Add status to bundle entries

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

@@ -42,61 +42,26 @@ public class BundleEntry extends BaseBundle {
 	//@formatter:on
 	private TagList myCategories;
 	private InstantDt myDeletedAt;
-	private CodeDt myDeletedResourceType;
-	private StringDt myDeletedResourceId;
-	private StringDt myDeletedResourceVersion;
-
-	public CodeDt getDeletedResourceType() {
-		if (myDeletedResourceType == null) {
-			myDeletedResourceType = new CodeDt();
-		}
-		return myDeletedResourceType;
-	}
-
-	public void setDeletedResourceType(CodeDt theDeletedResourceType) {
-		myDeletedResourceType = theDeletedResourceType;
-	}
-
-	public StringDt getDeletedResourceId() {
-		if (myDeletedResourceId == null) {
-			myDeletedResourceId = new StringDt();
-		}
-		return myDeletedResourceId;
-	}
-
-	public void setDeletedResourceId(StringDt theDeletedResourceId) {
-		myDeletedResourceId = theDeletedResourceId;
-	}
-
-	public StringDt getDeletedResourceVersion() {
-		if (myDeletedResourceVersion == null) {
-			myDeletedResourceVersion = new StringDt();
-		}
-		return myDeletedResourceVersion;
-	}
-
-	public void setDeletedResourceVersion(StringDt theDeletedResourceVersion) {
-		myDeletedResourceVersion = theDeletedResourceVersion;
-	}
-
 	private StringDt myDeletedByEmail;
 	private StringDt myDeletedByName;
 	private StringDt myDeletedComment;
+	private StringDt myDeletedResourceId;
+	private CodeDt myDeletedResourceType;
+	private StringDt myDeletedResourceVersion;
 	private StringDt myLinkAlternate;
+	private StringDt myLinkBase;
 	private StringDt myLinkSearch;
 	private StringDt myLinkSelf;
-	private StringDt myLinkBase;
 	private InstantDt myPublished;
 	private IResource myResource;
+	private DecimalDt myScore;
+	private BoundCodeDt<BundleEntryStatusEnum> myStatus;
 	private XhtmlDt mySummary;
 	private StringDt myTitle;
 	private InstantDt myUpdated;
-	private BoundCodeDt<BundleEntryStatusEnum> myStatus;
-	private DecimalDt myScore;
 
 	/**
-	 * @deprecated Tags wil become immutable in a future release of HAPI, so
+	 * @deprecated Tags wil become immutable in a future release of HAPI, so {@link #addCategory(String, String, String)} should be used instead
-	 *             {@link #addCategory(String, String, String)} should be used instead
 	 */
 	public Tag addCategory() {
 		Tag retVal = new Tag();
@@ -150,6 +115,27 @@ public class BundleEntry extends BaseBundle {
 		return myDeletedComment;
 	}
 
+	public StringDt getDeletedResourceId() {
+		if (myDeletedResourceId == null) {
+			myDeletedResourceId = new StringDt();
+		}
+		return myDeletedResourceId;
+	}
+
+	public CodeDt getDeletedResourceType() {
+		if (myDeletedResourceType == null) {
+			myDeletedResourceType = new CodeDt();
+		}
+		return myDeletedResourceType;
+	}
+
+	public StringDt getDeletedResourceVersion() {
+		if (myDeletedResourceVersion == null) {
+			myDeletedResourceVersion = new StringDt();
+		}
+		return myDeletedResourceVersion;
+	}
+
 	public StringDt getLinkAlternate() {
 		if (myLinkAlternate == null) {
 			myLinkAlternate = new StringDt();
@@ -189,6 +175,13 @@ public class BundleEntry extends BaseBundle {
 		return myResource;
 	}
 
+	public DecimalDt getScore() {
+		if (myScore == null) {
+			myScore = new DecimalDt();
+		}
+		return myScore;
+	}
+
 	public BoundCodeDt<BundleEntryStatusEnum> getStatus() {
 		if (myStatus == null) {
 			myStatus = new BoundCodeDt<BundleEntryStatusEnum>(BundleEntryStatusEnum.VALUESET_BINDER);
@@ -211,9 +204,8 @@ public class BundleEntry extends BaseBundle {
 	}
 
 	/**
-	 * @deprecated <b>DSTU2 Note:</b> As of DSTU2, bundle entries no longer have an updated time (this bit of metadata has been moved
+	 * @deprecated <b>DSTU2 Note:</b> As of DSTU2, bundle entries no longer have an updated time (this bit of metadata has been moved to the resource &lt;meta/&gt; element so it is redundant here). In
-	 * to the resource &lt;meta/&gt; element so it is redundant here). In preparation for DSTU2, it is recommended that you
+	 *             preparation for DSTU2, it is recommended that you migrate code away from using this method and over to using resource metadata instead.
-	 * migrate code away from using this method and over to using resource metadata instead. 
 	 */
 	public InstantDt getUpdated() {
 		if (myUpdated == null) {
@@ -221,7 +213,7 @@ public class BundleEntry extends BaseBundle {
 		}
 		if (myUpdated.isEmpty() && myResource != null) {
 			InstantDt resourceUpdated = ResourceMetadataKeyEnum.UPDATED.get(myResource);
-			if (resourceUpdated!=null && !resourceUpdated.isEmpty()) {
+			if (resourceUpdated != null && !resourceUpdated.isEmpty()) {
 				return resourceUpdated;
 			}
 		}
@@ -258,6 +250,18 @@ public class BundleEntry extends BaseBundle {
 		myDeletedComment = theDeletedComment;
 	}
 
+	public void setDeletedResourceId(StringDt theDeletedResourceId) {
+		myDeletedResourceId = theDeletedResourceId;
+	}
+
+	public void setDeletedResourceType(CodeDt theDeletedResourceType) {
+		myDeletedResourceType = theDeletedResourceType;
+	}
+
+	public void setDeletedResourceVersion(StringDt theDeletedResourceVersion) {
+		myDeletedResourceVersion = theDeletedResourceVersion;
+	}
+
 	public void setLinkAlternate(StringDt theLinkAlternate) {
 		myLinkAlternate = theLinkAlternate;
 	}
@@ -286,14 +290,17 @@ public class BundleEntry extends BaseBundle {
 		myResource = theResource;
 	}
 
