Work on build

examples/src/main/java/example/ClientExamples.java

@@ -20,8 +20,15 @@ public class ClientExamples {
    public void createProxy() {
       // START SNIPPET: proxy
       FhirContext ctx = new FhirContext();
+
+      // Set connections to access the network via the HTTP proxy at
+      // example.com : 8888
       ctx.getRestfulClientFactory().setProxy("example.com", 8888);
 
+      // If the proxy requires authentication, use the following as well
+      ctx.getRestfulClientFactory().setProxyCredentials("theUsername", "thePassword");
+      
+      // Create the client
       IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
       // END SNIPPET: proxy
    }

examples/src/main/java/example/HttpProxy.java

@@ -18,7 +18,10 @@ import ca.uhn.fhir.rest.client.IGenericClient;
 public class HttpProxy {
 
    public static void main(String[] args) {
-      
+      /*
+       * This is out ot date - Just keeping
+       * it in case it's helpful...
+       */
       final String authUser = "username"; 
       final String authPassword = "password"; 
       CredentialsProvider credsProvider = new BasicCredentialsProvider();

hapi-fhir-android/pom.xml

@@ -12,7 +12,7 @@
 	<artifactId>hapi-fhir-android</artifactId>
 	<packaging>jar</packaging>
 
-	<name>HAPI FHIR - Distribution Archive</name>
+	<name>HAPI FHIR - Android</name>
 
 	<dependencies>
 		<dependency>

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java

@@ -488,7 +488,7 @@ class ModelScanner {
 
 			Class<?> nextElementType = determineElementType(next);
 
-			if (IAnyResource.class.isAssignableFrom(nextElementType)) {
+			if (IAnyResource.class.isAssignableFrom(nextElementType) || IResource.class.equals(nextElementType)) {
 				/*
 				 * Child is a resource as a direct child, as in Bundle.entry.resource
 				 */

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

@@ -38,18 +38,23 @@ import java.util.Set;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.IBase;
 import org.hl7.fhir.instance.model.IBaseResource;
+import org.hl7.fhir.instance.model.IPrimitiveType;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IDomainResource;
 import org.hl7.fhir.instance.model.api.IReference;
 
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.BundleEntry;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -266,6 +271,57 @@ public abstract class BaseParser implements IParser {
 		return parseResource(null, theReader);
 	}
 
+	protected abstract <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) throws DataFormatException;
+	
+	public <T extends IBaseResource> T parseResource(Class<T> theResourceType, Reader theReader) throws DataFormatException {
+		T retVal = doParseResource(theResourceType, theReader);
+		
+		RuntimeResourceDefinition def = myContext.getResourceDefinition(retVal);
+		if ("Bundle".equals(def.getName())) {
+			List<IBase> base = def.getChildByName("base").getAccessor().getValues(retVal);
+			if (base != null && base.size() > 0) {
+				IPrimitiveType<?> baseType = (IPrimitiveType<?>) base.get(0);
+				IResource res = ((IResource)retVal);
+				res.setId(new IdDt(baseType.getValueAsString(), def.getName(), res.getId().getIdPart(), res.getId().getVersionIdPart()));
+			}
+			
+			BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
+			BaseRuntimeElementCompositeDefinition<?> entryDef = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
+			List<IBase> entries = entryChild.getAccessor().getValues(retVal);
+			if (entries != null) {
+				for (IBase nextEntry : entries) {
+					List<IBase> entryBase = entryDef.getChildByName("base").getAccessor().getValues(nextEntry);
+					
+					if (entryBase == null || entryBase.isEmpty()) {
+						entryBase = base;
+					}
+					
+					if (entryBase != null && entryBase.size() > 0) {
+						IPrimitiveType<?> baseType = (IPrimitiveType<?>) entryBase.get(0);
+						
+						List<IBase> entryResources = entryDef.getChildByName("resource").getAccessor().getValues(nextEntry);
+						if (entryResources != null && entryResources.size() > 0) {
+							IResource res = (IResource) entryResources.get(0);
+							RuntimeResourceDefinition resDef = myContext.getResourceDefinition(res);
+							String versionIdPart = res.getId().getVersionIdPart();
+							if (isBlank(versionIdPart)) {
+								versionIdPart = ResourceMetadataKeyEnum.VERSION.get(res);
+							}
+							
+							res.setId(new IdDt(baseType.getValueAsString(), resDef.getName(), res.getId().getIdPart(), versionIdPart));
+						}
+						
+					}
+					
+					
+				}
+			}
+			
+		}
+		
+		return retVal;
+	}
+	
 	@Override
 	public IResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException {
 		return parseResource(null, theMessageString);

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

@@ -277,6 +277,13 @@ public class JsonParser extends BaseParser implements IParser {
 
 			writeOptionalTagWithTextNode(theEventWriter, "base", determineResourceBaseUrl(theBundle.getLinkBase().getValue(), nextEntry));
 
+			boolean deleted = nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false;
+			IResource resource = nextEntry.getResource();
+			if (resource != null && !resource.isEmpty() && !deleted) {
+				RuntimeResourceDefinition resDef = myContext.getResourceDefinition(resource);
+				encodeResourceToJsonStreamWriter(resDef, resource, theEventWriter, "resource", false);
+			}
+			
 			if (nextEntry.getSearchMode().isEmpty() == false || nextEntry.getScore().isEmpty() == false) {
 				theEventWriter.writeStartObject("search");
 				writeOptionalTagWithTextNode(theEventWriter, "mode", nextEntry.getSearchMode().getValueAsString());
@@ -288,11 +295,10 @@ public class JsonParser extends BaseParser implements IParser {
 			if (nextEntry.getTransactionOperation().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
 				theEventWriter.writeStartObject("transaction");
 				writeOptionalTagWithTextNode(theEventWriter, "operation", nextEntry.getTransactionOperation().getValue());
-				writeOptionalTagWithTextNode(theEventWriter, "match", nextEntry.getLinkSearch().getValue());
+				writeOptionalTagWithTextNode(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
 				theEventWriter.writeEnd();
 			}
 
-			boolean deleted = nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false;
 			if (deleted) {
 				theEventWriter.writeStartObject("deleted");
 				if (nextEntry.getResource() != null) {
@@ -319,11 +325,6 @@ public class JsonParser extends BaseParser implements IParser {
 			//
 			// writeAuthor(nextEntry, theEventWriter);
 
