Add custom extension example

examples/src/main/java/example/customtype/CustomCompositeExtension.java

@@ -0,0 +1,84 @@
+package example.customtype;
+
+import org.hl7.fhir.dstu3.model.BackboneElement;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.util.ElementUtil;
+
+//START SNIPPET: resource
+@ResourceDef(name = "Patient")
+public class CustomCompositeExtension extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * A custom extension
+	 */
+	@Child(name = "foo")
+	@Extension(url="http://acme.org/fooParent", definedLocally = false, isModifier = false)
+	protected FooParentExtension fooParentExtension;
+
+	public FooParentExtension getFooParentExtension() {
+		return fooParentExtension;
+	}
+
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && ElementUtil.isEmpty(fooParentExtension);
+	}
+
+	public void setFooParentExtension(FooParentExtension theFooParentExtension) {
+		fooParentExtension = theFooParentExtension;
+	}
+
+	@Block
+	public static class FooParentExtension extends BackboneElement {
+
+		private static final long serialVersionUID = 4522090347756045145L;
+
+		@Child(name = "childA")
+		@Extension(url = "http://acme.org/fooChildA", definedLocally = false, isModifier = false)
+		private StringType myChildA;
+
+		@Child(name = "childB")
+		@Extension(url = "http://acme.org/fooChildB", definedLocally = false, isModifier = false)
+		private StringType myChildB;
+
+		@Override
+		public FooParentExtension copy() {
+			FooParentExtension copy = new FooParentExtension();
+			copy.myChildA = myChildA;
+			copy.myChildB = myChildB;
+			return copy;
+		}
+
+		@Override
+		public boolean isEmpty() {
+			return super.isEmpty() && ElementUtil.isEmpty(myChildA, myChildB);
+		}
+
+		public StringType getChildA() {
+			return myChildA;
+		}
+
+		public StringType getChildB() {
+			return myChildB;
+		}
+
+		public void setChildA(StringType theChildA) {
+			myChildA = theChildA;
+		}
+
+		public void setChildB(StringType theChildB) {
+			myChildB = theChildB;
+		}
+
+	}
+
+}
+//END SNIPPET: resource

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/DatabaseBackedPagingProvider.java

@@ -58,7 +58,7 @@ public class DatabaseBackedPagingProvider extends FifoMemoryPagingProvider {
 			if (!provider.ensureSearchEntityLoaded()) {
 				return null;
 			}
-			return provider;
+			retVal = provider;
 		}
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -14,46 +14,16 @@ import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 
 import java.math.BigDecimal;
-import java.util.Date;
+import java.util.*;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.dstu3.model.Appointment;
+import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.CodeType;
-import org.hl7.fhir.dstu3.model.CodeableConcept;
-import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
-import org.hl7.fhir.dstu3.model.DateTimeType;
-import org.hl7.fhir.dstu3.model.DateType;
-import org.hl7.fhir.dstu3.model.Device;
-import org.hl7.fhir.dstu3.model.DiagnosticRequest;
-import org.hl7.fhir.dstu3.model.DiagnosticReport;
-import org.hl7.fhir.dstu3.model.Encounter;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
-import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.dstu3.model.Immunization;
-import org.hl7.fhir.dstu3.model.Location;
-import org.hl7.fhir.dstu3.model.Medication;
-import org.hl7.fhir.dstu3.model.MedicationOrder;
-import org.hl7.fhir.dstu3.model.Observation;
-import org.hl7.fhir.dstu3.model.Organization;
-import org.hl7.fhir.dstu3.model.Patient;
-import org.hl7.fhir.dstu3.model.Period;
-import org.hl7.fhir.dstu3.model.Practitioner;
-import org.hl7.fhir.dstu3.model.Quantity;
-import org.hl7.fhir.dstu3.model.Reference;
-import org.hl7.fhir.dstu3.model.StringType;
-import org.hl7.fhir.dstu3.model.Subscription;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
-import org.hl7.fhir.dstu3.model.Substance;
-import org.hl7.fhir.dstu3.model.TemporalPrecisionEnum;
-import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -63,35 +33,13 @@ import org.junit.Test;
 
