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

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

hapi-fhir-base/examples/.classpath

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<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"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-base"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

hapi-fhir-base/examples/.gitignore

@@ -0,0 +1 @@
+/target/

hapi-fhir-base/examples/.project

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+	<name>hapi-fhir-base-examples</name>
+	<comment></comment>
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+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
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hapi-fhir-base/examples/.settings/org.eclipse.core.resources.prefs

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+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding/<project>=UTF-8

hapi-fhir-base/examples/.settings/org.eclipse.jdt.core.prefs

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+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert
+org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.join_lines_in_comments=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.lineSplit=160
+org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
+org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
+org.eclipse.jdt.core.formatter.tabulation.char=space
+org.eclipse.jdt.core.formatter.tabulation.size=3
+org.eclipse.jdt.core.formatter.use_on_off_tags=false
+org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=true
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true

hapi-fhir-base/examples/.settings/org.eclipse.jdt.ui.prefs

@@ -0,0 +1,3 @@
+eclipse.preferences.version=1
+formatter_profile=_examples-format
+formatter_settings_version=12

hapi-fhir-base/examples/.settings/org.eclipse.m2e.core.prefs

@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

hapi-fhir-base/examples/pom.xml

@@ -0,0 +1,47 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir</artifactId>
+		<version>0.6-SNAPSHOT</version>
+		<relativePath>../../pom.xml</relativePath>
+	</parent>
+
+	<artifactId>hapi-fhir-base-examples</artifactId>
+	<packaging>jar</packaging>
+
+	<name>HAPI FHIR - Examples (for site)</name>
+
+	<dependencies>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>0.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<version>3.1.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>${junit_version}</version>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-deploy-plugin</artifactId>
+				<configuration>
+					<skip>true</skip>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+
+</project>

hapi-fhir-base/examples/src/main/java/example/ClientExamples.java

@@ -0,0 +1,89 @@
+package example;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.IRestfulClientFactory;
+import ca.uhn.fhir.rest.client.api.IBasicClient;
+import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.EncodingEnum;
+
+public class ClientExamples {
+
+   public interface IPatientClient extends IBasicClient {
+      // nothing yet
+   }
+
+   @SuppressWarnings("unused")
+   public void createProxy() {
+      // START SNIPPET: proxy
+      FhirContext ctx = new FhirContext();
+      ctx.getRestfulClientFactory().setProxy("example.com", 8888);
+
+      IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
+      // END SNIPPET: proxy
+   }
+
+   @SuppressWarnings("unused")
+   public void createSecurity() {
+      // START SNIPPET: security
+      // Create a context and get the client factory so it can be configured
+      FhirContext ctx = new FhirContext();
+      IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
+
+      // Create an HTTP basic auth interceptor
+      String username = "foobar";
+      String password = "boobear";
+      BasicAuthInterceptor authInterceptor = new BasicAuthInterceptor(username, password);
+
+      // Register the interceptor with your client (either style)
+      IPatientClient annotationClient = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/fhir");
+      annotationClient.registerInterceptor(authInterceptor);
+
+      IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
+      annotationClient.registerInterceptor(authInterceptor);
+      // END SNIPPET: security
+   }
+
+   @SuppressWarnings("unused")
+   public void createLogging() {
+      {
+         // START SNIPPET: logging
+         // Create a context and get the client factory so it can be configured
+         FhirContext ctx = new FhirContext();
+         IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
+
+         // Create a logging interceptor
+         LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
+
+         // Optionally you may configure the interceptor (by default only
+         // summary info is logged)
+         loggingInterceptor.setLogRequestSummary(true);
+         loggingInterceptor.setLogRequestBody(true);
+
+         // Register the interceptor with your client (either style)
+         IPatientClient annotationClient = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/fhir");
+         annotationClient.registerInterceptor(loggingInterceptor);
+
+         IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
+         genericClient.registerInterceptor(loggingInterceptor);
+         // END SNIPPET: logging
+      }
+
+      /******************************/
+      {
+         // START SNIPPET: clientConfig
+         // Create a client
+         FhirContext ctx = new FhirContext();
+         IPatientClient client = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/");
+
+         // Request JSON encoding from the server (_format=json)
+         client.setEncoding(EncodingEnum.JSON);
+
+         // Request pretty printing from the server (_pretty=true)
+         client.setPrettyPrint(true);
+         // END SNIPPET: clientConfig
+      }
+   }
+
+}

hapi-fhir-base/examples/src/main/java/example/CompleteExampleClient.java

@@ -0,0 +1,66 @@
+package example;
+
+//START SNIPPET: client
+import java.io.IOException;
+import java.util.List;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.client.api.IRestfulClient;
+
+public class CompleteExampleClient {
+
+   /**
+    * This is a simple client interface. It can have many methods for various
+    * searches but in this case it has only 1.
+    */
+   public static interface ClientInterface extends IRestfulClient {
+
+      /**
+       * This is translated into a URL similar to the following:
+       * http://fhir.healthintersections.com.au/open/Patient?identifier=urn:oid:1.2.36.146.595.217.0.1%7C12345
+       */
+      @Search
+      List<Patient> findPatientsForMrn(@RequiredParam(name = Patient.SP_IDENTIFIER) IdentifierDt theIdentifier);
+
+   }
+
+   /**
+    * The main method here will directly call an open FHIR server and retrieve a
+    * list of resources matching a given criteria, then load a linked resource.
+    */
+   public static void main(String[] args) throws IOException {
+
+      // Create a client factory
+      FhirContext ctx = new FhirContext();
+
+      // Create the client
+      String serverBase = "http://fhir.healthintersections.com.au/open";
+      ClientInterface client = ctx.newRestfulClient(ClientInterface.class, serverBase);
+
+      // Invoke the client to search for patient
+      List<Patient> patients = client.findPatientsForMrn(new IdentifierDt("urn:oid:1.2.36.146.595.217.0.1", "12345"));
+
+      System.out.println("Found " + patients.size() + " patients");
+
+      // Print a value from the loaded resource
+      Patient patient = patients.get(0);
+      System.out.println("Patient Last Name: " + patient.getName().get(0).getFamily().get(0).getValue());
+
+      // Load a referenced resource
+      ResourceReferenceDt managingRef = patient.getManagingOrganization();
+      Organization org = (Organization) managingRef.loadResource(client);
+
+      // Print organization name
+      System.out.println(org.getName().getValue());
+
+   }
+
+}
+// END SNIPPET: client
+

hapi-fhir-base/examples/src/main/java/example/GenericClientExample.java

@@ -17,22 +17,19 @@ import ca.uhn.fhir.rest.method.SearchStyleEnum;
 
 public class GenericClientExample {
 
-@SuppressWarnings("unused")
 public static void simpleExample() {
 // START SNIPPET: simple
 FhirContext ctx = new FhirContext();
-String serverBase = "http://fhir.healthintersections.com.au/open";
+String serverBase = "http://fhirtest.uhn.ca/base";
 IGenericClient client = ctx.newRestfulGenericClient(serverBase);
 
-// Read a patient
+// Perform a search
-Patient patient = client.read(Patient.class, "1");
+Bundle results = client.search()
+      .forResource(Patient.class)
+      .where(Patient.FAMILY.matches().value("duck"))
+      .execute();
 
-// Change the patient and update it to the server
+System.out.println("Found " + results.size() + " patients named 'duck'");
-patient.getNameFirstRep().getFamilyFirstRep().setValue("Jones");
-client.update("1", patient);
-
-// Return the version history for that patient
-Bundle versions = client.history(Patient.class, "1",null,null);
 // END SNIPPET: simple	
 }
 
@@ -177,7 +174,7 @@ List<IResource> response = client.transaction()
 }
 
 	public static void main(String[] args) {
-		// nothing
+		simpleExample();
 	}
 
 }

hapi-fhir-base/examples/src/main/java/example/MyPatientUse.java

@@ -0,0 +1,86 @@
+package example;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.DateTimeDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+
+public class MyPatientUse {
+
+   @ResourceDef
+   public static class MyPatient extends Patient {
+
+      @Child(name="petName")  
+      @Extension(url="http://example.com/dontuse#petname", definedLocally=false, isModifier=false)
+      @Description(shortDefinition="The name of the patient's favourite pet")
+      private StringDt myPetName;
+      
+      public StringDt getPetName() {
+         if(myPetName==null) {
+            myPetName = new StringDt();
+         }
+         return myPetName;
+      }
+
+      public void setPetName(StringDt thePetName) {
+         myPetName = thePetName;
+      }
+
+      public List<DateTimeDt> getImportantDates() {
+         if (myImportantDates==null) {
+            myImportantDates=new ArrayList<DateTimeDt>();
+         }
+         return myImportantDates;
+      }
+
+      public void setImportantDates(List<DateTimeDt> theImportantDates) {
+         myImportantDates = theImportantDates;
+      }
+
+      @Child(name="importantDates", max=Child.MAX_UNLIMITED)   
+      @Extension(url="http://example.com/dontuse#importantDates", definedLocally=false, isModifier=true)
+      @Description(shortDefinition="Some dates of note for the patient")
+      private List<DateTimeDt> myImportantDates;
+
+   }
+   
+@SuppressWarnings("unused")
+public static void main(String[] args) throws DataFormatException, IOException {
+//START SNIPPET: patientUse
+MyPatient patient = new MyPatient();
+patient.setPetName(new StringDt("Fido"));
+patient.getImportantDates().add(new DateTimeDt("2010-01-02"));
+patient.getImportantDates().add(new DateTimeDt("2014-01-26T11:11:11"));
+
+patient.addName().addFamily("Smith").addGiven("John").addGiven("Quincy").addSuffix("Jr");
+
+IParser p = new FhirContext().newXmlParser().setPrettyPrint(true);
+String messageString = p.encodeResourceToString(patient);
+
+System.out.println(messageString);
+//END SNIPPET: patientUse
+	
+//START SNIPPET: patientParse
+IParser parser = new FhirContext().newXmlParser();
+MyPatient newPatient = parser.parseResource(MyPatient.class, messageString);
+//END SNIPPET: patientParse
+
+{
+	FhirContext ctx2 = new FhirContext();
+	RuntimeResourceDefinition def = ctx2.getResourceDefinition(patient);
+	System.out.println(ctx2.newXmlParser().setPrettyPrint(true).encodeResourceToString(def.toProfile()));
+}
+}
+	
+}

hapi-fhir-base/examples/src/main/java/example/RestfulPatientResourceProviderMore.java

@@ -19,7 +19,7 @@ import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.model.api.annotation.TagListParam;
+import ca.uhn.fhir.rest.annotation.TagListParam;
 import ca.uhn.fhir.model.dstu.composite.CodingDt;
 import ca.uhn.fhir.model.dstu.resource.Conformance;
 import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
@@ -57,7 +57,6 @@ import ca.uhn.fhir.rest.annotation.Validate;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.client.ITestClient;
 import ca.uhn.fhir.rest.client.api.IBasicClient;
 import ca.uhn.fhir.rest.client.api.IRestfulClient;
 import ca.uhn.fhir.rest.param.CompositeParam;
@@ -78,6 +77,14 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 @SuppressWarnings("unused")
 public abstract class RestfulPatientResourceProviderMore implements IResourceProvider {
 
+   public interface ITestClient extends IBasicClient
+   {
+
+      @Search
+      List<Patient> getPatientByDob(@RequiredParam(name=Patient.SP_BIRTHDATE) DateParam theParam);
+      
+   }
+   
 private boolean detectedVersionConflict;
 private boolean conflictHappened;
 private boolean couldntFindThisId;

hapi-fhir-base/examples/src/main/java/example/ServerMetadataExamples.java

@@ -0,0 +1,56 @@
+package example;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.rest.annotation.Search;
+
+public class ServerMetadataExamples {
+
+   // START SNIPPET: serverMethod
+   @Search
+   public List<Patient> getAllPatients() {
+      ArrayList<Patient> retVal = new ArrayList<Patient>();
+      
+      // Create a patient to return
+      Patient patient = new Patient();
+      retVal.add(patient);
+      patient.setId("Patient/123");
+      patient.addName().addFamily("Smith").addGiven("John");
+      
+      // Create a tag list and add it to the resource
+      TagList tags = new TagList();
+      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag1.html", "Some tag");
+      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag2.html", "Another tag");
+      ResourceMetadataKeyEnum.TAG_LIST.put(patient, tags);
+      
+      // Set some links (these can be provided as relative links or absolute)
+      // and the server will convert to absolute as appropriate
+      String linkAlternate = "Patient/7736";
+      ResourceMetadataKeyEnum.LINK_ALTERNATE.put(patient, linkAlternate);
+      String linkSearch = "Patient?name=smith&name=john";
+      ResourceMetadataKeyEnum.LINK_SEARCH.put(patient, linkSearch);
+      
+      // Set the published and updated dates
+      InstantDt pubDate = new InstantDt("2011-02-22");
+      ResourceMetadataKeyEnum.PUBLISHED.put(patient, pubDate);
+      InstantDt updatedDate = new InstantDt("2014-07-12T11:22:27Z");
+      ResourceMetadataKeyEnum.UPDATED.put(patient, updatedDate);
+      
+      // Set the resource title (note that if you are using HAPI's narrative
+      // generation capability, the narrative generator will often create
+      // useful titles automatically, and the server will create a default
+      // title if none is provided)
+      String title = "Patient John SMITH";
+      ResourceMetadataKeyEnum.TITLE.put(patient, title);
+      
+      return retVal;
+   }
+   // END SNIPPET: serverMethod
+   
+}

hapi-fhir-base/examples/src/main/java/example/TagsExamples.java

@@ -0,0 +1,71 @@
+package example;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.client.IGenericClient;
+
+public class TagsExamples {
+
+   public static void main(String[] args) {
+      new TagsExamples().getResourceTags();
+   }
+
+   @SuppressWarnings("unused")
+   public void getResourceTags() {
+      // START SNIPPET: getResourceTags
+      IGenericClient client = new FhirContext().newRestfulGenericClient("http://fhir.healthintersections.com.au/open");
+      Patient p = client.read(Patient.class, "1");
+
+      // Retrieve the list of tags from the resource metadata
+      TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(p);
+
+      // tags may be null if no tags were read in
+      if (tags == null) {
+         System.out.println("No tags!");
+      } else {
+
+         // You may iterate over all the tags
+         for (Tag next : tags) {
+            System.out.println(next.getScheme() + " - " + next.getTerm());
+         }
+
+         // You may also get a list of tags matching a given scheme
+         List<Tag> someTags = tags.getTagsWithScheme("http://hl7.org/fhir/tag");
+         
+         // Or a specific tag (by scheme and term)
+         Tag specificTag = tags.getTag("http://hl7.org/fhir/tag", "http://foo");
+         
+      }
+      // END SNIPPET: getResourceTags
+   }
+
+   // START SNIPPET: serverMethod
+   @Search
+   public List<Patient> getAllPatients() {
+      ArrayList<Patient> retVal = new ArrayList<Patient>();
+      
+      // Create a patient to return
+      Patient patient = new Patient();
+      patient.setId("Patient/123");
+      patient.addName().addFamily("Smith").addGiven("John");
+      
+      // Create a tag list and add it to the resource
+      TagList tags = new TagList();
+      ResourceMetadataKeyEnum.TAG_LIST.put(patient, tags);
+
+      // Add some tags to the list
+      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag1.html", "Some tag");
+      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag2.html", "Another tag");
+      
+      return retVal;
+   }
+   // END SNIPPET: serverMethod
+   
+}

hapi-fhir-base/pom.xml

@@ -8,10 +8,10 @@
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
-	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-base</artifactId>
 	<packaging>jar</packaging>
-	<url>http://hl7api.sourceforge.net/hapi-fhir/</url>
+	
+	<url>http://jamesagnew.github.io/hapi-fhir/</url>
  
 	<name>HAPI FHIR - Core Library</name>
 
@@ -20,14 +20,11 @@
 			<id>git.server</id>
 			<url>scm:git:git@github.com:jamesagnew/hapi-fhir.git</url>
 		</site>
-
-		<!-- <site> <id>hl7api.sf.net</id> <url>scp://shell.sourceforge.net/home/project-web/hl7api/htdocs/hapi-fhir</url> </site> -->
 	</distributionManagement>
 
 	<dependencies>
 
 		<!-- JSON -->
-		<!-- <dependency> <groupId>com.google.code.gson</groupId> <artifactId>gson</artifactId> <version>2.2.4</version> </dependency> -->
 		<dependency>
 			<groupId>javax.json</groupId>
 			<artifactId>javax.json-api</artifactId>

hapi-fhir-base/src/changes/changes.xml

@@ -7,9 +7,11 @@
 	</properties>
 	<body>
 		<release version="0.6" date="TBD">
+			<!-- 
 			<action type="add">
 				Allow generic client  ... OAUTH
 			</action>
+			-->
 			<action type="fix">
 				Tester UI created double _format and _pretty param entries in searches. Thanks to Gered King of University
 				Health Network for reporting!   
@@ -72,14 +74,26 @@
 				is "yyyy-mm-dd" anyhow, and this is correctly handled). Thanks to Jeffrey Ting of Systems Made Simple
 				for reporting! 
 			</action>
-			<action type="add">
-				Server now adds a profile tag to returned results if the resource being returned
-				doesn't already have one			
-			</action>
 			<action type="fix">
 				Server search method for an unnamed query gets called if the client requests a named query
 				with the same parameter list. Thanks to Neal Acharya of University Health Network for reporting!			
 			</action>
+			<action type="fix">
+				Category header (for tags) is correctly read in client for "read" operation
+			</action>
+			<action type="add">
+				Transaction method in server can now have parameter type Bundle instead of
+				List&lt;IResource&gt;
+			</action>
+			<action type="add">
+				HAPI parsers now use field access to get/set values instead of method accessors and mutators.
+				This should give a small performance boost.
+			</action>
+			<action type="fix">
+				JSON parser encodes resource references incorrectly, using the name "resource" instead
+				of the name "reference" for the actual reference. Thanks to
+				Ricky Nguyen for reporting and tracking down the issue!
+			</action>
 		</release>
 		<release version="0.5" date="2014-Jul-30">
 			<action type="add">

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

@@ -204,8 +204,7 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
 				if (values == null) {
 					return Collections.emptyList();
 				}
-				@SuppressWarnings("unchecked")
+				List<? extends IElement> retVal = (List<? extends IElement>) Collections.singletonList((IElement)values);
-				List<? extends IElement> retVal = (List<? extends IElement>) Collections.singletonList(values);
 				return retVal;
 			} catch (IllegalArgumentException e) {
 				throw new ConfigurationException("Failed to get value", e);

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

@@ -585,24 +585,36 @@ class ModelScanner {
 	private String scanResource(Class<? extends IResource> theClass, ResourceDef resourceDefinition) {
 		ourLog.debug("Scanning resource class: {}", theClass.getName());
 
+		boolean primaryNameProvider = true;
 		String resourceName = resourceDefinition.name();
 		if (isBlank(resourceName)) {
-			throw new ConfigurationException("Resource type @" + ResourceDef.class.getSimpleName() + " annotation contains no resource name: " + theClass.getCanonicalName());
+			Class<?> parent = theClass.getSuperclass();
+			primaryNameProvider=false;
+			while (parent.equals(Object.class)==false && isBlank(resourceName)) {
+				ResourceDef nextDef = parent.getAnnotation(ResourceDef.class);
+				if (nextDef != null) {
+					resourceName = nextDef.name();
+				}
+				parent = parent.getSuperclass();
+			}
+			if (isBlank(resourceName)) {
+				throw new ConfigurationException("Resource type @" + ResourceDef.class.getSimpleName() + " annotation contains no resource name(): " + theClass.getCanonicalName() + " - This is only allowed for types that extend other resource types ");
+			}
 		}
 