-			IResource resource = nextEntry.getResource();
-			if (resource != null && !resource.isEmpty() && !deleted) {
-				RuntimeResourceDefinition resDef = myContext.getResourceDefinition(resource);
-				encodeResourceToJsonStreamWriter(resDef, resource, theEventWriter, "resource", false);
-			}
 
 			if (nextEntry.getSummary().isEmpty() == false) {
 				theEventWriter.write("summary", nextEntry.getSummary().getValueAsString());
@@ -1096,7 +1097,7 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	@Override
-	public <T extends IBaseResource> T parseResource(Class<T> theResourceType, Reader theReader) {
+	public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
 		JsonReader reader = Json.createReader(theReader);
 		JsonObject object = reader.readObject();
 

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

@@ -1121,7 +1121,7 @@ class ParserState<T> {
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			if ("operation".equals(theLocalPart)) {
 				push(new PrimitiveState(getPreResourceState(), myEntry.getTransactionOperation()));
-			} else if ("match".equals(theLocalPart)) {
+			} else if ("url".equals(theLocalPart)) {
 				push(new PrimitiveState(getPreResourceState(), myEntry.getLinkSearch()));
 			} else {
 				throw new DataFormatException("Unexpected element in Bundle.entry.search: " + theLocalPart);
@@ -1658,6 +1658,8 @@ class ParserState<T> {
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			if (theLocalPart.equals("versionId")) {
 				push(new MetaVersionElementState(getPreResourceState(), myMap));
+//			} else if (theLocalPart.equals("profile")) {
+//				
 			} else if (theLocalPart.equals("lastUpdated")) {
 				InstantDt updated = new InstantDt();
 				push(new PrimitiveState(getPreResourceState(), updated));
@@ -1759,10 +1761,23 @@ class ParserState<T> {
 		@Override
 		public void wereBack() {
 			super.wereBack();
-
 			if (myEntry == null) {
 				myObject = (T) getCurrentElement();
 			}
+
+			IResource nextResource = (IResource) getCurrentElement();
+			String version = ResourceMetadataKeyEnum.VERSION.get(nextResource);
+			String resourceName = myContext.getResourceDefinition(nextResource).getName();
+			String bundleIdPart = nextResource.getId().getIdPart();
+			if (isNotBlank(bundleIdPart)) {
+//				if (isNotBlank(entryBaseUrl)) {
+//					nextResource.setId(new IdDt(entryBaseUrl, resourceName, bundleIdPart, version));
+//				} else {
+					nextResource.setId(new IdDt(null, resourceName, bundleIdPart, version));
+//				}
+			}
+
+			
 		}
 
 		@Override

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

@@ -81,6 +81,7 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
+import ca.uhn.fhir.rest.method.BaseMethodBinding;
 import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.XmlUtil;
@@ -385,8 +386,22 @@ public class XmlParser extends BaseParser implements IParser {
 		for (BundleEntry nextEntry : theBundle.getEntries()) {
 			theEventWriter.writeStartElement("entry");
 
+			boolean deleted = false;
+			if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
+				deleted = true;
+			}
+			
 			writeOptionalTagWithValue(theEventWriter, "base", determineResourceBaseUrl(bundleBaseUrl, nextEntry));
 
+			IResource resource = nextEntry.getResource();
+			if (resource != null && !resource.isEmpty() && !deleted) {
+				theEventWriter.writeStartElement("resource");
+				encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
+				theEventWriter.writeEndElement(); // content
+			} else {
+				ourLog.debug("Bundle entry contains null resource");
+			}
+
 			if (nextEntry.getSearchMode().isEmpty() == false || nextEntry.getScore().isEmpty() == false) {
 				theEventWriter.writeStartElement("search");
 				writeOptionalTagWithValue(theEventWriter, "mode", nextEntry.getSearchMode().getValueAsString());
@@ -398,13 +413,11 @@ public class XmlParser extends BaseParser implements IParser {
 			if (nextEntry.getTransactionOperation().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
 				theEventWriter.writeStartElement("transaction");
 				writeOptionalTagWithValue(theEventWriter, "operation", nextEntry.getTransactionOperation().getValue());
-				writeOptionalTagWithValue(theEventWriter, "match", nextEntry.getLinkSearch().getValue());
+				writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
 				theEventWriter.writeEndElement();
 			}
 
-			boolean deleted = false;
+			if (deleted) {
-			if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
-				deleted = true;
 				theEventWriter.writeStartElement("deleted");
 				writeOptionalTagWithValue(theEventWriter, "type", nextEntry.getId().getResourceType());
 				writeOptionalTagWithValue(theEventWriter, "id", nextEntry.getId().getIdPart());
@@ -413,15 +426,6 @@ public class XmlParser extends BaseParser implements IParser {
 				theEventWriter.writeEndElement();
 			}
 
-			IResource resource = nextEntry.getResource();
-			if (resource != null && !resource.isEmpty() && !deleted) {
-				theEventWriter.writeStartElement("resource");
-				encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
-				theEventWriter.writeEndElement(); // content
-			} else {
-				ourLog.debug("Bundle entry contains null resource");
-			}
-
 			theEventWriter.writeEndElement(); // entry
 		}
 
@@ -488,7 +492,11 @@ public class XmlParser extends BaseParser implements IParser {
 			break;
 		}
 		case RESOURCE: {
-			throw new IllegalStateException(); // should not happen
+			theEventWriter.writeStartElement(childName);
+			IBaseResource resource = (IBaseResource) nextValue;
+			encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
+			theEventWriter.writeEndElement();
+			break;
 		}
 		case PRIMITIVE_XHTML: {
 			XhtmlDt dt = (XhtmlDt) nextValue;
@@ -703,7 +711,11 @@ public class XmlParser extends BaseParser implements IParser {
 			IdDt resourceId = resource.getId();
 			if (resourceId != null && isNotBlank(resourceId.getVersionIdPart()) || (updated != null && !updated.isEmpty())) {
 				theEventWriter.writeStartElement("meta");
-				writeOptionalTagWithValue(theEventWriter, "versionId", resourceId.getVersionIdPart());
+				String versionIdPart = resourceId.getVersionIdPart();
+				if (isBlank(versionIdPart)) {
+					versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
+				}
+				writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
 				if (updated != null) {
 					writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
 				}
@@ -922,7 +934,7 @@ public class XmlParser extends BaseParser implements IParser {
 	}
 
 	@Override
-	public <T extends IBaseResource> T parseResource(Class<T> theResourceType, Reader theReader) {
+	public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
 		XMLEventReader streamReader = createStreamReader(theReader);
 		return parseResource(theResourceType, streamReader);
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/IRestfulClientFactory.java