+	public void setScore(DecimalDt theScore) {
+		myScore = theScore;
+	}
+
 	public void setStatus(BoundCodeDt<BundleEntryStatusEnum> theStatus) {
 		myStatus = theStatus;
 	}
 
 	/**
-	 * @deprecated <b>DSTU2 Note:</b> As of DSTU2, bundle entries no longer have an updated time (this bit of metadata has been moved
+	 * @deprecated <b>DSTU2 Note:</b> As of DSTU2, bundle entries no longer have an updated time (this bit of metadata has been moved to the resource &lt;meta/&gt; element so it is redundant here). In
-	 * to the resource &lt;meta/&gt; element so it is redundant here). In preparation for DSTU2, it is recommended that you
+	 *             preparation for DSTU2, it is recommended that you migrate code away from using this method and over to using resource metadata instead.
-	 * migrate code away from using this method and over to using resource metadata instead. 
 	 */
 	public void setUpdated(InstantDt theUpdated) {
 		Validate.notNull(theUpdated, "Updated may not be null");
@@ -312,15 +319,4 @@ public class BundleEntry extends BaseBundle {
 		return b.toString();
 	}
 
-	public DecimalDt getScore() {
-		if (myScore == null) {
-			myScore = new DecimalDt();
-		}
-		return myScore;
-	}
-
-	public void setScore(DecimalDt theScore) {
-		myScore = theScore;
-	}
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.rest.server;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.ProvidedResourceScanner;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.*;
@@ -30,6 +31,7 @@ import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu.resource.Binary;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.annotation.Destroy;
 import ca.uhn.fhir.rest.annotation.IdParam;
@@ -1116,7 +1118,7 @@ public class RestfulServer extends HttpServlet {
 		bundle.getLinkBase().setValue(theServerBase);
 		bundle.getLinkSelf().setValue(theCompleteUrl);
 
-		List<IResource> addedResources = new ArrayList<IResource>();
+		List<IResource> includedResources = new ArrayList<IResource>();
 		Set<IdDt> addedResourceIds = new HashSet<IdDt>();
 		for (IResource next : theResult) {
 
@@ -1172,7 +1174,7 @@ public class RestfulServer extends HttpServlet {
 					references.addAll(newReferences);
 				}
 
-				addedResources.addAll(addedResourcesThisPass);
+				includedResources.addAll(addedResourcesThisPass);
 
 			} while (references.isEmpty() == false);
 
@@ -1183,8 +1185,11 @@ public class RestfulServer extends HttpServlet {
 		/*
 		 * Actually add the resources to the bundle
 		 */
-		for (IResource next : addedResources) {
+		for (IResource next : includedResources) {
-			bundle.addResource(next, theContext, theServerBase);
+			BundleEntry entry = bundle.addResource(next, theContext, theServerBase);
+			if (theContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
+				entry.getStatus().setValueAsEnum(BundleEntryStatusEnum.INCLUDE);
+			}
 		}
 
 		bundle.getTotalResults().setValue(theTotalResults);

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

@@ -53,7 +53,18 @@ public class TestRestfulServer extends RestfulServer {
 		ETagSupportEnum etagSupport;
 		String baseUrlProperty;
 		switch (fhirVersionParam.trim().toUpperCase()) {
-		case "DSTU":
+		case "BASE": {
+			setFhirContext(FhirContext.forDstu1());
+			beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
+			systemProvider = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProvider.class);
+			systemDao = myAppCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
+			etagSupport = ETagSupportEnum.DISABLED;
+			JpaConformanceProviderDstu1 confProvider = new JpaConformanceProviderDstu1(this, systemDao);
+			confProvider.setImplementationDescription(implDesc);
+			setServerConformanceProvider(confProvider);
+			baseUrlProperty = "fhir.baseurl";
+			break;
+		}
 		case "DSTU1": {
 			setFhirContext(FhirContext.forDstu1());
 			beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
@@ -66,7 +77,7 @@ public class TestRestfulServer extends RestfulServer {
 			baseUrlProperty = "fhir.baseurl.dstu1";
 			break;
 		}
-		case "DEV": {
+		case "DSTU2": {
 			setFhirContext(FhirContext.forDev());
 			beans = myAppCtx.getBean("myResourceProvidersDev", List.class);
 			systemProvider = myAppCtx.getBean("mySystemProviderDev", JpaSystemProvider.class);
@@ -82,32 +93,61 @@ public class TestRestfulServer extends RestfulServer {
 			throw new ServletException("Unknown FHIR version specified in init-param[FhirVersion]: " + fhirVersionParam);
 		}
 		
+		/*
+		 * On the DSTU2 endpoint, we want to enable ETag support 
+		 */
 		setETagSupport(etagSupport);
 
+		/*
+		 * This server tries to dynamically generate narratives
+		 */
 		FhirContext ctx = getFhirContext();
 		ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 		
-
+		/*
+		 * The resource and system providers (which actually implement the various FHIR 
+		 * operations in this server) are all retrieved from the spring context above
+		 * and are provided to the server here.
+		 */
 		for (IResourceProvider nextResourceProvider : beans) {
 			ourLog.info(" * Have resource provider for: {}", nextResourceProvider.getResourceType().getSimpleName());
 		}
 		setResourceProviders(beans);
 		setPlainProviders(systemProvider);
 
+		/*
+		 * This tells the server to use "incorrect" MIME types if it detects that the
+		 * request is coming from a browser in the hopes that the browser won't just treat
+		 * the content as a binary payload and try to download it (which is what generally
+		 * happens if you load a FHIR URL in a browser)
+		 */
 		setUseBrowserFriendlyContentTypes(true);
 