-		if (myNameToResourceDefinitions.containsKey(resourceName)) {
+//		if (myNameToResourceDefinitions.containsKey(resourceName)) {
-			if (!myNameToResourceDefinitions.get(resourceName).getImplementingClass().equals(theClass)) {
+//			if (!myNameToResourceDefinitions.get(resourceName).getImplementingClass().equals(theClass)) {
-				// throw new
+//				// throw new
-				// ConfigurationException("Detected duplicate element name '" +
+//				// ConfigurationException("Detected duplicate element name '" +
-				// resourceName + "' in types '" + theClass.getCanonicalName() +
+//				// resourceName + "' in types '" + theClass.getCanonicalName() +
-				// "' and '"
+//				// "' and '"
-				// +
+//				// +
-				// myNameToResourceDefinitions.get(resourceName).getImplementingClass()
+//				// myNameToResourceDefinitions.get(resourceName).getImplementingClass()
-				// + "'");
+//				// + "'");
-			} else {
+//			} else {
-				return resourceName;
+//				return resourceName;
-			}
+//			}
-		}
+//		}
 
 		String resourceId = resourceDefinition.id();
 		if (isBlank(resourceId)) {
@@ -619,10 +631,11 @@ class ModelScanner {
 
 		String profile = resourceDefinition.profile();
 
-		RuntimeResourceDefinition resourceDef = new RuntimeResourceDefinition(theClass, resourceDefinition);
+		RuntimeResourceDefinition resourceDef = new RuntimeResourceDefinition(resourceName, theClass, resourceDefinition);
 		myClassToElementDefinitions.put(theClass, resourceDef);
+		if (primaryNameProvider) {
 			myNameToResourceDefinitions.put(resourceName, resourceDef);
-
+		}
 		scanCompositeElementForChildren(theClass, resourceDef);
 
 		myIdToResourceDefinition.put(resourceId, resourceDef);

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

@@ -34,6 +34,7 @@ import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 
 public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefinition {
 
@@ -103,6 +104,11 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
 			if (alternateElementName != null) {
 				myNameToChildDefinition.put(alternateElementName, nextDef);
 			}
+			
+			if (IResource.class.isAssignableFrom(next)) {
+				myDatatypeToElementDefinition.put(ResourceReferenceDt.class, nextDef);
+			}
+			
 			myDatatypeToElementDefinition.put(next, nextDef);
 			myDatatypeToElementName.put(next, elementName);
 		}

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

@@ -60,8 +60,8 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 	private List<RuntimeSearchParam> mySearchParams;
 	private String myId;
 
-	public RuntimeResourceDefinition(Class<? extends IResource> theClass, ResourceDef theResourceAnnotation) {
+	public RuntimeResourceDefinition(String theResourceName, Class<? extends IResource> theClass, ResourceDef theResourceAnnotation) {
-		super(theResourceAnnotation.name(), theClass);
+		super(theResourceName, theClass);
 		myResourceProfile = theResourceAnnotation.profile();
 		myId = theResourceAnnotation.id();
 	}

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

@@ -20,7 +20,7 @@ package ca.uhn.fhir.model.api;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.*;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -38,16 +38,12 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.UrlUtil;
 
 public class Bundle extends BaseBundle /* implements IElement */{
 
 	private volatile transient Map<IdDt, IResource> myIdToEntries;
 
-	//@formatter:off
-	/* ****************************************************
-	 * NB: add any new fields to the isEmpty() method!!!
-	 *****************************************************/
-	//@formatter:on
 	private List<BundleEntry> myEntries;
 	private StringDt myBundleId;
 	private StringDt myLinkBase;
@@ -60,6 +56,7 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	private StringDt myTitle;
 	private IntegerDt myTotalResults;
 	private InstantDt myUpdated;
+	private TagList myCategories;
 
 	/**
 	 * Returns true if this bundle contains zero entries
@@ -69,6 +66,16 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		return getEntries().isEmpty();
 	}
 
+	public Tag addCategory() {
+		Tag retVal = new Tag();
+		getCategories().add(retVal);
+		return retVal;
+	}
+
+	public void addCategory(Tag theTag) {
+		getCategories().add(theTag);
+	}
+
 	/**
 	 * Adds and returns a new bundle entry
 	 */
@@ -81,12 +88,15 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	/**
 	 * Retrieves a resource from a bundle given its logical ID.
 	 * <p>
-	 * <b>Important usage notes</b>: This method ignores base URLs (so passing in an ID of <code>http://foo/Patient/123</code> will return a resource if it has the logical ID of
+	 * <b>Important usage notes</b>: This method ignores base URLs (so passing in an ID of
-	 * <code>http://bar/Patient/123</code>. Also, this method is intended to be used for bundles which have already been populated. It will cache its results for fast performance, but that means that
+	 * <code>http://foo/Patient/123</code> will return a resource if it has the logical ID of
-	 * modifications to the bundle after this method is called may not be accurately reflected.
+	 * <code>http://bar/Patient/123</code>. Also, this method is intended to be used for bundles which have already been
+	 * populated. It will cache its results for fast performance, but that means that modifications to the bundle after
+	 * this method is called may not be accurately reflected.
 	 * </p>
 	 * 
-	 * @param theId The resource ID
+	 * @param theId
+	 *            The resource ID
 	 * @return Returns the resource with the given ID, or <code>null</code> if none is found
 	 */
 	public IResource getResourceById(IdDt theId) {
@@ -128,6 +138,18 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	// c.update().resource(txt).withId("1665").execute();
 	// }
 	//
+
+	public TagList getCategories() {
+		if (myCategories == null) {
+			myCategories = new TagList();
+		}
+		return myCategories;
+	}
+
+	public void setCategories(TagList theCategories) {
+		myCategories = theCategories;
+	}
+
 	public List<BundleEntry> getEntries() {
 		if (myEntries == null) {
 			myEntries = new ArrayList<BundleEntry>();
@@ -269,8 +291,6 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		BundleEntry entry = addEntry();
 		entry.setResource(theResource);
 
-		entry.setResource(theResource);
-
 		RuntimeResourceDefinition def = theContext.getResourceDefinition(theResource);
 
 		String title = ResourceMetadataKeyEnum.TITLE.get(theResource);
@@ -312,6 +332,24 @@ public class Bundle extends BaseBundle /* implements IElement */{
 			String qualifiedId = b.toString();
 			entry.getLinkSelf().setValue(qualifiedId);
 
+			// String resourceType = theContext.getResourceDefinition(theResource).getName();
+
+			String linkSearch = ResourceMetadataKeyEnum.LINK_SEARCH.get(theResource);
+			if (isNotBlank(linkSearch)) {
+				if (!UrlUtil.isAbsolute(linkSearch)) {
+					linkSearch = (theServerBase + "/" + linkSearch);
+				}
+				entry.getLinkSearch().setValue(linkSearch);
+			}
+
+			String linkAlternate = ResourceMetadataKeyEnum.LINK_ALTERNATE.get(theResource);
+			if (isNotBlank(linkAlternate)) {
+				if (!UrlUtil.isAbsolute(linkAlternate)) {
+					linkSearch = (theServerBase + "/" + linkAlternate);
+				}
+				entry.getLinkAlternate().setValue(linkSearch);
+			}
+
 		}
 
 		InstantDt published = ResourceMetadataKeyEnum.PUBLISHED.get(theResource);
@@ -346,9 +384,9 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		return entry;
 	}
 
-	public static Bundle withResources(ArrayList<IResource> theUploadBundle, FhirContext theContext, String theServerBase) {
+	public static Bundle withResources(List<IResource> theResources, FhirContext theContext, String theServerBase) {
 		Bundle retVal = new Bundle();
-		for (IResource next : theUploadBundle) {
+		for (IResource next : theResources) {
 			retVal.addResource(next, theContext, theServerBase);
 		}
 		return retVal;

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

@@ -197,6 +197,52 @@ public abstract class ResourceMetadataKeyEnum<T> {
 		}
 	};
 	
+	/**
+	 * If present and populated with a string, provides the "search link" (the link
+	 * element in the bundle entry with <code>rel="search"</code>). Server implementations
+	 * may populate this with a complete URL, in which case the URL will be
+	 * placed as-is in the bundle. They may alternately specify a
+	 * resource relative URL (e.g. "Patient?name=tester") in which case the
+	 * server will convert this to an absolute URL at runtime.  
+	 * <p>
+	 * Values for this key are of type <b>{@link String}</b>
+	 * </p>
+	 */
+	public static final ResourceMetadataKeyEnum<String> LINK_SEARCH = new ResourceMetadataKeyEnum<String>("LINK_SEARCH") {
+		@Override
+		public String get(IResource theResource) {
+			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_SEARCH);
+		}
+
+		@Override
+		public void put(IResource theResource, String theObject) {
+			theResource.getResourceMetadata().put(LINK_SEARCH, theObject);
+		}
+	};
+
+	/**
+	 * If present and populated with a string, provides the "alternate link" (the link
+	 * element in the bundle entry with <code>rel="alternate"</code>). Server implementations
+	 * may populate this with a complete URL, in which case the URL will be
+	 * placed as-is in the bundle. They may alternately specify a
+	 * resource relative URL (e.g. "Patient/1243") in which case the
+	 * server will convert this to an absolute URL at runtime.  
+	 * <p>
+	 * Values for this key are of type <b>{@link String}</b>
+	 * </p>
+	 */
+	public static final ResourceMetadataKeyEnum<String> LINK_ALTERNATE = new ResourceMetadataKeyEnum<String>("LINK_ALTERNATE") {
+		@Override
+		public String get(IResource theResource) {
+			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_ALTERNATE);
+		}
+
+		@Override
+		public void put(IResource theResource, String theObject) {
+			theResource.getResourceMetadata().put(LINK_ALTERNATE, theObject);
+		}
+	};
+	
 	private final String myValue;
 
 	public ResourceMetadataKeyEnum(String theValue) {

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

@@ -35,6 +35,18 @@ public class Tag extends BaseElement implements IElement {
 	 */
 	public static final String HL7_ORG_FHIR_TAG = "http://hl7.org/fhir/tag";
 
+	/**
+	 * Convenience constant containing the "http://hl7.org/fhir/tag/security" scheme
+	 * value
+	 */
+	public static final String HL7_ORG_SECURITY_TAG = "http://hl7.org/fhir/tag/security";
+
+	/**
+	 * Convenience constant containing the "http://hl7.org/fhir/tag/profile" scheme
+	 * value
+	 */
+	public static final String HL7_ORG_PROFILE_TAG = "http://hl7.org/fhir/tag/profile";
+
 	public static final String ATTR_TERM = "term";
 	public static final String ATTR_LABEL = "label";
 	public static final String ATTR_SCHEME = "scheme";

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.model.api;
  */
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class TagList extends ArrayList<Tag> {
 
@@ -48,7 +49,7 @@ public class TagList extends ArrayList<Tag> {
 		return null;
 	}
 
-	public ArrayList<Tag> getTagsWithScheme(String theScheme) {
+	public List<Tag> getTagsWithScheme(String theScheme) {
 		ArrayList<Tag> retVal = new ArrayList<Tag>();
 		for (Tag next : this) {
 			if (theScheme.equals(next.getScheme())) {

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

@@ -35,7 +35,7 @@ public @interface ResourceDef {
 	/**
 	 * The name of the resource (e.g. "Patient" or "DiagnosticReport")
 	 */
-	String name();
+	String name() default "";
 
 	/**
 	 * Not currently used

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/IdDt.java

@@ -34,6 +34,7 @@ import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.api.annotation.SimpleSetter;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.UrlUtil;
 
 /**
  * Represents the FHIR ID type. This is the actual resource ID, meaning the ID that will be used in RESTful URLs,
@@ -253,6 +254,14 @@ public class IdDt extends BasePrimitive<String> {
 		return isNotBlank(getVersionIdPart());
 	}
 
+	/**
+	 * Returns <code>true</code> if this ID contains an absolute URL (in other words, a URL starting with "http://" or
+	 * "https://"
+	 */
+	public boolean isAbsolute() {
+		return UrlUtil.isAbsolute(getValue());
+	}
+
 	/**
 	 * Returns <code>true</code> if the unqualified ID is a valid {@link Long} value (in other words, it consists only
 	 * of digits)

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/view/ViewGenerator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.model.view;
 
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import java.util.List;
 
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;

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

@@ -167,6 +167,8 @@ public class JsonParser extends BaseParser implements IParser {
 			eventWriter.writeEnd();
 		}
 		
+		writeCategories(eventWriter, theBundle.getCategories());
+
 		writeOptionalTagWithTextNode(eventWriter, "totalResults", theBundle.getTotalResults());
 
 		writeAuthor(theBundle, eventWriter);
@@ -193,17 +195,7 @@ public class JsonParser extends BaseParser implements IParser {
 			writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
 			writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
 
-			if (nextEntry.getCategories() != null && nextEntry.getCategories().size() > 0) {
+			writeCategories(eventWriter, nextEntry.getCategories());
-				eventWriter.writeStartArray("category");
-				for (Tag next : nextEntry.getCategories()) {
-					eventWriter.writeStartObject();
-					eventWriter.write("term", defaultString(next.getTerm()));
-					eventWriter.write("label", defaultString(next.getLabel()));
-					eventWriter.write("scheme", defaultString(next.getScheme()));
-					eventWriter.writeEnd();
-				}
-				eventWriter.writeEnd();
-			}
 
 			writeAuthor(nextEntry, eventWriter);
 
@@ -221,6 +213,20 @@ public class JsonParser extends BaseParser implements IParser {
 		eventWriter.flush();
 	}
 
+	private void writeCategories(JsonGenerator eventWriter, TagList categories) {
+		if (categories != null && categories.size() > 0) {
+			eventWriter.writeStartArray("category");
+			for (Tag next : categories) {
+				eventWriter.writeStartObject();
+				eventWriter.write("term", defaultString(next.getTerm()));
+				eventWriter.write("label", defaultString(next.getLabel()));
+				eventWriter.write("scheme", defaultString(next.getScheme()));
+				eventWriter.writeEnd();
+			}
+			eventWriter.writeEnd();
+		}
+	}
+
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theWriter, IElement theValue, BaseRuntimeElementDefinition<?> theChildDef,
 			String theChildName) throws IOException {
 
@@ -291,10 +297,10 @@ public class JsonParser extends BaseParser implements IParser {
 			}
 
 			if (StringUtils.isNotBlank(reference)) {
-				theWriter.write("resource", reference);
+				theWriter.write(XmlParser.RESREF_REFERENCE, reference);
 			}
 			if (referenceDt.getDisplay().isEmpty() == false) {
-				theWriter.write("display", referenceDt.getDisplay().getValueAsString());
+				theWriter.write(XmlParser.RESREF_DISPLAY, referenceDt.getDisplay().getValueAsString());
 			}
 			theWriter.writeEnd();
 			break;

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

@@ -20,8 +20,7 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.*;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -67,6 +66,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.IModelVisitor;
 
 class ParserState<T> {
 
@@ -474,6 +474,12 @@ class ParserState<T> {
 					metadata.put(ResourceMetadataKeyEnum.VERSION_ID, linkSelf);
 				}
 			}
+			if (!myEntry.getLinkAlternate().isEmpty()) {
+				ResourceMetadataKeyEnum.LINK_ALTERNATE.put(myEntry.getResource(), myEntry.getLinkAlternate().getValue());
+			}
+			if (!myEntry.getLinkSearch().isEmpty()) {
+				ResourceMetadataKeyEnum.LINK_SEARCH.put(myEntry.getResource(), myEntry.getLinkSearch().getValue());
+			}
 
 		}
 
@@ -622,6 +628,8 @@ class ParserState<T> {
 				push(new AtomPrimitiveState(myInstance.getUpdated()));
 			} else if ("author".equals(theLocalPart)) {
 				push(new AtomAuthorState(myInstance));
+			} else if ("category".equals(theLocalPart)) {
+				push(new AtomCategoryState(myInstance.getCategories().addTag()));
 			} else if ("deleted-entry".equals(theLocalPart) && verifyNamespace(XmlParser.TOMBSTONES_NS, theNamespaceURI)) {
 				push(new AtomDeletedEntryState(myInstance, myResourceType));
 			} else {
@@ -902,7 +910,7 @@ class ParserState<T> {
 		public void attributeValue(String theName, String theValue) throws DataFormatException {
 			if ("id".equals(theName)) {
 				if (myInstance instanceof IIdentifiableElement) {
-					((IIdentifiableElement) myInstance).setId(new IdDt(theValue));
+					((IIdentifiableElement) myInstance).setElementSpecificId((theValue));
 				} else if (myInstance instanceof IResource) {
 					((IResource) myInstance).setId(new IdDt(theValue));
 				}
@@ -1249,7 +1257,17 @@ class ParserState<T> {
 				myObject = (T) myInstance;
 			}
 
-			for (ResourceReferenceDt nextRef : myResourceReferences) {
+			myContext.newTerser().visit(myInstance, new IModelVisitor() {
+				
+				@Override
+				public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+					acceptElement(theNextExt.getValue(), null, null);
+				}
+				
+				@Override
+				public void acceptElement(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
+					if (theElement instanceof ResourceReferenceDt) {
+						ResourceReferenceDt nextRef = (ResourceReferenceDt)theElement;
 						String ref = nextRef.getReference().getValue();
 						if (isNotBlank(ref)) {
 							if (ref.startsWith("#")) {
@@ -1262,6 +1280,8 @@ class ParserState<T> {
 							}
 						}
 					}
+				}
+			});
 			
 		}
 

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

@@ -80,6 +80,8 @@ import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
 
 public class XmlParser extends BaseParser implements IParser {
+	static final String RESREF_DISPLAY = "display";
+	static final String RESREF_REFERENCE = "reference";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
 	static final String ATOM_NS = "http://www.w3.org/2005/Atom";
 	static final String FHIR_NS = "http://hl7.org/fhir";
@@ -144,6 +146,8 @@ public class XmlParser extends BaseParser implements IParser {
 				eventWriter.writeEndElement();
 			}
 
+			writeCategories(eventWriter, theBundle.getCategories());
+
 			for (BundleEntry nextEntry : theBundle.getEntries()) {
 				boolean deleted = false;
 				if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
@@ -182,15 +186,7 @@ public class XmlParser extends BaseParser implements IParser {
 				writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
 				writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
 
-				if (nextEntry.getCategories() != null) {
+				writeCategories(eventWriter, nextEntry.getCategories());
-					for (Tag next : nextEntry.getCategories()) {
-						eventWriter.writeStartElement("category");
-						eventWriter.writeAttribute("term", defaultString(next.getTerm()));
-						eventWriter.writeAttribute("label", defaultString(next.getLabel()));
-						eventWriter.writeAttribute("scheme", defaultString(next.getScheme()));
-						eventWriter.writeEndElement();
-					}
-				}
 
 				if (!nextEntry.getLinkSelf().isEmpty()) {
 					writeAtomLink(eventWriter, "self", nextEntry.getLinkSelf());
@@ -224,6 +220,18 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
+	private void writeCategories(XMLStreamWriter eventWriter,  TagList categories) throws XMLStreamException {
+		if (categories != null) {
+			for (Tag next : categories) {
+				eventWriter.writeStartElement("category");
+				eventWriter.writeAttribute("term", defaultString(next.getTerm()));
+				eventWriter.writeAttribute("label", defaultString(next.getLabel()));
+				eventWriter.writeAttribute("scheme", defaultString(next.getScheme()));
+				eventWriter.writeEndElement();
+			}
+		}
+	}
+
 	@Override
 	public String encodeResourceToString(IResource theResource) throws DataFormatException {
 		if (theResource == null) {
@@ -550,12 +558,12 @@ public class XmlParser extends BaseParser implements IParser {
 		// }
 
 		if (!(theRef.getDisplay().isEmpty())) {
-			theEventWriter.writeStartElement("display");
+			theEventWriter.writeStartElement(RESREF_DISPLAY);
 			theEventWriter.writeAttribute("value", theRef.getDisplay().getValue());
 			theEventWriter.writeEndElement();
 		}
 		if (StringUtils.isNotBlank(reference)) {
-			theEventWriter.writeStartElement("reference");
+			theEventWriter.writeStartElement(RESREF_REFERENCE);
 			theEventWriter.writeAttribute("value", reference);
 			theEventWriter.writeEndElement();
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/TransactionParam.java

@@ -24,7 +24,15 @@ import java.lang.annotation.ElementType;
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
 import java.lang.annotation.Target;
+import java.util.List;
 