@@ -150,6 +150,14 @@ public interface IRestfulClientFactory {
 	 */
 	void setProxy(String theHost, Integer thePort);
 
+	/**
+	 * Sets the credentials to use to authenticate with the HTTP proxy,
+	 * if one is defined. Set to null to use no authentication with the proxy.
+	 * @param theUsername The username
+	 * @param thePassword The password
+	 */
+	void setProxyCredentials(String theUsername, String thePassword);
+
 	/**
 	 * Sets the server validation mode for any clients created from this factory. Server 
 	 * validation involves the client requesting the server's conformance statement

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/RestfulClientFactory.java

@@ -23,6 +23,7 @@ package ca.uhn.fhir.rest.client;
 import java.lang.reflect.InvocationHandler;
 import java.lang.reflect.Method;
 import java.lang.reflect.Proxy;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
@@ -32,9 +33,15 @@ import java.util.concurrent.TimeUnit;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.HttpHost;
+import org.apache.http.auth.AuthScope;
+import org.apache.http.auth.UsernamePasswordCredentials;
+import org.apache.http.client.CredentialsProvider;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.config.RequestConfig;
+import org.apache.http.impl.client.BasicCredentialsProvider;
+import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.http.impl.client.HttpClients;
+import org.apache.http.impl.client.ProxyAuthenticationStrategy;
 import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 
 import ca.uhn.fhir.context.ConfigurationException;
@@ -100,18 +107,35 @@ public class RestfulClientFactory implements IRestfulClientFactory {
 				    .setProxy(myProxy)
 				    .build();
 			
-			myHttpClient = HttpClients.custom()
+			HttpClientBuilder builder = HttpClients.custom()
 				.setConnectionManager(connectionManager)
 				.setDefaultRequestConfig(defaultRequestConfig)
-				.disableCookieManagement()
+				.disableCookieManagement();
-				.build();
+			
+			if (myProxy != null && StringUtils.isNotBlank(myProxyUsername) && StringUtils.isNotBlank(myProxyPassword)) {
+				CredentialsProvider credsProvider = new BasicCredentialsProvider();
+				credsProvider.setCredentials(new AuthScope(myProxy.getHostName(), myProxy.getPort()), new UsernamePasswordCredentials(myProxyUsername, myProxyPassword));
+				builder.setProxyAuthenticationStrategy(new ProxyAuthenticationStrategy());
+				builder.setDefaultCredentialsProvider(credsProvider);
+			}
+			
+			myHttpClient = builder.build();
 			//@formatter:on
 
 		}
 
 		return myHttpClient;
 	}
+	
+	private String myProxyUsername;
+	private String myProxyPassword;
 
+	@Override
+	public void setProxyCredentials(String theUsername, String thePassword) {
+		myProxyUsername=theUsername;
+		myProxyPassword=thePassword;
+	}
+	
 	@Override
 	public ServerValidationModeEnum getServerValidationModeEnum() {
 		return myServerValidationMode;

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseBundle.java

@@ -0,0 +1,7 @@
+package org.hl7.fhir.instance.model.api;
+
+import org.hl7.fhir.instance.model.IBaseResource;
+
+public interface IBaseBundle extends IBaseResource {
+
+}

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/client/HttpProxyTest.java

@@ -86,25 +86,27 @@ public class HttpProxyTest {
 		server.start();
 		try {
 
-			final String authUser = "username";
+//			final String authUser = "username";
-			final String authPassword = "password";
+//			final String authPassword = "password";
-			CredentialsProvider credsProvider = new BasicCredentialsProvider();
+//			CredentialsProvider credsProvider = new BasicCredentialsProvider();
-			credsProvider.setCredentials(new AuthScope("127.0.0.1", port), new UsernamePasswordCredentials(authUser, authPassword));
+//			credsProvider.setCredentials(new AuthScope("127.0.0.1", port), new UsernamePasswordCredentials(authUser, authPassword));
-
+//
-			HttpHost myProxy = new HttpHost("127.0.0.1", port);
+//			HttpHost myProxy = new HttpHost("127.0.0.1", port);
-
+//
-			//@formatter:off
+//			//@formatter:off
-			HttpClientBuilder clientBuilder = HttpClientBuilder.create();
+//			HttpClientBuilder clientBuilder = HttpClientBuilder.create();
-			clientBuilder
+//			clientBuilder
-				.setProxy(myProxy)
+//				.setProxy(myProxy)
-				.setProxyAuthenticationStrategy(new ProxyAuthenticationStrategy())
+//				.setProxyAuthenticationStrategy(new ProxyAuthenticationStrategy())
-				.setDefaultCredentialsProvider(credsProvider)
+//				.setDefaultCredentialsProvider(credsProvider)
-				.disableCookieManagement();
+//				.disableCookieManagement();
-			CloseableHttpClient httpClient = clientBuilder.build();
+//			CloseableHttpClient httpClient = clientBuilder.build();
-			//@formatter:on
+//			//@formatter:on
-
+//			ourCtx.getRestfulClientFactory().setHttpClient(httpClient);
-			ourCtx.getRestfulClientFactory().setHttpClient(httpClient);
 
+			ourCtx.getRestfulClientFactory().setProxy("127.0.0.1", port);
+			ourCtx.getRestfulClientFactory().setProxyCredentials("username", "password");
+			
 			String baseUri = "http://99.99.99.99:" + port + "/rootctx/rcp2/fhirctx/fcp2";
 			IGenericClient client = ourCtx.newRestfulGenericClient(baseUri);
 

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

@@ -62,17 +62,17 @@ public class TransactionWithBundleParamTest {
 		Patient p1 = new Patient();
 		p1.addName().addFamily("Family1");
 		BundleEntry entry = b.addEntry();
-		entry.getId().setValue("1");
+		p1.getId().setValue("1");
 		entry.setResource(p1);
 
 		Patient p2 = new Patient();
 		p2.addName().addFamily("Family2");
 		entry = b.addEntry();
-		entry.getId().setValue("2");
+		p2.getId().setValue("2");
 		entry.setResource(p2);
 		
 		BundleEntry deletedEntry = b.addEntry();
-		deletedEntry.setId(new IdDt("Patient/3"));
+		deletedEntry.setDeletedResourceId(new IdDt("Patient/3"));
 		deletedEntry.setDeleted(nowInstant);
 		
 		String bundleString = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
@@ -92,17 +92,17 @@ public class TransactionWithBundleParamTest {
 		assertEquals(3, bundle.size());
 
 		BundleEntry entry0 = bundle.getEntries().get(0);
-		assertEquals("http://localhost:" + ourPort + "/Patient/81", entry0.getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getResource().getId().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getLinkSelf().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/1", entry0.getLinkAlternate().getValue());
 		
