Many bugfixes

hapi-fhir-base/TODO.txt

@@ -33,6 +33,8 @@
  
  * Support "Binary" resource, which is a special resource type
  
+ * Submit "_pretty" as possible parameter to HL7
+ 
 ---------
 Issues:
  * Need to be able to bind Identifier.system to a set of allowable values in a profile. Graeme

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

@@ -8,7 +8,6 @@ import java.util.Set;
 import ca.uhn.fhir.model.api.ICodeEnum;
 import ca.uhn.fhir.model.api.IDatatype;
 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;
 
@@ -35,7 +34,8 @@ public abstract class BaseRuntimeChildDatatypeDefinition extends BaseRuntimeDecl
 
 	@Override
 	public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IElement> theDatatype) {
-		if (myDatatype.equals(theDatatype)) {
+		Class<? extends IElement> datatype = theDatatype;
+		if (myDatatype.equals(datatype)) {
 			return myElementDefinition;
 		}
 		return null;
@@ -74,4 +74,11 @@ public abstract class BaseRuntimeChildDatatypeDefinition extends BaseRuntimeDecl
 		}
 		myCodeType = theType;
 	}
+	
+	@Override
+	public String toString() {
+		return getClass().getSimpleName() + "[" + getElementName() + "]";
+	}
+
+	
 }

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

@@ -13,5 +13,4 @@ public class RuntimeChildCompositeDatatypeDefinition extends BaseRuntimeChildDat
 	}
 
 
-
 }

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

@@ -83,4 +83,9 @@ public class RuntimeChildResourceDefinition extends BaseRuntimeDeclaredChildDefi
 
 		myValidChildNames = Collections.unmodifiableSet(myValidChildNames);
 	}
+
+	@Override
+	public String toString() {
+		return getClass().getSimpleName() + "[" + getElementName() + "]";
+	}
 }

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

@@ -30,7 +30,7 @@ public class BoundCodeableConceptDt<T extends Enum<?>> extends CodeableConceptDt
 			return;
 		}
 		for (T next : theValues) {
-			getCoding().add(new BoundCodingDt<T>(myBinder, next));
+			getCoding().add(new CodingDt(myBinder.toSystemString(next), myBinder.toCodeString(next)));
 		}
 	}
 

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

@@ -5,16 +5,16 @@ import ca.uhn.fhir.model.api.IValueSetEnumBinder;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.dstu.composite.CodingDt;
 
-@DatatypeDef(name = "Coding")
+@DatatypeDef(name = "Coding", isSpecialization=true)
-public class BoundCodingDt<T extends Enum<?>> extends CodingDt {
+public class BoundCodingDt__<T extends Enum<?>> extends CodingDt {
 
 	private IValueSetEnumBinder<T> myBinder;
 
-	public BoundCodingDt(IValueSetEnumBinder<T> theBinder) {
+	public BoundCodingDt__(IValueSetEnumBinder<T> theBinder) {
 		myBinder = theBinder;
 	}
 	
-	public BoundCodingDt(IValueSetEnumBinder<T> theBinder, T theValue) {
+	public BoundCodingDt__(IValueSetEnumBinder<T> theBinder, T theValue) {
 		myBinder = theBinder;
 		setValueAsEnum(theValue);
 	}

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

@@ -8,9 +8,7 @@ import ca.uhn.fhir.model.api.annotation.SimpleSetter;
 import ca.uhn.fhir.parser.DataFormatException;
 
 /**
- * Represents the FHIR ID type. This is the actual resource ID, meaning the ID that
+ * Represents the FHIR ID type. This is the actual resource ID, meaning the ID that will be used in RESTful URLs, Resource References, etc. to represent a specific instance of a resource.
- * will be used in RESTful URLs, Resource References, etc. to represent a specific
- * instance of a resource.
  * 
  * <p>
  * <b>Description</b>: A whole number in the range 0 to 2^64-1 (optionally represented in hex), a uuid, an oid, or any other combination of lowercase letters, numerals, "-" and ".", with a length
@@ -32,6 +30,17 @@ public class IdDt extends BasePrimitive<String> {
 		super();
 	}
 