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
+import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
-import ca.uhn.fhir.jpa.entity.ResourceLink;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
 import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.param.CompositeParam;
+import ca.uhn.fhir.rest.param.*;
-import ca.uhn.fhir.rest.param.DateParam;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.param.HasParam;
-import ca.uhn.fhir.rest.param.NumberParam;
-import ca.uhn.fhir.rest.param.ParamPrefixEnum;
-import ca.uhn.fhir.rest.param.QuantityParam;
-import ca.uhn.fhir.rest.param.ReferenceParam;
-import ca.uhn.fhir.rest.param.StringAndListParam;
-import ca.uhn.fhir.rest.param.StringOrListParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.TokenAndListParam;
-import ca.uhn.fhir.rest.param.TokenOrListParam;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.param.TokenParamModifier;
-import ca.uhn.fhir.rest.param.UriParam;
-import ca.uhn.fhir.rest.param.UriParamQualifierEnum;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsInRelativeOrder;
@@ -95,9 +96,11 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.core.NestedExceptionUtils;
 
 import com.google.common.collect.Lists;
 
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.parser.IParser;
@@ -128,6 +131,47 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 	}
 
 
+	@Test
+	public void testSearchPagingKeepsOldSearches() throws Exception {
+		String methodName = "testSearchPagingKeepsOldSearches";
+		IIdType pid1;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("0");
+			patient.addName().addFamily(methodName).addGiven("Joe");
+			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		for (int i = 1; i <= 20; i++) {
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue(Integer.toString(i));
+			patient.addName().addFamily(methodName).addGiven("Joe");
+			myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		
+		List<String> linkNext = Lists.newArrayList(); 
+		for (int i = 0 ; i < 100; i++) {
+			Bundle bundle = ourClient
+				.search()
+				.forResource(Patient.class)
+				.where(Patient.NAME.matches().value("testSearchPagingKeepsOldSearches"))
+				.count(5)
+				.returnBundle(Bundle.class)
+				.execute();
+			assertTrue(isNotBlank(bundle.getLink("next").getUrl()));
+			assertEquals(5, bundle.getEntry().size());
+			linkNext.add(bundle.getLink("next").getUrl());
+		}
+
+		int index = 0;
+		for (String nextLink : linkNext) {
+			ourLog.info("Fetching index {}", index++);
+			Bundle b = ourClient.fetchResourceFromUrl(Bundle.class, nextLink);
+			assertEquals(5, b.getEntry().size());
+		}
+	}
+
+	
 	@Test
 	public void testHasParameter() throws Exception {
 		IIdType pid0;

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -200,11 +201,10 @@ public class TestRestfulServer extends RestfulServer {
 		setServerAddressStrategy(new MyHardcodedServerAddressStrategy(baseUrl));
 		
 		/*
-		 * This is a simple paging strategy that keeps the last 10 
+		 * Spool results to the database 
-		 * searches in memory
 		 */
-		setPagingProvider(new FifoMemoryPagingProvider(10).setMaximumPageSize(500));
+		setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
-
+		
 		/*
 		 * Load interceptors for the server from Spring
 		 */

