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

.gitignore

@@ -16,6 +16,7 @@ nohup.out
 tmp.txt
 *.hprof
 tmp.txt
+ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString/
 
 # Vagrant stuff.
 .vagrant

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

@@ -2,6 +2,8 @@ package ca.uhn.fhir.model.api;
 
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
+import ch.qos.logback.core.db.dialect.MySQLDialect;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -34,7 +36,7 @@ public class Include {
 
 	private boolean myRecurse;
 	private String myValue;
-	private boolean myImmutable;
+	private final boolean myImmutable;
 
 	/**
 	 * Constructor for <b>non-recursive</b> include
@@ -44,10 +46,11 @@ public class Include {
 	 */
 	public Include(String theValue) {
 		myValue = theValue;
+		myImmutable = false;
 	}
 
 	/**
-	 * Constructor for <b>non-recursive</b> include
+	 * Constructor for an include
 	 * 
 	 * @param theValue
 	 *           The <code>_include</code> value, e.g. "Patient:name"
@@ -57,6 +60,21 @@ public class Include {
 	public Include(String theValue, boolean theRecurse) {
 		myValue = theValue;
 		myRecurse = theRecurse;
+		myImmutable = false;
+	}
+
+	/**
+	 * Constructor for an include
+	 * 
+	 * @param theValue
+	 *           The <code>_include</code> value, e.g. "Patient:name"
+	 * @param theRecurse
+	 *           Should the include recurse
+	 */
+	public Include(String theValue, boolean theRecurse, boolean theImmutable) {
+		myValue = theValue;
+		myRecurse = theRecurse;
+		myImmutable = theImmutable;
 	}
 
 	/**
@@ -132,9 +150,18 @@ public class Include {
 		myValue = theValue;
 	}
 
+	/**
+	 * Is this object {@link #toLocked() locked}?
+	 */
+	public boolean isLocked() {
+		return myImmutable;
+	}
+
+	/**
+	 * Return a new 
+	 */
 	public Include toLocked() {
-		Include retVal = new Include(myValue, myRecurse);
+		Include retVal = new Include(myValue, myRecurse, true);
-		retVal.myImmutable = true;
 		return retVal;
 	}
 	
@@ -145,4 +172,36 @@ public class Include {
 		builder.append("recurse", myRecurse);
 		return builder.toString();
 	}
+	
+	/**
+	 * Creates and returns a new copy of this Include with the given type. The 
+	 * following table shows what will be returned:
+	 * <table>
+	 * <tr><th>Initial Contents</th><th>theResourceType</th><th>Output</th></tr>
+	 * <tr><td>Patient:careProvider</th><th>Organization</th><th>Patient:careProvider:Organization</th></tr>
+	 * <tr><td>Patient:careProvider:Practitioner</th><th>Organization</th><th>Patient:careProvider:Organization</th></tr>
+	 * <tr><td>Patient</th><th>(any)</th><th>{@link IllegalStateException}</th></tr>
+	 * </table>
+	 * 
+	 * @param theResourceType The resource type (e.g. "Organization")
+	 * @return A new copy of the include. Note that if this include is {@link #toLocked() locked}, the returned include will be too
+	 */
+	public Include withType(String theResourceType) {
+		StringBuilder b = new StringBuilder();
+		b.append(myValue);
+		int firstColon = myValue.indexOf(':');
+		if (firstColon == -1 || firstColon == b.length() - 1) {
+			throw new IllegalStateException("This include does not contain a value in the format [ResourceType]:[paramName]");
+		}
+		int secondColon = myValue.indexOf(':', firstColon + 1);
+		if (secondColon != -1) {
+			b.delete(secondColon, b.length());
+		}
+		
+		b.append(":");
+		b.append(theResourceType);
+		Include retVal = new Include(b.toString(), myRecurse, myImmutable);
+		return retVal;
+	}
+	
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java