+	/**
+	 * Create a new ID, using a BigDecimal input. Uses {@link BigDecimal#toPlainString()} to generate the string representation.
+	 */
+	public IdDt(BigDecimal thePid) {
+		if (thePid != null) {
+			setValue(thePid.toPlainString());
+		} else {
+			setValue(null);
+		}
+	}
+
 	/**
 	 * Create a new ID using a long
 	 */
@@ -56,14 +65,24 @@ public class IdDt extends BasePrimitive<String> {
 	}
 
 	/**
-	 * Create a new ID, using a BigDecimal input. Uses {@link BigDecimal#toPlainString()} to generate the string representation.
+	 * Returns the value of this ID as a big decimal, or <code>null</code> if the value is null
+	 * 
+	 * @throws NumberFormatException
+	 *             If the value is not a valid BigDecimal
 	 */
-	public IdDt(BigDecimal thePid) {
+	public BigDecimal asBigDecimal() {
-		if (thePid != null) {
+		if (getValue() == null) {
-			setValue(thePid.toPlainString());
+			return null;
-		} else {
-			setValue(null);
 		}
+		return new BigDecimal(getValueAsString());
+	}
+
+	/**
+	 * Returns a reference to <code>this</code> IdDt. It is generally not neccesary to use this method but it is provided for consistency with the rest of the API.
+	 */
+	@Override
+	public IdDt getId() {
+		return this;
 	}
 
 	@Override
@@ -76,6 +95,14 @@ public class IdDt extends BasePrimitive<String> {
 		return myValue;
 	}
 
+	/**
+	 * Copies the value from the given IdDt to <code>this</code> IdDt. It is generally not neccesary to use this method but it is provided for consistency with the rest of the API.
+	 */
+	@Override
+	public void setId(IdDt theId) {
+		setValue(theId.getValue());
+	}
+
 	/**
 	 * Set the value
 	 * 
@@ -114,16 +141,4 @@ public class IdDt extends BasePrimitive<String> {
 		return myValue;
 	}
 
-	/**
-	 * Returns the value of this ID as a big decimal, or <code>null</code> if the value is null
-	 * 
-	 * @throws NumberFormatException If the value is not a valid BigDecimal
-	 */
-	public BigDecimal asBigDecimal() {
-		if (getValue() == null){
-			return null;
-		}
-		return new BigDecimal(getValueAsString());
-	}
-
 }

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

@@ -101,5 +101,13 @@ public class StringDt extends BasePrimitive<String> implements IQueryParameterTy
 		return getValue();
 	}
 	
+	/**
+	 * Returns <code>true</code> if this datatype has no extensions, and has either a <code>null</code>
+	 * value or an empty ("") value.
+	 */
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && StringUtils.isBlank(getValue());
+	}
 
 }

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

@@ -99,7 +99,7 @@ public class JsonParser extends BaseParser implements IParser {
 			writeTagWithTextNode(eventWriter, "id", nextEntry.getEntryId());
 
 			eventWriter.writeStartArray("link");
-			writeAtomLink(eventWriter, "self", theBundle.getLinkSelf());
+			writeAtomLink(eventWriter, "self", nextEntry.getLinkSelf());
 			eventWriter.writeEnd();
 
 			writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());

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

@@ -100,7 +100,7 @@ public class XmlParser extends BaseParser implements IParser {
 			writeAtomLink(eventWriter, "fhir-base", theBundle.getLinkBase());
 
 			if (theBundle.getTotalResults().getValue() != null) {
-				eventWriter.writeStartElement("os", "totalResults",OPENSEARCH_NS);
+				eventWriter.writeStartElement("os", "totalResults", OPENSEARCH_NS);
 				eventWriter.writeNamespace("os", OPENSEARCH_NS);
 				eventWriter.writeCharacters(theBundle.getTotalResults().getValue().toString());
 				eventWriter.writeEndElement();
@@ -119,6 +119,13 @@ public class XmlParser extends BaseParser implements IParser {
 			for (BundleEntry nextEntry : theBundle.getEntries()) {
 				eventWriter.writeStartElement("entry");
 