+		/*
+		 * The server's base URL (e.g. http://fhirtest.uhn.ca/baseDstu2) is 
+		 * pulled from a system property, which is helpful if you want to try
+		 * hosting your own copy of this server.
+		 */
 		String baseUrl = System.getProperty(baseUrlProperty);
 		if (StringUtils.isBlank(baseUrl)) {
-			// Fall back to the old URL
+			// Try to fall back in case the property isn't set
 			baseUrl = System.getProperty("fhir.baseurl");
 			if (StringUtils.isBlank(baseUrl)) {
 				throw new ServletException("Missing system property: " + baseUrlProperty);
 			}
 		}
-
 		setServerAddressStrategy(new HardcodedServerAddressStrategy(baseUrl));
+		
+		/*
+		 * This is a simple paging strategy that keeps the last 10 
+		 * searches in memory
+		 */
 		setPagingProvider(new FifoMemoryPagingProvider(10));
 
+		/*
+		 * Do some fancy logging to create a nice access log that has details
+		 * about each incoming request. 
+		 */
 		LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
 		loggingInterceptor.setLoggerName("fhirtest.access");
 		loggingInterceptor.setMessageFormat("Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]");

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/web.xml

@@ -33,6 +33,20 @@
 		<load-on-startup>2</load-on-startup>
 	</servlet>
 
+	<servlet>
+		<servlet-name>fhirServletBase</servlet-name>
+		<servlet-class>ca.uhn.fhirtest.TestRestfulServer</servlet-class>
+		<init-param>
+			<param-name>ImplementationDescription</param-name>
+			<param-value>UHN Test Server (Base / DSTU1 Resources)</param-value>
+		</init-param>
+		<init-param>
+			<param-name>FhirVersion</param-name>
+			<param-value>BASE</param-value>
+		</init-param>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+	
 	<servlet>
 		<servlet-name>fhirServletDstu1</servlet-name>
 		<servlet-class>ca.uhn.fhirtest.TestRestfulServer</servlet-class>
@@ -48,21 +62,21 @@
 	</servlet>
 
 	<servlet>
-		<servlet-name>fhirServletDev</servlet-name>
+		<servlet-name>fhirServletDstu2</servlet-name>
 		<servlet-class>ca.uhn.fhirtest.TestRestfulServer</servlet-class>
 		<init-param>
 			<param-name>ImplementationDescription</param-name>
-			<param-value>UHN Test Server (DEV Resources)</param-value>
+			<param-value>UHN Test Server (DSTU2 Resources)</param-value>
 		</init-param>
 		<init-param>
 			<param-name>FhirVersion</param-name>
-			<param-value>DEV</param-value>
+			<param-value>DSTU2</param-value>
 		</init-param>
 		<load-on-startup>1</load-on-startup>
 	</servlet>
 
 	<servlet-mapping>
-		<servlet-name>fhirServletDstu1</servlet-name>
+		<servlet-name>fhirServletBase</servlet-name>
 		<url-pattern>/base/*</url-pattern>
 	</servlet-mapping>
 
@@ -72,12 +86,12 @@
 	</servlet-mapping>
 
 	<servlet-mapping>
-		<servlet-name>fhirServletDev</servlet-name>
+		<servlet-name>fhirServletDstu2</servlet-name>
 		<url-pattern>/baseDstu2/*</url-pattern>
 	</servlet-mapping>
 	
 	<servlet-mapping>
-		<servlet-name>fhirServletDev</servlet-name>
+		<servlet-name>fhirServletDstu2</servlet-name>
 		<url-pattern>/baseDev/*</url-pattern>
 	</servlet-mapping>
 

hapi-fhir-structures-dev/.project

@@ -16,12 +16,12 @@
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>

hapi-fhir-structures-dev/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java

@@ -50,6 +50,7 @@ public class XmlParserTest {
 
 		assertEquals(1, parsed.getEntries().size());
 		assertEquals("update", parsed.getEntries().get(0).getStatus().getValue());
+		assertEquals("http://foo?search", parsed.getEntries().get(0).getLinkSearch().getValue());
 
 		MedicationPrescription p = (MedicationPrescription) parsed.getEntries().get(0).getResource();
 		assertEquals("Patient/example", p.getPatient().getReference().getValue());