+import ca.uhn.fhir.model.api.Bundle;
+
+/**
+ * Parameter annotation for the "transaction" operation. The parameter annotated with this
+ * annotation must be either of type <code>{@link Bundle}</code> or of type 
+ * <code>{@link List}&lt;IResource&gt;</code>
+ */
 @Target(value=ElementType.PARAMETER)
 @Retention(RetentionPolicy.RUNTIME)
 public @interface TransactionParam {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseOutcomeReturningMethodBinding.java

@@ -20,8 +20,6 @@ package ca.uhn.fhir.rest.method;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
-
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Writer;
@@ -39,7 +37,6 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.dstu.valueset.RestfulOperationTypeEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -54,9 +51,7 @@ import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
 abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<MethodOutcome> {
-	private static final String LABEL = "label=\"";
 	static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseOutcomeReturningMethodBinding.class);
-	private static final String SCHEME = "scheme=\"";
 
 	private boolean myReturnVoid;
 
@@ -118,7 +113,7 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
 			TagList tagList = new TagList();
 			for (Enumeration<String> enumeration = theRequest.getServletRequest().getHeaders(Constants.HEADER_CATEGORY); enumeration.hasMoreElements();) {
 				String nextTagComplete = enumeration.nextElement();
-				parseTagValue(tagList, nextTagComplete);
+				MethodUtil.parseTagValue(tagList, nextTagComplete);
 			}
 			if (tagList.isEmpty() == false) {
 				resource.getResourceMetadata().put(ResourceMetadataKeyEnum.TAG_LIST, tagList);
@@ -218,19 +213,25 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
 		// getMethod().in
 	}
 
-	static void parseTagValue(TagList tagList, String nextTagComplete) {
+	public boolean isReturnVoid() {
-		StringBuilder next = new StringBuilder(nextTagComplete);
+		return myReturnVoid;
-		parseTagValue(tagList, nextTagComplete, next);
 	}
 
-	/**
+	private void addLocationHeader(Request theRequest, HttpServletResponse theResponse, MethodOutcome response) {
-	 * @throws IOException
+		StringBuilder b = new StringBuilder();
-	 */
+		b.append(theRequest.getFhirServerBase());
-	protected IResource parseIncomingServerResource(Request theRequest) throws IOException {
+		b.append('/');
-		EncodingEnum encoding = RestfulServer.determineRequestEncoding(theRequest);
+		b.append(getResourceName());
-		IParser parser = encoding.newParser(getContext());
+		b.append('/');
-		IResource resource = parser.parseResource(theRequest.getServletRequest().getReader());
+		b.append(response.getId().getIdPart());
-		return resource;
+		if (response.getId().hasVersionIdPart()) {
+			b.append("/" + Constants.PARAM_HISTORY + "/");
+			b.append(response.getId().getVersionIdPart());
+		} else if (response.getVersionId() != null && response.getVersionId().isEmpty() == false) {
+			b.append("/" + Constants.PARAM_HISTORY + "/");
+			b.append(response.getVersionId().getValue());
+		}
+		theResponse.addHeader(Constants.HEADER_LOCATION, b.toString());
 	}
 
 	/*
@@ -257,99 +258,6 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
 	 * encoding.newParser(getContext()); parser.encodeResourceToWriter(outcome, writer); } } finally { writer.close(); } // getMethod().in }
 	 */
 
-	public boolean isReturnVoid() {
-		return myReturnVoid;
-	}
-
-	private void addLocationHeader(Request theRequest, HttpServletResponse theResponse, MethodOutcome response) {
-		StringBuilder b = new StringBuilder();
-		b.append(theRequest.getFhirServerBase());
-		b.append('/');
-		b.append(getResourceName());
-		b.append('/');
-		b.append(response.getId().getIdPart());
-		if (response.getId().hasVersionIdPart()) {
-			b.append("/" + Constants.PARAM_HISTORY + "/");
-			b.append(response.getId().getVersionIdPart());
-		} else if (response.getVersionId() != null && response.getVersionId().isEmpty() == false) {
-			b.append("/" + Constants.PARAM_HISTORY + "/");
-			b.append(response.getVersionId().getValue());
-		}
-		theResponse.addHeader(Constants.HEADER_LOCATION, b.toString());
-	}
-
-	private static void parseTagValue(TagList theTagList, String theCompleteHeaderValue, StringBuilder theBuffer) {
-		int firstSemicolon = theBuffer.indexOf(";");
-		int deleteTo;
-		if (firstSemicolon == -1) {
-			firstSemicolon = theBuffer.indexOf(",");
-			if (firstSemicolon == -1) {
-				firstSemicolon = theBuffer.length();
-				deleteTo = theBuffer.length();
-			} else {
-				deleteTo = firstSemicolon;
-			}
-		} else {
-			deleteTo = firstSemicolon + 1;
-		}
-
-		String term = theBuffer.substring(0, firstSemicolon);
-		String scheme = null;
-		String label = null;
-		if (isBlank(term)) {
-			return;
-		}
-
-		theBuffer.delete(0, deleteTo);
-		while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
-			theBuffer.deleteCharAt(0);
-		}
-
-		while (theBuffer.length() > 0) {
-			boolean foundSomething = false;
-			if (theBuffer.length() > SCHEME.length() && theBuffer.substring(0, SCHEME.length()).equals(SCHEME)) {
-				int closeIdx = theBuffer.indexOf("\"", SCHEME.length());
-				scheme = theBuffer.substring(SCHEME.length(), closeIdx);
-				theBuffer.delete(0, closeIdx + 1);
-				foundSomething = true;
-			}
-			if (theBuffer.length() > LABEL.length() && theBuffer.substring(0, LABEL.length()).equals(LABEL)) {
-				int closeIdx = theBuffer.indexOf("\"", LABEL.length());
-				label = theBuffer.substring(LABEL.length(), closeIdx);
-				theBuffer.delete(0, closeIdx + 1);
-				foundSomething = true;
-			}
-			// TODO: support enc2231-string as described in
-			// http://tools.ietf.org/html/draft-johnston-http-category-header-02
-			// TODO: support multiple tags in one header as described in
-			// http://hl7.org/implement/standards/fhir/http.html#tags
-
-			while (theBuffer.length() > 0 && (theBuffer.charAt(0) == ' ' || theBuffer.charAt(0) == ';')) {
-				theBuffer.deleteCharAt(0);
-			}
-
-			if (!foundSomething) {
-				break;
-			}
-		}
-
-		if (theBuffer.length() > 0 && theBuffer.charAt(0) == ',') {
-			theBuffer.deleteCharAt(0);
-			while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
-				theBuffer.deleteCharAt(0);
-			}
-			theTagList.add(new Tag(scheme, term, label));
-			parseTagValue(theTagList, theCompleteHeaderValue, theBuffer);
-		} else {
-			theTagList.add(new Tag(scheme, term, label));
-		}
-
-		if (theBuffer.length() > 0) {
-			ourLog.warn("Ignoring extra text at the end of " + Constants.HEADER_CATEGORY + " tag '" + theBuffer.toString() + "' - Complete tag value was: " + theCompleteHeaderValue);
-		}
-
-	}
-
 	protected abstract void addParametersForServerRequest(Request theRequest, Object[] theParams);
 
 	/**
@@ -366,6 +274,16 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
 	 */
 	protected abstract String getMatchingOperation();
 
+	/**
+	 * @throws IOException
+	 */
+	protected IResource parseIncomingServerResource(Request theRequest) throws IOException {
+		EncodingEnum encoding = RestfulServer.determineRequestEncoding(theRequest);
+		IParser parser = encoding.newParser(getContext());
+		IResource resource = parser.parseResource(theRequest.getServletRequest().getReader());
+		return resource;
+	}
+
 	protected abstract Set<RequestType> provideAllowableRequestTypes();
 
 	/**
@@ -425,4 +343,5 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
 		}
 	}
 
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/MethodUtil.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.rest.method;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.*;
 
 import java.io.IOException;
 import java.io.PushbackReader;
@@ -79,6 +79,8 @@ import ca.uhn.fhir.util.ReflectionUtil;
  */
 
 public class MethodUtil {
+	private static final String LABEL = "label=\"";
+	private static final String SCHEME = "scheme=\"";
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MethodUtil.class);
 
@@ -132,7 +134,94 @@ public class MethodUtil {
 			String headerValue = clHeaders.get(0);
 			resource.getId().setValue(headerValue);
 		}
+		
+		List<String> categoryHeaders = theHeaders.get(Constants.HEADER_CATEGORY_LC);
+		if (categoryHeaders != null && categoryHeaders.size() > 0 && StringUtils.isNotBlank(categoryHeaders.get(0))) {
+			TagList tagList = new TagList();
+			for (String header : categoryHeaders) {
+				parseTagValue(tagList, header);
 			}
+			ResourceMetadataKeyEnum.TAG_LIST.put(resource, tagList);
+		}
+	}
+
+	public static void parseTagValue(TagList tagList, String nextTagComplete) {
+		StringBuilder next = new StringBuilder(nextTagComplete);
+		parseTagValue(tagList, nextTagComplete, next);
+	}
+
+	private static void parseTagValue(TagList theTagList, String theCompleteHeaderValue, StringBuilder theBuffer) {
+		int firstSemicolon = theBuffer.indexOf(";");
+		int deleteTo;
+		if (firstSemicolon == -1) {
+			firstSemicolon = theBuffer.indexOf(",");
+			if (firstSemicolon == -1) {
+				firstSemicolon = theBuffer.length();
+				deleteTo = theBuffer.length();
+			} else {
+				deleteTo = firstSemicolon;
+			}
+		} else {
+			deleteTo = firstSemicolon + 1;
+		}
+
+		String term = theBuffer.substring(0, firstSemicolon);
+		String scheme = null;
+		String label = null;
+		if (isBlank(term)) {
+			return;
+		}
+
+		theBuffer.delete(0, deleteTo);
+		while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
+			theBuffer.deleteCharAt(0);
+		}
+
+		while (theBuffer.length() > 0) {
+			boolean foundSomething = false;
+			if (theBuffer.length() > SCHEME.length() && theBuffer.substring(0, SCHEME.length()).equals(SCHEME)) {
+				int closeIdx = theBuffer.indexOf("\"", SCHEME.length());
+				scheme = theBuffer.substring(SCHEME.length(), closeIdx);
+				theBuffer.delete(0, closeIdx + 1);
+				foundSomething = true;
+			}
+			if (theBuffer.length() > LABEL.length() && theBuffer.substring(0, LABEL.length()).equals(LABEL)) {
+				int closeIdx = theBuffer.indexOf("\"", LABEL.length());
+				label = theBuffer.substring(LABEL.length(), closeIdx);
+				theBuffer.delete(0, closeIdx + 1);
+				foundSomething = true;
+			}
+			// TODO: support enc2231-string as described in
+			// http://tools.ietf.org/html/draft-johnston-http-category-header-02
+			// TODO: support multiple tags in one header as described in
+			// http://hl7.org/implement/standards/fhir/http.html#tags
+
+			while (theBuffer.length() > 0 && (theBuffer.charAt(0) == ' ' || theBuffer.charAt(0) == ';')) {
+				theBuffer.deleteCharAt(0);
+			}
+
+			if (!foundSomething) {
+				break;
+			}
+		}
+
+		if (theBuffer.length() > 0 && theBuffer.charAt(0) == ',') {
+			theBuffer.deleteCharAt(0);
+			while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
+				theBuffer.deleteCharAt(0);
+			}
+			theTagList.add(new Tag(scheme, term, label));
+			parseTagValue(theTagList, theCompleteHeaderValue, theBuffer);
+		} else {
+			theTagList.add(new Tag(scheme, term, label));
+		}
+
+		if (theBuffer.length() > 0) {
+			ourLog.warn("Ignoring extra text at the end of " + Constants.HEADER_CATEGORY + " tag '" + theBuffer.toString() + "' - Complete tag value was: " + theCompleteHeaderValue);
+		}
+
+	}
+
 	
 	static void addTagsToPostOrPut(IResource resource, BaseHttpClientInvocation retVal) {
 		TagList list = (TagList) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/TransactionMethodBinding.java

@@ -20,11 +20,11 @@ package ca.uhn.fhir.rest.method;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.*;
 
 import java.io.IOException;
 import java.lang.reflect.Method;
-import java.util.ArrayList;
+import java.util.IdentityHashMap;
 import java.util.List;
 
 import ca.uhn.fhir.context.ConfigurationException;
@@ -72,7 +72,6 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 		return RestfulOperationSystemEnum.TRANSACTION;
 	}
 
-
 	@Override
 	public boolean incomingServerRequestMatchesMethod(Request theRequest) {
 		if (theRequest.getRequestType() != RequestType.POST) {
@@ -95,16 +94,24 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 	@SuppressWarnings("unchecked")
 	@Override
 	public IBundleProvider invokeServer(Request theRequest, Object[] theMethodParams) throws InvalidRequestException, InternalErrorException {
-		List<IResource> resources = (List<IResource>) theMethodParams[myTransactionParamIndex];
+		// Grab the IDs of all of the resources in the transaction
-		
+		List<IResource> resources;
-		List<IdDt> oldIds= new ArrayList<IdDt>();
+		if (theMethodParams[myTransactionParamIndex] instanceof Bundle) {
-		for (IResource next : resources) {
+			resources = ((Bundle) theMethodParams[myTransactionParamIndex]).toListOfResources();
-			oldIds.add(next.getId());
+		} else {
+			resources = (List<IResource>) theMethodParams[myTransactionParamIndex];
 		}
 		
+		IdentityHashMap<IResource, IdDt> oldIds = new IdentityHashMap<IResource, IdDt>();
+		for (IResource next : resources) {
+			oldIds.put(next, next.getId());
+		}
+
+		// Call the server implementation method
 		Object response = invokeServerMethod(theMethodParams);
 		IBundleProvider retVal = toResourceList(response);
 
+		/*
 		int offset = 0;
 		if (retVal.size() != resources.size()) {
 			if (retVal.size() > 0 && retVal.getResources(0, 1).get(0) instanceof OperationOutcome) {
@@ -113,14 +120,17 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 				throw new InternalErrorException("Transaction bundle contained " + resources.size() + " entries, but server method response contained " + retVal.size() + " entries (must be the same)");
 			}
 		}
+		 */
 		
-		List<IResource> retResources = retVal.getResources(offset, retVal.size()); 
+		List<IResource> retResources = retVal.getResources(0, retVal.size());
-		for (int i =0; i < resources.size(); i++) {
+		for (int i = 0; i < retResources.size(); i++) {
-			IdDt oldId = oldIds.get(i);
+			IdDt oldId = oldIds.get(retResources.get(i));
 			IResource newRes = retResources.get(i);
 			if (newRes.getId() == null || newRes.getId().isEmpty()) {
+				if (!(newRes instanceof OperationOutcome)) {
 					throw new InternalErrorException("Transaction method returned resource at index " + i + " with no id specified - IResource#setId(IdDt)");
 				}
+			}
 
 			if (oldId != null && !oldId.isEmpty()) {
 				if (!oldId.equals(newRes.getId())) {
@@ -130,6 +140,9 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 		}
 
 		return retVal;
+
+		
+		
 			}
 
 	@Override
@@ -147,12 +160,16 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 
 	@Override
 	public BaseHttpClientInvocation invokeClient(Object[] theArgs) throws InternalErrorException {
+		FhirContext context = getContext();
+		if (theArgs[myTransactionParamIndex] instanceof Bundle) {
+			Bundle bundle = (Bundle) theArgs[myTransactionParamIndex];
+			return createTransactionInvocation(bundle, context);
+		} else {
 			@SuppressWarnings("unchecked")
 			List<IResource> resources = (List<IResource>) theArgs[myTransactionParamIndex];
-		FhirContext context = getContext();
-		
 			return createTransactionInvocation(resources, context);
 		}
+	}
 
 	public static BaseHttpClientInvocation createTransactionInvocation(List<IResource> theResources, FhirContext theContext) {
 		return new HttpPostClientInvocation(theContext, theResources);

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/TransactionParamBinder.java

@@ -38,6 +38,8 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 class TransactionParamBinder implements IParameter {
 
+	private boolean myParamIsBundle;
+
 	public TransactionParamBinder() {
 	}
 
@@ -50,6 +52,9 @@ class TransactionParamBinder implements IParameter {
 	@Override
 	public Object translateQueryParametersIntoServerArgument(Request theRequest, Object theRequestContents) throws InternalErrorException, InvalidRequestException {
 		Bundle resource = (Bundle) theRequestContents;
+		if (myParamIsBundle) {
+			return resource;
+		}
 
 		ArrayList<IResource> retVal = new ArrayList<IResource>();
 		for (BundleEntry next : resource.getEntries()) {
@@ -66,11 +71,22 @@ class TransactionParamBinder implements IParameter {
 		if (theOuterCollectionType != null) {
 			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + TransactionParam.class.getName() + " but can not be a collection of collections");
 		}
+		if (theParameterType.equals(Bundle.class)) {
+			myParamIsBundle=true;
+			if (theInnerCollectionType!=null) {
+				throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + TransactionParam.class.getName() + " but is not of type List<" + IResource.class.getCanonicalName()
+						+ "> or Bundle");
+			}
+		} else {
+			myParamIsBundle=false;
 			if (theInnerCollectionType.equals(List.class) == false) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + TransactionParam.class.getName() + " but is not of type List<" + IResource.class.getCanonicalName()+">");
+				throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + TransactionParam.class.getName() + " but is not of type List<" + IResource.class.getCanonicalName()
+						+ "> or Bundle");
 			}
 			if (theParameterType.equals(IResource.class) == false) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + TransactionParam.class.getName() + " but is not of type List<" + IResource.class.getCanonicalName()+">");
+				throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + TransactionParam.class.getName() + " but is not of type List<" + IResource.class.getCanonicalName()
+						+ "> or Bundle");
+			}
 		}
 	}
 

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.param;
 
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.server.Constants;
 

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

@@ -48,6 +48,7 @@ public class Constants {
 	public static final String HEADER_ACCEPT_ENCODING = "Accept-Encoding";
 	public static final String HEADER_AUTHORIZATION = "Authorization";
 	public static final String HEADER_CATEGORY = "Category";
+	public static final String HEADER_CATEGORY_LC = HEADER_CATEGORY.toLowerCase();
 	public static final String HEADER_CONTENT_DISPOSITION = "Content-Disposition";
 	public static final String HEADER_CONTENT_ENCODING = "Content-Encoding";
 	public static final String HEADER_CONTENT_LOCATION = "Content-Location";
@@ -97,8 +98,6 @@ public class Constants {
 	public static final int STATUS_HTTP_500_INTERNAL_ERROR = 500;
 	public static final int STATUS_HTTP_501_NOT_IMPLEMENTED = 501;
 	public static final String URL_TOKEN_HISTORY = "_history";
-	public static final String TAG_SCHEME_PROFILE = "http://hl7.org/fhir/tag/profile	";
-	
 
 	static {
 		Map<String, EncodingEnum> valToEncoding = new HashMap<String, EncodingEnum>();

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

@@ -856,8 +856,8 @@ public class RestfulServer extends HttpServlet {
 				
 			} while (references.isEmpty() == false);
 			
-			BundleEntry entry = bundle.addResource(next, theContext, theServerBase);
+			bundle.addResource(next, theContext, theServerBase);
-			addProfileToBundleEntry(theContext, next, entry);
+//			addProfileToBundleEntry(theContext, next, entry);
 			