+				writeTagWithTextNode(eventWriter, "title", nextEntry.getTitle());
+				writeTagWithTextNode(eventWriter, "id", nextEntry.getEntryId());
+
+				if (!nextEntry.getLinkSelf().isEmpty()) {
+					writeAtomLink(eventWriter, "self", nextEntry.getLinkSelf());
+				}
+
 				eventWriter.writeStartElement("content");
 				eventWriter.writeAttribute("type", "text/xml");
 
@@ -138,7 +145,7 @@ public class XmlParser extends BaseParser implements IParser {
 
 	@Override
 	public String encodeResourceToString(IResource theResource) throws DataFormatException {
-		if (theResource==null) {
+		if (theResource == null) {
 			throw new NullPointerException("Resource can not be null");
 		}
 
@@ -200,8 +207,6 @@ public class XmlParser extends BaseParser implements IParser {
 		return parseResource(theResourceType, streamReader);
 	}
 
-
-
 	@Override
 	public IParser setPrettyPrint(boolean thePrettyPrint) {
 		myPrettyPrint = thePrettyPrint;
@@ -290,7 +295,8 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
-	private void encodeChildElementToStreamWriter(XMLStreamWriter theEventWriter, IElement nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl) throws XMLStreamException, DataFormatException {
+	private void encodeChildElementToStreamWriter(XMLStreamWriter theEventWriter, IElement nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl)
+			throws XMLStreamException, DataFormatException {
 		if (nextValue.isEmpty()) {
 			return;
 		}
@@ -355,7 +361,8 @@ public class XmlParser extends BaseParser implements IParser {
 
 	}
 
-	private void encodeCompositeElementChildrenToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children) throws XMLStreamException, DataFormatException {
+	private void encodeCompositeElementChildrenToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children) throws XMLStreamException,
+			DataFormatException {
 		for (BaseRuntimeChildDefinition nextChild : children) {
 			List<? extends IElement> values = nextChild.getAccessor().getValues(theElement);
 			if (values == null || values.isEmpty()) {
@@ -392,7 +399,8 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
-	private void encodeCompositeElementToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef) throws XMLStreamException, DataFormatException {
+	private void encodeCompositeElementToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef) throws XMLStreamException,
+			DataFormatException {
 		encodeExtensionsIfPresent(theEventWriter, theElement);
 		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getExtensions());
 		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getChildren());
@@ -419,7 +427,6 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
-
 	private void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter theEventWriter, boolean theIncludeResourceId) throws XMLStreamException, DataFormatException {
 		super.containResourcesForEncoding(theResource);
 
@@ -449,7 +456,7 @@ public class XmlParser extends BaseParser implements IParser {
 				IElement nextValue = next.getValue();
 				RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
 				String childName = extDef.getChildNameByDatatype(nextValue.getClass());
-				if (childName==null) {
+				if (childName == null) {
 					throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + nextValue.getClass().getCanonicalName());
 				}
 				BaseRuntimeElementDefinition<?> childDef = extDef.getChildElementDefinitionByDatatype(nextValue.getClass());
@@ -579,7 +586,6 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
-
 	private void writeTagWithTextNode(XMLStreamWriter theEventWriter, String theElementName, StringDt theStringDt) throws XMLStreamException {
 		theEventWriter.writeStartElement(theElementName);
 		if (StringUtils.isNotBlank(theStringDt.getValue())) {