@@ -1322,7 +1322,7 @@ public class SearchBuilder {
 	 * 
 	 * @param theLastUpdated
 	 */
-	private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode, EverythingModeEnum theEverythingModeEnum, DateRangeParam theLastUpdated) {
+	private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode, DateRangeParam theLastUpdated) {
 		if (theMatches.size() == 0) {
 			return new HashSet<Long>();
 		}
@@ -1595,7 +1595,7 @@ public class SearchBuilder {
 		final Set<Long> revIncludedPids;
 		if (theParams.getEverythingMode() == null) {
 			if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
-				revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true, null, lu);
+				revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true, lu);
 			} else {
 				revIncludedPids = new HashSet<Long>();
 			}
@@ -1623,7 +1623,7 @@ public class SearchBuilder {
 
 						// Load includes
 						pidsSubList = new ArrayList<Long>(pidsSubList);
-						revIncludedPids.addAll(loadReverseIncludes(pidsSubList, theParams.getIncludes(), false, null, theParams.getLastUpdated()));
+						revIncludedPids.addAll(loadReverseIncludes(pidsSubList, theParams.getIncludes(), false, theParams.getLastUpdated()));
 
 						// Execute the query and make sure we return distinct results
 						List<IBaseResource> resources = new ArrayList<IBaseResource>();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java

@@ -4,7 +4,9 @@ import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
 import static org.mockito.Mockito.mock;
 
 import java.util.List;
@@ -14,9 +16,8 @@ import javax.servlet.http.HttpServletRequest;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
 
-import ca.uhn.fhir.jpa.dao.FhirSearchDao;
-import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.model.dstu2.resource.Device;
 import ca.uhn.fhir.model.dstu2.resource.Media;
 import ca.uhn.fhir.model.dstu2.resource.Observation;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -1430,25 +1430,36 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		{
 			Organization org = new Organization();
 			org.getNameElement().setValue(methodName + "_O1Parent");
-			parentOrgId = myOrganizationDao.create(org).getId();
+			parentOrgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
 		}
+		IIdType orgId;
+		IIdType patientId;
 		{
 			Organization org = new Organization();
 			org.getNameElement().setValue(methodName + "_O1");
 			org.setPartOf(new ResourceReferenceDt(parentOrgId));
-			IIdType orgId = myOrganizationDao.create(org).getId();
+			orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
 
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester_" + methodName + "_P1").addGiven("Joe");
 			patient.getManagingOrganization().setReference(orgId);
-			myPatientDao.create(patient);
+			patient.addCareProvider().setReference(orgId);
+			patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
 		}
+		IIdType practId2;
+		{
+			Practitioner pract = new Practitioner();
+			pract.getName().addFamily(methodName + "_PRACT1");
+			practId2 = myPractitionerDao.create(pract).getId().toUnqualifiedVersionless();
+		}
+		IIdType patientId2;
 		{
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("Tester_" + methodName + "_P2").addGiven("John");
-			myPatientDao.create(patient);
+			patient.addCareProvider().setReference(practId2);
+			patientId2 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
 		}
 
 		{
@@ -1527,6 +1538,20 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			assertEquals(1, patients.size());
 			assertEquals(Patient.class, patients.get(0).getClass());
 		}
+		{
+			// Untyped include
+			SearchParameterMap params = new SearchParameterMap();
+			params.addInclude(Patient.INCLUDE_CAREPROVIDER);
+			List<IIdType> ids = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(ids, containsInAnyOrder(orgId, patientId, patientId2, practId2));
+		}
+		{
+//			// Typed include
+//			SearchParameterMap params = new SearchParameterMap();
+//			params.addInclude(Patient.INCLUDE_CAREPROVIDER.withType("Practitioner"));
+//			List<IIdType> ids = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+//			assertThat(ids, containsInAnyOrder(patientId, patientId2, practId2));
+		}
 	}
 
 	@SuppressWarnings("unused")

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/IncludeTest.java

@@ -1,7 +1,10 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -51,56 +54,21 @@ import ca.uhn.fhir.util.PortUtil;
 public class IncludeTest {
 
 	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(IncludeTest.class);
 	private static int ourPort;
 	private static Server ourServer;
-	private static FhirContext ourCtx;
 