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

@@ -0,0 +1,490 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.Include;
+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.model.dev.resource.DiagnosticReport;
+import ca.uhn.fhir.model.dev.resource.Observation;
+import ca.uhn.fhir.model.dev.resource.Organization;
+import ca.uhn.fhir.model.dev.resource.Patient;
+import ca.uhn.fhir.model.dev.resource.Practitioner;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
+import ca.uhn.fhir.rest.annotation.IncludeParam;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.util.ElementUtil;
+import ca.uhn.fhir.util.PortUtil;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class IncludeTest {
+
+	private static CloseableHttpClient ourClient;
+	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 {
+		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());
+
+		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);
+		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 testIIncludedResourcesNonContained() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=normalInclude&_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(3, 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(BundleEntryStatusEnum.INCLUDE, bundle.getEntries().get(2).getStatus().getValueAsEnum());
+		
+		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");
+		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(3, 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(BundleEntryStatusEnum.INCLUDE, bundle.getEntries().get(2).getStatus().getValueAsEnum());
+		
+		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 testIIncludedResourcesNonContainedInExtensionJson() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=extInclude&_pretty=true&_format=json");
+		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.newJsonParser().parseBundle(responseContent);
+		
+		ourLog.info(responseContent);
+		
+		assertEquals(3, 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(BundleEntryStatusEnum.INCLUDE, bundle.getEntries().get(2).getStatus().getValueAsEnum());
+
+		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 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());
+		assertEquals(BundleEntryStatusEnum.INCLUDE, bundle.getEntries().get(2).getStatus().getValueAsEnum());
+		assertEquals(BundleEntryStatusEnum.INCLUDE, bundle.getEntries().get(3).getStatus().getValueAsEnum());
+
+		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 testTwoInclude() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo&_include=bar");
+		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(2, p.getName().size());
+		assertEquals("Hello", p.getId().getIdPart());
+
+		Set<String> values = new HashSet<String>();
+		values.add( p.getName().get(0).getFamilyFirstRep().getValue());
+		values.add( p.getName().get(1).getFamilyFirstRep().getValue());
+		assertThat(values, containsInAnyOrder("foo", "bar"));
+		
+	}
+
+	@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());
+	}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		
+		ourCtx = new FhirContext();
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer();
+		servlet.setFhirContext(ourCtx);
+		servlet.setResourceProviders(patientProvider, new DummyDiagnosticReportResourceProvider());
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	@ResourceDef(name="Patient")
+	public static class ExtPatient extends Patient
+	{
+		@Child(name="secondOrg")
+		@Extension(url="http://foo#secondOrg", definedLocally = false, isModifier = false)
+		private ResourceReferenceDt mySecondOrg;
+
+		@Override
+		public boolean isEmpty() {
+			return super.isEmpty() && ElementUtil.isEmpty(mySecondOrg);
+		}
+
+		public ResourceReferenceDt getSecondOrg() {
+			if (mySecondOrg==null) {
+				mySecondOrg= new ResourceReferenceDt();
+			}
+			return mySecondOrg;
+		}
+
+		public void setSecondOrg(ResourceReferenceDt theSecondOrg) {
+			mySecondOrg = theSecondOrg;
+		}
+		
+	}
+	
+	/**
+	 * Created by dsotnikov on 2/25/2014.
+	 */
+	public static class DummyDiagnosticReportResourceProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IResource> getResourceType() {
+			return DiagnosticReport.class;
+		}
+		
+		@Search(queryName = "stitchedInclude")
+		public List<DiagnosticReport> stitchedInclude() {
+			Practitioner pr1 = new Practitioner();
+			pr1.setId("Practitioner/001");
+			pr1.getName().addFamily("Pract1");
+
+			Practitioner pr2 = new Practitioner();
+			pr2.setId("Practitioner/002");
+			pr2.getName().addFamily("Pract2");
+
+			Practitioner pr3 = new Practitioner();
+			pr3.setId("Practitioner/003");
+			pr3.getName().addFamily("Pract3");
+
+			Observation o1 = new Observation();
+			o1.getName().setText("Obs1");
+			o1.addPerformer().setResource(pr1);
+			
+			Observation o2 = new Observation();
+			o2.getName().setText("Obs2");
+			o2.addPerformer().setResource(pr2);
+			
+			Observation o3 = new Observation();
+			o3.getName().setText("Obs3");
+			o3.addPerformer().setResource(pr3);
+
+			DiagnosticReport rep = new DiagnosticReport();
+			rep.setId("DiagnosticReport/999");
+			rep.getName().setText("Rep");
+			rep.addResult().setResource(o1);
+			rep.addResult().setResource(o2);
+			rep.addResult().setResource(o3);
+			
+			return Collections.singletonList(rep);
+		}
+		
+		
+		
+	}
+	
+	
+	/**
+	 * Created by dsotnikov on 2/25/2014.
+	 */
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		@Search(queryName = "normalInclude")
+		public List<Patient> normalInclude() {
+			Organization o1 = new Organization();
+			o1.getNameElement().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);
+		}
+		
+		
+		@Search(queryName = "extInclude")
+		public List<Patient> extInclude() {
+			Organization o1 = new Organization();
+			o1.getNameElement().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();
+			o1.getNameElement().setValue("o1");
+			o1.setId("o1");
+
+			Organization o2 = new Organization();
+			o2.getNameElement().setValue("o2");
+			o2.setId("o2");
+			o1.getPartOf().setResource(o2);
+			
+			ExtPatient p1 = new ExtPatient();
+			p1.setId("p1");
+			p1.addIdentifier().setLabel("p1");
+			p1.getSecondOrg().setResource(o1);
+
+			ExtPatient p2 = new ExtPatient();
+			p2.setId("p2");
+			p2.addIdentifier().setLabel("p2");
+			p2.getSecondOrg().setResource(o1);
+
+			return Arrays.asList(p1, p2);
+		}
+
+		
+		@Search(queryName = "containedInclude")
+		public List<Patient> containedInclude() {
+			Organization o1 = new Organization();
+			o1.getNameElement().setValue("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);
+		}
+		
+		@Search
+		public List<Patient> findPatient(@RequiredParam(name = Patient.SP_NAME) StringDt theName, @IncludeParam(allow = { "foo", "bar" }) Set<Include> theIncludes) {
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+
+			Patient p = new Patient();
+			p.addIdentifier().setSystem("foo").setValue("bar");
+
+			p.setId(theName.getValue());
+
+			if (theIncludes != null) {
+				for (Include next : theIncludes) {
+					p.addName().addFamily().setValue(next.getValue());
+				}
+			}
+			retVal.add(p);
+
+			return retVal;
+		}
+
+		@Override
+		public Class<? extends IResource> getResourceType() {
+			return Patient.class;
+		}
+
+	}
+
+	
+	public static void main(String[] args) {
+		
+		Organization org = new Organization();
+		org.setId("Organization/65546");
+		org.getNameElement().setValue("Contained Test Organization");
+		
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
+		patient.getManagingOrganization().setResource(patient);
+		
+		
+		System.out.println(new FhirContext().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
+		
+		patient.getManagingOrganization().getReference();
+		
+	}
+	
+}

hapi-fhir-structures-dev/src/test/resources/bundle-example(example).xml

@@ -17,6 +17,7 @@
   </link>
   <entry>
     <status value="update"/>
+    <search value="http://foo?search"/>
     <resource>
       <MedicationPrescription>
         <id value="3123"/>

