
 				} else {
 					resourceType = q.substring(1);
 				}
 			} else if (q.startsWith(".")) {
 				myChain = q.substring(1);
+				// type not defined but this is a chain, so treat value as opaque
+				myId.setParts(null, null, theValue, null);
+				skipSetValue = true;
 			}
 		}
 
+		if (!skipSetValue) {
 			setValue(theValue);
 
 			if (isNotBlank(resourceType) && isBlank(getResourceType())) {
 				setValue(resourceType + '/' + theValue);
 			}
 		}
+	}
 
 
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -1,5 +1,40 @@
 package ca.uhn.fhir.parser;
 
+import static org.hamcrest.CoreMatchers.equalTo;
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.hamcrest.core.IsInstanceOf.instanceOf;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.*;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hamcrest.Matchers;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.AfterClass;
+import org.junit.Assert;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Mockito;
+import org.mockito.internal.stubbing.answers.ThrowsException;
+import org.slf4j.LoggerFactory;
+
+import com.google.common.collect.Sets;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.*;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
@@ -1886,6 +1921,113 @@ public class JsonParserDstu2Test {
 		//@formatter:off
 
 		assertEquals("Smith", p.getName().get(0).getGiven().get(0).getValue());
+		assertExtensionMetadata(p, "fhir-request-method", false, StringDt.class, "POST");
+		assertExtensionMetadata(p, "fhir-request-uri", false, UriDt.class, "Patient");
+		assertExtensionMetadata(p, "modified-fhir-request-method", true, StringDt.class, "POST");
+		assertExtensionMetadata(p, "modified-fhir-request-uri", true, UriDt.class, "Patient");
+	}
+
+	private void assertExtensionMetadata(
+		BaseResource resource,
+		String url,
+		boolean isModifier,
+		Class<?> expectedType,
+		String expectedValue) {
+		ExtensionDt extension = (ExtensionDt) resource.getResourceMetadata().get(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(url));
+		assertThat(extension.getValue(), instanceOf(expectedType));
+		assertThat(extension.isModifier(), equalTo(isModifier));
+		assertThat(extension.getValueAsPrimitive().getValueAsString(), equalTo(expectedValue));
+	}
+
+	@Test
+	public void testEncodeResourceWithExtensionMetadata() throws Exception {
+		ProcedureRequest procedureRequest = new ProcedureRequest();
+		procedureRequest.setStatus(ProcedureRequestStatusEnum.ACCEPTED);
+		ExtensionDt timestamp = new ExtensionDt(false, "http://fhir.sjanic.com/timestamp");
+		timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/user", new ResourceReferenceDt("sjanic"));
+		timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/instance", new InstantDt("2012-01-01T13:00:00Z"));
+		timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/organization", new ResourceReferenceDt("sjanic_org"));
+		timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/role", new CodeableConceptDt().addCoding(new CodingDt("sjanic", "Doctor").setDisplay("Doctorin")));
+		ExtensionDt payment = new ExtensionDt(true, "http://fhir.sjanic.com/procedureRequest/requiresPatientPayment", new BooleanDt(true));
+		procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(timestamp.getUrl()), timestamp);
+		procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(payment.getUrl()), payment);
+
+		String json = ourCtx.newJsonParser().encodeResourceToString(procedureRequest);
+
+		// @formatter:off
+		assertThat(json, stringContainsInOrder(
+			"\"meta\":{"+
+				"\"extension\":["+
+				"{"+
+				"\"url\":\"http://fhir.sjanic.com/timestamp\","+
+				"\"extension\":["+
+				"{"+
+				"\"url\":\"http://fhir.sjanic.com/timestamp/user\","+
+				"\"valueReference\":{"+
+				"\"reference\":\"sjanic\""+
+				"}"+
+				"},"+
+				"{"+
+				"\"url\":\"http://fhir.sjanic.com/timestamp/instance\","+
+				"\"valueInstant\":\"2012-01-01T13:00:00Z\""+
+				"},"+
+				"{"+
+				"\"url\":\"http://fhir.sjanic.com/timestamp/organization\","+
+				"\"valueReference\":{"+
+				"\"reference\":\"sjanic_org\""+
+				"}"+
+				"},"+
+				"{"+
+				"\"url\":\"http://fhir.sjanic.com/timestamp/role\","+
+				"\"valueCodeableConcept\":{"+
+				"\"coding\":["+
+				"{"+
+				"\"system\":\"sjanic\","+
+				"\"code\":\"Doctor\","+
+				"\"display\":\"Doctorin\""+
+				"}"+
+				"]"+
+				"}"+
+				"}"+
+				"]"+
+				"}"+
+				"],"+
+				"\"modifierExtension\":["+
+				"{"+
+				"\"url\":\"http://fhir.sjanic.com/procedureRequest/requiresPatientPayment\","+
+				"\"valueBoolean\":true"+
+				"}"+
+				"]"+
+				"},"));
+		// @formatter:on
+	}
+
+	@Test
+	public void testParseResourceWithExtensionMetadata() throws Exception {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/procedure-request.json"));
+		IParser parser = ourCtx.newJsonParser();
+		IParserErrorHandler peh = mock(IParserErrorHandler.class);
+		parser.setParserErrorHandler(peh);
+
+		ProcedureRequest p = parser.parseResource(ProcedureRequest.class, input);
+
+		ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
+		verify(peh, Mockito.never()).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
+		assertParsedResourcesExtensionMetadata(p);
+	}
+
+	private void assertParsedResourcesExtensionMetadata(ProcedureRequest resource) throws Exception {
+		ExtensionDt payment = (ExtensionDt) resource.getResourceMetadata().get(
+			new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://fhir.sjanic.com/procedureRequest/requiresPatientPayment"));
+		assertThat(payment.isModifier(), equalTo(true));
+		assertThat(((BooleanDt)payment.getValue()).getValue(), equalTo(true));
+
+		TimestampFields timestampFields = new TimestampFields(resource);
+		assertThat(timestampFields.user.getReference().getIdPart(), equalTo("sjanic"));
+		assertThat(timestampFields.instance.getValue(), equalTo(new InstantDt("2012-01-01T13:00:00Z").getValue()));
+		assertThat(timestampFields.organization.getReference().getIdPart(), equalTo("sjanic_org"));
+		assertThat(timestampFields.role.getCodingFirstRep().getSystem(), equalTo("sjanic"));
+		assertThat(timestampFields.role.getCodingFirstRep().getCode(), equalTo("Doctor"));
 	}
 