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

@@ -0,0 +1,82 @@
+package ca.uhn.fhir.parser;
+
+import org.hl7.fhir.dstu3.model.BackboneElement;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.util.ElementUtil;
+
+@ResourceDef(name = "Patient")
+public class PatientWithCustomCompositeExtension extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * A custom extension
+	 */
+	@Child(name = "foo")
+	@Extension(url="http://acme.org/fooParent", definedLocally = false, isModifier = false)
+	protected FooParentExtension fooParentExtension;
+
+	public FooParentExtension getFooParentExtension() {
+		return fooParentExtension;
+	}
+
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && ElementUtil.isEmpty(fooParentExtension);
+	}
+
+	public void setFooParentExtension(FooParentExtension theFooParentExtension) {
+		fooParentExtension = theFooParentExtension;
+	}
+
+	@Block
+	public static class FooParentExtension extends BackboneElement {
+
+		private static final long serialVersionUID = 4522090347756045145L;
+
+		@Child(name = "childA")
+		@Extension(url = "http://acme.org/fooChildA", definedLocally = false, isModifier = false)
+		private StringType myChildA;
+
+		@Child(name = "childB")
+		@Extension(url = "http://acme.org/fooChildB", definedLocally = false, isModifier = false)
+		private StringType myChildB;
+
+		@Override
+		public FooParentExtension copy() {
+			FooParentExtension copy = new FooParentExtension();
+			copy.myChildA = myChildA;
+			copy.myChildB = myChildB;
+			return copy;
+		}
+
+		@Override
+		public boolean isEmpty() {
+			return super.isEmpty() && ElementUtil.isEmpty(myChildA, myChildB);
+		}
+
+		public StringType getChildA() {
+			return myChildA;
+		}
+
+		public StringType getChildB() {
+			return myChildB;
+		}
+
+		public void setChildA(StringType theChildA) {
+			myChildA = theChildA;
+		}
+
+		public void setChildB(StringType theChildB) {
+			myChildB = theChildB;
+		}
+
+	}
+
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -66,6 +66,7 @@ import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.parser.FooMessageHeaderWithExplicitField.FooMessageSourceComponent;
 import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
+import ca.uhn.fhir.parser.PatientWithCustomCompositeExtension.FooParentExtension;
 import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.util.TestUtil;
@@ -82,159 +83,6 @@ public class XmlParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
-	@Test
-	public void testEncodeReferenceWithUuid() {
-		
-		Practitioner pract = new Practitioner();
-		pract.setId(IdType.newRandomUuid());
-		pract.addName().addFamily("PRACT FAMILY");
-		
-		Patient patient = new Patient();
-		patient.addGeneralPractitioner().setResource(pract);
-		
-		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(encoded);
-		
-		assertThat(pract.getId(), startsWith("urn:uuid:"));
-		assertThat(encoded, containsString("<reference value=\"" + pract.getId() + "\"/>"));
-	}
-	
-	@Test
-	public void testEncodeAndParseContainedCustomTypes() {
-		ourCtx = FhirContext.forDstu3();
-		ourCtx.setDefaultTypeForProfile(CustomObservation.PROFILE, CustomObservation.class);
-		ourCtx.setDefaultTypeForProfile(CustomDiagnosticReport.PROFILE, CustomDiagnosticReport.class);
-		
-		CustomObservation obs = new CustomObservation();
-		obs.setStatus(ObservationStatus.FINAL);
-		
-		CustomDiagnosticReport dr = new CustomDiagnosticReport();
-		dr.setStatus(DiagnosticReportStatus.FINAL);
-		dr.addResult().setResource(obs);
-		
-		IParser parser = ourCtx.newXmlParser();
-		parser.setPrettyPrint(true);
-		
-		String output = parser.encodeResourceToString(dr);
-		ourLog.info(output);
-		
-		//@formatter:off
-		assertThat(output,stringContainsInOrder(
-			"<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
-				"<meta>",
-				"<profile value=\"http://custom_DiagnosticReport\"/>",
-				"</meta>",
-				"<contained>",
-					"<Observation xmlns=\"http://hl7.org/fhir\">",
-						"<id value=\"1\"/>",
-						"<meta>",
-							"<profile value=\"http://custom_Observation\"/>",
-						"</meta>",
-						"<status value=\"final\"/>",
-					"</Observation>",
-				"</contained>",
-				"<status value=\"final\"/>",
-				"<result>",
-					"<reference value=\"#1\"/>",
-				"</result>",
-			"</DiagnosticReport>"));
-		//@formatter:on
-		
-		/*
-		 * Now PARSE!
-		 */
-		
-		dr = (CustomDiagnosticReport) parser.parseResource(output);
-		assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
-
-		assertEquals("#1", dr.getResult().get(0).getReference());
-		obs = (CustomObservation) dr.getResult().get(0).getResource();
-		assertEquals(ObservationStatus.FINAL, obs.getStatus());
-
-		ourCtx = null;
-	}
-	
-	@Test
-	public void testEncodeAndParseContainedNonCustomTypes() {
-		ourCtx = FhirContext.forDstu3();
-		
-		Observation obs = new Observation();
-		obs.setStatus(ObservationStatus.FINAL);
-		
-		DiagnosticReport dr = new DiagnosticReport();
-		dr.setStatus(DiagnosticReportStatus.FINAL);
-		dr.addResult().setResource(obs);
-		
-		IParser parser = ourCtx.newXmlParser();
-		parser.setPrettyPrint(true);
-		
-		String output = parser.encodeResourceToString(dr);
-		ourLog.info(output);
-		
-		//@formatter:off
-		assertThat(output,stringContainsInOrder(
-			"<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
-				"<contained>",
-					"<Observation xmlns=\"http://hl7.org/fhir\">",
-						"<id value=\"1\"/>",
-						"<status value=\"final\"/>",
-					"</Observation>",
-				"</contained>",
-				"<status value=\"final\"/>",
-				"<result>",
-					"<reference value=\"#1\"/>",
-				"</result>",
-			"</DiagnosticReport>"));
-		//@formatter:on
-		
-		/*
-		 * Now PARSE!
-		 */
-		
-		dr = (DiagnosticReport) parser.parseResource(output);
-		assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
-
-		assertEquals("#1", dr.getResult().get(0).getReference());
-		obs = (Observation) dr.getResult().get(0).getResource();
-		assertEquals(ObservationStatus.FINAL, obs.getStatus());
-
-		ourCtx = null;
-	}
-
-	@Test
-	public void testEncodeHistoryEncodeVersionsAtPath3() {
-		ourCtx = FhirContext.forDstu3();
-		
-		assertNull(ourCtx.newXmlParser().getStripVersionsFromReferences());
-		
-		AuditEvent auditEvent = new AuditEvent();
-		auditEvent.addEntity().setReference(new Reference("http://foo.com/Organization/2/_history/1"));
-		
-		IParser parser = ourCtx.newXmlParser();
-		
-		parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
-		String enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-		ourLog.info(enc);
-		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2/_history/1\"/>"));
-		
-		parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
-		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-		ourLog.info(enc);
-		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
-
-		parser.setDontStripVersionsFromReferencesAtPaths((String[])null);
-		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-		ourLog.info(enc);
-		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
-
-		parser.setDontStripVersionsFromReferencesAtPaths((List<String>)null);
-		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-		ourLog.info(enc);
-		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
-		
-	}
-
-
 	@Test
 	public void testBundleWithBinary() {
 		//@formatter:off
@@ -265,7 +113,7 @@ public class XmlParserDstu3Test {
 		assertArrayEquals(new byte[] { 1, 2, 3, 4 }, bin.getContent());
 