 		}
 
@@ -865,24 +865,26 @@ public class RestfulServer extends HttpServlet {
 		 * Actually add the resources to the bundle
 		 */
 		for (IResource next : addedResources) {
-			BundleEntry entry = bundle.addResource(next, theContext, theServerBase);
+			bundle.addResource(next, theContext, theServerBase);
-			addProfileToBundleEntry(theContext, next, entry);
+//			addProfileToBundleEntry(theContext, next, entry);
 		}
 
 		bundle.getTotalResults().setValue(theTotalResults);
 		return bundle;
 	}
 
+	/*
 	private static void addProfileToBundleEntry(FhirContext theContext, IResource next, BundleEntry entry) {
-		ArrayList<Tag> profileTags = entry.getCategories().getTagsWithScheme(Constants.TAG_SCHEME_PROFILE);
+		List<Tag> profileTags = entry.getCategories().getTagsWithScheme(Tag.HL7_ORG_PROFILE_TAG);
 		if (profileTags.isEmpty()) {
 			RuntimeResourceDefinition nextDef = theContext.getResourceDefinition(next);
 			String profile = nextDef.getResourceProfile();
 			if (isNotBlank(profile)) {
-				entry.addCategory(new Tag(Constants.TAG_SCHEME_PROFILE, profile, null));
+				entry.addCategory(new Tag(Tag.HL7_ORG_PROFILE_TAG, profile, null));
 			}
 		}
 	}
+	*/
 	
 	public static String createPagingLink(String theServerBase, String theSearchId, int theOffset, int theCount, EncodingEnum theResponseEncoding, boolean thePrettyPrint) {
 		StringBuilder b = new StringBuilder();

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

@@ -1,7 +1,5 @@
 package ca.uhn.fhir.rest.server.exceptions;
 
-import java.text.ParseException;
-
 import ca.uhn.fhir.rest.server.Constants;
 
 /*
@@ -41,7 +39,7 @@ public class AuthenticationException extends BaseServerResponseException {
 		super(STATUS_CODE, theMessage);
 	}
 
-	public AuthenticationException(String theMessage, ParseException theCause) {
+	public AuthenticationException(String theMessage, Throwable theCause) {
 		super(STATUS_CODE, theMessage, theCause);
 	}
 

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

@@ -27,9 +27,8 @@ import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
  */
 
 /**
- * Base class for RESTful client and server exceptions. RESTful client methods
+ * Base class for RESTful client and server exceptions. RESTful client methods will only throw exceptions which are
- * will only throw exceptions which are subclasses of this exception type, and
+ * subclasses of this exception type, and RESTful server methods should also only call subclasses of this exception
- * RESTful server methods should also only call subclasses of this exception
  * type.
  */
 public abstract class BaseServerResponseException extends RuntimeException {
@@ -50,10 +49,8 @@ public abstract class BaseServerResponseException extends RuntimeException {
 	}
 
 	private final OperationOutcome myOperationOutcome;
-
 	private String myResponseBody;
 	private String myResponseMimeType;
-
 	private int myStatusCode;
 
 	/**
@@ -77,6 +74,9 @@ public abstract class BaseServerResponseException extends RuntimeException {
 	 *            The HTTP status code corresponding to this problem
 	 * @param theMessage
 	 *            The message
+	 * @param theOperationOutcome
+	 *            An OperationOutcome resource to return to the calling client (in a server) or the OperationOutcome
+	 *            that was returned from the server (in a client)
 	 */
 	public BaseServerResponseException(int theStatusCode, String theMessage, OperationOutcome theOperationOutcome) {
 		super(theMessage);
@@ -100,6 +100,25 @@ public abstract class BaseServerResponseException extends RuntimeException {
 		myOperationOutcome = null;
 	}
 
+	/**
+	 * Constructor
+	 * 
+	 * @param theStatusCode
+	 *            The HTTP status code corresponding to this problem
+	 * @param theMessage
+	 *            The message
+	 * @param theCause
+	 *            The underlying cause exception
+	 * @param theOperationOutcome
+	 *            An OperationOutcome resource to return to the calling client (in a server) or the OperationOutcome
+	 *            that was returned from the server (in a client)
+	 */
+	public BaseServerResponseException(int theStatusCode, String theMessage, Throwable theCause, OperationOutcome theOperationOutcome) {
+		super(theMessage, theCause);
+		myStatusCode = theStatusCode;
+		myOperationOutcome = theOperationOutcome;
+	}
+
 	/**
 	 * Constructor
 	 * 
@@ -115,17 +134,32 @@ public abstract class BaseServerResponseException extends RuntimeException {
 	}
 
 	/**
-	 * Returns the {@link OperationOutcome} resource if any which was supplied
+	 * Constructor
-	 * in the response, or <code>null</code>
+	 * 
+	 * @param theStatusCode
+	 *            The HTTP status code corresponding to this problem
+	 * @param theCause
+	 *            The underlying cause exception
+	 * @param theOperationOutcome
+	 *            An OperationOutcome resource to return to the calling client (in a server) or the OperationOutcome
+	 *            that was returned from the server (in a client)
+	 */
+	public BaseServerResponseException(int theStatusCode, Throwable theCause, OperationOutcome theOperationOutcome) {
+		super(theCause.toString(), theCause);
+		myStatusCode = theStatusCode;
+		myOperationOutcome = theOperationOutcome;
+	}
+
+	/**
+	 * Returns the {@link OperationOutcome} resource if any which was supplied in the response, or <code>null</code>
 	 */
 	public OperationOutcome getOperationOutcome() {
 		return myOperationOutcome;
 	}
 
 	/**
-	 * In a RESTful client, this method will be populated with the body of the
+	 * In a RESTful client, this method will be populated with the body of the HTTP respone if one was provided by the
-	 * HTTP respone if one was provided by the server, or <code>null</code>
+	 * server, or <code>null</code> otherwise.
-	 * otherwise.
 	 * <p>
 	 * In a restful server, this method is currently ignored.
 	 * </p>
@@ -135,8 +169,8 @@ public abstract class BaseServerResponseException extends RuntimeException {
 	}
 
 	/**
-	 * In a RESTful client, this method will be populated with the HTTP status
+	 * In a RESTful client, this method will be populated with the HTTP status code that was returned with the HTTP
-	 * code that was returned with the HTTP response.
+	 * response.
 	 * <p>
 	 * In a restful server, this method is currently ignored.
 	 * </p>
@@ -153,16 +187,14 @@ public abstract class BaseServerResponseException extends RuntimeException {
 	}
 
 	/**
-	 * This method is currently only called internally by HAPI, it should not be
+	 * This method is currently only called internally by HAPI, it should not be called by user code.
-	 * called by user code.
 	 */
 	public void setResponseBody(String theResponseBody) {
 		myResponseBody = theResponseBody;
 	}
 
 	/**
-	 * This method is currently only called internally by HAPI, it should not be
+	 * This method is currently only called internally by HAPI, it should not be called by user code.
-	 * called by user code.
 	 */
 	public void setResponseMimeType(String theResponseMimeType) {
 		myResponseMimeType = theResponseMimeType;

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java

@@ -37,6 +37,7 @@ import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 import ca.uhn.fhir.model.dstu.composite.ContainedDt;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
 
@@ -108,30 +109,68 @@ public class FhirTerser {
 	}
 
 	/**
-	 * Returns a list containing all child elements (including the resource itself) which are <b>non-empty</b>
+	 * Visit all elements in a given resource
-	 * and are either of the exact type specified, or are a subclass of that type.
+	 * 
-	 * <p>
+	 * @param theResource The resource to visit
-	 * For example, specifying a type of {@link StringDt} would return all non-empty string instances within
+	 * @param theVisitor The visitor
-	 * the message. Specifying a type of {@link IResource} would return the resource itself, as well as any contained resources. 
-	 * </p>  
-	 * @param theResourceT The resource instance to search. Must not be null.
-	 * @param theType The type to search for. Must not be null.
-	 * @return
 	 */
-	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(IResource theResource, Class<T> theType) {
+	public void visit(IResource theResource, IModelVisitor theVisitor) {
-		ArrayList<T> retVal = new ArrayList<T>();
 		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
-		getAllChildElementsOfType(theResource, def, theType, retVal);
+		visit(theResource, null, def, theVisitor);
-		return retVal;
 	}
 
-	private <T extends IElement> void getAllChildElementsOfType(IElement theElement, BaseRuntimeElementDefinition<?> theDefinition, Class<T> theType, ArrayList<T> theList) {
+	/**
+	 * Returns a list containing all child elements (including the resource itself) which are <b>non-empty</b> and are
+	 * either of the exact type specified, or are a subclass of that type.
+	 * <p>
+	 * For example, specifying a type of {@link StringDt} would return all non-empty string instances within the
+	 * message. Specifying a type of {@link IResource} would return the resource itself, as well as any contained
+	 * resources.
+	 * </p>
+	 * 
+	 * @param theResourceT
+	 *            The resource instance to search. Must not be null.
+	 * @param theType
+	 *            The type to search for. Must not be null.
+	 * @return
+	 */
+	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(IResource theResource, final Class<T> theType) {
+		final ArrayList<T> retVal = new ArrayList<T>();
+		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
+		visit(theResource, null, def, new IModelVisitor() {
+			@SuppressWarnings("unchecked")
+			@Override
+			public void acceptElement(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
 				if (theElement.isEmpty()) {
 					return;
 				}
 
-		addIfCorrectType(theElement, theType, theList);
+				if (theElement != null && theType.isAssignableFrom(theElement.getClass())) {
-		addUndeclaredExtensions(theElement, theType, theList);
+					retVal.add((T) theElement);
+				}
+			}
+
+			@SuppressWarnings("unchecked")
+			@Override
+			public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+				if (theType.isAssignableFrom(theNextExt.getClass())) {
+					retVal.add((T) theNextExt);
+				}
+				if (theNextExt.getValue() != null && theType.isAssignableFrom(theNextExt.getValue().getClass())) {
+					retVal.add((T) theNextExt.getValue());
+				}
+			}
+		});
+		return retVal;
+	}
+
+	private <T extends IElement> void visit(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
+		theCallback.acceptElement(theElement, theChildDefinition, theDefinition);
+		addUndeclaredExtensions(theElement, theDefinition, theChildDefinition, theCallback);
+
+//		if (theElement.isEmpty()) {
+//			return;
+//		}
 		
 		switch (theDefinition.getChildType()) {
 		case PRIMITIVE_XHTML:
@@ -153,7 +192,9 @@ public class FhirTerser {
 						if (nextValue.isEmpty()) {
 							continue;
 						}
-						BaseRuntimeElementDefinition<?> childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
+						BaseRuntimeElementDefinition<?> childElementDef;
+						childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
+						
 						if (childElementDef == null) {
 							StringBuilder b = new StringBuilder();
 							b.append("Found value of type[");
@@ -171,7 +212,7 @@ public class FhirTerser {
 							}
 							throw new DataFormatException(b.toString());
 						}
-						getAllChildElementsOfType(nextValue, childElementDef, theType, theList);
+						visit(nextValue, nextChild, childElementDef, theCallback);
 					}
 				}
 			}
@@ -181,7 +222,7 @@ public class FhirTerser {
 			ContainedDt value = (ContainedDt) theElement;
 			for (IResource next : value.getContainedResources()) {
 				BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
-				getAllChildElementsOfType(next, def, theType, theList);
+				visit(next, null, def, theCallback);
 			}
 			break;
 		}
@@ -192,22 +233,14 @@ public class FhirTerser {
 		}
 	}
 
-	private <T extends IElement> void addUndeclaredExtensions(IElement theElement, Class<T> theType, ArrayList<T> theList) {
+	private <T extends IElement> void addUndeclaredExtensions(IElement theElement, BaseRuntimeElementDefinition<?> theDefinition, BaseRuntimeChildDefinition theChildDefinition, IModelVisitor theCallback) {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
-			ISupportsUndeclaredExtensions elem = (ISupportsUndeclaredExtensions) theElement;
+			ISupportsUndeclaredExtensions containingElement = (ISupportsUndeclaredExtensions) theElement;
-			for (ExtensionDt nextExt : elem.getUndeclaredExtensions()) {
+			for (ExtensionDt nextExt : containingElement.getUndeclaredExtensions()) {
-				addIfCorrectType(nextExt, theType, theList);
+				theCallback.acceptUndeclaredExtension(containingElement, theChildDefinition, theDefinition, nextExt);
-				addIfCorrectType(nextExt.getValue(), theType, theList);
+				addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
-				addUndeclaredExtensions(nextExt, theType, theList);
 			}
 		}
 	}
 
-	@SuppressWarnings("unchecked")
-	private <T extends IElement> void addIfCorrectType(IElement theElement, Class<T> theType, ArrayList<T> theList) {
-		if (theElement != null && theType.isAssignableFrom(theElement.getClass())) {
-			theList.add((T) theElement);
-		}
-	}
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/IModelVisitor.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.util;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.IElement;
+import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
+
+/**
+ * @see FhirTerser#visit(ca.uhn.fhir.model.api.IResource, IModelVisitor)
+ */
+public interface IModelVisitor {
+
+	/**
+	 * 
+	 * @param theElement
+	 * @param theChildDefinition May be null if this is a root element
+	 * @param theDefinition
+	 */
+	void acceptElement(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition);
+
+	/**
+	 * 
+	 * @param theContainingElement
+	 * @param theChildDefinition May be null if this is a root element
+	 * @param theDefinition
+	 * @param theNextExt
+	 */
+	void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt);
+
+	
+	
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.util;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+public class UrlUtil {
+
+	public static boolean isAbsolute(String theValue) {
+		String value = theValue.toLowerCase();
+		return value.startsWith("http://") || value.startsWith("https://");
+	}
+
+}

hapi-fhir-base/src/site/example/java/example/ClientExamples.java

@@ -1,90 +0,0 @@
-package example;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.client.IGenericClient;
-import ca.uhn.fhir.rest.client.IRestfulClientFactory;
-import ca.uhn.fhir.rest.client.api.IBasicClient;
-import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
-import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.EncodingEnum;
-
-public class ClientExamples {
-
-	public interface IPatientClient extends IBasicClient {
-		// nothing yet
-	}
-
-	@SuppressWarnings("unused")
-	public void createProxy() {
-//START SNIPPET: proxy
-FhirContext ctx = new FhirContext();
-ctx.getRestfulClientFactory().setProxy("example.com", 8888);
-
-IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
-//START SNIPPET: end
-	}
-	
-	@SuppressWarnings("unused")
-	public void createSecurity() {
-//START SNIPPET: security
-// Create a context and get the client factory so it can be configured
-FhirContext ctx = new FhirContext();
-IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
-
-//Create an HTTP basic auth interceptor 
-String username = "foobar";
-String password = "boobear";
-BasicAuthInterceptor authInterceptor = new BasicAuthInterceptor(username, password);
-
-// Register the interceptor with your client (either style)
-IPatientClient annotationClient = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/fhir");
-annotationClient.registerInterceptor(authInterceptor);
-
-IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
-annotationClient.registerInterceptor(authInterceptor);
-//END SNIPPET: security
-}
-
-@SuppressWarnings("unused")
-public void createLogging() {
-{
-//START SNIPPET: logging
-//Create a context and get the client factory so it can be configured
-FhirContext ctx = new FhirContext();
-IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
-
-//Create a logging interceptor 
-LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
-
-// Optionally you may configure the interceptor (by default only summary info is logged)
-loggingInterceptor.setLogRequestSummary(true);
-loggingInterceptor.setLogRequestBody(true);
-
-//Register the interceptor with your client (either style)
-IPatientClient annotationClient = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/fhir");
-annotationClient.registerInterceptor(loggingInterceptor);
-
-IGenericClient genericClient = ctx.newRestfulGenericClient("http://localhost:9999/fhir");
-genericClient.registerInterceptor(loggingInterceptor);
-//END SNIPPET: logging
-}
-
-
-
-/******************************/
-{
-//START SNIPPET: clientConfig
-//Create a client
-FhirContext ctx = new FhirContext();
-IPatientClient client = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/");
-
-// Request JSON encoding from the server (_format=json)
-client.setEncoding(EncodingEnum.JSON);
-
-// Request pretty printing from the server (_pretty=true)
-client.setPrettyPrint(true);
-//END SNIPPET: clientConfig
-}
-	}
-	
-}

hapi-fhir-base/src/site/example/java/example/CompleteExampleClient.java

@@ -1,68 +0,0 @@
-package example;
-
-//START SNIPPET: client
-import java.io.IOException;
-import java.util.List;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
-import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
-import ca.uhn.fhir.model.dstu.resource.Organization;
-import ca.uhn.fhir.model.dstu.resource.Patient;
-import ca.uhn.fhir.rest.annotation.RequiredParam;
-import ca.uhn.fhir.rest.annotation.Search;
-import ca.uhn.fhir.rest.client.api.IRestfulClient;
-
-public class CompleteExampleClient {
-
-	/**
-	 * This is a simple client interface. It can have many methods
-	 * for various searches but in this case it has only 1.
-	 */
-	public static interface ClientInterface extends IRestfulClient
-	{ 
-	 
-		/**
-		 * This is translated into a URL similar to the following:
-		 * http://fhir.healthintersections.com.au/open/Patient?identifier=urn:oid:1.2.36.146.595.217.0.1%7C12345 
-		 */
-		@Search
-		List<Patient> findPatientsForMrn(@RequiredParam(name=Patient.SP_IDENTIFIER) IdentifierDt theIdentifier);
-		
-	}
-
-	/**
-	 * The main method here will directly call an open FHIR server
-	 * and retrieve a list of resources matching a given criteria,
-	 * then load a linked resource.
-	 */
-	public static void main(String[] args) throws IOException {
-		
-		// Create a client factory
-		FhirContext ctx = new FhirContext();
-		
-		//Create the client
-		String serverBase = "http://fhir.healthintersections.com.au/open";
-		ClientInterface client = ctx.newRestfulClient(ClientInterface.class, serverBase);
-		
-		// Invoke the client to search for patient
-		List<Patient> patients = client.findPatientsForMrn(new IdentifierDt("urn:oid:1.2.36.146.595.217.0.1", "12345"));
-		
-		System.out.println("Found "+ patients.size() + " patients");
-		
-		// Print a value from the loaded resource
-		Patient patient = patients.get(0);
-		System.out.println("Patient Last Name: " + patient.getName().get(0).getFamily().get(0).getValue());
-		
-		// Load a referenced resource
-		ResourceReferenceDt managingRef = patient.getManagingOrganization();
-		Organization org = (Organization) managingRef.loadResource(client);
-		
-		// Print organization name
-		System.out.println(org.getName().getValue());
-		
-	}
-
-}
-//END SNIPPET: client
-

hapi-fhir-base/src/site/example/java/example/MyPatientUse.java

@@ -1,43 +0,0 @@
-package example;
-
-import java.io.IOException;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
-import ca.uhn.fhir.model.primitive.StringDt;
-import ca.uhn.fhir.parser.DataFormatException;
-import ca.uhn.fhir.parser.IParser;
-import ca.uhn.fhir.parser.MyPatient;
-
-public class MyPatientUse {
-
-@SuppressWarnings("unused")
-public static void main(String[] args) throws DataFormatException, IOException {
-//START SNIPPET: patientUse
-MyPatient patient = new MyPatient();
-patient.setPetName(new StringDt("Fido"));
-patient.getImportantDates().add(new DateTimeDt("2010-01-02"));
-patient.getImportantDates().add(new DateTimeDt("2014-01-26T11:11:11"));
-
-patient.addName().addFamily("Smith").addGiven("John").addGiven("Quincy").addSuffix("Jr");
-
-IParser p = new FhirContext().newXmlParser().setPrettyPrint(true);
-String messageString = p.encodeResourceToString(patient);
-
-System.out.println(messageString);
-//END SNIPPET: patientUse
-	
-//START SNIPPET: patientParse
-IParser parser = new FhirContext().newXmlParser();
-MyPatient newPatient = parser.parseResource(MyPatient.class, messageString);
-//END SNIPPET: patientParse
-
-{
-	FhirContext ctx2 = new FhirContext();
-	RuntimeResourceDefinition def = ctx2.getResourceDefinition(patient);
-	System.out.println(ctx2.newXmlParser().setPrettyPrint(true).encodeResourceToString(def.toProfile()));
-}
-}
-	
-}

hapi-fhir-base/src/site/site.xml

@@ -61,6 +61,7 @@
 			<item name="The Data Model" href="./doc_fhirobjects.html">
 				<item name="Extensions" href="./doc_extensions.html" />
 				<item name="Resource References" href="./doc_resource_references.html" />
+				<item name="Tags" href="./doc_tags.html" />
 			</item>
 			<item name="RESTful Client" href="./doc_rest_client.html" />
 			<item name="RESTful Server" href="./doc_rest_server.html" >

hapi-fhir-base/src/site/xdoc/doc_extensions.xml

@@ -28,7 +28,7 @@
 			</p>
 			<macro name="snippet">
 				<param name="id" value="resourceExtension" />
-				<param name="file" value="src/site/example/java/example/Extensions.java" />
+				<param name="file" value="examples/src/main/java/example/Extensions.java" />
 			</macro>
 			