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

@@ -10,11 +10,23 @@ import java.lang.annotation.Target;
  * be populated with the "_include" values for a search param.  
  * <p>
  * Only one parameter may be annotated with this annotation, and that
- * parameter should be of type Collection, List, or Set.
+ * parameter should be one of the following:
  * </p> 
+ * <ul>
+ * <li><code>Collection&lt;PathSpecification&gt;</code></li> 
+ * <li><code>List&lt;PathSpecification&gt;</code></li> 
+ * <li><code>Set&lt;PathSpecification&gt;</code></li> 
+ * </ul>
  */
 @Retention(RetentionPolicy.RUNTIME)
 @Target(value= {ElementType.PARAMETER})
 public @interface Include {
 
+	/**
+	 * Optional parameter, if provided the server will only allow the values
+	 * within the given set. If an _include parameter is passed to the server
+	 * which does not match any allowed values the server will return an error. 
+	 */
+	String[] allow() default {};
+	
 }

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

@@ -106,6 +106,9 @@ public class SearchMethodBinding extends BaseMethodBinding {
 			IParameter param = myParameters.get(i);
 			String[] value = parameterValues.get(param.getName());
 			if (value == null || value.length == 0) {
+				if (param.handlesMissing()) {
+					params[i] = param.parse(new ArrayList<List<String>>(0));
+				}
 				continue;
 			}
 			

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

@@ -8,14 +8,20 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public interface IParameter {
 
-	public abstract List<List<String>> encode(Object theObject) throws InternalErrorException;
+	List<List<String>> encode(Object theObject) throws InternalErrorException;
 
-	public abstract String getName();
+	String getName();
 
-	public abstract Object parse(List<List<String>> theString) throws InternalErrorException, InvalidRequestException;
+	Object parse(List<List<String>> theString) throws InternalErrorException, InvalidRequestException;
 
-	public abstract boolean isRequired();
+	boolean isRequired();
 	
-	public abstract SearchParamTypeEnum getParamType();
+	/**
+	 * Parameter should return true if {@link #parse(List)} should be called even
+	 * if the query string contained no values for the given parameter 
+	 */
+	boolean handlesMissing();
+
+	SearchParamTypeEnum getParamType();
 
 }

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

@@ -3,19 +3,29 @@ package ca.uhn.fhir.rest.param;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
+import java.util.TreeSet;
 
 import ca.uhn.fhir.model.api.PathSpecification;
 import ca.uhn.fhir.model.dstu.valueset.SearchParamTypeEnum;
+import ca.uhn.fhir.rest.annotation.Include;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public class IncludeParameter implements IParameter {
 
 	private Class<? extends Collection<PathSpecification>> myInstantiableCollectionType;
+	private HashSet<String> myAllow;
 
-	public IncludeParameter(Class<? extends Collection<PathSpecification>> theInstantiableCollectionType) {
+	public IncludeParameter(Include theAnnotation, Class<? extends Collection<PathSpecification>> theInstantiableCollectionType) {
 		myInstantiableCollectionType = theInstantiableCollectionType;
+		if (theAnnotation.allow().length > 0) {
+			myAllow = new HashSet<String>();
+			for (String next : theAnnotation.allow()) {
+				myAllow.add(next);
+			}
+		}
 	}
 
 	@SuppressWarnings("unchecked")
@@ -53,7 +63,13 @@ public class IncludeParameter implements IParameter {
 				throw new InvalidRequestException("'OR' query parameters (values containing ',') are not supported in _include parameters");
 			}
 			
-			retVal.add(new PathSpecification(nextParamList.get(0)));
+			String value = nextParamList.get(0);
+			if (myAllow != null) {
+				if (!myAllow.contains(value)) {
+					throw new InvalidRequestException("Invalid _include parameter value: '" + value + "'. Valid values are: " + new TreeSet<String>(myAllow));
+				}
+			}
+			retVal.add(new PathSpecification(value));
 		}
 		
 		return retVal;
@@ -69,4 +85,9 @@ public class IncludeParameter implements IParameter {
 		return null;
 	}
 