 	@Test
@@ -1989,4 +2131,189 @@ public class JsonParserDstu2Test {
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
+	
+	/**
+	 * See #537
+	 */
+	@Test
+	public void testEncodeNestedContained() {
+		
+		Organization org04 = new Organization();
+		org04.setName("LEVEL04");
+		
+		Organization org03 = new Organization();
+		org03.setName("LEVEL03");
+		org03.getPartOf().setResource(org04);
+		
+		Organization org02 = new Organization();
+		org02.setName("LEVEL02");
+		org02.getPartOf().setResource(org03);
+		
+		Organization org01 = new Organization();
+		org01.setName("LEVEL01");
+		org01.getPartOf().setResource(org02);
+		
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(org01);
+		ourLog.info(encoded);
+		
+		assertThat(encoded, stringContainsInOrder("LEVEL02","LEVEL03","LEVEL04","LEVEL01" ));
+	}
+	
+	
+	/**
+	 * See #505
+	 */
+	@Test
+	public void testIncludeResourceWhenEncoding() {
+		Condition condition = new Condition();
+		condition.setDateRecorded(new DateDt("2011-01-01"));
+		
+		Goal goal = new Goal();
+		goal.setId("Goal1");
+		ResourceReferenceDt resourceReferenceDt = new ResourceReferenceDt(condition);
+		goal.setAddresses(Collections.singletonList(resourceReferenceDt));
+
+		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
+		Entry entry = bundle.addEntry();
+		entry.setResource(goal);
+		
+		IParser parser = ourCtx.newJsonParser();
+		
+		String resourceToString = parser.setPrettyPrint(true).encodeResourceToString(bundle);
+		ourLog.info(resourceToString);
+		
+		assertThat(resourceToString, containsString("2011-01-01"));
+		
+		bundle = parser.parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, resourceToString);
+		assertEquals(1, bundle.getEntry().size());
+		goal = (Goal) bundle.getEntry().get(0).getResource();
+		
+		condition = (Condition) goal.getAddresses().get(0).getResource();
+		
+		assertEquals("2011-01-01", condition.getDateRecordedElement().getValueAsString());
+	}
+
+	/**
+	 * Test for the url generated based on the server config
+	 */
+	@Test
+	public void testGeneratedUrls() {
+		final IParser jsonParser = ourCtx.newJsonParser().setPrettyPrint(true);
+		jsonParser.setServerBaseUrl("http://myserver.com");
+
+		final CustomPatientDstu2 patient = new CustomPatientDstu2();
+		patient.setHomeless(new BooleanDt(true));
+
+		final String parsedPatient = jsonParser.encodeResourceToString(patient);
+
+		assertTrue(parsedPatient.contains("http://myserver.com/StructureDefinition/Patient"));
+		assertTrue(parsedPatient.contains("http://myserver.com/StructureDefinition/homeless"));
+	}	
+  
+	/**
+	 * Test for the url generated based on the server config
+	 */
+	@Test
+	public void testCustomUrlExtension() {
+		final String expected = "{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}";
+
+		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+		patient.setPetName(new StringDt("myName"));
+
+		final IParser jsonParser = ourCtx.newJsonParser();
+		jsonParser.setServerBaseUrl("http://www.example.com");
+
+		final String parsedPatient = jsonParser.encodeResourceToString(patient);
+		System.out.println(parsedPatient);
+		assertEquals(expected, parsedPatient);
+
+		// Parse with string
+		MyPatientWithCustomUrlExtension newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, parsedPatient);
+		assertEquals("myName", newPatient.getPetName().getValue());
+
+		// Parse with stream
+		newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