 	}
-
+	
 	@Test
 	public void testContainedResourceInExtensionUndeclared() {
 		Patient p = new Patient();
@@ -287,7 +135,7 @@ public class XmlParserDstu3Test {
 		o = (Organization) rr.getResource();
 		assertEquals("ORG", o.getName());
 	}
-
+	
 	@Test
 	public void testDuration() {
 		Encounter enc = new Encounter();
@@ -301,7 +149,7 @@ public class XmlParserDstu3Test {
 		assertThat(str, not(containsString("meta")));
 		assertThat(str, containsString("<length><value value=\"123\"/><unit value=\"day\"/></length>"));
 	}
-
+	
 	@Test
 	public void testEncodeAndParseBundleWithResourceRefs() {
 
@@ -339,6 +187,24 @@ public class XmlParserDstu3Test {
 		assertSame(org, pt.getManagingOrganization().getResource());
 	}
 
+	@Test
+	public void testEncodeAndParseCompositeExtension() {
+		PatientWithCustomCompositeExtension pat = new PatientWithCustomCompositeExtension();
+		pat.setId("123");
+		pat.setFooParentExtension(new FooParentExtension());
+		pat.getFooParentExtension().setChildA(new StringType("ValueA"));
+		pat.getFooParentExtension().setChildB(new StringType("ValueB"));
+		
+		String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pat);
+		ourLog.info(enc);
+		
+		pat = ourCtx.newXmlParser().parseResource(PatientWithCustomCompositeExtension.class, enc);
+		
+		assertEquals("ValueA", pat.getFooParentExtension().getChildA().getValue());
+		assertEquals("ValueB", pat.getFooParentExtension().getChildB().getValue());
+	}
+
+
 	@Test
 	public void testEncodeAndParseContained() {
 		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
@@ -408,6 +274,108 @@ public class XmlParserDstu3Test {
 