 	@Test
-	public void testNoIncludes() throws Exception {
+	public void testBadInclude() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo&_include=baz");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-		assertEquals(1, bundle.size());
-
-		Patient p = bundle.getResources(Patient.class).get(0);
-		assertEquals(0, p.getName().size());
-		assertEquals("Hello", p.getId().getIdPart());
-	}
-
-	@Test
-	public void testOneInclude() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-		assertEquals(1, bundle.size());
-
-		Patient p = bundle.getResources(Patient.class).get(0);
-		assertEquals(1, p.getName().size());
-		assertEquals("Hello", p.getId().getIdPart());
-		assertEquals("foo", p.getName().get(0).getFamilyFirstRep().getValue());
-	}
-
-	// @Test
-	public void testMixedContainedAndNonContained() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/DiagnosticReport?_query=stitchedInclude&_pretty=true");
 		HttpResponse status = ourClient.execute(httpGet);
+		assertEquals(400, status.getStatusLine().getStatusCode());
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info(responseContent);
-
+		assertThat(responseContent, containsString("Invalid _include parameter value"));
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-		assertEquals(4, bundle.size());
 	}
 
 	@Test
@@ -128,6 +96,32 @@ public class IncludeTest {
 
 	}
 
+	@Test
+	public void testIIncludedResourcesNonContainedInDeclaredExtension() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=declaredExtInclude&_pretty=true");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+
+		ourLog.info(responseContent);
+
+		assertEquals(4, bundle.size());
+		assertEquals(new IdDt("Patient/p1"), bundle.toListOfResources().get(0).getId().toUnqualifiedVersionless());
+		assertEquals(new IdDt("Patient/p2"), bundle.toListOfResources().get(1).getId().toUnqualifiedVersionless());
+		assertEquals(new IdDt("Organization/o1"), bundle.toListOfResources().get(2).getId().toUnqualifiedVersionless());
+		assertEquals(new IdDt("Organization/o2"), bundle.toListOfResources().get(3).getId().toUnqualifiedVersionless());
+
+		Patient p1 = (Patient) bundle.toListOfResources().get(0);
+		assertEquals(0, p1.getContained().getContainedResources().size());
+
+		Patient p2 = (Patient) bundle.toListOfResources().get(1);
+		assertEquals(0, p2.getContained().getContainedResources().size());
+
+	}
+
 	@Test
 	public void testIIncludedResourcesNonContainedInExtension() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=extInclude&_pretty=true");
@@ -179,29 +173,79 @@ public class IncludeTest {
 	}
 
 	@Test
-	public void testIIncludedResourcesNonContainedInDeclaredExtension() throws Exception {
+	public void testIncludeWithType() {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=declaredExtInclude&_pretty=true");
+		assertEquals("Patient:careProvider:Practitioner", new Include("Patient:careProvider", true).withType("Practitioner").getValue());
+		assertEquals(true, new Include("Patient:careProvider", true).withType("Practitioner").isRecurse());
+		assertEquals(false, new Include("Patient:careProvider:Organization", true).withType("Practitioner").isLocked());
+
+		assertEquals("Patient:careProvider:Practitioner", new Include("Patient:careProvider:Organization", true).withType("Practitioner").getValue());
+		assertEquals(true, new Include("Patient:careProvider:Organization", true).toLocked().withType("Practitioner").isLocked());
+
+		try {
+			new Include("").withType("Patient");
+			fail();
+		} catch (IllegalStateException e) {
+			// good
+		}
+		try {
+			new Include("Patient").withType("Patient");
+			fail();
+		} catch (IllegalStateException e) {
+			// good
+		}
+		try {
+			new Include("Patient:").withType("Patient");
+			fail();
+		} catch (IllegalStateException e) {
+			// good
+		}
+	}
+
+	// @Test
+	public void testMixedContainedAndNonContained() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/DiagnosticReport?_query=stitchedInclude&_pretty=true");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		ourLog.info(responseContent);
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+		assertEquals(4, bundle.size());
+	}
+
+	@Test
+	public void testNoIncludes() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");
 		HttpResponse status = ourClient.execute(httpGet);
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
 