 			<p>
@@ -36,7 +36,7 @@
 			</p>
 			<macro name="snippet">
 				<param name="id" value="resourceStringExtension" />
-				<param name="file" value="src/site/example/java/example/Extensions.java" />
+				<param name="file" value="examples/src/main/java/example/Extensions.java" />
 			</macro>
 			
 			<subsection name="Sub-Extensions">
@@ -48,7 +48,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="subExtension" />
-					<param name="file" value="src/site/example/java/example/Extensions.java" />
+					<param name="file" value="examples/src/main/java/example/Extensions.java" />
 				</macro>
 			
 			</subsection>
@@ -61,7 +61,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="parseExtension" />
-					<param name="file" value="src/site/example/java/example/Extensions.java" />
+					<param name="file" value="examples/src/main/java/example/Extensions.java" />
 				</macro>
 			
 			</subsection>
@@ -78,7 +78,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="patientDef" />
-					<param name="file" value="src/site/example/java/example/MyPatient.java" />
+					<param name="file" value="examples/src/main/java/example/MyPatient.java" />
 				</macro>
 
 				<p>
@@ -88,7 +88,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="patientUse" />
-					<param name="file" value="src/site/example/java/example/MyPatientUse.java" />
+					<param name="file" value="examples/src/main/java/example/MyPatientUse.java" />
 				</macro>
 			
 				<p>
@@ -121,7 +121,7 @@
 			
 				<macro name="snippet">
 					<param name="id" value="patientParse" />
-					<param name="file" value="src/site/example/java/example/MyPatientUse.java" />
+					<param name="file" value="examples/src/main/java/example/MyPatientUse.java" />
 				</macro>
 
 			<subsection name="Documentation">

hapi-fhir-base/src/site/xdoc/doc_fhirobjects.xml

@@ -31,7 +31,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="datatypes" />
-				<param name="file" value="src/site/example/java/example/FhirDataModel.java" />
+				<param name="file" value="examples/src/main/java/example/FhirDataModel.java" />
 			</macro>
 
 			<subsection name="Navigating Structures">
@@ -45,7 +45,7 @@
 			
 				<macro name="snippet">
 					<param name="id" value="nonNull" />
-					<param name="file" value="src/site/example/java/example/FhirDataModel.java" />
+					<param name="file" value="examples/src/main/java/example/FhirDataModel.java" />
 				</macro>
 
 			</subsection>
@@ -65,7 +65,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="codes" />
-					<param name="file" value="src/site/example/java/example/FhirDataModel.java" />
+					<param name="file" value="examples/src/main/java/example/FhirDataModel.java" />
 				</macro>
 
 			</subsection>
@@ -87,7 +87,7 @@
 			
 				<macro name="snippet">
 					<param name="id" value="namesHard" />
-					<param name="file" value="src/site/example/java/example/FhirDataModel.java" />
+					<param name="file" value="examples/src/main/java/example/FhirDataModel.java" />
 				</macro>
 			
 				<p>
@@ -97,7 +97,7 @@
 			
 				<macro name="snippet">
 					<param name="id" value="namesEasy" />
-					<param name="file" value="src/site/example/java/example/FhirDataModel.java" />
+					<param name="file" value="examples/src/main/java/example/FhirDataModel.java" />
 				</macro>
 			
 			</subsection>

hapi-fhir-base/src/site/xdoc/doc_intro.xml

@@ -70,7 +70,7 @@
 	
 				<macro name="snippet">
 					<param name="id" value="creatingContext" />
-					<param name="file" value="src/site/example/java/example/FhirContextIntro.java" />
+					<param name="file" value="examples/src/main/java/example/FhirContextIntro.java" />
 				</macro>
 
 			</subsection>
@@ -93,7 +93,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="parseMsg" />
-					<param name="file" value="src/site/example/java/example/FhirContextIntro.java" />
+					<param name="file" value="examples/src/main/java/example/FhirContextIntro.java" />
 				</macro>
 
 			</subsection>
@@ -107,7 +107,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="encodeMsg" />
-					<param name="file" value="src/site/example/java/example/FhirContextIntro.java" />
+					<param name="file" value="examples/src/main/java/example/FhirContextIntro.java" />
 				</macro>
 				
 				<!-- ****** The section below on fluent references the snippet above
@@ -147,7 +147,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="encodeMsgFluent" />
-					<param name="file" value="src/site/example/java/example/FhirContextIntro.java" />
+					<param name="file" value="examples/src/main/java/example/FhirContextIntro.java" />
 				</macro>
 			
 			</subsection>
@@ -160,7 +160,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="encodeMsgJson" />
-					<param name="file" value="src/site/example/java/example/FhirContextIntro.java" />
+					<param name="file" value="examples/src/main/java/example/FhirContextIntro.java" />
 				</macro>
 
 				<p>

hapi-fhir-base/src/site/xdoc/doc_narrative.xml

@@ -28,7 +28,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="simple" />
-				<param name="file" value="src/site/example/java/example/Narrative.java" />
+				<param name="file" value="examples/src/main/java/example/Narrative.java" />
 			</macro>
 
 		</section>			
@@ -64,7 +64,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="example1" />
-					<param name="file" value="src/site/example/java/example/Narrative.java" />
+					<param name="file" value="examples/src/main/java/example/Narrative.java" />
 				</macro>
 				
 				<p>
@@ -163,7 +163,7 @@ humanname.narrative=classpath:ca/uhn/fhir/narrative/HumanNameDt.html]]></source>
 
 			<macro name="snippet">
 				<param name="id" value="gen" />
-				<param name="file" value="src/site/example/java/example/NarrativeGenerator.java" />
+				<param name="file" value="examples/src/main/java/example/NarrativeGenerator.java" />
 			</macro>
 		
 		</section>

hapi-fhir-base/src/site/xdoc/doc_rest_client.xml

@@ -27,8 +27,9 @@
 				There are two types of clients provided by HAPI: Generic and Annotation-driven.
 				The generic client (introduced in HAPI-FHIR 0.3) is much simpler to create
 				and generally provides the faster way to get started. The annotation-driven
-				client is more powerful and can rely on code generation to give better
+				client can rely on code generation and static binding to specific operations to 
-				compile-time checking. 
+				give better	compile-time checking against servers with a specific set of capabilities
+				exposed. 
 			</p>
 
 		</section>
@@ -47,7 +48,7 @@
 			<macro name="snippet">
 				<param name="id" value="simple" />
 				<param name="file"
-					value="src/site/example/java/example/GenericClientExample.java" />
+					value="examples/src/main/java/example/GenericClientExample.java" />
 			</macro>
 			
 			<p> 
@@ -76,27 +77,19 @@
 				</p>
 			</subsection>
 						
-			<subsection name="Type - Create">
-				<p>
-					The following example shows how to perform a create
-					operation using the generic client:
-				</p>
-				<macro name="snippet">
-					<param name="id" value="create" />
-					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
-				</macro>
-			</subsection>			
-						
 			<subsection name="Type - Search/Query">
 				
+				<p>
+					Searching for resources is probably the most common initial scenario for
+					client applications, so we'll start the demonstration there.
+				</p>
 				<p>
 					The following example shows how to query using the generic client:
 				</p>
 				<macro name="snippet">
 					<param name="id" value="search" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 				
 				<h4>Search - Multi-valued Parameters (ANY/OR)</h4>
@@ -108,7 +101,7 @@
 				<macro name="snippet">
 					<param name="id" value="searchOr" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 
 				<h4>Search - Multi-valued Parameters (ALL/AND)</h4>
@@ -120,7 +113,7 @@
 				<macro name="snippet">
 					<param name="id" value="searchOr" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 
 				<h4>Search - Paging</h4>
@@ -131,7 +124,7 @@
 				<macro name="snippet">
 					<param name="id" value="searchPaging" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 				
 				<h4>Search - Composite Parameters</h4>
@@ -144,7 +137,7 @@
 				<macro name="snippet">
 					<param name="id" value="searchComposite" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 				
 				<h4>Search - Other Query Options</h4>
@@ -155,7 +148,7 @@
 				<macro name="snippet">
 					<param name="id" value="searchAdv" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 
 				<h4>Search - Using HTTP POST or GET with _search</h4>
@@ -168,11 +161,23 @@
 				<macro name="snippet">
 					<param name="id" value="searchPost" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 				
 			</subsection>			
 
+			<subsection name="Type - Create">
+				<p>
+					The following example shows how to perform a create
+					operation using the generic client:
+				</p>
+				<macro name="snippet">
+					<param name="id" value="create" />
+					<param name="file"
+						value="examples/src/main/java/example/GenericClientExample.java" />
+				</macro>
+			</subsection>			
+
 			<subsection name="Instance - Delete">
 				<p>
 					The following example shows how to perform a delete
@@ -181,7 +186,7 @@
 				<macro name="snippet">
 					<param name="id" value="delete" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 			</subsection>			
 
@@ -198,7 +203,7 @@
 				<macro name="snippet">
 					<param name="id" value="update" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 			</subsection>			
 
@@ -210,7 +215,7 @@
 				<macro name="snippet">
 					<param name="id" value="conformance" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 			</subsection>			
 			
@@ -221,7 +226,7 @@
 				<macro name="snippet">
 					<param name="id" value="transaction" />
 					<param name="file"
-						value="src/site/example/java/example/GenericClientExample.java" />
+						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
 			</subsection>			
 			
@@ -295,7 +300,7 @@
 				<macro name="snippet">
 					<param name="id" value="provider" />
 					<param name="file"
-						value="src/site/example/java/example/IRestfulClient.java" />
+						value="examples/src/main/java/example/IRestfulClient.java" />
 				</macro>
 
 				<p>
@@ -321,7 +326,7 @@
 				<macro name="snippet">
 					<param name="id" value="client" />
 					<param name="file"
-						value="src/site/example/java/example/ExampleRestfulClient.java" />
+						value="examples/src/main/java/example/ExampleRestfulClient.java" />
 				</macro>
 
 			</subsection>
@@ -343,7 +348,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="clientConfig" />
-					<param name="file" value="src/site/example/java/example/ClientExamples.java" />
+					<param name="file" value="examples/src/main/java/example/ClientExamples.java" />
 				</macro>
 
 			</subsection>
@@ -359,7 +364,7 @@
 				<macro name="snippet">
 					<param name="id" value="client" />
 					<param name="file"
-						value="src/site/example/java/example/CompleteExampleClient.java" />
+						value="examples/src/main/java/example/CompleteExampleClient.java" />
 				</macro>
 				
 			</subsection>
@@ -412,7 +417,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="security" />
-					<param name="file" value="src/site/example/java/example/ClientExamples.java" />
+					<param name="file" value="examples/src/main/java/example/ClientExamples.java" />
 				</macro>
 
 			</subsection>
@@ -429,7 +434,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="logging" />
-					<param name="file" value="src/site/example/java/example/ClientExamples.java" />
+					<param name="file" value="examples/src/main/java/example/ClientExamples.java" />
 				</macro>
 
 			</subsection>
@@ -443,7 +448,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="logging" />
-					<param name="file" value="src/site/example/java/example/ClientExamples.java" />
+					<param name="file" value="examples/src/main/java/example/ClientExamples.java" />
 				</macro>
 			
 			</subsection>

hapi-fhir-base/src/site/xdoc/doc_rest_operations.xml

@@ -202,7 +202,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="read" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -218,7 +218,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="clientReadInterface" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<a name="instance_vread" />
@@ -243,7 +243,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="vread" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -294,7 +294,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="update" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -311,7 +311,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="updateClient" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<a name="instance_delete" />
@@ -336,7 +336,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="delete" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -407,7 +407,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="create" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -424,7 +424,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="createClient" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<a name="type_search" />
@@ -456,7 +456,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="searchAll" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -495,7 +495,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="searchStringParam" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -517,7 +517,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="searchIdentifierParam" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -550,7 +550,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="dates" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -565,7 +565,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="dateClient" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 			</subsection>
@@ -597,7 +597,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="dateRange" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -612,7 +612,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="dateClient" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<h4>Unbounded Ranges</h4>
@@ -658,7 +658,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="quantity" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -699,7 +699,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="reference" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -722,7 +722,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="referenceChain" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 			</subsection>
@@ -744,7 +744,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="searchComposite" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -800,7 +800,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="searchOptionalParam" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -878,7 +878,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="searchMultiple" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -910,7 +910,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="searchMultipleAnd" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 				
 				<h4>AND Relationship Query Parameters for Dates</h4>
@@ -940,7 +940,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="pathSpec" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -957,7 +957,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="pathSpecSimple" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 			</subsection>
@@ -979,7 +979,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="searchNamedQuery" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -1016,7 +1016,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="sort" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 				<p>
@@ -1041,7 +1041,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="searchWithDocs" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 
 			</subsection>
@@ -1108,7 +1108,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="validate" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -1150,7 +1150,7 @@
 			</p>
 			<macro name="snippet">
 				<param name="id" value="metadataProvider" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -1160,7 +1160,7 @@
 			</p>
 			<macro name="snippet">
 				<param name="id" value="metadataClient" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -1171,7 +1171,7 @@
 			</p>
 			<macro name="snippet">
 				<param name="id" value="metadataClientUsage" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<a name="system_transaction" />
@@ -1198,9 +1198,14 @@
 			</p>
 			<macro name="snippet">
 				<param name="id" value="transaction" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 			
+			<p>
+				Transaction methods require one parameter annotated with @TransactionParam, and that
+				parameter may be of type List&lt;IResource&gt; or Bundle.
+			</p>
+			
 			<p>
 				Example URL to invoke this method:
 				<br />
@@ -1315,7 +1320,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="history" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<p>
@@ -1324,7 +1329,7 @@
 
 			<macro name="snippet">
 				<param name="id" value="historyClient" />
-				<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 			</macro>
 
 			<a name="exceptions" />
@@ -1406,7 +1411,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="readTags" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 				
 				<p>
@@ -1417,7 +1422,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="clientReadTags" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 				
 			</subsection>
@@ -1444,7 +1449,7 @@
 
 				<macro name="snippet">
 					<param name="id" value="createTags" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 				
 			</subsection>
@@ -1464,7 +1469,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="tagMethodProvider" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 				
 				<p>

hapi-fhir-base/src/site/xdoc/doc_rest_server.xml

@@ -57,7 +57,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="provider" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProvider.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProvider.java" />
 				</macro>
 
 			</subsection>
@@ -88,7 +88,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="servlet" />
-					<param name="file" value="src/site/example/java/example/ExampleRestfulServlet.java" />
+					<param name="file" value="examples/src/main/java/example/ExampleRestfulServlet.java" />
 				</macro>
 
 				<a name="plain_providers"/>
@@ -120,7 +120,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="plainProvider" />
-					<param name="file" value="src/site/example/java/example/ExampleProviders.java" />
+					<param name="file" value="examples/src/main/java/example/ExampleProviders.java" />
 				</macro>
 			
 				<p>
@@ -136,7 +136,7 @@
 				</p>
 				<macro name="snippet">
 					<param name="id" value="plainProviderServer" />
-					<param name="file" value="src/site/example/java/example/ExampleProviders.java" />
+					<param name="file" value="examples/src/main/java/example/ExampleProviders.java" />
 				</macro>
 			
 			</subsection>
@@ -258,7 +258,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="provider" />
-					<param name="file" value="src/site/example/java/example/PagingServer.java" />
+					<param name="file" value="examples/src/main/java/example/PagingServer.java" />
 				</macro>
 			
 			</subsection>			
@@ -290,7 +290,7 @@
 				
 				<macro name="snippet">
 					<param name="id" value="provider" />
-					<param name="file" value="src/site/example/java/example/PagingPatientProvider.java" />
+					<param name="file" value="examples/src/main/java/example/PagingPatientProvider.java" />
 				</macro>
 			
 			</subsection>
@@ -323,7 +323,7 @@
 			
 				<macro name="snippet">
 					<param name="id" value="underlyingReq" />
-					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+					<param name="file" value="examples/src/main/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 			
 			
@@ -435,6 +435,41 @@
 		
 		</section>
 		
+		<section name="Populating Resource Metadata">
+		
+			<p>
+				Server operations will often return a resource or a bundle of resources. These
+				types will contain one or more resource instances, but also specify a set of 
+				metadata describing that resource.   
+			</p>
+			
+			<p>
+				For example, resources have a "published" and "updated" date, referring to 
+				the date/time the resource was originally created and the date/time the 
+				resource was last updated respectively. For operations which return a single
+				resource, these values are returned via HTTP headers. For operations which
+				return a bundle, these values are returned via elements within the 
+				bundle's "entry" tag. 	
+			</p>
+			
+			<p>
+				Bundles may also contain a set of links, such as an "alternate" link to
+				a resource, or a "search" link.
+			</p>
+			
+			<p>
+				Populating these metadata elements is done via the
+				<code><a href="http://jamesagnew.github.io/hapi-fhir/apidocs/ca/uhn/fhir/model/api/IResource.html#getResourceMetadata()">IResource#getResourceMetadata()</a></code>
+				method. The following example shows how to set various metadata elements on 
+				a resource being returned.
+			</p>
+			<macro name="snippet">
+				<param name="id" value="serverMethod" />
+				<param name="file" value="examples/src/main/java/example/ServerMetadataExamples.java" />
+			</macro>
+				
+		</section>
+
 		<section name="A Complete Example">
 		
 			<p>

hapi-fhir-base/src/site/xdoc/doc_tags.xml

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
+
+	<properties>
+		<title>Resource Tags - HAPI FHIR</title>
+		<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
+	</properties>
+
+	<body>
+
+		<section name="Working With Tags">
+
+			<p>
+				FHIR defines a useful framework for adding/updating/removing 
+				<a href="http://www.hl7.org/implement/standards/fhir/extras.html#tag">Tags</a>
+				against resource instances. A tag is a pair of URLs (a scheme, and a term) which 
+				can optionally have a textual "label" as well.
+			</p>
+			
+			<p>
+				A specific resource instance's tags can be found in the resource
+				<a href="http://jamesagnew.github.io/hapi-fhir/apidocs/ca/uhn/fhir/model/api/IResource.html#getResourceMetadata()">metadata</a>
+				map, using the key of 
+				<a href="http://jamesagnew.github.io/hapi-fhir/apidocs/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.html#TAG_LIST">ResourceMetadataKeyEnum.TAG_LIST</a>. 
+				The following example shows how to access the tags in a client
+				following a "read" operation:
+			</p>
+			<macro name="snippet">
+				<param name="id" value="getResourceTags" />
+				<param name="file" value="examples/src/main/java/example/TagsExamples.java" />
+			</macro>
+
+			<subsection name="Adding Tags to a Resource">
+			
+				<p>
+					In a server implementation, you might want to 
+					add tags to a resource being returned. This is done
+					by adding a TagList instance to the resource's
+					metadata, as shown in the example below.
+				</p>
+				
+				<p>
+					The server will then do the "right thing" with the tags. If the method
+					is for a <code>search</code> operation, the tags will be added to the category 
+					element in the
+					returned bundle. If the method is for a <code>read</code> operation, the
+					tags will be added to the response "Category" headers.
+				</p>
+				<macro name="snippet">
+					<param name="id" value="serverMethod" />
+					<param name="file" value="examples/src/main/java/example/TagsExamples.java" />
+				</macro>
+				
+			</subsection>
+			
+		</section>
+		
+	</body>
+
+</document>

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/ModelExtensionTest.java

@@ -30,6 +30,9 @@ public class ModelExtensionTest {
 		MyPatient parsed = ourCtx.newXmlParser().parseResource(MyPatient.class, str);
 		assertEquals("foo", parsed.getIdentifierFirstRep().getSystem().getValueAsString());
 