 		BundleEntry entry1 = bundle.getEntries().get(1);
-		assertEquals("http://localhost:" + ourPort + "/Patient/82", entry1.getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getResource().getId().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getLinkSelf().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/2", entry1.getLinkAlternate().getValue());
 
 		BundleEntry entry2 = bundle.getEntries().get(2);
-		assertEquals("http://localhost:" + ourPort + "/Patient/3", entry2.getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getResource().getId().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getLinkSelf().getValue());
 		assertEquals(nowInstant.getValueAsString(), entry2.getDeletedAt().getValueAsString());
 }
@@ -118,17 +118,17 @@ public class TransactionWithBundleParamTest {
 		Patient p1 = new Patient();
 		p1.addName().addFamily("Family1");
 		BundleEntry entry = b.addEntry();
-		entry.getId().setValue("1");
+		p1.getId().setValue("1");
 		entry.setResource(p1);
 
 		Patient p2 = new Patient();
 		p2.addName().addFamily("Family2");
 		entry = b.addEntry();
-		entry.getId().setValue("2");
+		p2.getId().setValue("2");
 		entry.setResource(p2);
 		
 		BundleEntry deletedEntry = b.addEntry();
-		deletedEntry.setId(new IdDt("Patient/3"));
+		deletedEntry.setDeletedResourceId(new IdDt("Patient/3"));
 		deletedEntry.setDeleted(nowInstant);
 		
 		String bundleString = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
@@ -151,17 +151,17 @@ public class TransactionWithBundleParamTest {
 		assertEquals("OperationOutcome (no ID)", bundle.getEntries().get(0).getTitle().getValue());
 		
 		BundleEntry entry0 = bundle.getEntries().get(1);
-		assertEquals("http://localhost:" + ourPort + "/Patient/81", entry0.getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getResource().getId().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getLinkSelf().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/1", entry0.getLinkAlternate().getValue());
 		
 		BundleEntry entry1 = bundle.getEntries().get(2);
-		assertEquals("http://localhost:" + ourPort + "/Patient/82", entry1.getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getResource().getId().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getLinkSelf().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/2", entry1.getLinkAlternate().getValue());
 
 		BundleEntry entry2 = bundle.getEntries().get(3);
-		assertEquals("http://localhost:" + ourPort + "/Patient/3", entry2.getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getResource().getId().getValue());
 		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getLinkSelf().getValue());
 		assertEquals(nowInstant.getValueAsString(), entry2.getDeletedAt().getValueAsString());
 }

hapi-fhir-structures-dstu2/pom.xml

@@ -204,7 +204,7 @@
 						<!--<baseResourceName>assessmentdefinition</baseResourceName>-->
 						<baseResourceName>basic</baseResourceName>
 						<!--<baseResourceName>binary</baseResourceName>-->
-						<!--<baseResourceName>bundle</baseResourceName>-->
+						<baseResourceName>bundle</baseResourceName>
 						<!--<baseResourceName>careactivity</baseResourceName>-->
 						<baseResourceName>careplan</baseResourceName>
 						<baseResourceName>careplan2</baseResourceName>

hapi-fhir-structures-dstu2/src/main/resources/ca/uhn/fhir/model/dstu2/schema/fhir-all.xsd

@@ -26,7 +26,7 @@ Copyright (c) 2011+, HL7, Inc
  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
  POSSIBILITY OF SUCH DAMAGE.
 
- Generated on Sat, Feb 7, 2015 18:18+0000 for FHIR v0.4.0
+ Generated on Sat, Feb 14, 2015 16:12-0500 for FHIR v0.4.0
 -->
 <xs:schema xmlns="http://hl7.org/fhir" xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://hl7.org/fhir" elementFormDefault="qualified" version="0.4.0">
   <xs:include schemaLocation="alert.xsd"/>
@@ -122,6 +122,7 @@ Copyright (c) 2011+, HL7, Inc
   <xs:include schemaLocation="specimen.xsd"/>
   <xs:include schemaLocation="statusrequest.xsd"/>
   <xs:include schemaLocation="statusresponse.xsd"/>
+  <xs:include schemaLocation="structuredefinition.xsd"/>
   <xs:include schemaLocation="subscription.xsd"/>
   <xs:include schemaLocation="substance.xsd"/>
   <xs:include schemaLocation="supply.xsd"/>