-		ourLog.info(responseContent);
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(0, p.getName().size());
+		assertEquals("Hello", p.getId().getIdPart());
+	}
 
-		assertEquals(4, bundle.size());
+	@Test
-		assertEquals(new IdDt("Patient/p1"), bundle.toListOfResources().get(0).getId().toUnqualifiedVersionless());
+	public void testOneInclude() throws Exception {
-		assertEquals(new IdDt("Patient/p2"), bundle.toListOfResources().get(1).getId().toUnqualifiedVersionless());
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo");
-		assertEquals(new IdDt("Organization/o1"), bundle.toListOfResources().get(2).getId().toUnqualifiedVersionless());
+		HttpResponse status = ourClient.execute(httpGet);
-		assertEquals(new IdDt("Organization/o2"), bundle.toListOfResources().get(3).getId().toUnqualifiedVersionless());
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
 
-		Patient p1 = (Patient) bundle.toListOfResources().get(0);
+		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertEquals(0, p1.getContained().getContainedResources().size());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-
+		assertEquals(1, bundle.size());
-		Patient p2 = (Patient) bundle.toListOfResources().get(1);
-		assertEquals(0, p2.getContained().getContainedResources().size());
 
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(1, p.getName().size());
+		assertEquals("Hello", p.getId().getIdPart());
+		assertEquals("foo", p.getName().get(0).getFamilyFirstRep().getValue());
 	}
 
 	@Test
@@ -226,18 +270,6 @@ public class IncludeTest {
 
 	}
 
-	@Test
-	public void testBadInclude() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo&_include=baz");
-		HttpResponse status = ourClient.execute(httpGet);
-		assertEquals(400, status.getStatusLine().getStatusCode());
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		ourLog.info(responseContent);
-		assertThat(responseContent, containsString("Invalid _include parameter value"));
-	}
-
 	@AfterClass
 	public static void afterClass() throws Exception {
 		ourServer.stop();
@@ -268,27 +300,20 @@ public class IncludeTest {
 
 	}
 
-	@ResourceDef(name = "Patient")
+	public static void main(String[] args) {
-	public static class ExtPatient extends Patient {
-		@Child(name = "secondOrg")
-		@Extension(url = "http://foo#secondOrg", definedLocally = false, isModifier = false)
-		private ResourceReferenceDt mySecondOrg;
 
-		@Override
+		Organization org = new Organization();
-		public boolean isEmpty() {
+		org.setId("Organization/65546");
-			return super.isEmpty() && ElementUtil.isEmpty(mySecondOrg);
+		org.getName().setValue("Contained Test Organization");
-		}
 
-		public ResourceReferenceDt getSecondOrg() {
+		Patient patient = new Patient();
-			if (mySecondOrg == null) {
+		patient.setId("Patient/1333");
-				mySecondOrg = new ResourceReferenceDt();
+		patient.addIdentifier("urn:mrns", "253345");
-			}
+		patient.getManagingOrganization().setResource(patient);
-			return mySecondOrg;
-		}
 
-		public void setSecondOrg(ResourceReferenceDt theSecondOrg) {
+		System.out.println(FhirContext.forDstu1().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
-			mySecondOrg = theSecondOrg;
+
-		}
+		patient.getManagingOrganization().getReference();
 
 	}
 
@@ -345,11 +370,10 @@ public class IncludeTest {
 	 */
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 
-		@Search(queryName = "normalInclude")
+		@Search(queryName = "containedInclude")
-		public List<Patient> normalInclude() {
+		public List<Patient> containedInclude() {
 			Organization o1 = new Organization();
 			o1.getName().setValue("o1");
-			o1.setId("o1");
 
 			Patient p1 = new Patient();
 			p1.setId("p1");
@@ -364,25 +388,6 @@ public class IncludeTest {
 			return Arrays.asList(p1, p2);
 		}
 