+//		assertEquals(MyOrganization.class, parsed.getManagingOrganization().getResource().getClass());
+//		MyOrganization parsedOrg = (MyOrganization) parsed.getManagingOrganization().getResource();
+//		assertEquals("arg0", parsedOrg.getName().getValue());
 	}
 
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/ModelScannerTest.java

@@ -5,7 +5,9 @@ import static org.junit.Assert.*;
 import org.junit.Test;
 
 import ca.uhn.fhir.model.dstu.resource.CarePlan;
+import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.MyPatient;
 
 public class ModelScannerTest {
 
@@ -15,6 +17,16 @@ public class ModelScannerTest {
 		new ModelScanner(CarePlan.class);
 	}
 	
+	@Test
+	public void testExtendedClass() {
+		FhirContext ctx = new FhirContext();
+		ctx.getResourceDefinition(MyPatient.class);
+		ctx.getResourceDefinition(Patient.class);
+		
+		RuntimeResourceDefinition patient = ctx.getResourceDefinition("Patient");
+		assertEquals(Patient.class, patient.getImplementingClass());
+	}
+	
 	
 	@Test
 	public void testScanExtensionTypes() throws DataFormatException {

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

@@ -363,6 +363,29 @@ public class JsonParserTest {
 	@Test
 	public void testEncodeBundleCategory() {
 
+		Bundle b = new Bundle();
+		BundleEntry e = b.addEntry();
+		e.setResource(new Patient());
+		b.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
+		
+		String val = new FhirContext().newJsonParser().setPrettyPrint(false).encodeBundleToString(b);
+		ourLog.info(val);
+
+		assertThat(val, StringContains.containsString("\"category\":[{\"term\":\"term\",\"label\":\"label\",\"scheme\":\"scheme\"}]"));
+		
+		b = new FhirContext().newJsonParser().parseBundle(val);
+		assertEquals(1,b.getEntries().size());
+		assertEquals(1,b.getCategories().size());
+		assertEquals("term", b.getCategories().get(0).getTerm());
+		assertEquals("label", b.getCategories().get(0).getLabel());
+		assertEquals("scheme", b.getCategories().get(0).getScheme());
+		assertNull(b.getEntries().get(0).getResource());
+
+	}
+
+	@Test
+	public void testEncodeBundleEntryCategory() {
+
 		Bundle b = new Bundle();
 		BundleEntry e = b.addEntry();
 		e.setResource(new Patient());
@@ -383,7 +406,6 @@ public class JsonParserTest {
 
 	}
 	
-	
 	@Test
 	public void testEncodeContainedResources() throws IOException {
 
@@ -542,7 +564,7 @@ public class JsonParserTest {
 
 		patient.setManagingOrganization(new ResourceReferenceDt("Organization/123"));
 		str = p.encodeResourceToString(patient);
-		assertThat(str, StringContains.containsString("\"managingOrganization\":{\"resource\":\"Organization/123\"}"));
+		assertThat(str, StringContains.containsString("\"managingOrganization\":{\"reference\":\"Organization/123\"}"));
 
 		Organization org = new Organization();
 		org.addIdentifier().setSystem("foo").setValue("bar");
@@ -671,6 +693,11 @@ public class JsonParserTest {
 		IParser p = ourCtx.newJsonParser();
 		Bundle bundle = p.parseBundle(msg);
 
+		assertEquals(1, bundle.getCategories().size());
+		assertEquals("http://scheme", bundle.getCategories().get(0).getScheme());
+		assertEquals("http://term", bundle.getCategories().get(0).getTerm());
+		assertEquals("label", bundle.getCategories().get(0).getLabel());
+		
 		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(bundle);
 		ourLog.info(encoded);
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/MyOrganization.java

@@ -3,7 +3,7 @@ package ca.uhn.fhir.parser;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import ca.uhn.fhir.model.dstu.resource.Organization;
 
-@ResourceDef(name="Organization")
+@ResourceDef()
 public class MyOrganization extends Organization {
 
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/MyPatient.java

@@ -12,7 +12,7 @@ import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 
-@ResourceDef(name="Patient")
+@ResourceDef()
 public class MyPatient extends Patient {
 	
 	@Child(name="petName")	

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

@@ -63,16 +63,19 @@ import ca.uhn.fhir.parser.JsonParserTest.MyPatientWithOneDeclaredExtension;
 
 public class XmlParserTest {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
 	private static FhirContext ourCtx;
-
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
 
 	@Test
-	public void testParseLanguage() {
+	public void testEncodeBinaryResource() {
-		String input = "<Patient xmlns=\"http://hl7.org/fhir\"><language value=\"zh-CN\"/><text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> 海生 <b>王 </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>URNo</td></tr><tr><td>Address</td><td><span>99 Houston Road </span><br/><span>BENTLEIGH </span><span>Victoria </span></td></tr><tr><td>Date of birth</td><td><span>01 January 1997</span></td></tr></tbody></table></div></text><identifier><use value=\"usual\"/><label value=\"URNo\"/><value value=\"89532\"/></identifier><name><text value=\"王海生\"/><family value=\"王\"/><given value=\"海生\"/></name><telecom><system value=\"phone\"/><value value=\"9899 9878\"/><use value=\"home\"/></telecom><telecom><system value=\"email\"/><value value=\"zimmerman@datacorp.com.au\"/><use value=\"home\"/></telecom><gender><coding><system value=\"http://hl7.org/fhir/v3/AdministrativeGender\"/><code value=\"M\"/><display value=\"Male\"/></coding><text value=\"Male\"/></gender><birthDate value=\"1997-01-01\"/><address><use value=\"home\"/><text value=\"99 Houston Road, BENTLEIGH, 3204\"/><line value=\"99 Houston Road\"/><city value=\"BENTLEIGH\"/><state value=\"Victoria\"/><zip value=\"3204\"/><period><start value=\"2006-06-16\"/></period></address><active value=\"true\"/></Patient>";
+
-		Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		Binary patient = new Binary();
+		patient.setContentType("foo");
+		patient.setContent(new byte[] {1,2,3,4});
+		
+		String val = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>", val);
 		
-		assertEquals("zh-CN", pt.getLanguage().getValue());
 	}
 	
 	@Test
@@ -88,283 +91,10 @@ public class XmlParserTest {
 
 	}
 
-	@Test
-	public void testNestedContainedResources() {
-
-		Observation A = new Observation();
-		A.getName().setText("A");
-		
-		Observation B = new Observation();
-		B.getName().setText("B");
-		A.addRelated().setTarget(new ResourceReferenceDt(B));
-		
-		Observation C = new Observation();
-		C.getName().setText("C");
-		B.addRelated().setTarget(new ResourceReferenceDt(C));
-
-		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(A);
-		ourLog.info(str);
-		
-		assertThat(str, stringContainsInOrder(Arrays.asList("<text value=\"B\"/>", "<text value=\"C\"/>", "<text value=\"A\"/>")));
-		assertThat(str, stringContainsInOrder(Arrays.asList("<contained>", "</contained>")));
-		
-		// Only one (outer) contained block
-		int idx0 = str.indexOf("<contained>");
-		int idx1 = str.indexOf("<contained>",idx0+1);
-		assertNotEquals(-1, idx0);
-		assertEquals(-1, idx1);
-		
-		Observation obs = ourCtx.newXmlParser().parseResource(Observation.class, str);
-		assertEquals("A",obs.getName().getText().getValue());
-		
-		Observation obsB = (Observation) obs.getRelatedFirstRep().getTarget().getResource();
-		assertEquals("B",obsB.getName().getText().getValue());
-
-		Observation obsC = (Observation) obsB.getRelatedFirstRep().getTarget().getResource();
-		assertEquals("C",obsC.getName().getText().getValue());
-
-		
-	}
-
-	
-
-	@Test
-	public void testParseQuery() {
-		String msg = "<Query xmlns=\"http://hl7.org/fhir\">\n" + 
-				"  <text>\n" + 
-				"    <status value=\"generated\"/>\n" + 
-				"    <div xmlns=\"http://www.w3.org/1999/xhtml\">[Put rendering here]</div>\n" + 
-				"  </text>\n" + 
-				"\n" + 
-				"  <!--   this is an extermely simple query - a request to execute the query 'example' on the\n" + 
-				"   responder   -->\n" + 
-				"  <identifier value=\"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\"/>\n" + 
-				"  <parameter url=\"http://hl7.org/fhir/query#_query\">\n" + 
-				"    <valueString value=\"example\"/>\n" + 
-				"  </parameter>\n" + 
-				"</Query>";
-		Query query = ourCtx.newXmlParser().parseResource(Query.class, msg);
-		
-		assertEquals("urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376", query.getIdentifier().getValueAsString());
-		assertEquals("http://hl7.org/fhir/query#_query", query.getParameterFirstRep().getUrlAsString());
-		assertEquals("example", query.getParameterFirstRep().getValueAsPrimitive().getValueAsString());
-		
-	}
-	
-	@Test
-	public void testEncodeQuery() {
-		Query q = new Query();
-		ExtensionDt parameter = q.addParameter();
-		parameter.setUrl("http://foo").setValue(new StringDt("bar"));
-		
-		
-		String val = ourCtx.newXmlParser().encodeResourceToString(q);
-		ourLog.info(val);
-
-		assertEquals("<Query xmlns=\"http://hl7.org/fhir\"><parameter url=\"http://foo\"><valueString value=\"bar\"/></parameter></Query>", val);
-		
-	}
-
-	
-	@Test
-	public void testEncodeBinaryResource() {
-
-		Binary patient = new Binary();
-		patient.setContentType("foo");
-		patient.setContent(new byte[] {1,2,3,4});
-		
-		String val = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>", val);
-		
-	}
-
-	
-	@Test
-	public void testParseBinaryResource() {
-
-		Binary val = ourCtx.newXmlParser().parseResource(Binary.class, "<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>");
-		assertEquals("foo", val.getContentType());
-		assertArrayEquals(new byte[] {1,2,3,4}, val.getContent());
-
-	}
-
-	@Test
-	public void testTagList() {
-		
-		//@formatter:off
-		String tagListStr = "<taglist xmlns=\"http://hl7.org/fhir\"> \n" + 
-				"    <category term=\"term0\" label=\"label0\" scheme=\"scheme0\" /> \n" + 
-				"    <category term=\"term1\" label=\"label1\" scheme=\"\" /> \n" + 
-				"    <category term=\"term2\" label=\"label2\" /> \n" + 
-				"</taglist>";
-		//@formatter:on
-		
-		TagList tagList = ourCtx.newXmlParser().parseTagList(tagListStr);
-		assertEquals(3, tagList.size());
-		assertEquals("term0", tagList.get(0).getTerm());
-		assertEquals("label0", tagList.get(0).getLabel());
-		assertEquals("scheme0", tagList.get(0).getScheme());
-		assertEquals("term1", tagList.get(1).getTerm());
-		assertEquals("label1", tagList.get(1).getLabel());
-		assertEquals(null, tagList.get(1).getScheme());
-		assertEquals("term2", tagList.get(2).getTerm());
-		assertEquals("label2", tagList.get(2).getLabel());
-		assertEquals(null, tagList.get(2).getScheme());
-		
-		/*
-		 * Encode
-		 */
-
-		//@formatter:off
-		String expected = "<taglist xmlns=\"http://hl7.org/fhir\">" + 
-				"<category term=\"term0\" label=\"label0\" scheme=\"scheme0\"/>" + 
-				"<category term=\"term1\" label=\"label1\"/>" + 
-				"<category term=\"term2\" label=\"label2\"/>" + 
-				"</taglist>";
-		//@formatter:on
-		
-		String encoded = ourCtx.newXmlParser().encodeTagListToString(tagList);
-		assertEquals(expected,encoded);
-		
-	}
-	
-	
-	@Test
-	public void testTotalResultsUsingOldNamespace() {
-
-		//@formatter:off
-		String bundle = "<feed xmlns=\"http://www.w3.org/2005/Atom\">\n" + 
-				"  <title>Search results for Patient</title>\n" + 
-				"  <id>urn:uuid:374f2876-0da7-4441-87da-526e2fc624f8</id>\n" + 
-				"  <totalResults xmlns=\"http://purl.org/atompub/tombstones/1.0\">15</totalResults>\n" + 
-				"  <updated>2014-05-04T13:19:47.027-04:00</updated>\n" + 
-				"  <author>\n" + 
-				"    <name>AEGIS Wildfhir Server</name>\n" + 
-				"  </author>" +
-				"</feed>";
-		//@formatter:off
-
-		Bundle bundleR = ourCtx.newXmlParser().parseBundle(bundle);
-		assertEquals(15, bundleR.getTotalResults().getValue().intValue());
-	}
-
-	@Test
-	public void testEncodeExtensionWithResourceContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		Patient patient = new Patient();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.addUndeclaredExtension(false, "urn:foo", new ResourceReferenceDt("Organization/123"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
-
-		Patient actual = parser.parseResource(Patient.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		List<ExtensionDt> ext = actual.getUndeclaredExtensionsByUrl("urn:foo");
-		assertEquals(1, ext.size());
-		ResourceReferenceDt ref = (ResourceReferenceDt) ext.get(0).getValue();
-		assertEquals("Organization/123", ref.getReference().getValue());
-
-	}
-
-	@Test
-	public void testEncodeDeclaredExtensionWithResourceContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		MyPatientWithOneDeclaredExtension patient = new MyPatientWithOneDeclaredExtension();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.setFoo(new ResourceReferenceDt("Organization/123"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
-
-		MyPatientWithOneDeclaredExtension actual = parser.parseResource(MyPatientWithOneDeclaredExtension.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		ResourceReferenceDt ref = actual.getFoo();
-		assertEquals("Organization/123", ref.getReference().getValue());
-
-	}
-
-	@Test
-	public void testEncodeDeclaredExtensionWithAddressContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		MyPatientWithOneDeclaredAddressExtension patient = new MyPatientWithOneDeclaredAddressExtension();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.setFoo(new AddressDt().addLine("line1"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
-
-		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		AddressDt ref = actual.getFoo();
-		assertEquals("line1", ref.getLineFirstRep().getValue());
-
-	}
-
-	@Test
-	public void testEncodeUndeclaredExtensionWithAddressContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		Patient patient = new Patient();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.addUndeclaredExtension(false, "urn:foo", new AddressDt().addLine("line1"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
-
-		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		AddressDt ref = actual.getFoo();
-		assertEquals("line1", ref.getLineFirstRep().getValue());
-
-	}
-
-	@Test
-	public void testEncodeBundleResultCount() {
-
-		Bundle b = new Bundle();
-		b.getTotalResults().setValue(123);
-
-		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
-		ourLog.info(val);
-
-		assertThat(val, StringContains.containsString("<os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">123</os:totalResults>"));
-
-	}
-
-	@Test
-	public void testEncodeBundleCategory() {
-
-		Bundle b = new Bundle();
-		BundleEntry e = b.addEntry();
-		e.setResource(new Patient());
-		e.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
-
-		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
-		ourLog.info(val);
-
-		assertThat(val, StringContains.containsString("<category term=\"term\" label=\"label\" scheme=\"scheme\"/>"));
-
-		b = ourCtx.newXmlParser().parseBundle(val);
-		assertEquals(1, b.getEntries().size());
-		assertEquals(1, b.getEntries().get(0).getCategories().size());
-		assertEquals("term", b.getEntries().get(0).getCategories().get(0).getTerm());
-		assertEquals("label", b.getEntries().get(0).getCategories().get(0).getLabel());
-		assertEquals("scheme", b.getEntries().get(0).getCategories().get(0).getScheme());
-		assertNull(b.getEntries().get(0).getResource());
-
-	}
-
 	@Test
 	public void testEncodeBundle() throws InterruptedException {
 		Bundle b= new Bundle();
+		b.getCategories().addTag("http://hl7.org/fhir/tag", "http://hl7.org/fhir/tag/message", "Message"); 
 
 		InstantDt pub = InstantDt.withCurrentTime();
 		b.setPublished(pub);
@@ -393,6 +123,7 @@ public class XmlParserTest {
 
 		List<String> strings = new ArrayList<String>();
 		strings.addAll(Arrays.asList("<published>", pub.getValueAsString(), "</published>"));
+		strings.add("<category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>");
 		strings.addAll(Arrays.asList("<entry>", "<id>1</id>", "</entry>"));
 		strings.addAll(Arrays.asList("<entry>", "<id>2</id>", "<link rel=\"alternate\" href=\"http://foo/bar\"/>", "<link rel=\"search\" href=\"http://foo/bar/search\"/>","</entry>"));
 		strings.addAll(Arrays.asList("<at:deleted-entry", "ref=\"Patient/3", "/>"));
@@ -402,6 +133,44 @@ public class XmlParserTest {
 	}
 
 	
+
+	@Test
+	public void testEncodeBundleCategory() {
+
+		Bundle b = new Bundle();
+		BundleEntry e = b.addEntry();
+		e.setResource(new Patient());
+		e.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
+
+		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(val);
+
+		assertThat(val, StringContains.containsString("<category term=\"term\" label=\"label\" scheme=\"scheme\"/>"));
+
+		b = ourCtx.newXmlParser().parseBundle(val);
+		assertEquals(1, b.getEntries().size());
+		assertEquals(1, b.getEntries().get(0).getCategories().size());
+		assertEquals("term", b.getEntries().get(0).getCategories().get(0).getTerm());
+		assertEquals("label", b.getEntries().get(0).getCategories().get(0).getLabel());
+		assertEquals("scheme", b.getEntries().get(0).getCategories().get(0).getScheme());
+		assertNull(b.getEntries().get(0).getResource());
+
+	}
+	
+	@Test
+	public void testEncodeBundleResultCount() {
+
+		Bundle b = new Bundle();
+		b.getTotalResults().setValue(123);
+
+		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(val);
+
+		assertThat(val, StringContains.containsString("<os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">123</os:totalResults>"));
+
+	}
+
+	
 	@Test
 	public void testEncodeContainedAndIncludedResources() {
 
@@ -421,8 +190,6 @@ public class XmlParserTest {
 	}
 
 	
-	
-	
 	@Test
 	public void testEncodeContainedResources() {
 
@@ -446,6 +213,66 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeDeclaredExtensionWithAddressContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		MyPatientWithOneDeclaredAddressExtension patient = new MyPatientWithOneDeclaredAddressExtension();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.setFoo(new AddressDt().addLine("line1"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
+
+		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		AddressDt ref = actual.getFoo();
+		assertEquals("line1", ref.getLineFirstRep().getValue());
+
+	}
+	
+	
+	@Test
+	public void testEncodeDeclaredExtensionWithResourceContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		MyPatientWithOneDeclaredExtension patient = new MyPatientWithOneDeclaredExtension();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.setFoo(new ResourceReferenceDt("Organization/123"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
+
+		MyPatientWithOneDeclaredExtension actual = parser.parseResource(MyPatientWithOneDeclaredExtension.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		ResourceReferenceDt ref = actual.getFoo();
+		assertEquals("Organization/123", ref.getReference().getValue());
+
+	}
+
+	@Test
+	public void testEncodeExtensionWithResourceContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.addUndeclaredExtension(false, "urn:foo", new ResourceReferenceDt("Organization/123"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
+
+		Patient actual = parser.parseResource(Patient.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		List<ExtensionDt> ext = actual.getUndeclaredExtensionsByUrl("urn:foo");
+		assertEquals(1, ext.size());
+		ResourceReferenceDt ref = (ResourceReferenceDt) ext.get(0).getValue();
+		assertEquals("Organization/123", ref.getReference().getValue());
+
+	}
+
 	@Test
 	public void testEncodeInvalidChildGoodException() {
 		Observation obs = new Observation();
@@ -502,6 +329,19 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeQuery() {
+		Query q = new Query();
+		ExtensionDt parameter = q.addParameter();
+		parameter.setUrl("http://foo").setValue(new StringDt("bar"));
+		
+		
+		String val = ourCtx.newXmlParser().encodeResourceToString(q);
+		ourLog.info(val);
+
+		assertEquals("<Query xmlns=\"http://hl7.org/fhir\"><parameter url=\"http://foo\"><valueString value=\"bar\"/></parameter></Query>", val);
+		
+	}
 