hapi-fhir-structures-dstu2/src/main/resources/ca/uhn/fhir/model/dstu2/schema/fhir-base.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Sat, Feb 7, 2015 18:18+0000 for FHIR v0.4.0 
+  Generated on Sat, Feb 14, 2015 16:12-0500 for FHIR v0.4.0 
 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://hl7.org/fhir" xmlns:xhtml="http://www.w3.org/1999/xhtml" targetNamespace="http://hl7.org/fhir" elementFormDefault="qualified" version="0.4.0">
   <xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
@@ -351,6 +351,7 @@
       <xs:element ref="Specimen"/>
       <xs:element ref="StatusRequest"/>
       <xs:element ref="StatusResponse"/>
+      <xs:element ref="StructureDefinition"/>
       <xs:element ref="Subscription"/>
       <xs:element ref="Substance"/>
       <xs:element ref="Supply"/>
@@ -358,6 +359,7 @@
       <xs:element ref="ValueSet"/>
       <xs:element ref="VisionClaim"/>
       <xs:element ref="VisionPrescription"/>
+      <xs:element ref="Parameters"/>
     </xs:choice>
   </xs:complexType>
   <xs:complexType name="Extension">
@@ -2301,7 +2303,7 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
   </xs:complexType>
   <xs:complexType name="DomainResource">
     <xs:annotation>
-      <xs:documentation></xs:documentation>
+      <xs:documentation>A resource that includes narrative, extensions, and contained resources.</xs:documentation>
     </xs:annotation>
     <xs:complexContent>
       <xs:extension base="Resource">
@@ -2330,6 +2332,41 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
+  <xs:simpleType name="ExtensionContext-list">
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="resource">
+        <xs:annotation>
+          <xs:documentation>The context is all elements matching a particular resource element path.</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="datatype">
+        <xs:annotation>
+          <xs:documentation>The context is all nodes matching a particular data type element path (root or repeating element) or all elements referencing a particular primitive data type (expressed as the datatype name).</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="mapping">
+        <xs:annotation>
+          <xs:documentation>The context is all nodes whose mapping to a specified reference model corresponds to a particular mapping structure.  The context identifies the mapping target. The mapping should clearly identify where such an extension could be used.</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+      <xs:enumeration value="extension">
+        <xs:annotation>
+          <xs:documentation>The context is a particular extension from a particular profile.  Expressed as uri#name, where uri identifies the profile and #name identifies the extension code.</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
+    </xs:restriction>
+  </xs:simpleType>
+  <xs:complexType name="ExtensionContext">
+    <xs:annotation>
+      <xs:documentation></xs:documentation>
+      <xs:documentation>If the element is present, it must have either a @value, an @id, or extensions</xs:documentation>
+    </xs:annotation>
+    <xs:complexContent>
+       <xs:extension base="Element">
+         <xs:attribute name="value" type="ExtensionContext-list" use="optional"/>
+       </xs:extension>
+     </xs:complexContent>
+  </xs:complexType>
   <xs:simpleType name="DataAbsentReason-list">
     <xs:restriction base="xs:string">
       <xs:enumeration value="unknown">
@@ -2447,7 +2484,7 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>The value is no longer available</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
-      <xs:enumeration value="nil known">
+      <xs:enumeration value="nil-known">
         <xs:annotation>
           <xs:documentation>The are no known applicable values in this context</xs:documentation>
         </xs:annotation>
@@ -2717,7 +2754,7 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>The Patient is present for the encounter, however is not currently meeting with a practitioner.</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
-      <xs:enumeration value="in progress">
+      <xs:enumeration value="in-progress">
         <xs:annotation>
           <xs:documentation>The Encounter has begun and the patient is present / the practitioner and the patient are meeting.</xs:documentation>
         </xs:annotation>
@@ -2912,7 +2949,7 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>The specified property of the code is in the set of codes or concepts specified in the provided value (comma separated list).</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
-      <xs:enumeration value="not in">
+      <xs:enumeration value="not-in">
         <xs:annotation>
           <xs:documentation>The specified property of the code is not in the set of codes or concepts specified in the provided value (comma separated list).</xs:documentation>
         </xs:annotation>
@@ -2942,7 +2979,7 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>This reference has been superseded by another reference.</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
-      <xs:enumeration value="entered in error">
+      <xs:enumeration value="entered-in-error">
         <xs:annotation>
           <xs:documentation>This reference was created in error.</xs:documentation>
         </xs:annotation>
@@ -3727,6 +3764,11 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>This resource provides processing status, errors and notes from the processing of a resource.</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
+      <xs:enumeration value="StructureDefinition">
+        <xs:annotation>
+          <xs:documentation>A Resource Profile - a statement of use of one or more FHIR Resources.  It may include constraints on Resources and Data Types, Terminology Binding Statements and Extension Definitions.</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
       <xs:enumeration value="Subscription">
         <xs:annotation>
           <xs:documentation>Todo.</xs:documentation>
@@ -4372,6 +4414,11 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>This resource provides processing status, errors and notes from the processing of a resource.</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
+      <xs:enumeration value="StructureDefinition">
+        <xs:annotation>
+          <xs:documentation>A Resource Profile - a statement of use of one or more FHIR Resources.  It may include constraints on Resources and Data Types, Terminology Binding Statements and Extension Definitions.</xs:documentation>
+        </xs:annotation>
+      </xs:enumeration>
       <xs:enumeration value="Subscription">
         <xs:annotation>
           <xs:documentation>Todo.</xs:documentation>
@@ -4442,7 +4489,7 @@ P.O. Box number, delivery hints, and similar address information.</xs:documentat
           <xs:documentation>The composition or document has been modified subsequent to being released as &quot;final&quot;, and is complete and verified by an authorized person.</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
-      <xs:enumeration value="entered in error">
+      <xs:enumeration value="entered-in-error">
         <xs:annotation>
           <xs:documentation>The composition or document was originally created/issued in error, and this is an amendment that marks that the entire series should not be considered as valid.</xs:documentation>
         </xs:annotation>

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

@@ -94,14 +94,6 @@ public class JsonParserTest {
 			"   }],\n" + 
 			"   \"entry\" : [{\n" + 
 			"      \"base\" : \"http://foo/fhirBase2\",\n" +
-			"      \"search\" : {\n" +
-			"         \"mode\" : \"match\",\n" +
-			"         \"score\" : 0.123\n" +
-			"      },\n" +
-			"      \"transaction\" : {\n" +
-			"         \"operation\" : \"create\",\n" +
-			"         \"match\" : \"http://foo/Patient?identifier=value\"\n" +
-			"      },\n" +
 			"      \"resource\" : {\n" + 
 			"         \"resourceType\" : \"Patient\",\n" + 
 			"         \"id\" : \"1\",\n" + 
@@ -110,7 +102,15 @@ public class JsonParserTest {
 			"            \"lastUpdated\" : \"2001-02-22T11:22:33-05:00\"\n" +
 			"         },\n" + 
 			"         \"birthDate\" : \"2012-01-02\"\n" + 
-			"      }\n" + 
+			"      },\n" + 
+			"      \"search\" : {\n" +
+			"         \"mode\" : \"match\",\n" +
+			"         \"score\" : 0.123\n" +
+			"      },\n" +
+			"      \"transaction\" : {\n" +
+			"         \"operation\" : \"create\",\n" +
+			"         \"url\" : \"http://foo/Patient?identifier=value\"\n" +
+			"      }\n" +
 			"   }]\n" + 
 			"}";
 		//@formatter:on
@@ -201,6 +201,48 @@ public class JsonParserTest {
 		assertEquals(exp, act);
 
 	}
+
+	
+	@Test
+	public void testParseAndEncodeBundleNewStyle() throws Exception {
+		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-example.json"));
+
+		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = ourCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, content);
+		assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
+		assertEquals("1", parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.VERSION));
+		assertEquals("1", parsed.getId().getVersionIdPart());
+		assertEquals(new InstantDt("2014-08-18T01:43:30Z"), parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
+		assertEquals("searchset", parsed.getType());
+		assertEquals(3, parsed.getTotal().intValue());
+		assertEquals("http://example.com/base", parsed.getBaseElement().getValueAsString());
+		assertEquals("https://example.com/base/MedicationPrescription?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink().get(0).getUrlElement().getValueAsString());
+		assertEquals("https://example.com/base/MedicationPrescription?patient=347&_include=MedicationPrescription.medication", parsed.getLink().get(1).getUrlElement().getValueAsString());
+
+		assertEquals(2, parsed.getEntry().size());
+
+		MedicationPrescription p = (MedicationPrescription) parsed.getEntry().get(0).getResource();
+		assertEquals("Patient/347", p.getPatient().getReference().getValue());
+		assertEquals("2014-08-16T05:31:17Z", ResourceMetadataKeyEnum.UPDATED.get(p).getValueAsString());
+		assertEquals("http://example.com/base/MedicationPrescription/3123/_history/1", p.getId().getValue());
+
+		String reencoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed);
+		ourLog.info(reencoded);
+
+		JsonConfig cfg = new JsonConfig();
+
+		JSON expected = JSONSerializer.toJSON(content.trim(), cfg);
+		JSON actual = JSONSerializer.toJSON(reencoded.trim(), cfg);
+
+		String exp = expected.toString().replace("\\r\\n", "\\n"); // .replace("§", "§");
+		String act = actual.toString().replace("\\r\\n", "\\n");
+
+		ourLog.info("Expected: {}", exp);
+		ourLog.info("Actual  : {}", act);
+
+		assertEquals(exp, act);
+
+	}
+
 	