 	}
 
+	@Test
+	public void testEncodeAndParseContainedCustomTypes() {
+		ourCtx = FhirContext.forDstu3();
+		ourCtx.setDefaultTypeForProfile(CustomObservation.PROFILE, CustomObservation.class);
+		ourCtx.setDefaultTypeForProfile(CustomDiagnosticReport.PROFILE, CustomDiagnosticReport.class);
+		
+		CustomObservation obs = new CustomObservation();
+		obs.setStatus(ObservationStatus.FINAL);
+		
+		CustomDiagnosticReport dr = new CustomDiagnosticReport();
+		dr.setStatus(DiagnosticReportStatus.FINAL);
+		dr.addResult().setResource(obs);
+		
+		IParser parser = ourCtx.newXmlParser();
+		parser.setPrettyPrint(true);
+		
+		String output = parser.encodeResourceToString(dr);
+		ourLog.info(output);
+		
+		//@formatter:off
+		assertThat(output,stringContainsInOrder(
+			"<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
+				"<meta>",
+				"<profile value=\"http://custom_DiagnosticReport\"/>",
+				"</meta>",
+				"<contained>",
+					"<Observation xmlns=\"http://hl7.org/fhir\">",
+						"<id value=\"1\"/>",
+						"<meta>",
+							"<profile value=\"http://custom_Observation\"/>",
+						"</meta>",
+						"<status value=\"final\"/>",
+					"</Observation>",
+				"</contained>",
+				"<status value=\"final\"/>",
+				"<result>",
+					"<reference value=\"#1\"/>",
+				"</result>",
+			"</DiagnosticReport>"));
+		//@formatter:on
+		
+		/*
+		 * Now PARSE!
+		 */
+		
+		dr = (CustomDiagnosticReport) parser.parseResource(output);
+		assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
+
+		assertEquals("#1", dr.getResult().get(0).getReference());
+		obs = (CustomObservation) dr.getResult().get(0).getResource();
+		assertEquals(ObservationStatus.FINAL, obs.getStatus());
+
+		ourCtx = null;
+	}
+
+	@Test
+	public void testEncodeAndParseContainedNonCustomTypes() {
+		ourCtx = FhirContext.forDstu3();
+		
+		Observation obs = new Observation();
+		obs.setStatus(ObservationStatus.FINAL);
+		
+		DiagnosticReport dr = new DiagnosticReport();
+		dr.setStatus(DiagnosticReportStatus.FINAL);
+		dr.addResult().setResource(obs);
+		
+		IParser parser = ourCtx.newXmlParser();
+		parser.setPrettyPrint(true);
+		
+		String output = parser.encodeResourceToString(dr);
+		ourLog.info(output);
+		
+		//@formatter:off
+		assertThat(output,stringContainsInOrder(
+			"<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
+				"<contained>",
+					"<Observation xmlns=\"http://hl7.org/fhir\">",
+						"<id value=\"1\"/>",
+						"<status value=\"final\"/>",
+					"</Observation>",
+				"</contained>",
+				"<status value=\"final\"/>",
+				"<result>",
+					"<reference value=\"#1\"/>",
+				"</result>",
+			"</DiagnosticReport>"));
+		//@formatter:on
+		
+		/*
+		 * Now PARSE!
+		 */
+		
+		dr = (DiagnosticReport) parser.parseResource(output);
+		assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
+
+		assertEquals("#1", dr.getResult().get(0).getReference());
+		obs = (Observation) dr.getResult().get(0).getResource();
+		assertEquals(ObservationStatus.FINAL, obs.getStatus());
+
+		ourCtx = null;
+	}
+
 	@Test
 	public void testEncodeAndParseExtensionOnCode() {
 		Organization o = new Organization();
@@ -1113,6 +1081,30 @@ public class XmlParserDstu3Test {
 		ourLog.info(parser.encodeResourceToString(gr));
 	}
 
+	@Test
+	public void testEncodeDeclaredBlock() throws Exception {
+		FooMessageSourceComponent source = new FooMessageHeaderWithExplicitField.FooMessageSourceComponent();
+		source.getMessageHeaderApplicationId().setValue("APPID");
+		source.setName("NAME");
+
+		FooMessageHeaderWithExplicitField header = new FooMessageHeaderWithExplicitField();
+		header.setSourceNew(source);
+
+		header.addDestination().setName("DEST");
+
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(header);
+
+		IParser p = ourCtx.newXmlParser();
+		p.setPrettyPrint(true);
+
+		String encode = p.encodeResourceToString(bundle);
+		ourLog.info(encode);
+
+		assertThat(encode, containsString("<value value=\"APPID\"/>"));
+		assertThat(encode, stringContainsInOrder("<source", "<dest"));
+	}
+
 	/**
 	 * Make sure whitespace is preserved for pre tags
 	 */
@@ -1341,6 +1333,39 @@ public class XmlParserDstu3Test {
 