 	@Test
 	public void testEncodeResourceRef() throws DataFormatException {
@@ -525,6 +365,76 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeUndeclaredExtensionWithAddressContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.addUndeclaredExtension(false, "urn:foo", new AddressDt().addLine("line1"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
+
+		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		AddressDt ref = actual.getFoo();
+		assertEquals("line1", ref.getLineFirstRep().getValue());
+
+	}
+
+	@Test
+	public void testExtensionOnComposite() throws Exception {
+
+		Patient patient = new Patient();
+
+		HumanNameDt name = patient.addName();
+		name.addFamily().setValue("Shmoe");
+		HumanNameDt given = name.addGiven("Joe");
+		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
+		given.addUndeclaredExtension(ext2);
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<name><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension><family value=\"Shmoe\"/><given value=\"Joe\"/></name>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
+		assertEquals(1, parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
+		ExtensionDt ext = parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
+		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
+
+	}
+
+	
+	@Test
+	public void testExtensionOnPrimitive() throws Exception {
+
+		Patient patient = new Patient();
+
+		HumanNameDt name = patient.addName();
+		StringDt family = name.addFamily();
+		family.setValue("Shmoe");
+
+		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
+		family.addUndeclaredExtension(ext2);
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<name><family value=\"Shmoe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension></family></name>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
+		assertEquals(1, parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
+		ExtensionDt ext = parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
+		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
+
+	}
+
+	
+	
+	
 	@Test
 	public void testExtensions() throws DataFormatException {
 
@@ -630,6 +540,7 @@ public class XmlParserTest {
 		assertTrue(d.toString(), d.identical());
 	}
 
+	
 	@Test
 	public void testLoadAndEncodeUndeclaredExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
 		IParser p = ourCtx.newXmlParser();
@@ -683,25 +594,6 @@ public class XmlParserTest {
 		assertTrue(d.toString(), d.identical());
 	}
 
-	
-	@Test
-	public void testParseWithXmlHeader() throws ConfigurationException, DataFormatException {
-		IParser p = ourCtx.newXmlParser();
-
-		//@formatter:off
-		String msg = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" +
-				"<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-				"	<identifier>\n" + 
-				"		<label value=\"IdentifierLabel\"/>\n" + 
-				"	</identifier>\n" + 
-				"</Patient>";
-		//@formatter:on
-
-		Patient resource = (Patient) p.parseResource(msg);
-		assertEquals("IdentifierLabel", resource.getIdentifier().get(0).getLabel().getValue());
-	}
-	
-	
 	@Test
 	public void testLoadObservation() throws ConfigurationException, DataFormatException, IOException {
 
@@ -767,6 +659,52 @@ public class XmlParserTest {
 
 	}
 
+	
+	@Test
+	public void testMoreExtensions() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier(IdentifierUseEnum.OFFICIAL, "urn:example", "7000135", null);
+
+		ExtensionDt ext = new ExtensionDt();
+		ext.setModifier(false);
+		ext.setUrl("http://example.com/extensions#someext");
+		ext.setValue(new DateTimeDt("2011-01-02T11:13:15"));
+
+		// Add the extension to the resource
+		patient.addUndeclaredExtension(ext);
+		// END SNIPPET: resourceExtension
+
+		// START SNIPPET: resourceStringExtension
+		HumanNameDt name = patient.addName();
+		name.addFamily().setValue("Shmoe");
+		StringDt given = name.addGiven();
+		given.setValue("Joe");
+		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("given"));
+		given.addUndeclaredExtension(ext2);
+		// END SNIPPET: resourceStringExtension
+
+		// START SNIPPET: subExtension
+		ExtensionDt parent = new ExtensionDt(false, "http://example.com#parent");
+		patient.addUndeclaredExtension(parent);
+
+		ExtensionDt child1 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
+		parent.addUndeclaredExtension(child1);
+
+		ExtensionDt child2 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
+		parent.addUndeclaredExtension(child2);
+		// END SNIPPET: subExtension
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
+		assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension></extension>"));
+		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
+	}
+	
+	
 	@Test
 	public void testNarrativeGeneration() throws DataFormatException {
 
@@ -791,12 +729,50 @@ public class XmlParserTest {
 	}
 
 	@Test
-	public void testParseBundleWithMixedReturnTypes() {
+	public void testNestedContainedResources() {
-		InputStreamReader str = new InputStreamReader(getClass().getResourceAsStream("/mixed-return-bundle.xml"));
+
-		Bundle b = ourCtx.newXmlParser().parseBundle(Patient.class, str);
+		Observation A = new Observation();
-		assertEquals(Patient.class, b.getEntries().get(0).getResource().getClass());
+		A.getName().setText("A");
-		assertEquals(Patient.class, b.getEntries().get(1).getResource().getClass());
+		
-		assertEquals(Organization.class, b.getEntries().get(2).getResource().getClass());
+		Observation B = new Observation();
+		B.getName().setText("B");
+		A.addRelated().setTarget(new ResourceReferenceDt(B));
+		
+		Observation C = new Observation();
+		C.getName().setText("C");
+		B.addRelated().setTarget(new ResourceReferenceDt(C));
+
+		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(A);
+		ourLog.info(str);
+		
+		assertThat(str, stringContainsInOrder(Arrays.asList("<text value=\"B\"/>", "<text value=\"C\"/>", "<text value=\"A\"/>")));
+		assertThat(str, stringContainsInOrder(Arrays.asList("<contained>", "</contained>")));
+		
+		// Only one (outer) contained block
+		int idx0 = str.indexOf("<contained>");
+		int idx1 = str.indexOf("<contained>",idx0+1);
+		assertNotEquals(-1, idx0);
+		assertEquals(-1, idx1);
+		
+		Observation obs = ourCtx.newXmlParser().parseResource(Observation.class, str);
+		assertEquals("A",obs.getName().getText().getValue());
+		
+		Observation obsB = (Observation) obs.getRelatedFirstRep().getTarget().getResource();
+		assertEquals("B",obsB.getName().getText().getValue());
+
+		Observation obsC = (Observation) obsB.getRelatedFirstRep().getTarget().getResource();
+		assertEquals("C",obsC.getName().getText().getValue());
+
+		
+	}
+
+	@Test
+	public void testParseBinaryResource() {
+
+		Binary val = ourCtx.newXmlParser().parseResource(Binary.class, "<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>");
+		assertEquals("foo", val.getContentType());
+		assertArrayEquals(new byte[] {1,2,3,4}, val.getContent());
+
 	}
 
 	@SuppressWarnings("deprecation")
@@ -814,6 +790,7 @@ public class XmlParserTest {
 				"  <title>FHIR Core Valuesets</title>\n" + 
 				"  <id>http://hl7.org/fhir/profile/valuesets</id>\n" + 
 				"  <link href=\"http://hl7.org/implement/standards/fhir/valuesets.xml\" rel=\"self\"/>\n" +
+				"  <category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>\n" + 
 				"  <updated>2014-02-10T04:11:24.435-00:00</updated>\n" + 
 				"  <entry>\n" + 
 				"    <title>Valueset &quot;256a5231-a2bb-49bd-9fea-f349d428b70d&quot; to support automated processing</title>\n" + 
@@ -867,6 +844,9 @@ public class XmlParserTest {
 		IParser p = new FhirContext(ValueSet.class).newXmlParser();
 		Bundle bundle = p.parseBundle(msg);
 
+		assertEquals(1, bundle.getCategories().size());
+		assertEquals("http://hl7.org/fhir/tag", bundle.getCategories().get(0).getScheme());
+		
 		assertEquals("FHIR Core Valuesets", bundle.getTitle().getValue());
 		assertEquals("http://hl7.org/implement/standards/fhir/valuesets.xml", bundle.getLinkSelf().getValue());
 		assertEquals("2014-02-10T04:11:24.435+00:00", bundle.getUpdated().getValueAsString());
@@ -946,7 +926,6 @@ public class XmlParserTest {
 		
 	}
 
-	
 	@Test
 	public void testParseBundleLarge() throws IOException {
 
@@ -961,6 +940,15 @@ public class XmlParserTest {
 
 	}
 	
+	@Test
+	public void testParseBundleWithMixedReturnTypes() {
+		InputStreamReader str = new InputStreamReader(getClass().getResourceAsStream("/mixed-return-bundle.xml"));
+		Bundle b = ourCtx.newXmlParser().parseBundle(Patient.class, str);
+		assertEquals(Patient.class, b.getEntries().get(0).getResource().getClass());
+		assertEquals(Patient.class, b.getEntries().get(1).getResource().getClass());
+		assertEquals(Organization.class, b.getEntries().get(2).getResource().getClass());
+	}
+
 	@Test
 	public void testParseContainedResources() throws IOException {
 
@@ -976,19 +964,6 @@ public class XmlParserTest {
 
 	}
 
-	/**
-	 * This sample has extra elements in <searchParam> that are not actually a
-	 * part of the spec any more..
-	 */
-	@Test
-	public void testParseFuroreMetadataWithExtraElements() throws IOException {
-		String msg = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/furore-conformance.xml"));
-
-		IParser p = new FhirContext(ValueSet.class).newXmlParser();
-		Conformance conf = p.parseResource(Conformance.class, msg);
-		RestResource res = conf.getRestFirstRep().getResourceFirstRep();
-		assertEquals("_id", res.getSearchParam().get(1).getName().getValue());
-	}
 	
 	@Test
 	public void testParseEncodeNarrative() {
@@ -1010,103 +985,66 @@ public class XmlParserTest {
 
 	}
 
-	@BeforeClass
+	/**
-	public static void beforeClass() {
+	 * This sample has extra elements in <searchParam> that are not actually a
-		XMLUnit.setIgnoreAttributeOrder(true);
+	 * part of the spec any more..
-		XMLUnit.setIgnoreComments(true);
+	 */
-		XMLUnit.setIgnoreWhitespace(true);
+	@Test
-		ourCtx = new FhirContext();
+	public void testParseFuroreMetadataWithExtraElements() throws IOException {
+		String msg = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/furore-conformance.xml"));
+
+		IParser p = new FhirContext(ValueSet.class).newXmlParser();
+		Conformance conf = p.parseResource(Conformance.class, msg);
+		RestResource res = conf.getRestFirstRep().getResourceFirstRep();
+		assertEquals("_id", res.getSearchParam().get(1).getName().getValue());
 	}
 
 	@Test
-	public void testMoreExtensions() throws Exception {
+	public void testParseLanguage() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\"><language value=\"zh-CN\"/><text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> 海生 <b>王 </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>URNo</td></tr><tr><td>Address</td><td><span>99 Houston Road </span><br/><span>BENTLEIGH </span><span>Victoria </span></td></tr><tr><td>Date of birth</td><td><span>01 January 1997</span></td></tr></tbody></table></div></text><identifier><use value=\"usual\"/><label value=\"URNo\"/><value value=\"89532\"/></identifier><name><text value=\"王海生\"/><family value=\"王\"/><given value=\"海生\"/></name><telecom><system value=\"phone\"/><value value=\"9899 9878\"/><use value=\"home\"/></telecom><telecom><system value=\"email\"/><value value=\"zimmerman@datacorp.com.au\"/><use value=\"home\"/></telecom><gender><coding><system value=\"http://hl7.org/fhir/v3/AdministrativeGender\"/><code value=\"M\"/><display value=\"Male\"/></coding><text value=\"Male\"/></gender><birthDate value=\"1997-01-01\"/><address><use value=\"home\"/><text value=\"99 Houston Road, BENTLEIGH, 3204\"/><line value=\"99 Houston Road\"/><city value=\"BENTLEIGH\"/><state value=\"Victoria\"/><zip value=\"3204\"/><period><start value=\"2006-06-16\"/></period></address><active value=\"true\"/></Patient>";
+		Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
 		
-		Patient patient = new Patient();
+		assertEquals("zh-CN", pt.getLanguage().getValue());
-		patient.addIdentifier(IdentifierUseEnum.OFFICIAL, "urn:example", "7000135", null);
-
-		ExtensionDt ext = new ExtensionDt();
-		ext.setModifier(false);
-		ext.setUrl("http://example.com/extensions#someext");
-		ext.setValue(new DateTimeDt("2011-01-02T11:13:15"));
-
-		// Add the extension to the resource
-		patient.addUndeclaredExtension(ext);
-		// END SNIPPET: resourceExtension
-
-		// START SNIPPET: resourceStringExtension
-		HumanNameDt name = patient.addName();
-		name.addFamily().setValue("Shmoe");
-		StringDt given = name.addGiven();
-		given.setValue("Joe");
-		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("given"));
-		given.addUndeclaredExtension(ext2);
-		// END SNIPPET: resourceStringExtension
-
-		// START SNIPPET: subExtension
-		ExtensionDt parent = new ExtensionDt(false, "http://example.com#parent");
-		patient.addUndeclaredExtension(parent);
-
-		ExtensionDt child1 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
-		parent.addUndeclaredExtension(child1);
-
-		ExtensionDt child2 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
-		parent.addUndeclaredExtension(child2);
-		// END SNIPPET: subExtension
-
-		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(output);
-
-		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
-		assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension></extension>"));
-		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
 	}
 
 	@Test
-	public void testExtensionOnComposite() throws Exception {
+	public void testParseQuery() {
+		String msg = "<Query xmlns=\"http://hl7.org/fhir\">\n" + 
+				"  <text>\n" + 
+				"    <status value=\"generated\"/>\n" + 
+				"    <div xmlns=\"http://www.w3.org/1999/xhtml\">[Put rendering here]</div>\n" + 
+				"  </text>\n" + 
+				"\n" + 
+				"  <!--   this is an extermely simple query - a request to execute the query 'example' on the\n" + 
+				"   responder   -->\n" + 
+				"  <identifier value=\"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\"/>\n" + 
+				"  <parameter url=\"http://hl7.org/fhir/query#_query\">\n" + 
+				"    <valueString value=\"example\"/>\n" + 
+				"  </parameter>\n" + 
+				"</Query>";
+		Query query = ourCtx.newXmlParser().parseResource(Query.class, msg);
 		
-		Patient patient = new Patient();
+		assertEquals("urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376", query.getIdentifier().getValueAsString());
-
+		assertEquals("http://hl7.org/fhir/query#_query", query.getParameterFirstRep().getUrlAsString());
-		HumanNameDt name = patient.addName();
+		assertEquals("example", query.getParameterFirstRep().getValueAsPrimitive().getValueAsString());
-		name.addFamily().setValue("Shmoe");
-		HumanNameDt given = name.addGiven("Joe");
-		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
-		given.addUndeclaredExtension(ext2);
-		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(output);
-
-		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertThat(enc, containsString("<name><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension><family value=\"Shmoe\"/><given value=\"Joe\"/></name>"));
-
-		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
-		assertEquals(1, parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
-		ExtensionDt ext = parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
-		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
 		
 	}
 	
 	@Test
-	public void testExtensionOnPrimitive() throws Exception {
+	public void testParseWithXmlHeader() throws ConfigurationException, DataFormatException {
+		IParser p = ourCtx.newXmlParser();
 
-		Patient patient = new Patient();
+		//@formatter:off
-
+		String msg = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" +
-		HumanNameDt name = patient.addName();
+				"<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-		StringDt family = name.addFamily();
+				"	<identifier>\n" + 
-		family.setValue("Shmoe");
+				"		<label value=\"IdentifierLabel\"/>\n" + 
-
+				"	</identifier>\n" + 
-		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
+				"</Patient>";
-		family.addUndeclaredExtension(ext2);
+		//@formatter:on
-		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(output);
-
-		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertThat(enc, containsString("<name><family value=\"Shmoe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension></family></name>"));
-
-		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
-		assertEquals(1, parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
-		ExtensionDt ext = parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
-		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
 
+		Patient resource = (Patient) p.parseResource(msg);
+		assertEquals("IdentifierLabel", resource.getIdentifier().get(0).getLabel().getValue());
 	}
 
 	@Test
@@ -1167,4 +1105,71 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testTagList() {
+		
+		//@formatter:off
+		String tagListStr = "<taglist xmlns=\"http://hl7.org/fhir\"> \n" + 
+				"    <category term=\"term0\" label=\"label0\" scheme=\"scheme0\" /> \n" + 
+				"    <category term=\"term1\" label=\"label1\" scheme=\"\" /> \n" + 
+				"    <category term=\"term2\" label=\"label2\" /> \n" + 
+				"</taglist>";
+		//@formatter:on
+		
+		TagList tagList = ourCtx.newXmlParser().parseTagList(tagListStr);
+		assertEquals(3, tagList.size());
+		assertEquals("term0", tagList.get(0).getTerm());
+		assertEquals("label0", tagList.get(0).getLabel());
+		assertEquals("scheme0", tagList.get(0).getScheme());
+		assertEquals("term1", tagList.get(1).getTerm());
+		assertEquals("label1", tagList.get(1).getLabel());
+		assertEquals(null, tagList.get(1).getScheme());
+		assertEquals("term2", tagList.get(2).getTerm());
+		assertEquals("label2", tagList.get(2).getLabel());
+		assertEquals(null, tagList.get(2).getScheme());
+		
+		/*
+		 * Encode
+		 */
+
+		//@formatter:off
+		String expected = "<taglist xmlns=\"http://hl7.org/fhir\">" + 
+				"<category term=\"term0\" label=\"label0\" scheme=\"scheme0\"/>" + 
+				"<category term=\"term1\" label=\"label1\"/>" + 
+				"<category term=\"term2\" label=\"label2\"/>" + 
+				"</taglist>";
+		//@formatter:on
+		
+		String encoded = ourCtx.newXmlParser().encodeTagListToString(tagList);
+		assertEquals(expected,encoded);
+		
+	}
+
+	@Test
+	public void testTotalResultsUsingOldNamespace() {
+
+		//@formatter:off
+		String bundle = "<feed xmlns=\"http://www.w3.org/2005/Atom\">\n" + 
+				"  <title>Search results for Patient</title>\n" + 
+				"  <id>urn:uuid:374f2876-0da7-4441-87da-526e2fc624f8</id>\n" + 
+				"  <totalResults xmlns=\"http://purl.org/atompub/tombstones/1.0\">15</totalResults>\n" + 
+				"  <updated>2014-05-04T13:19:47.027-04:00</updated>\n" + 
+				"  <author>\n" + 
+				"    <name>AEGIS Wildfhir Server</name>\n" + 
+				"  </author>" +
+				"</feed>";
+		//@formatter:off
+
+		Bundle bundleR = ourCtx.newXmlParser().parseBundle(bundle);
+		assertEquals(15, bundleR.getTotalResults().getValue().intValue());
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		XMLUnit.setIgnoreAttributeOrder(true);
+		XMLUnit.setIgnoreComments(true);
+		XMLUnit.setIgnoreWhitespace(true);
+		ourCtx = new FhirContext();
+	}
+
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/ClientTest.java

@@ -1,9 +1,7 @@
 package ca.uhn.fhir.rest.client;
 
 import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -581,9 +579,11 @@ public class ClientTest {
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
 		when(httpClient.execute(capt.capture())).thenReturn(httpResponse);
 		when(httpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
-		Header[] headers = new Header[2];
+		Header[] headers = new Header[] {
-		headers[0] = new BasicHeader(Constants.HEADER_LAST_MODIFIED, "Wed, 15 Nov 1995 04:58:08 GMT");
+			new BasicHeader(Constants.HEADER_LAST_MODIFIED, "Wed, 15 Nov 1995 04:58:08 GMT"),
-		headers[1] = new BasicHeader(Constants.HEADER_CONTENT_LOCATION, "http://foo.com/Patient/123/_history/2333");
+			new BasicHeader(Constants.HEADER_CONTENT_LOCATION, "http://foo.com/Patient/123/_history/2333"),				
+			new BasicHeader(Constants.HEADER_CATEGORY, "http://foo/tagdefinition.html; scheme=\"http://hl7.org/fhir/tag\"; label=\"Some tag\"")
+		};
 	
 		when(httpResponse.getAllHeaders()).thenReturn(headers);
 		when(httpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
@@ -603,6 +603,13 @@ public class ClientTest {
 		lm.setTimeZoneZulu(true);
 		assertEquals("1995-11-15T04:58:08.000Z", lm.getValueAsString());
 