 	@Test
 	public void testParseAndEncodeNewExtensionFormat() {

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

@@ -85,6 +85,38 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testParseAndEncodeBundleNewStyle() throws Exception {
+		String content = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/bundle-example.xml"));
+
+		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, content);
+		assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
+		assertEquals("1", parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.VERSION));
+		assertEquals(new InstantDt("2014-08-18T01:43:30Z"), parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
+		assertEquals("searchset", parsed.getType());
+		assertEquals(3, parsed.getTotal().intValue());
+		assertEquals("http://example.com/base", parsed.getBaseElement().getValueAsString());
+		assertEquals("https://example.com/base/MedicationPrescription?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink().get(0).getUrlElement().getValueAsString());
+		assertEquals("https://example.com/base/MedicationPrescription?patient=347&_include=MedicationPrescription.medication", parsed.getLink().get(1).getUrlElement().getValueAsString());
+
+		assertEquals(2, parsed.getEntry().size());
+		assertEquals("http://foo?search", parsed.getEntry().get(0).getTransaction().getUrlElement().getValueAsString());
+
+		MedicationPrescription p = (MedicationPrescription) parsed.getEntry().get(0).getResource();
+		assertEquals("Patient/347", p.getPatient().getReference().getValue());
+		assertEquals("2014-08-16T05:31:17Z", ResourceMetadataKeyEnum.UPDATED.get(p).getValueAsString());
+		assertEquals("http://example.com/base/MedicationPrescription/3123/_history/1", p.getId().getValue());
+//		assertEquals("3123", p.getId().getValue());
+
+		String reencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
+		ourLog.info(reencoded);
+
+		Diff d = new Diff(new StringReader(content), new StringReader(reencoded));
+		assertTrue(d.toString(), d.identical());
+
+	}
+
+	
 	@Test
 	public void testEncodeAndParseBundleWithoutResourceIds() {
 		Organization org = new Organization();
@@ -144,14 +176,6 @@ public class XmlParserTest {
 			"   </link>\n" + 
 			"   <entry>\n" + 
 			"      <base value=\"http://foo/fhirBase2\"/>\n" + 
-			"      <search>\n" +
-			"         <mode value=\"match\"/>\n" +
-			"         <score value=\"0.123\"/>\n" +
-			"      </search>\n" +
-			"      <transaction>\n" +
-			"         <operation value=\"create\"/>\n" +
-			"         <match value=\"http://foo/Patient?identifier=value\"/>\n" +
-			"      </transaction>\n" +
 			"      <resource>\n" + 
 			"         <Patient xmlns=\"http://hl7.org/fhir\">\n" + 
 			"            <id value=\"1\"/>\n" + 
@@ -162,6 +186,14 @@ public class XmlParserTest {
 			"            <birthDate value=\"2012-01-02\"/>\n" + 
 			"         </Patient>\n" + 
 			"      </resource>\n" + 
+			"      <search>\n" +
+			"         <mode value=\"match\"/>\n" +
+			"         <score value=\"0.123\"/>\n" +
+			"      </search>\n" +
+			"      <transaction>\n" +
+			"         <operation value=\"create\"/>\n" +
+			"         <url value=\"http://foo/Patient?identifier=value\"/>\n" +
+			"      </transaction>\n" +
 			"   </entry>\n" + 
 			"</Bundle>";
 		//@formatter:on

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/TransactionWithBundleResourceParamTest.java