hapi-fhir-structures-dev/src/test/resources/bundle-example.xml

@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Bundle xmlns="http://hl7.org/fhir">
+  <id value="example"/>
+  <meta>
+    <versionId value="1"/>
+    <lastUpdated value="2014-08-18T01:43:30Z"/>
+  </meta> 
+  <type value="transaction"/>  
+  <base value="http://example.com/base"/>
+  <total value="3"/>
+  <link>
+    <relation value="next"/>
+    <url value="https://example.com/base/MedicationPrescription?patient=347&amp;searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&amp;page=2"/>
+  </link>
+  <link>
+    <relation value="self"/>
+    <url value="https://example.com/base/MedicationPrescription?patient=347"/>
+  </link>
+  <entry>
+    <status value="update"/>
+    <resource>
+      <MedicationPrescription>
+        <id value="3123"/>
+        <meta>
+          <versionId value="1"/>
+          <lastUpdated value="2014-08-16T05:31:17Z"/>      
+        </meta> 
+        <text>
+          <status value="generated"/>
+          <div xmlns="http://www.w3.org/1999/xhtml">
+            <p>Penicillin VK 5ml suspension to be administered by oral route</p>
+            <p>ONE 5ml spoonful to be taken THREE times a day</p>
+            <p>100ml bottle</p>
+            <p>to patient ref: a23</p>
+            <p>by doctor X</p>
+          </div>
+        </text>
+        <status value="active"/>
+        <patient>
+          <reference value="Patient/example"/>
+        </patient>
+        <prescriber>
+          <reference value="Practitioner/example"/>
+        </prescriber>
+
+        <medication>
+          <reference value="Medication/example"/>
+        </medication>
+
+        <dosageInstruction>
+          <scheduledTiming>
+            <repeat>
+              <frequency value="3"/>
+              <duration value="1"/>
+              <units value="d"/>
+            </repeat>
+          </scheduledTiming>
+          <route>
+            <coding>
+              <system value="http://snomed.info/sct"/>
+              <code value="394899003"/>
+              <display value="oral administration of treatment"/>
+            </coding>
+          </route>
+          <doseQuantity>
+            <value value="5"/>
+            <units value="ml"/>
+            <system value="http://unitsofmeasure.org"/>
+            <code value="ml"/>
+          </doseQuantity>
+        </dosageInstruction>
+
+        <dispense>
+          <quantity>
+            <value value="100"/>
+            <units value="ml"/>
+            <system value="http://unitsofmeasure.org"/>
+            <code value="ml"/>
+          </quantity>
+        </dispense>
+
+      </MedicationPrescription>
+    </resource>
+  </entry>
+</Bundle>