+		TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(response);
+		assertNotNull(tags);
+		assertEquals(1,tags.size());
+		assertEquals("http://foo/tagdefinition.html", tags.get(0).getTerm());
+		assertEquals("http://hl7.org/fhir/tag",tags.get(0).getScheme());
+		assertEquals("Some tag",tags.get(0).getLabel());
+
 	}
 
 	@Test

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/GenericClientTest.java

@@ -270,9 +270,11 @@ public class GenericClientTest {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
-		Header[] headers = new Header[2];
+		Header[] headers = new Header[] {
-		headers[0] = new BasicHeader(Constants.HEADER_LAST_MODIFIED, "Wed, 15 Nov 1995 04:58:08 GMT");
+				new BasicHeader(Constants.HEADER_LAST_MODIFIED, "Wed, 15 Nov 1995 04:58:08 GMT"),
-		headers[1] = new BasicHeader(Constants.HEADER_CONTENT_LOCATION, "http://foo.com/Patient/123/_history/2333");
+				new BasicHeader(Constants.HEADER_CONTENT_LOCATION, "http://foo.com/Patient/123/_history/2333"),				
+				new BasicHeader(Constants.HEADER_CATEGORY, "http://foo/tagdefinition.html; scheme=\"http://hl7.org/fhir/tag\"; label=\"Some tag\"")
+		};
 		when(myHttpResponse.getAllHeaders()).thenReturn(headers);
 	
 		IGenericClient client = myCtx.newRestfulGenericClient("http://example.com/fhir");
@@ -289,6 +291,13 @@ public class GenericClientTest {
 		lm.setTimeZoneZulu(true);
 		assertEquals("1995-11-15T04:58:08.000Z", lm.getValueAsString());
 
+		TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(response);
+		assertNotNull(tags);
+		assertEquals(1,tags.size());
+		assertEquals("http://foo/tagdefinition.html", tags.get(0).getTerm());
+		assertEquals("http://hl7.org/fhir/tag",tags.get(0).getScheme());
+		assertEquals("Some tag",tags.get(0).getLabel());
+		
 	}
 	
 	@SuppressWarnings("unused")

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/TransactionClientTest.java

@@ -75,7 +75,7 @@ public class TransactionClientTest {
 		when(httpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_ATOM_XML + "; charset=UTF-8"));
 		when(httpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(createBundle()), Charset.forName("UTF-8")));
 
-		client.searchWithParam(resources);
+		client.transaction(resources);
 
 		assertEquals(HttpPost.class, capt.getValue().getClass());
 		HttpPost post = (HttpPost) capt.getValue();
@@ -92,6 +92,47 @@ public class TransactionClientTest {
 		assertTrue(bundle.getEntries().get(1).getId().isEmpty());
 
 	}
+
+	
+	@Test
+	public void testSimpleTransactionWithBundleParam() throws Exception {
+		Patient patient = new Patient();
+		patient.setId(new IdDt("Patient/testPersistWithSimpleLinkP01"));
+		patient.addIdentifier("urn:system", "testPersistWithSimpleLinkP01");
+		patient.addName().addFamily("Tester").addGiven("Joe");
+
+		Observation obs = new Observation();
+		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
+		obs.setSubject(new ResourceReferenceDt("Patient/testPersistWithSimpleLinkP01"));
+
+		Bundle transactionBundle = Bundle.withResources(Arrays.asList((IResource)patient, obs), ctx, "http://foo");
+		
+		IBundleClient client = ctx.newRestfulClient(IBundleClient.class, "http://foo");
+		
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(httpClient.execute(capt.capture())).thenReturn(httpResponse);
+		when(httpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(httpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_ATOM_XML + "; charset=UTF-8"));
+		when(httpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(createBundle()), Charset.forName("UTF-8")));
+
+		client.transaction(transactionBundle);
+
+		assertEquals(HttpPost.class, capt.getValue().getClass());
+		HttpPost post = (HttpPost) capt.getValue();
+		assertEquals("http://foo/", post.getURI().toString());
+
+		Bundle bundle = ctx.newXmlParser().parseBundle(new InputStreamReader(post.getEntity().getContent()));
+		ourLog.info(ctx.newXmlParser().setPrettyPrint(true).encodeBundleToString(bundle));
+		
+		assertEquals(2, bundle.size());
+		assertEquals("http://foo/Patient/testPersistWithSimpleLinkP01", bundle.getEntries().get(0).getId().getValue());
+		assertEquals("http://foo/Patient/testPersistWithSimpleLinkP01", bundle.getEntries().get(0).getLinkSelf().getValue());
+		assertEquals(null, bundle.getEntries().get(0).getLinkAlternate().getValue());
+
+		assertTrue(bundle.getEntries().get(1).getId().isEmpty());
+
+	}
+
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TransactionClientTest.class);
 	private String createBundle() {
 		return ctx.newXmlParser().encodeBundleToString(new Bundle());
@@ -100,7 +141,15 @@ public class TransactionClientTest {
 	private interface IClient extends IBasicClient {
 
 		@Transaction
-		public List<IResource> searchWithParam(@TransactionParam List<IResource> theResources);
+		public List<IResource> transaction(@TransactionParam List<IResource> theResources);
+
+	
+	}
+
+	private interface IBundleClient extends IBasicClient {
+
+		@Transaction
+		public List<IResource> transaction(@TransactionParam Bundle theResources);
 
 	
 	}

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/method/BaseOutcomeReturningMethodBindingTest.java

@@ -14,7 +14,7 @@ public class BaseOutcomeReturningMethodBindingTest {
 		
 		String headerString = "http://britsystems.com/fhir/tag/4567; scheme=\"http://britsystems.com/fhir\"; label=\"Tag-4567\",http://client/scheme/tag/123; scheme=\"http://client/scheme\"; label=\"tag 123\",http://client/scheme/tag/456; scheme=\"http://client/scheme\"; label=\"tag 456\",http://fhir.healthintersections.com.au/open/Patient/1; scheme=\"http://hl7.org/fhir/tag\"; label=\"GET <host>/<resourceType>/<id>\",http://hl7.fhir/example; scheme=\"http://hl7.org/fhir/tag\"; label=\"FHIR example\",http://hl7.org/fhir/sid/us-ssn; scheme=\"http://hl7.org/fhir/tag\"; label=\"POST <host>/<resourceType>\",http://hl7.org/fhir/tools/tag/test; scheme=\"http://hl7.org/fhir/tag\"; label=\"Test Tag\",http://hl7.org/implement/standards/fhir/v3/ActCode/InformationSensitivityPolicy#GDIS; scheme=\"http://hl7.org/fhir/tag\"; label=\"GDIS\",http://hl7.org/implement/standards/fhir/v3/Confidentiality#N; scheme=\"http://hl7.org/fhir/tag\"; label=\"N (Normal)\",http://hl7.org/implement/standards/fhir/v3/Confidentiality#R; scheme=\"http://hl7.org/fhir/tag\"; label=\"restricted\",http://nu.nl/testname; scheme=\"http://hl7.org/fhir/tag\"; label=\"TestCreateEditDelete\",http://readtag.nu.nl; scheme=\"http://hl7.org/fhir/tag\"; label=\"readTagTest\",http://spark.furore.com/fhir; scheme=\"http://hl7.org/fhir/tag\"; label=\"GET <host>/<resourceType>/<id>\",http://www.healthintersections.com.au/fhir/tags/invalid; scheme=\"http://hl7.org/fhir/tag\"; label=\"Non-conformant Resource\",urn:happytag; scheme=\"http://hl7.org/fhir/tag\"; label=\"This is a happy resource\",condition; scheme=\"http://hl7.org/fhir/tag/profile\"; label=\"Profile condition\",device; scheme=\"http://hl7.org/fhir/tag/profile\"; label=\"Profile device\",http://fhir.healthintersections.com.au/open/Profile/condition; scheme=\"http://hl7.org/fhir/tag/profile\"; label=\"Profile condition\",http://fhir.healthintersections.com.au/open/Profile/device; scheme=\"http://hl7.org/fhir/tag/profile\"; label=\"Profile device\",http://hl7.org/fhir/v3/ActCode#CEL; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Celebrity / VIP\",http://hl7.org/fhir/v3/ActCode#DEMO; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Contact/Employment Confidential\",http://hl7.org/fhir/v3/ActCode#DIA; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Diagnosis is/would be Confidential\",http://hl7.org/fhir/v3/ActCode#EMP; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Employee / Staff member\",http://hl7.org/fhir/v3/ActCode#ORCON; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Author only\",http://hl7.org/fhir/v3/ActCode#TABOO; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Patient/Carer Only\",http://hl7.org/fhir/v3/Confidentiality#L; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Confidentiality = Low\",http://hl7.org/fhir/v3/Confidentiality#M; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Confidentiality = Moderate\",http://hl7.org/fhir/v3/Confidentiality#N; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Confidentiality = Normal\",http://hl7.org/fhir/v3/Confidentiality#R; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Confidentiality = Restricted\",http://hl7.org/fhir/v3/Confidentiality#U; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Confidentiality = none\",http://hl7.org/fhir/v3/Confidentiality#V; scheme=\"http://hl7.org/fhir/tag/security\"; label=\"Confidentiality = Very Restricted\",http://term.com; scheme=\"http://scheme.com\"; label=\"Some good ole term\"";
 		TagList parsedFromHeader = new TagList();
-		BaseOutcomeReturningMethodBinding.parseTagValue(parsedFromHeader, headerString);
+		MethodUtil.parseTagValue(parsedFromHeader, headerString);
 		
 		//@formatter:off
 		String resourceString = "{\n" + 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/CustomTypeTest.java

@@ -63,7 +63,7 @@ public class CustomTypeTest {
 		assertEquals(1, bundle.getEntries().size());
 
 		BundleEntry entry = bundle.getEntries().get(0);
-		ArrayList<Tag> profileTags = entry.getCategories().getTagsWithScheme(Constants.TAG_SCHEME_PROFILE);
+		List<Tag> profileTags = entry.getCategories().getTagsWithScheme(Tag.HL7_ORG_PROFILE_TAG);
 		assertEquals(1, profileTags.size());
 		assertEquals("http://foo/profiles/Profile", profileTags.get(0).getTerm());
 		

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/SearchTest.java

@@ -10,6 +10,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.impl.client.CloseableHttpClient;
@@ -26,9 +27,11 @@ 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.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.dstu.composite.CodingDt;
 import ca.uhn.fhir.model.dstu.resource.Observation;
 import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
 import ca.uhn.fhir.rest.annotation.RequiredParam;
@@ -149,6 +152,29 @@ public class SearchTest {
 		assertEquals("AAANamed", p.getIdentifierFirstRep().getValue().getValue());
 	}
 	
+	@Test
+	public void testReturnLinks() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort+"/Patient?_query=findWithLinks");
+		
+		CloseableHttpResponse 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.getEntries().size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals("AAANamed", p.getIdentifierFirstRep().getValue().getValue());
+		assertEquals("http://foo/Patient?_id=1", bundle.getEntries().get(0).getLinkSearch().getValue());
+		assertEquals("http://localhost:" + ourPort+"/Patient/9988", bundle.getEntries().get(0).getLinkAlternate().getValue());
+		
+		assertEquals("http://foo/Patient?_id=1", ResourceMetadataKeyEnum.LINK_SEARCH.get(p));
+		assertEquals("http://localhost:" + ourPort+"/Patient/9988", ResourceMetadataKeyEnum.LINK_ALTERNATE.get(p));
+		
+		
+	}
+
+	
 	@AfterClass
 	public static void afterClass() throws Exception {
 		ourServer.stop();
@@ -206,7 +232,7 @@ public class SearchTest {
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 		
 		@Search
-		public List<Patient> findPatient(@OptionalParam(name = "_id") StringParam theParam) {
+		public List<Patient> findPatient(@RequiredParam(name = "_id") StringParam theParam) {
 			ArrayList<Patient> retVal = new ArrayList<Patient>();
 
 			Patient patient = new Patient();
@@ -220,7 +246,7 @@ public class SearchTest {
 		}
 
 		@Search
-		public List<Patient> findPatientByAAA01(@OptionalParam(name = "AAA") StringParam theParam) {
+		public List<Patient> findPatientByAAA01(@RequiredParam(name = "AAA") StringParam theParam) {
 			ArrayList<Patient> retVal = new ArrayList<Patient>();
 
 			Patient patient = new Patient();
@@ -241,6 +267,19 @@ public class SearchTest {
 			return retVal;
 		}
 
+		@Search(queryName="findWithLinks")
+		public List<Patient> findWithLinks() {
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+
+			Patient patient = new Patient();
+			patient.setId("1");
+			patient.addIdentifier("system", "AAANamed");
+			ResourceMetadataKeyEnum.LINK_SEARCH.put(patient, ("http://foo/Patient?_id=1"));
+			ResourceMetadataKeyEnum.LINK_ALTERNATE.put(patient, ("Patient/9988"));
+			retVal.add(patient);
+			return retVal;
+		}
+
 		@Override
 		public Class<? extends IResource> getResourceType() {
 			return Patient.class;

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/TransactionTest.java

@@ -41,17 +41,16 @@ public class TransactionTest {
 
 	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx = new FhirContext();
+	private static boolean ourDropFirstResource;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TransactionTest.class);
 	private static int ourPort;
 	private static boolean ourReturnOperationOutcome;
-
 	private static Server ourServer;
 
-	
-	
 	@Before
 	public void before() {
 		ourReturnOperationOutcome = false;
+		ourDropFirstResource = false;
 	}
 
 	@Test
@@ -82,7 +81,8 @@ public class TransactionTest {
 		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());
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		assertEquals(200, status.getStatusLine().getStatusCode());
 
@@ -107,6 +107,56 @@ public class TransactionTest {
 		assertEquals(nowInstant.getValueAsString(), entry2.getDeletedAt().getValueAsString());
 	}
 
+	@Test
+	public void testTransactionWithFewerResponseElements() throws Exception {
+		ourDropFirstResource =true;
+		
+		Bundle b = new Bundle();
+		InstantDt nowInstant = InstantDt.withCurrentTime();
+
+		Patient p1 = new Patient();
+		p1.addName().addFamily("Family1");
+		BundleEntry entry = b.addEntry();
+		entry.getId().setValue("1");
+		entry.setResource(p1);
+
+		Patient p2 = new Patient();
+		p2.addName().addFamily("Family2");
+		entry = b.addEntry();
+		entry.getId().setValue("2");
+		entry.setResource(p2);
+
+		BundleEntry deletedEntry = b.addEntry();
+		deletedEntry.setId(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(2, bundle.size());
+
+		BundleEntry entry1 = bundle.getEntries().get(0);
+		assertEquals("http://localhost:" + ourPort + "/Patient/82", entry1.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(1);
+		assertEquals("http://localhost:" + ourPort + "/Patient/3", entry2.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 {
@@ -138,7 +188,8 @@ public class TransactionTest {
 		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());
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		assertEquals(200, status.getStatusLine().getStatusCode());
 
@@ -214,19 +265,21 @@ public class TransactionTest {
 				index++;
 			}
 
-			List<IResource> retVal = theResources;
+			List<IResource> retVal = new ArrayList<IResource>(theResources);
+
+			if (ourDropFirstResource) {
+				retVal.remove(0);
+			}
+
 			if (ourReturnOperationOutcome) {
-				retVal = new ArrayList<IResource>();
 				OperationOutcome oo = new OperationOutcome();
 				oo.addIssue().setDetails("AAAAA");
-				retVal.add(oo);
+				retVal.add(0, oo);
-				retVal.addAll(theResources);
 			}
 
 			return retVal;
 		}
 
-	
 	}
 
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/TransactionWithBundleParamTest.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.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.dstu.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu.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.testutil.RandomServerPortProvider;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class TransactionWithBundleParamTest {
+
+	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx = new FhirContext();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TransactionWithBundleParamTest.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");
+		BundleEntry entry = b.addEntry();
+		entry.getId().setValue("1");
+		entry.setResource(p1);
+
+		Patient p2 = new Patient();
+		p2.addName().addFamily("Family2");
+		entry = b.addEntry();
+		entry.getId().setValue("2");
+		entry.setResource(p2);
+		
+		BundleEntry deletedEntry = b.addEntry();
+		deletedEntry.setId(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(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.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.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.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();
+		entry.getId().setValue("1");
+		entry.setResource(p1);
+
+		Patient p2 = new Patient();
+		p2.addName().addFamily("Family2");
+		entry = b.addEntry();
+		entry.getId().setValue("2");
+		entry.setResource(p2);
+		
+		BundleEntry deletedEntry = b.addEntry();
+		deletedEntry.setId(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", entry0.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.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.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 = RandomServerPortProvider.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-base/src/test/resources/atom-document-large.json

@@ -25,6 +25,11 @@
     }
   ],
   "updated" : "2014-03-22T15:37:12Z",
+  "category" : [{
+    "term" : "http://term",
+    "label" : "label",
+    "scheme" : "http://scheme"
+  }],
   "totalResults" : "356",
   "entry" : [
     {

hapi-fhir-jpaserver-uhnfhirtest/.settings/org.eclipse.wst.common.component

@@ -12,7 +12,7 @@
         <dependent-module archiveName="hapi-fhir-base-0.6-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/hapi-fhir-base/hapi-fhir-base">
             <dependency-type>uses</dependency-type>
         </dependent-module>
-        <dependent-module deploy-path="/" handle="module:/overlay/prj/hapi-fhir-testpage-overlay?includes=**/**&amp;excludes=META-INF/MANIFEST.MF">
+        <dependent-module deploy-path="/" handle="module:/overlay/var/M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-testpage-overlay/0.6-SNAPSHOT/hapi-fhir-testpage-overlay-0.6-SNAPSHOT.war?unpackFolder=target/m2e-wtp/overlays&amp;includes=**/**&amp;excludes=META-INF/MANIFEST.MF">
             <dependency-type>consumes</dependency-type>
         </dependent-module>
         <dependent-module deploy-path="/" handle="module:/overlay/slf/?includes=**/**&amp;excludes=META-INF/MANIFEST.MF">

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

@@ -110,6 +110,7 @@ public class TinderStructuresMojo extends AbstractMojo {
 			ourLog.info("Loading profiles...");
 			ProfileParser pp = new ProfileParser();
 			for (ProfileFileDefinition next : resourceProfileFiles) {
+				ourLog.info("Parsing file: {}", next.profileFile);
 				pp.parseSingleProfile(new File(next.profileFile), next.profileSourceUrl);
 			}
 			
@@ -182,6 +183,10 @@ public class TinderStructuresMojo extends AbstractMojo {
 
 	public static void main(String[] args) throws Exception {
 
+		ProfileParser pp = new ProfileParser();
+			pp.parseSingleProfile(new File("../hapi-tinder-test/src/test/resources/profile/patient.xml"), "http://foo");
+
+		
 		 ValueSetGenerator vsp = new ValueSetGenerator();
 //		 vsp.setDirectory("src/test/resources/vs/");
 		 vsp.parse();
@@ -194,8 +199,9 @@ public class TinderStructuresMojo extends AbstractMojo {
 		 dtp.writeAll(new File(dtOutputDir), "ca.uhn.fhir.model.dstu");
 		
 		 ResourceGeneratorUsingSpreadsheet rp = new ResourceGeneratorUsingSpreadsheet();
-		 rp.setBaseResourceNames(Arrays.asList("observation"));
+		 rp.setBaseResourceNames(Arrays.asList("patient"));
 		 rp.parse();
+		 
 //		 rp.bindValueSets(vsp);
 		
 		 String rpOutputDir = "target/generated/valuesets/ca/uhn/fhir/model/dstu/resource";

pom.xml

@@ -57,6 +57,7 @@
 
 	<modules>
 		<module>hapi-fhir-base</module>
+		<module>hapi-fhir-base/examples</module>
 		<module>hapi-tinder-plugin</module>
 		<module>hapi-tinder-test</module>
 		<module>hapi-fhir-structures-dstu</module>