+		assertEquals("myName", newPatient.getPetName().getValue());
+
+		//Check no NPE if base server not configure
+		newPatient = ourCtx.newJsonParser().parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
+		assertNull("myName", newPatient.getPetName().getValue());
+		assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+	}
+
+	@Test
+	public void testCustomUrlExtensioninBundle() {
+		final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
+
+		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+		patient.setPetName(new StringDt("myName"));
+
+		final Bundle bundle = new Bundle();
+		final Entry entry = new Entry();
+		entry.setResource(patient);
+		bundle.addEntry(entry);
+
+		final IParser jsonParser = ourCtx.newJsonParser();
+		jsonParser.setServerBaseUrl("http://www.example.com");
+
+		final String parsedBundle = jsonParser.encodeResourceToString(bundle);
+		System.out.println(parsedBundle);
+		assertEquals(expected, parsedBundle);
+
+		// Parse with string
+		Bundle newBundle = jsonParser.parseResource(Bundle.class, parsedBundle);
+		assertNotNull(newBundle);
+		assertEquals(1, newBundle.getEntry().size());
+		Patient newPatient = (Patient) newBundle.getEntry().get(0).getResource();
+		assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+
+		// Parse with stream
+		newBundle = jsonParser.parseResource(Bundle.class, new StringReader(parsedBundle));
+		assertNotNull(newBundle);
+		assertEquals(1, newBundle.getEntry().size());
+		newPatient = (Patient) newBundle.getEntry().get(0).getResource();
+		assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+
+	}  
+
+	@Test
+	public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
+		String refVal = "http://my.org/FooBar";
+
+		Patient fhirPat = new Patient();
+		fhirPat.addUndeclaredExtension(false, "x1").setValue(new ResourceReferenceDt(refVal));
+
+		IParser parser = ourCtx.newJsonParser();
+
+		String output = parser.encodeResourceToString(fhirPat);
+		System.out.println("output: " + output);
+
+		// Deserialize then check that valueReference value is still correct
+		fhirPat = parser.parseResource(Patient.class, output);
+
+		List<ExtensionDt> extlst = fhirPat.getUndeclaredExtensionsByUrl("x1");
+		Assert.assertEquals(1, extlst.size());
+		Assert.assertEquals(refVal, ((ResourceReferenceDt) extlst.get(0).getValue()).getReference().getValue());
+	}
+
+	private static final class TimestampFields {
+		ResourceReferenceDt user;
+		InstantDt instance;
+		ResourceReferenceDt organization;
+		CodeableConceptDt role;
+
+		TimestampFields(BaseResource resource) {
+			ExtensionDt timestamp = (ExtensionDt) resource.getResourceMetadata().get(
+				new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://fhir.sjanic.com/timestamp"));
+
+			Map<String, ExtensionDt> timestampFields = new HashMap<>(timestamp.getExtension().size());
+			for (ExtensionDt extensionDt : timestamp.getExtension()) {
+				timestampFields.put(extensionDt.getUrl(), extensionDt);
+			}
+			user = ((ResourceReferenceDt)timestampFields.get("http://fhir.sjanic.com/timestamp/user").getValue());
+			instance = (InstantDt) timestampFields.get("http://fhir.sjanic.com/timestamp/instance").getValue();
+			organization = (ResourceReferenceDt) timestampFields.get("http://fhir.sjanic.com/timestamp/organization").getValue();
+			role = (CodeableConceptDt) timestampFields.get("http://fhir.sjanic.com/timestamp/role").getValue();
+		}
+	}
 }