pom.xml.orig

@@ -0,0 +1,694 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+
+	<parent>
+		<groupId>org.sonatype.oss</groupId>
+		<artifactId>oss-parent</artifactId>
+		<version>9</version>
+	</parent>
+
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>ca.uhn.hapi.fhir</groupId>
+	<artifactId>hapi-fhir</artifactId>
+	<packaging>pom</packaging>
+	<version>0.9-SNAPSHOT</version>
+	<name>HAPI-FHIR</name>
+	<url>http://hl7api.sourceforge.net/hapi-fhir/</url>
+
+	<organization>
+		<name>University Health Network</name>
+		<url>http://www.uhn.ca</url>
+	</organization>
+
+	<inceptionYear>2014</inceptionYear>
+
+	<issueManagement>
+		<system>GitHub</system>
+		<url>https://github.com/jamesagnew/hapi-fhir/issues/</url>
+	</issueManagement>
+
+	<distributionManagement>
+		<site>
+			<id>git.server</id>
+			<url>scm:git:git@github.com:jamesagnew/hapi-fhir.git</url>
+		</site>
+	</distributionManagement>
+
+	<scm>
+		<connection>scm:git:git@github.com:jamesagnew/hapi-fhir.git</connection>
+		<url>scm:git:git@github.com:jamesagnew/hapi-fhir.git</url>
+		<developerConnection>scm:git:git@github.com:jamesagnew/hapi-fhir.git</developerConnection>
+	</scm>
+
+	<description>
+	</description>
+
+	<dependencies>
+	</dependencies>
+
+	<prerequisites>
+		<maven>3.0.1</maven>
+	</prerequisites>
+
+	<developers>
+		<developer>
+			<id>jamesagnew</id>
+			<name>James Agnew</name>
+			<organization>University Health Network</organization>
+		</developer>
+		<developer>
+			<name>Dmitri Sotnikov</name>
+			<organization>University Health Network</organization>
+		</developer>
+		<developer>
+			<name>Lisa Wong</name>
+			<organization>University Health Network</organization>
+		</developer>
+		<developer>
+			<name>Josh Mandel</name>
+			<organization>Boston Children's Hospital</organization>
+		</developer>
+		<developer>
+			<id>lmds</id>
+			<name>Laura MacDougall Sookraj</name>
+			<organization>University Health Network</organization>
+		</developer>
+		<developer>
+			<name>Neal Acharya</name>
+			<organization>University Health Network</organization>
+		</developer>
+		<developer>
+			<name>David Hay</name>
+			<organization>Orion Health</organization>
+		</developer>
+		<developer>
+			<id>suranga</id>
+			<name>Suranga Nath Kasthurirathne</name>
+			<organization>OpenMRS / Regenstrief Center for Biomedical Informatics</organization>
+		</developer>
+		<developer>
+			<id>dougmartin</id>
+			<name>Doug Martin</name>
+			<organization>Regenstrief Center for Biomedical Informatics</organization>
+		</developer>
+		<developer>
+			<id>akley</id>
+			<name>Alexander Kley</name>
+		</developer>
+		<developer>
+			<id>preston</id>
+			<name>Preston Lee</name>
+			<organization>Arizona State University</organization>
+		</developer>
+		<developer>
+			<id>jjathman</id>
+			<name>Joe Athman</name>
+		</developer>
+		<developer>
+			<id>petromykhailysyn</id>
+			<name>Petro Mykhailyshyn</name>
+		</developer>
+		<developer>
+			<id>tahurac</id>
+			<name>Tahura Chaudhry</name>
+			<organization>University Health Network</organization>
+		</developer>
+		<developer>
+			<id>b.debeaubien</id>
+			<name>Bill de Beaubien</name>
+			<organization>Systems Made Simple</organization>
+		</developer>
+	</developers>
+
+	<licenses>
+		<license>
+			<name>Apache Software License 2.0</name>
+			<url>https://www.apache.org/licenses/LICENSE-2.0.txt</url>
+		</license>
+	</licenses>
+
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		
+		<!-- For site-deploy -->
+		<siteMainDirectory>${user.home}/sites/hapi-fhir</siteMainDirectory>
+		<scmPubCheckoutDirectory>${user.home}/sites/scm/hapi-fhir</scmPubCheckoutDirectory>
+
+		<!-- Plugin Versions -->
+		<apache_httpclient_version>4.3.6</apache_httpclient_version>
+		<apache_httpcore_version>4.4</apache_httpcore_version>
+		<commons_io_version>2.4</commons_io_version>
+		<commons_lang_version>3.3.2</commons_lang_version>
+		<commons_codec_version>1.10</commons_codec_version>
+		<derby_version>10.11.1.1</derby_version>
+		<guava_version>18.0</guava_version>
+		<hamcrest_version>1.3</hamcrest_version>
+		<hibernate_version>4.3.7.Final<!-- 4.2.12.Final --></hibernate_version>
+		<hibernate_validator_version>5.1.0.Final</hibernate_validator_version>
+		<jetty_version>9.2.6.v20141205</jetty_version>
+		<jscience_version>4.3.1</jscience_version>
+		<junit_version>4.12</junit_version>
+		<logback_version>1.1.2</logback_version>
+		<maven_assembly_plugin_version>2.4.1</maven_assembly_plugin_version>
+		<maven_javadoc_plugin_version>2.10.1</maven_javadoc_plugin_version>
+		<maven_license_plugin_version>1.7</maven_license_plugin_version>
+		<maven_surefire_plugin_version>2.18.1</maven_surefire_plugin_version>
+		<maven_site_plugin_version>3.4</maven_site_plugin_version>
+		<maven_source_plugin_version>2.3</maven_source_plugin_version>
+		<mitreid-connect-version>1.1.8</mitreid-connect-version>
+		<mockito_version>1.10.17</mockito_version>
+		<phloc_schematron_version>2.7.1</phloc_schematron_version>
+		<phloc_commons_version>4.3.5</phloc_commons_version>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<servlet_api_version>3.1.0</servlet_api_version>
+		<slf4j_version>1.7.9</slf4j_version>
+		<spring_version>4.1.3.RELEASE</spring_version>
+		<spring_security_version>3.2.4.RELEASE</spring_security_version>
+		<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
+		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
+		<woodstox_version>4.4.0</woodstox_version>
+	</properties>
+
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-compiler-plugin</artifactId>
+					<version>3.2</version>
+					<configuration>
+						<source>1.6</source>
+						<target>1.6</target>
+					</configuration>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-surefire-plugin</artifactId>
+					<version>${maven_surefire_plugin_version}</version>
+					<configuration>
+						<redirectTestOutputToFile>true</redirectTestOutputToFile>
+						<runOrder>random</runOrder>
+<<<<<<< HEAD
+=======
+						<!--<argLine>-Dfile.encoding=ISO-8859-1</argLine> -->
+>>>>>>> 8c96bf7d9ef6d6c590c3c7420c293b815935b336
+						<argLine>-Dfile.encoding=UTF-8</argLine>
+					</configuration>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-site-plugin</artifactId>
+					<version>${maven_site_plugin_version}</version>
+					<dependencies>
+						<dependency>
+							<groupId>org.apache.maven.wagon</groupId>
+							<artifactId>wagon-ssh</artifactId>
+							<version>1.0</version>
+						</dependency>
+						<dependency>
+							<groupId>org.apache.maven.doxia</groupId>
+							<artifactId>doxia-module-markdown</artifactId>
+							<version>1.6</version>
+						</dependency>
+					</dependencies>
+					<configuration>
+						<skip>true</skip>