@@ -0,0 +1,234 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+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.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.rest.annotation.Transaction;
+import ca.uhn.fhir.rest.annotation.TransactionParam;
+import ca.uhn.fhir.util.PortUtil;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class TransactionWithBundleResourceParamTest {
+
+	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx = new FhirContext();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TransactionWithBundleResourceParamTest.class);
+	private static int ourPort;
+	private static boolean ourReturnOperationOutcome;
+
+	private static Server ourServer;
+	
+	
+	
+	@Before
+	public void before() {
+		ourReturnOperationOutcome = false;
+	}
+	
+	@Test
+	public void testTransaction() throws Exception {
+		Bundle b = new Bundle();
+		InstantDt nowInstant = InstantDt.withCurrentTime();
+		
+		Patient p1 = new Patient();
+		p1.addName().addFamily("Family1");
+		Entry entry = b.addEntry();
+		p1.getId().setValue("1");
+		entry.setResource(p1);
+
+		Patient p2 = new Patient();
+		p2.addName().addFamily("Family2");
+		entry = b.addEntry();
+		p2.getId().setValue("2");
+		entry.setResource(p2);
+		
+		Entry deletedEntry = b.addEntry();
+		deletedEntry.getTransaction().getMethodElement().setDeletedResourceId(new IdDt("Patient/3"));
+		deletedEntry.setDeleted(nowInstant);
+		
+		String bundleString = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
+		ourLog.info(bundleString);
+		
+		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/");
+		httpPost.addHeader("Accept", Constants.CT_ATOM_XML + "; pretty=true"); 
+		httpPost.setEntity(new StringEntity(bundleString, ContentType.create(Constants.CT_ATOM_XML, "UTF-8")));
+		HttpResponse status = ourClient.execute(httpPost);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		
+		ourLog.info(responseContent);
+		
+		Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
+		assertEquals(3, bundle.size());
+
+		BundleEntry entry0 = bundle.getEntries().get(0);
+		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getResource().getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getLinkSelf().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/1", entry0.getLinkAlternate().getValue());
+		
+		BundleEntry entry1 = bundle.getEntries().get(1);
+		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getResource().getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getLinkSelf().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/2", entry1.getLinkAlternate().getValue());
+
+		BundleEntry entry2 = bundle.getEntries().get(2);
+		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getResource().getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getLinkSelf().getValue());
+		assertEquals(nowInstant.getValueAsString(), entry2.getDeletedAt().getValueAsString());
+}
+	
+	
+	@Test
+	public void testTransactionWithOperationOutcome() throws Exception {
+		ourReturnOperationOutcome = true;
+		
+		Bundle b = new Bundle();
+		InstantDt nowInstant = InstantDt.withCurrentTime();
+		
+		Patient p1 = new Patient();
+		p1.addName().addFamily("Family1");
+		BundleEntry entry = b.addEntry();
+		p1.getId().setValue("1");
+		entry.setResource(p1);
+
+		Patient p2 = new Patient();
+		p2.addName().addFamily("Family2");
+		entry = b.addEntry();
+		p2.getId().setValue("2");
+		entry.setResource(p2);
+		
+		BundleEntry deletedEntry = b.addEntry();
+		deletedEntry.setDeletedResourceId(new IdDt("Patient/3"));
+		deletedEntry.setDeleted(nowInstant);
+		
+		String bundleString = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(bundleString);
+		
+		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/");
+		httpPost.addHeader("Accept", Constants.CT_ATOM_XML + "; pretty=true"); 
+		httpPost.setEntity(new StringEntity(bundleString, ContentType.create(Constants.CT_ATOM_XML, "UTF-8")));
+		HttpResponse status = ourClient.execute(httpPost);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		
+		ourLog.info(responseContent);
+		
+		Bundle bundle = new FhirContext().newXmlParser().parseBundle(responseContent);
+		assertEquals(4, bundle.size());
+
+		assertEquals(OperationOutcome.class, bundle.getEntries().get(0).getResource().getClass());
+		assertEquals("OperationOutcome (no ID)", bundle.getEntries().get(0).getTitle().getValue());
+		
+		BundleEntry entry0 = bundle.getEntries().get(1);
+		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getResource().getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/81/_history/91", entry0.getLinkSelf().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/1", entry0.getLinkAlternate().getValue());
+		
+		BundleEntry entry1 = bundle.getEntries().get(2);
+		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getResource().getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/82/_history/92", entry1.getLinkSelf().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/2", entry1.getLinkAlternate().getValue());
+
+		BundleEntry entry2 = bundle.getEntries().get(3);
+		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getResource().getId().getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/3/_history/93", entry2.getLinkSelf().getValue());
+		assertEquals(nowInstant.getValueAsString(), entry2.getDeletedAt().getValueAsString());
+}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		DummyProvider patientProvider = new DummyProvider();
+		RestfulServer server = new RestfulServer();
+		server.setProviders(patientProvider);
+		
+		org.eclipse.jetty.servlet.ServletContextHandler proxyHandler = new org.eclipse.jetty.servlet.ServletContextHandler();
+		proxyHandler.setContextPath("/");
+
+		ServletHolder handler = new ServletHolder();
+		handler.setServlet(server);
+		proxyHandler.addServlet(handler, "/*");
+
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+		
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+	
+	
+	
+	/**
+	 * Created by dsotnikov on 2/25/2014.
+	 */
+	public static class DummyProvider  {
+
+		@Transaction
+		public List<IResource> transaction(@TransactionParam Bundle theResources) {
+			int index=1;
+			for (IResource next : theResources.toListOfResources()) {
+				String newId = "8"+Integer.toString(index);
+				if (next.getResourceMetadata().containsKey(ResourceMetadataKeyEnum.DELETED_AT)) {
+					newId = next.getId().getIdPart();
+				}
+				next.setId(new IdDt("Patient", newId, "9"+Integer.toString(index)));
+				index++;
+			}
+			
+			List<IResource> retVal = theResources.toListOfResources();
+			if (ourReturnOperationOutcome) {
+				retVal = new ArrayList<IResource>();
+				OperationOutcome oo = new OperationOutcome();
+				oo.addIssue().setDetails("AAAAA");
+				retVal.add(oo);
+				retVal.addAll(theResources.toListOfResources());
+			}
+			
+			return retVal;
+		}
+
+	
+	}
+
+}

hapi-fhir-structures-dstu2/src/test/resources/bundle-example.json

@@ -20,10 +20,6 @@
   ],
   "entry": [
     {
-      "search": {
-        "mode": "match",
-        "score": 1
-      },
       "resource": {
         "resourceType": "MedicationPrescription",
         "id": "3123",
@@ -37,15 +33,19 @@
         "medication": {
           "reference": "Medication/example"
         }
+      },
+      "search": {
+        "mode": "match",
+        "score": 1
       }
     },
     {
-      "search": {
-        "mode": "include"
-      },
       "resource": {
         "resourceType": "Medication",
         "id": "example"
+      },
+      "search": {
+        "mode": "include"
       }
     }
   ]

hapi-fhir-structures-dstu2/src/test/resources/bundle-example.xml

@@ -3,7 +3,7 @@
   <meta>
     <versionId value="1"/> 
     <lastUpdated value="2014-08-18T01:43:30Z"/>
-  </meta> 
+  </meta>
   <type value="searchset"/>  
   <base value="http://example.com/base"/> 
   <total value="3"/>
@@ -16,13 +16,6 @@
     <url value="https://example.com/base/MedicationPrescription?patient=347&amp;_include=MedicationPrescription.medication"/>
   </link>
   <entry>
-    <search>
-      <mode value="match"/> 
-      <score value="1"/>
-    </search>
-    <transaction>
-      <match value="http://foo?search"/>
-    </transaction>
     <resource>
       <MedicationPrescription>
         <id value="3123"/>
@@ -38,15 +31,22 @@
         </medication>
       </MedicationPrescription>
     </resource>
+    <search>
+      <mode value="match"/> 
+      <score value="1"/>
+    </search>
+    <transaction>
+      <url value="http://foo?search"/>
+    </transaction>
   </entry>
   <entry>
-    <search>
-      <mode value="include"/> 
-    </search>
     <resource>
       <Medication>
         <id value="example"/>
       </Medication>
     </resource>
+    <search>
+      <mode value="include"/> 
+    </search>
   </entry>
 </Bundle>

hapi-fhir-structures-hl7org-dstu2/.classpath

@@ -13,6 +13,7 @@
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry kind="src" path="src/test/resources"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/model/Bundle.java