hapi-fhir-structures-dstu2/src/test/resources/patient1.json

@@ -13,11 +13,11 @@
     ],
     "modifierExtension": [
       {
-        "url": "fhir-request-method",
+        "url": "modified-fhir-request-method",
         "valueString": "POST"
       },
       {
-        "url": "fhir-request-uri",
+        "url": "modified-fhir-request-uri",
         "valueUri": "Patient"
       }
     ],

hapi-fhir-structures-dstu2/src/test/resources/procedure-request.json

@@ -0,0 +1,47 @@
+{
+	"resourceType": "ProcedureRequest",
+	"meta": {
+		"extension": [
+			{
+				"url": "http://fhir.sjanic.com/timestamp",
+				"extension": [
+					{
+						"url": "http://fhir.sjanic.com/timestamp/user",
+						"valueReference": {
+							"reference": "sjanic"
+						}
+					},
+					{
+						"url": "http://fhir.sjanic.com/timestamp/instance",
+						"valueInstant": "2012-01-01T13:00:00Z"
+					},
+					{
+						"url": "http://fhir.sjanic.com/timestamp/organization",
+						"valueReference": {
+							"reference": "sjanic_org"
+						}
+					},
+					{
+						"url": "http://fhir.sjanic.com/timestamp/role",
+						"valueCodeableConcept": {
+							"coding": [
+								{
+									"system": "sjanic",
+									"code": "Doctor",
+									"display": "Doctorin"
+								}
+							]
+						}
+					}
+				]
+			}
+		],
+		"modifierExtension": [
+			{
+				"url": "http://fhir.sjanic.com/procedureRequest/requiresPatientPayment",
+				"valueBoolean": true
+			}
+		]
+	},
+	"status": "accepted"
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/param/ReferenceParamTest.java

@@ -19,10 +19,62 @@ public class ReferenceParamTest {
 		rp.setValueAsQueryToken(ourCtx, null, null, "Location/123");
 		assertEquals("Location", rp.getResourceType());
 		assertEquals("123", rp.getIdPart());
+		assertEquals("Location/123", rp.getValue());
 		assertEquals(null, rp.getQueryParameterQualifier());
 		