+	@Override
+	public boolean handlesMissing() {
+		return true;
+	}
+
 }

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

@@ -100,6 +100,8 @@ public class SearchParameter implements IParameter {
 			throw new ConfigurationException("Unknown search parameter type: " + type);
 		}
 		
+		// NB: Once this is enabled, we should return true from handlesMissing if
+		// it's a collection type
 //		if (theInnerCollectionType != null) {
 //			this.parser = new CollectionBinder(this.parser, theInnerCollectionType);
 //		}
@@ -115,4 +117,9 @@ public class SearchParameter implements IParameter {
 		return myParamType;
 	}
 
+	@Override
+	public boolean handlesMissing() {
+		return false;
+	}
+
 }

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

@@ -16,6 +16,8 @@ public class Constants {
 	public static final Set<String> FORMAT_VAL_XML;
 	public static final Set<String> FORMAT_VAL_JSON;
 	public static final Map<String, EncodingUtil> FORMAT_VAL_TO_ENCODING;
+	public static final String CT_XML = "application/xml";
+	public static final String CT_JSON = "application/json";
 
 	static {
 		Map<String, EncodingUtil> valToEncoding = new HashMap<String, EncodingUtil>();

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

@@ -2,16 +2,20 @@ package ca.uhn.fhir.rest.server;
 
 public enum EncodingUtil {
 
-	XML(Constants.CT_FHIR_XML, Constants.CT_ATOM_XML),
+	XML(Constants.CT_FHIR_XML, Constants.CT_ATOM_XML, Constants.CT_XML),
 
-	JSON(Constants.CT_FHIR_JSON, Constants.CT_FHIR_JSON);
+	JSON(Constants.CT_FHIR_JSON, Constants.CT_FHIR_JSON, Constants.CT_JSON)
+	
+	;
 
 	private String myResourceContentType;
 	private String myBundleContentType;
+	private String myBrowserFriendlyContentType;
 	
-	EncodingUtil(String theResourceContentType, String theBundleContentType) {
+	EncodingUtil(String theResourceContentType, String theBundleContentType, String theBrowserFriendlyContentType) {
 		myResourceContentType = theResourceContentType;
 		myBundleContentType = theBundleContentType;
+		myBrowserFriendlyContentType = theBrowserFriendlyContentType;
 	}
 
 	public String getBundleContentType() {
@@ -22,4 +26,8 @@ public enum EncodingUtil {
 		return myResourceContentType;
 	}
 
+	public String getBrowserFriendlyBundleContentType() {
+		return myBrowserFriendlyContentType;
+	}
+
 }

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

@@ -40,11 +40,24 @@ import ca.uhn.fhir.rest.server.provider.ServerProfileProvider;
 
 public abstract class RestfulServer extends HttpServlet {
 
+	private static final String PARAM_HISTORY = "_history";
+	private static final String PARAM_PRETTY = "_pretty";
+
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestfulServer.class);
 
 	private static final long serialVersionUID = 1L;
 
 	private FhirContext myFhirContext;
+	private boolean myUseBrowserFriendlyContentTypes;
+
+	/**
+	 * If set to <code>true</code> (default is false), the server will use browser friendly
+	 * content-types (instead of standard FHIR ones) when it detects that the request
+	 * is coming from a browser instead of a FHIR
+	 */
+	public void setUseBrowserFriendlyContentTypes(boolean theUseBrowserFriendlyContentTypes) {
+		myUseBrowserFriendlyContentTypes = theUseBrowserFriendlyContentTypes;
+	}
 
 	private Map<Class<? extends IResource>, IResourceProvider> myTypeToProvider = new HashMap<Class<? extends IResource>, IResourceProvider>();
 
@@ -81,7 +94,6 @@ public abstract class RestfulServer extends HttpServlet {
 		handleRequest(SearchMethodBinding.RequestType.DELETE, request, response);
 	}
 