-		@Search(queryName = "extInclude")
-		public List<Patient> extInclude() {
-			Organization o1 = new Organization();
-			o1.getName().setValue("o1");
-			o1.setId("o1");
-
-			Patient p1 = new Patient();
-			p1.setId("p1");
-			p1.addIdentifier().setLabel("p1");
-			p1.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
-
-			Patient p2 = new Patient();
-			p2.setId("p2");
-			p2.addIdentifier().setLabel("p2");
-			p2.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
-
-			return Arrays.asList(p1, p2);
-		}
-
 		@Search(queryName = "declaredExtInclude")
 		public List<ExtPatient> declaredExtInclude() {
 			Organization o1 = new Organization();
@@ -407,20 +412,21 @@ public class IncludeTest {
 			return Arrays.asList(p1, p2);
 		}
 
-		@Search(queryName = "containedInclude")
+		@Search(queryName = "extInclude")
-		public List<Patient> containedInclude() {
+		public List<Patient> extInclude() {
 			Organization o1 = new Organization();
 			o1.getName().setValue("o1");
+			o1.setId("o1");
 
 			Patient p1 = new Patient();
 			p1.setId("p1");
 			p1.addIdentifier().setLabel("p1");
-			p1.getManagingOrganization().setResource(o1);
+			p1.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
 
 			Patient p2 = new Patient();
 			p2.setId("p2");
 			p2.addIdentifier().setLabel("p2");
-			p2.getManagingOrganization().setResource(o1);
+			p2.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
 
 			return Arrays.asList(p1, p2);
 		}
@@ -449,22 +455,48 @@ public class IncludeTest {
 			return Patient.class;
 		}
 
+		@Search(queryName = "normalInclude")
+		public List<Patient> normalInclude() {
+			Organization o1 = new Organization();
+			o1.getName().setValue("o1");
+			o1.setId("o1");
+
+			Patient p1 = new Patient();
+			p1.setId("p1");
+			p1.addIdentifier().setLabel("p1");
+			p1.getManagingOrganization().setResource(o1);
+
+			Patient p2 = new Patient();
+			p2.setId("p2");
+			p2.addIdentifier().setLabel("p2");
+			p2.getManagingOrganization().setResource(o1);
+
+			return Arrays.asList(p1, p2);
+		}
+
 	}
 
-	public static void main(String[] args) {
+	@ResourceDef(name = "Patient")
+	public static class ExtPatient extends Patient {
+		@Child(name = "secondOrg")
+		@Extension(url = "http://foo#secondOrg", definedLocally = false, isModifier = false)
+		private ResourceReferenceDt mySecondOrg;
 
-		Organization org = new Organization();
+		public ResourceReferenceDt getSecondOrg() {
-		org.setId("Organization/65546");
+			if (mySecondOrg == null) {
-		org.getName().setValue("Contained Test Organization");
+				mySecondOrg = new ResourceReferenceDt();
+			}
+			return mySecondOrg;
+		}
 
-		Patient patient = new Patient();
+		@Override
-		patient.setId("Patient/1333");
+		public boolean isEmpty() {
-		patient.addIdentifier("urn:mrns", "253345");
+			return super.isEmpty() && ElementUtil.isEmpty(mySecondOrg);
-		patient.getManagingOrganization().setResource(patient);
+		}
 
-		System.out.println(FhirContext.forDstu1().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
+		public void setSecondOrg(ResourceReferenceDt theSecondOrg) {
-
+			mySecondOrg = theSecondOrg;
-		patient.getManagingOrganization().getReference();
+		}
 