 	}
 
+	@Test
+	public void testWithResourceType_AbsoluteUrl() {
+		
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, null, "http://a.b/c/d/e");
+		assertEquals("d", rp.getResourceType());
+		assertEquals("e", rp.getIdPart());
+		assertEquals("http://a.b/c/d/e", rp.getValue());
+		assertEquals(null, rp.getQueryParameterQualifier());
+		
+	}
+
+	@Test
+	public void testWithNoResourceTypeAsQualifierAndChain() {
+
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ".name", "FOO");
+		assertEquals(null, rp.getResourceType());
+		assertEquals("FOO", rp.getIdPart());
+		assertEquals("FOO", rp.getValue());
+		assertEquals(".name", rp.getQueryParameterQualifier());
+		assertEquals("name", rp.getChain());
+
+	}
+
+	@Test
+	public void testWithNoResourceTypeAsQualifierAndChain_RelativeUrl() {
+
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ".name", "Patient/1233");
+		assertEquals(null, rp.getResourceType());
+		assertEquals("Patient/1233", rp.getIdPart());
+		assertEquals("Patient/1233", rp.getValue());
+		assertEquals(".name", rp.getQueryParameterQualifier());
+		assertEquals("name", rp.getChain());
+
+	}
+
+	@Test
+	public void testWithNoResourceTypeAsQualifierAndChain_AbsoluteUrl() {
+
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ".name", "http://something.strange/a/b/c");
+		assertEquals(null, rp.getResourceType());
+		assertEquals("http://something.strange/a/b/c", rp.getIdPart());
+		assertEquals("http://something.strange/a/b/c", rp.getValue());
+		assertEquals(".name", rp.getQueryParameterQualifier());
+		assertEquals("name", rp.getChain());
+
+	}
+	
 	@Test
 	public void testWithResourceTypeAsQualifier() {
 		
@@ -30,6 +82,34 @@ public class ReferenceParamTest {
 		rp.setValueAsQueryToken(ourCtx, null, ":Location", "123");
 		assertEquals("Location", rp.getResourceType());
 		assertEquals("123", rp.getIdPart());
+		assertEquals("Location/123", rp.getValue());
+		assertEquals(null, rp.getQueryParameterQualifier());
+
+	}
+
+	// TODO: verify this behavior is correct. If type is explicitly specified (i.e. :Location), should it be
+	// an error if it gets overriden by the resourceType in the url?
+	@Test
+	public void testWithResourceTypeAsQualifier_RelativeUrl() {
+		
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ":Location", "Patient/123");
+		assertEquals("Patient", rp.getResourceType());
+		assertEquals("123", rp.getIdPart());
+		assertEquals("Patient/123", rp.getValue());
+		assertEquals(null, rp.getQueryParameterQualifier());
+
+	}
+
+	// TODO: verify this behavior is correct. Same case as testWithResourceTypeAsQualifier_RelativeUrl()
+	@Test
+	public void testWithResourceTypeAsQualifier_AbsoluteUrl() {
+		
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ":Location", "http://a.b/c/d/e");
+		assertEquals("d", rp.getResourceType());
+		assertEquals("e", rp.getIdPart());
+		assertEquals("http://a.b/c/d/e", rp.getValue());
 		assertEquals(null, rp.getQueryParameterQualifier());
 
 	}
@@ -42,11 +122,51 @@ public class ReferenceParamTest {
 		rp.setValueAsQueryToken(ourCtx, null, ":Location.name", "FOO");
 		assertEquals("Location", rp.getResourceType());
 		assertEquals("FOO", rp.getIdPart());
+		assertEquals("Location/FOO", rp.getValue());
 		assertEquals(":Location.name", rp.getQueryParameterQualifier());
 		assertEquals("name", rp.getChain());
 
 	}
 
+	@Test
+	public void testWithResourceTypeAsQualifierAndChain_IdentifierUrlAndValue() {
+
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "http://hey.there/a/b|123");
+		assertEquals("Patient", rp.getResourceType());
+		assertEquals("http://hey.there/a/b|123", rp.getIdPart());
+		assertEquals("Patient/http://hey.there/a/b|123", rp.getValue());
+		assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
+		assertEquals("identifier", rp.getChain());
+
+	}
+
+	@Test
+	public void testWithResourceTypeAsQualifierAndChain_IdentifierUrlOnly() {
+
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "http://hey.there/a/b|");
+		assertEquals("Patient", rp.getResourceType());
+		assertEquals("http://hey.there/a/b|", rp.getIdPart());
+		assertEquals("Patient/http://hey.there/a/b|", rp.getValue());
+		assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
+		assertEquals("identifier", rp.getChain());
+
+	}
+
+	@Test
+	public void testWithResourceTypeAsQualifierAndChain_ValueOnlyNoUrl() {
+
+		ReferenceParam rp = new ReferenceParam();
+		rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "|abc");
+		assertEquals("Patient", rp.getResourceType());
+		assertEquals("|abc", rp.getIdPart());
+		assertEquals("Patient/|abc", rp.getValue());
+		assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
+		assertEquals("identifier", rp.getChain());
+
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();