@@ -40,12 +40,13 @@ import org.hl7.fhir.instance.model.annotations.Child;
 import org.hl7.fhir.instance.model.annotations.Description;
 import org.hl7.fhir.instance.model.annotations.ResourceDef;
 import org.hl7.fhir.instance.model.annotations.SearchParamDefinition;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.utilities.Utilities;
 /**
  * A container for a group of resources.
  */
 @ResourceDef(name="Bundle", profile="http://hl7.org/fhir/Profile/Bundle")
-public class Bundle extends Resource {
+public class Bundle extends Resource implements IBaseBundle {
 
     public enum BundleType {
         /**

hapi-fhir-structures-hl7org-dstu2/src/test/resources/bundle-example.xml

@@ -0,0 +1,52 @@
+<Bundle xmlns="http://hl7.org/fhir">
+  <id value="example"/>
+  <meta>
+    <versionId value="1"/> 
+    <lastUpdated value="2014-08-18T01:43:30Z"/>
+  </meta>
+  <type value="searchset"/>  
+  <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&amp;_include=MedicationPrescription.medication"/>
+  </link>
+  <entry>
+    <resource>
+      <MedicationPrescription>
+        <id value="3123"/>
+        <meta>
+        	<versionId value="1"/>
+        	<lastUpdated value="2014-08-16T05:31:17Z"/>
+        </meta>
+        <patient>
+          <reference value="Patient/347"/>
+        </patient>
+        <medication>
+          <reference value="Medication/example"/>
+        </medication>
+      </MedicationPrescription>
+    </resource>
+    <search>
+      <mode value="match"/> 
+      <score value="1"/>
+    </search>
+    <transaction>
+      <url value="http://foo?search"/>
+    </transaction>
+  </entry>
+  <entry>
+    <resource>
+      <Medication>
+        <id value="example"/>
+      </Medication>
+    </resource>
+    <search>
+      <mode value="include"/> 
+    </search>
+  </entry>
+</Bundle>

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderJpaRestServerMojo.java

@@ -92,6 +92,9 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
 			}
 			for (String next : keys) {
 				if (next.startsWith("resource.")) {
+					if (next.endsWith(".Bundle")) {
+						continue;
+					}
 					baseResourceNames.add(next.substring("resource.".length()).toLowerCase());
 				}
 			}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/BaseElement.java

@@ -91,7 +91,7 @@ public abstract class BaseElement {
 		return toStringConstant(myDefinition);
 	}
 
-	private String toStringConstant(String theDefinition) {
+	static String toStringConstant(String theDefinition) {
 		if (theDefinition == null) {
 			return "";
 		}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/Child.java

@@ -129,6 +129,11 @@ public abstract class Child extends BaseElement {
 		// } else {
 		// retVal = (elemName + getTypeSuffix());
 		// }
+		
+		if (retVal.equals("ResourceDt")) {
+			retVal = "IResource";
+		}
+		
 		return retVal;
 	}
 

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/SearchParameter.java

@@ -40,7 +40,7 @@ public class SearchParameter {
 	}
 
 	public String getDescription() {
-		return StringUtils.defaultString(myDescription);
+		return BaseElement.toStringConstant(myDescription);
 	}
 
 	public String getFluentConstantName() {

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/BaseStructureParser.java

@@ -217,6 +217,9 @@ public abstract class BaseStructureParser {
 //		if ("ResourceReferenceDt".equals(theNextType)) {
 //			return "ca.uhn.fhir.model." + myVersion + ".composite." + ResourceReferenceDt.class.getSimpleName();
 //		}
+		if ("ResourceDt".equals(theNextType)) {
+			return IResource.class.getCanonicalName();
+		}
 		if ("Binary".equals(theNextType)) {
 			return "ca.uhn.fhir.model." + myVersion + ".resource." + Binary.class.getSimpleName();
 		}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/DatatypeGeneratorUsingSpreadsheet.java

@@ -102,6 +102,7 @@ public class DatatypeGeneratorUsingSpreadsheet extends BaseStructureSpreadsheetP
 		}
 		
 		if (!version.equals("dstu")) {			
+			retVal.add(("/dt/" + version + "/meta.xml"));
 			retVal.add(("/dt/" + version + "/attachment.xml"));
 			retVal.add(("/dt/" + version + "/contactpoint.xml"));
 			retVal.add(("/dt/" + version + "/elementdefinition.xml"));

hapi-tinder-plugin/src/main/resources/vm/jpa_resource_provider.vm

@@ -15,7 +15,8 @@ import ca.uhn.fhir.rest.annotation.*;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.model.dstu.resource.Binary;
- 
+// import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.api.Bundle;
 
 public class ${className}ResourceProvider extends JpaResourceProvider<${className}> {
 

hapi-tinder-plugin/src/main/resources/vm/resource.vm

@@ -40,7 +40,10 @@ import ${import};
  */
 @ResourceDef(name="${elementName}", profile="${profile}", id="${id}")
 public class ${className} extends ca.uhn.fhir.model.${version}.resource.BaseResource
-    implements #{if}( ${className}=="OperationOutcome" || ${className}=="Conformance" || ${className}=="SecurityEvent" ) ca.uhn.fhir.model.base.resource.Base${className} #{else} IResource #{end} 
+    implements #{if}( ${className}=="OperationOutcome" || ${className}=="Conformance" || ${className}=="SecurityEvent" ) ca.uhn.fhir.model.base.resource.Base${className} #{else} IResource #{end}
+#if ( ${className} == "Bundle" )
+    , org.hl7.fhir.instance.model.api.IBaseBundle
+#end
     {
 
 #foreach ( $param in $searchParams )

hapi-tinder-plugin/src/main/resources/vm/templates.vm

@@ -51,7 +51,20 @@
 	}
 
 #foreach ( $child in $childElements )
-#if ( $child.primitive && $child.repeatable == false )
+#if ( $child.referenceType == 'IResource' )
+	/**
+	 * Gets the value(s) for <b>${child.elementName}</b> ($esc.html(${child.shortName})).
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * $esc.html(${child.definition})
+     * </p> 
+	 */
+	public ${child.referenceType} get${child.methodName}() {  
+		return ${child.variableName};
+	}
+
+#elseif ( $child.primitive && $child.repeatable == false )
 	/**
 	 * Gets the value(s) for <b>${child.elementName}</b> ($esc.html(${child.shortName})).
 	 * creating it if it does

pom.xml

@@ -714,6 +714,7 @@
 				<module>hapi-fhir-structures-dstu2</module>
 				<module>hapi-fhir-structures-dev</module>
 				<module>hapi-fhir-jpaserver-base</module>
+				<module>hapi-fhir-jpaserver-example</module>
 				<module>restful-server-example</module>
 				<module>restful-server-example-test</module>
 				<module>hapi-fhir-testpage-overlay</module>