+						<skipDeploy>true</skipDeploy>
+					</configuration>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-deploy-plugin</artifactId>
+					<version>2.8.1</version>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-javadoc-plugin</artifactId>
+					<version>${maven_javadoc_plugin_version}</version>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-source-plugin</artifactId>
+					<version>${maven_source_plugin_version}</version>
+				</plugin>
+				<plugin>
+					<groupId>org.codehaus.mojo</groupId>
+					<artifactId>license-maven-plugin</artifactId>
+					<version>${maven_license_plugin_version}</version>
+					<configuration>
+						<verbose>true</verbose>
+						<addSvnKeyWords>false</addSvnKeyWords>
+					</configuration>
+				</plugin>
+				<plugin>
+					<artifactId>maven-site-plugin</artifactId>
+					<version>${maven_site_plugin_version}</version>
+					<configuration>
+						<skip>false</skip>
+						<skipDeploy>true</skipDeploy>
+					</configuration>
+					<dependencies>
+						<dependency>
+							<groupId>org.apache.maven.wagon</groupId>
+							<artifactId>wagon-scm</artifactId>
+							<version>2.2</version>
+						</dependency>
+						<dependency>
+							<groupId>org.apache.maven.scm</groupId>
+							<artifactId>maven-scm-manager-plexus</artifactId>
+							<version>1.9</version>
+						</dependency>
+						<dependency>
+							<groupId>org.apache.maven.scm</groupId>
+							<artifactId>maven-scm-provider-gitexe</artifactId>
+							<version>1.9</version>
+						</dependency>
+						<dependency>
+							<groupId>org.apache.maven.scm</groupId>
+							<artifactId>maven-scm-api</artifactId>
+							<version>1.9</version>
+						</dependency>
+					</dependencies>
+				</plugin>
+				<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
+				<plugin>
+					<groupId>org.eclipse.m2e</groupId>
+					<artifactId>lifecycle-mapping</artifactId>
+					<version>1.0.0</version>
+					<configuration>
+						<lifecycleMappingMetadata>
+							<pluginExecutions>
+								<pluginExecution>
+									<pluginExecutionFilter>
+										<groupId>
+											ca.uhn.hapi.fhir
+										</groupId>
+										<artifactId>
+											hapi-tinder-plugin
+										</artifactId>
+										<versionRange>
+											[0.8-SNAPSHOT,)
+										</versionRange>
+										<goals>
+											<goal>
+												generate-jparest-server
+											</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<ignore></ignore>
+									</action>
+								</pluginExecution>
+								<pluginExecution>
+									<pluginExecutionFilter>
+										<groupId>
+											org.apache.maven.plugins
+										</groupId>
+										<artifactId>
+											maven-antrun-plugin
+										</artifactId>
+										<versionRange>
+											[1.7,)
+										</versionRange>
+										<goals>
+											<goal>run</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<ignore></ignore>
+									</action>
+								</pluginExecution>
+							</pluginExecutions>
+						</lifecycleMappingMetadata>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+		<plugins>
+			<plugin>
+				<artifactId>maven-antrun-plugin</artifactId>
+				<version>1.7</version>
+				<inherited>false</inherited>
+				<executions>
+					<execution>
+						<id>copySubProjects</id>
+						<phase>site</phase>
+						<goals>
+							<goal>run</goal>
+						</goals>
+						<configuration>
+							<target>
+								<copy todir="target/site/apidocs">
+									<fileset dir="hapi-fhir-base/target/site/apidocs"/>
+								</copy>
+								<copy todir="target/site/apidocs-dstu">
+									<fileset dir="hapi-fhir-structures-dstu/target/site/apidocs"/>
+								</copy>
+								<copy todir="target/site/apidocs-dev">
+									<fileset dir="hapi-fhir-structures-dev/target/site/apidocs"/>
+								</copy>
+							</target>
+						</configuration>
+					</execution>
+					<execution>
+						<id>addSyntaxHighlighter</id>
+						<phase>site</phase>
+						<goals>
+							<goal>run</goal>
+						</goals>
+						<configuration>
+							<target>
+								<echo>Adding Syntax Highlighter</echo>
+								<replace dir="target/site" summary="true">
+									<include name="*.html"></include>
+									<replacetoken><![CDATA[</body>]]></replacetoken>
+									<replacevalue><![CDATA[
+<script type="text/javascript">
+	var elements = document.getElementsByClassName("source");
+	for (var i=0; i < elements.length; i++) {
+		var pres = elements[i].getElementsByTagName("pre");
+		for (var j = 0; j < pres.length; j++) {
+			var pre = pres[j];
+			if (pre.innerHTML.match(/\/\*/)) {
+				pre.className = 'brush: java';
+			} else if (pre.innerHTML.match(/^\/\//)) {
+				pre.className = 'brush: java';
+			} else if (pre.innerHTML.match(/^\{/)) {
+				pre.className = 'brush: jscript';
+			} else if (pre.innerHTML.match(/^\#/)) {
+				pre.className = 'brush: bash';
+			} else if (pre.innerHTML.match(/\&lt\;\//)) {
+				pre.className = 'brush: xml';
+			} else {
+				pre.className = 'brush: java';
+			}
+		}
+	}
+
+	SyntaxHighlighter.all();
+</script>
+</body>
+									]]></replacevalue>
+								</replace>
+							</target>
+						</configuration>
+					</execution>
+					<execution>
+						<id>addAnalytics</id>
+						<phase>post-site</phase>
+						<configuration>
+							<target>
+								<echo>Adding Google analytics in target/site for &lt;body&gt;</echo>
+								<replace dir="target/site" summary="true">
+									<include name="**/*.html"></include>
+									<replacefilter token="#build#" value="${label}" />
+									<replacefilter token="#version#" value="${project.version}" />
+									<replacetoken><![CDATA[</body>]]></replacetoken>
+									<replacevalue><![CDATA[
+<script>
+  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
+
+  ga('create', 'UA-1395874-5', 'auto');
+  ga('require', 'displayfeatures');
+  ga('require', 'linkid', 'linkid.js');
+  ga('send', 'pageview');
+
+</script>
+                </body >
+                ]]></replacevalue>
+								</replace>
+								<echo>Adding Google analytics in target/site for &lt;BODY&gt;</echo>
+								<replace dir="target/site" summary="true">
+									<include name="**/*.html"></include>
+									<replacetoken><![CDATA[</BODY>]]></replacetoken>
+									<replacevalue><![CDATA[
+<script>
+  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
+
+  ga('create', 'UA-1395874-5', 'auto');
+  ga('require', 'displayfeatures');
+  ga('require', 'linkid', 'linkid.js');
+  ga('send', 'pageview');
+
+</script>
+                </BODY >
+                ]]></replacevalue>
+								</replace>
+								<echo>Adding social plugins for HAPI</echo>
+								<replace dir="target/site/" summary="true">
+									<include name="**/*.html"></include>