 	}
 

pom.xml

@@ -240,7 +240,7 @@
 		<jetty_version>9.2.14.v20151106</jetty_version> 
 		<!-- Note on Hibernate versions: Hibernate 4.3+ uses JPA 2.1, which is too new for a number of platforms including JBoss EAP 6.x and Glassfish 3.0. Upgrade this version with caution! Also note that if 
 			you change this, you may get a failure in hibernate4-maven-plugin. See the note in hapi-fhir-jpaserver-base/pom.xml's configuration for that plugin... -->
-		<hibernate_version>5.0.3.Final</hibernate_version>
+		<hibernate_version>5.0.5.Final</hibernate_version>
 		<hibernate_validator_version>5.2.2.Final</hibernate_validator_version>
 		<maven_assembly_plugin_version>2.5.3</maven_assembly_plugin_version>
 		<maven_failsafe_plugin_version>2.18.1</maven_failsafe_plugin_version>
@@ -251,7 +251,7 @@
 		<mitreid-connect-version>1.1.8</mitreid-connect-version>
 		<phloc_schematron_version>2.7.1</phloc_schematron_version>
 		<phloc_commons_version>4.3.6</phloc_commons_version>
-		<spring_version>4.2.2.RELEASE</spring_version>
+		<spring_version>4.2.3.RELEASE</spring_version>
 		<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
 		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
 		<xmlunit_version>1.6</xmlunit_version>
@@ -277,7 +277,7 @@
 			<dependency>
 				<groupId>com.google.guava</groupId>
 				<artifactId>guava</artifactId>
-				<version>18.0</version>
+				<version>19.0</version>
 			</dependency>
 			<dependency>
 				<groupId>com.phloc</groupId>
@@ -392,12 +392,12 @@
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
 				<artifactId>lucene-highlighter</artifactId>
-				<version>5.3.0</version>
+				<version>5.3.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
 				<artifactId>lucene-analyzers-phonetic</artifactId>
-				<version>5.3.0</version>
+				<version>5.3.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.doxia</groupId>
@@ -407,17 +407,17 @@
 			<dependency>
 				<groupId>org.apache.maven.scm</groupId>
 				<artifactId>maven-scm-api</artifactId>
-				<version>1.9</version>
+				<version>1.9.4</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.scm</groupId>
 				<artifactId>maven-scm-manager-plexus</artifactId>
-				<version>1.9</version>
+				<version>1.9.4</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.scm</groupId>
 				<artifactId>maven-scm-provider-gitexe</artifactId>
-				<version>1.9</version>
+				<version>1.9.4</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.wagon</groupId>
@@ -552,7 +552,7 @@
 			<dependency>
 				<groupId>org.hibernate</groupId>
 				<artifactId>hibernate-search-orm</artifactId>
-				<version>5.5.0.Final</version>
+				<version>5.5.1.Final</version>
 			</dependency>
 			<dependency>
 				<groupId>org.javassist</groupId>
@@ -562,17 +562,17 @@
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-android</artifactId>
-				<version>1.7.12</version>
+				<version>1.7.13</version>
 			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-api</artifactId>
-				<version>1.7.12</version>
+				<version>1.7.13</version>
 			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>jcl-over-slf4j</artifactId>
-				<version>1.7.12</version>
+				<version>1.7.13</version>
 			</dependency>
 			<dependency>
 				<groupId>org.springframework</groupId>
@@ -663,7 +663,7 @@
 				<plugin>
 					<groupId>org.apache.felix</groupId>
 					<artifactId>maven-bundle-plugin</artifactId>
-					<version>3.0.0</version>
+					<version>3.0.1</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -931,12 +931,12 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-checkstyle-plugin</artifactId>
-					<version>2.15</version>
+					<version>2.17</version>
 					<dependencies>
 						<dependency>
 							<groupId>com.puppycrawl.tools</groupId>
 							<artifactId>checkstyle</artifactId>
-							<version>6.11.2</version>
+							<version>6.13</version>
 						</dependency>
 					</dependencies>
 					<configuration>

src/changes/changes.xml

@@ -7,6 +7,16 @@
 	</properties>
 	<body>
 		<release version="1.4" date="TBD">
+			<action type="add">
+            Bump the version of a few dependencies to the
+            latest versions (dependent HAPI modules listed in brackets):
+            <![CDATA[
+               <ul>
+                  <li>Hibernate (JPA, Web Tester): 5.0.3 -&gt; 5.0.5</li>
+                  <li>Springframework (JPA, Web Tester): 4.2.2 -&gt; 4.2.3</li>
+               </ul>
+            ]]>
+			</action>
 			<action type="fix">
 				Remove a dependency on a Java 1.7 class 
 				(ReflectiveOperationException) in several spots in the