 	}
 
+	@Test
+	public void testEncodeHistoryEncodeVersionsAtPath3() {
+		ourCtx = FhirContext.forDstu3();
+		
+		assertNull(ourCtx.newXmlParser().getStripVersionsFromReferences());
+		
+		AuditEvent auditEvent = new AuditEvent();
+		auditEvent.addEntity().setReference(new Reference("http://foo.com/Organization/2/_history/1"));
+		
+		IParser parser = ourCtx.newXmlParser();
+		
+		parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
+		String enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2/_history/1\"/>"));
+		
+		parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
+		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
+
+		parser.setDontStripVersionsFromReferencesAtPaths((String[])null);
+		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
+
+		parser.setDontStripVersionsFromReferencesAtPaths((List<String>)null);
+		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
+		
+	}
+
 	@Test
 	public void testEncodeNarrativeSuppressed() {
 		Patient patient = new Patient();
@@ -1471,6 +1496,23 @@ public class XmlParserDstu3Test {
 		assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
 	}
 
+	@Test
+	public void testEncodeReferenceWithUuid() {
+		
+		Practitioner pract = new Practitioner();
+		pract.setId(IdType.newRandomUuid());
+		pract.addName().addFamily("PRACT FAMILY");
+		
+		Patient patient = new Patient();
+		patient.addGeneralPractitioner().setResource(pract);
+		
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+		
+		assertThat(pract.getId(), startsWith("urn:uuid:"));
+		assertThat(encoded, containsString("<reference value=\"" + pract.getId() + "\"/>"));
+	}
+
 	@Test
 	public void testEncodeSummary() {
 		Patient patient = new Patient();
@@ -1534,30 +1576,6 @@ public class XmlParserDstu3Test {
 		assertThat(encode, stringContainsInOrder("<source", "<dest"));
 	}
 
-	@Test
-	public void testEncodeDeclaredBlock() throws Exception {
-		FooMessageSourceComponent source = new FooMessageHeaderWithExplicitField.FooMessageSourceComponent();
-		source.getMessageHeaderApplicationId().setValue("APPID");
-		source.setName("NAME");
-
-		FooMessageHeaderWithExplicitField header = new FooMessageHeaderWithExplicitField();
-		header.setSourceNew(source);
-
-		header.addDestination().setName("DEST");
-
-		Bundle bundle = new Bundle();
-		bundle.addEntry().setResource(header);
-
-		IParser p = ourCtx.newXmlParser();
-		p.setPrettyPrint(true);
-
-		String encode = p.encodeResourceToString(bundle);
-		ourLog.info(encode);
-
-		assertThat(encode, containsString("<value value=\"APPID\"/>"));
-		assertThat(encode, stringContainsInOrder("<source", "<dest"));
-	}
-
 	@Test
 	public void testEncodeUndeclaredExtensionWithEnumerationContent() {
 		IParser parser = ourCtx.newXmlParser();

src/site/xdoc/doc_extensions.xml

@@ -240,6 +240,36 @@
 				</macro>
 
 			</subsection>
+
+			<subsection name="Custom Type Examples: Composite Extensions">
+			
+				<p>
+					The following example shows a resource containing a composite
+					extension.
+				</p>
+			
+				<macro name="snippet">
+					<param name="id" value="resource" />
+					<param name="file" value="examples/src/main/java/example/customtype/CustomCompositeExtension.java" />
+				</macro>
+			
+				<p>
+					This could be used to create a resource such as the
+					following:
+				</p>
+				<source><![CDATA[<Patient xmlns="http://hl7.org/fhir">
+   <id value="123"/>
+   <extension url="http://acme.org/fooParent">
+      <extension url="http://acme.org/fooChildA">
+         <valueString value="ValueA"/>
+      </extension>
+      <extension url="http://acme.org/fooChildB">
+         <valueString value="ValueB"/>
+      </extension>
+   </extension>
+</Patient>]]></source>
+			
+			</subsection>
 			
 		</section>