+									<replacetoken><![CDATA[SOCIALPLUGINSHEREFHIR]]></replacetoken>
+									<replacevalue><![CDATA[
+            	<table cellpadding="0" cellspacing="0" border="0"><tr>
+            	<td><div class="g-plusone" data-annotation="inline" data-width="300" data-href="http://hl7api.sourceforge.net/"></div></td>
+            	<td><div class="fb-like" data-href="http://hl7api.sourceforge.net/" data-send="false" data-layout="button_count" data-width="450" data-show-faces="true"></div></td>
+            	</tr></table>
+
+            	</p><p>
+            	<!-- Place this tag after the last +1 button tag. -->
+            	<script type="text/javascript">
+            	  (function() {
+            	    var po = document.createElement('script'); po.type = 'text/javascript'; po.async = true;
+            	    po.src = 'https://apis.google.com/js/plusone.js';
+            	    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(po, s);
+            	  })();
+            	</script>
+            	<div id="fb-root"></div>
+            	<script>(function(d, s, id) {
+            	  var js, fjs = d.getElementsByTagName(s)[0];
+            	  if (d.getElementById(id)) return;
+            	  js = d.createElement(s); js.id = id;
+            	  js.src = "//connect.facebook.net/en_US/all.js#xfbml=1";
+            	  fjs.parentNode.insertBefore(js, fjs);
+            	}(document, 'script', 'facebook-jssdk'));</script>
+				]]></replacevalue>
+								</replace>
+
+
+							</target>
+						</configuration>
+						<goals>
+							<goal>run</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>animal-sniffer-maven-plugin</artifactId>
+				<version>1.12</version>
+				<inherited>true</inherited>
+				<configuration>
+					<signature>
+						<groupId>org.codehaus.mojo.signature</groupId>
+						<artifactId>java16</artifactId>
+						<version>1.01</version>
+					</signature>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-site-plugin</artifactId>
+				<inherited>false</inherited>
+				<executions>
+					<execution>
+						<id>stage-for-scm-publish</id>
+						<phase>post-site</phase>
+						<goals>
+							<goal>stage</goal>
+						</goals>
+						<configuration>
+							<stagingDirectory>${siteMainDirectory}</stagingDirectory>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-scm-publish-plugin</artifactId>
+				<version>1.1</version>
+				<inherited>false</inherited>
+				<configuration>
+					<checkoutDirectory>${scmPubCheckoutDirectory}</checkoutDirectory>
+					<content>\${siteMainDirectory}</content>
+					<tryUpdate>true</tryUpdate>
+					<scmBranch>gh-pages</scmBranch>
+					<pubScmUrl>scm:git:git@github.com:jamesagnew/hapi-fhir.git</pubScmUrl>
+				</configuration>
+				<executions>
+					<execution>
+						<id>scm-publish</id>
+						<phase>site-deploy</phase>
+						<goals>
+							<goal>publish-scm</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-changes-plugin</artifactId>
+				<version>2.11</version>
+				<inherited>false</inherited>
+				<reportSets>
+					<reportSet>
+						<reports>
+							<report>changes-report</report>
+						</reports>
+					</reportSet>
+				</reportSets>
+				<configuration>
+					<feedType>atom_1.0</feedType>
+					<issueLinkTemplatePerSystem>
+						<default>https://github.com/jamesagnew/hapi-fhir/issues/%ISSUE%</default>
+					</issueLinkTemplatePerSystem>
+					<escapeHTML>false</escapeHTML>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-report-plugin</artifactId>
+				<version>${maven_surefire_plugin_version}</version>
+				<configuration>
+					<aggregate>true</aggregate>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-project-info-reports-plugin</artifactId>
+				<version>2.7</version>
+				<inherited>false</inherited>
+				<reportSets>
+					<reportSet>
+						<reports>
+							<report>project-team</report>
+							<report>issue-tracking</report>
+							<report>license</report>
+							<report>scm</report>
+						</reports>
+					</reportSet>
+				</reportSets>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>findbugs-maven-plugin</artifactId>
+				<version>3.0.0</version>
+				<configuration>
+					<classFilesDirectory>./hapi-fhir-base/target/classes</classFilesDirectory>
+				</configuration>
+				<reportSets>
+					<reportSet>
+						<reports>
+							<report>findbugs</report>
+						</reports>
+					</reportSet>
+				</reportSets>
+			</plugin>
+	
+			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-linkcheck-plugin</artifactId> 
+				<version>1.1</version> </plugin> -->
+		</plugins>
+	</reporting>
+
+	<profiles>
+		<profile>
+			<id>ROOT</id>
+			<modules>
+			</modules>
+			<build>
+				<plugins>
+					<!-- 
+					<plugin>
+						<artifactId>maven-assembly-plugin</artifactId>
+						<version>${maven_assembly_plugin_version}</version>
+						<executions>
+							<execution>
+								<phase>package</phase>
+								<goals>
+									<goal>single</goal>
+								</goals>
+								<configuration>
+									<attach>false</attach>
+									<descriptors>
+										<descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor>
+									</descriptors>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+					 -->
+				</plugins>
+			</build>
+		</profile>
+		<profile>
+			<id>SIGN_ARTIFACTS</id>
+			<activation>
+				<property>
+					<name>gpg.passphrase</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-gpg-plugin</artifactId>
+						<version>1.5</version>
+						<executions>
+							<execution>
+								<id>sign-artifacts</id>
+								<phase>verify</phase>
+								<goals>
+									<goal>sign</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+		<profile>
+			<id>SITE</id>
+			<modules>
+				<module>hapi-fhir-base</module>
+				<module>hapi-fhir-structures-dstu</module>
+				<module>hapi-fhir-structures-dev</module>
+				<module>examples</module>
+			</modules>
+		</profile>
+		<profile>
+			<id>ALLMODULES</id>
+			<activation>
+				<activeByDefault>true</activeByDefault>
+			</activation>
+			<modules>
+				<module>hapi-deployable-pom</module>
+				<module>hapi-fhir-base</module>
+				<!--<module>hapi-fhir-oauth2</module>-->
+				<module>hapi-fhir-base/testmindeps</module>
+				<module>hapi-tinder-plugin</module>
+				<module>hapi-tinder-test</module>
+				<module>hapi-fhir-structures-dstu</module>
+				<module>hapi-fhir-structures-dev</module>
+				<module>hapi-fhir-jpaserver-base</module>
+				<module>hapi-fhir-jpaserver-test</module>
+				<module>restful-server-example</module>
+				<module>restful-server-example-test</module>
+				<module>hapi-fhir-testpage-overlay</module>
+				<module>hapi-fhir-jpaserver-uhnfhirtest</module>
+			<!--	<module>hapi-fhir-dist</module> -->
+			</modules>
+		</profile>
+	</profiles>
+
+</project>