-	
 	@Override
 	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
 		handleRequest(SearchMethodBinding.RequestType.GET, request, response);
@@ -102,7 +114,6 @@ public abstract class RestfulServer extends HttpServlet {
 		handleRequest(SearchMethodBinding.RequestType.PUT, request, response);
 	}
 
-
 	private void findResourceMethods(IResourceProvider theProvider) throws Exception {
 
 		Class<? extends IResource> resourceType = theProvider.getResourceType();
@@ -131,12 +142,11 @@ public abstract class RestfulServer extends HttpServlet {
 		}
 	}
 
-
 	public FhirContext getFhirContext() {
 		return myFhirContext;
 	}
 
-	private IParser getNewParser(EncodingUtil theResponseEncoding) {
+	private IParser getNewParser(EncodingUtil theResponseEncoding, boolean thePrettyPrint) {
 		IParser parser;
 		switch (theResponseEncoding) {
 		case JSON:
@@ -147,7 +157,7 @@ public abstract class RestfulServer extends HttpServlet {
 			parser = myFhirContext.newXmlParser();
 			break;
 		}
-		return parser;
+		return parser.setPrettyPrint(thePrettyPrint);
 	}
 
 	public Collection<ResourceBinding> getResourceBindings() {
@@ -160,8 +170,7 @@ public abstract class RestfulServer extends HttpServlet {
 	public abstract Collection<IResourceProvider> getResourceProviders();
 
 	/**
-	 * This method should be overridden to provide a security manager instance.
+	 * This method should be overridden to provide a security manager instance. By default, returns null.
-	 * By default, returns null.
 	 */
 	public ISecurityManager getSecurityManager() {
 		return null;
@@ -182,9 +191,16 @@ public abstract class RestfulServer extends HttpServlet {
 				securityManager.authenticate(request);
 			}
 			
+			String uaHeader = request.getHeader("user-agent");
+			boolean requestIsBrowser = false;
+			if (uaHeader != null && uaHeader.contains("Mozilla")) {
+				requestIsBrowser = true;
+			}
+			
+
 			String resourceName = null;
 			String requestFullPath = StringUtils.defaultString(request.getRequestURI());
-//			String contextPath = StringUtils.defaultString(request.getContextPath());
+			// String contextPath = StringUtils.defaultString(request.getContextPath());
 			String servletPath = StringUtils.defaultString(request.getServletPath());
 			StringBuffer requestUrl = request.getRequestURL();
 			String servletContextPath = "";
@@ -208,13 +224,27 @@ public abstract class RestfulServer extends HttpServlet {
 				requestPath = requestPath.substring(1);
 			}
 
-			int contextIndex = requestUrl.indexOf(servletPath);
+			int contextIndex;
+			if (servletPath.length()==0) {
+				contextIndex = requestUrl.indexOf(requestPath);
+			}else {
+				contextIndex = requestUrl.indexOf(servletPath);
+			}
+			
 			String fhirServerBase = requestUrl.substring(0, contextIndex + servletPath.length());
 			String completeUrl = StringUtils.isNotBlank(request.getQueryString()) ? requestUrl + "?" + request.getQueryString() : requestUrl.toString();
 
 			Map<String, String[]> params = new HashMap<String, String[]>(request.getParameterMap());
 			EncodingUtil responseEncoding = determineResponseEncoding(request, params);
 
+			String[] pretty = params.remove(PARAM_PRETTY);
+			boolean prettyPrint = false;
+			if (pretty != null && pretty.length > 0) {
+				if ("true".equals(pretty[0])) {
+					prettyPrint = true;
+				}
+			}
+
 			StringTokenizer tok = new StringTokenizer(requestPath, "/");
 			if (!tok.hasMoreTokens()) {
 				throw new MethodNotFoundException("No resource name specified");
@@ -244,7 +274,7 @@ public abstract class RestfulServer extends HttpServlet {
 
 			if (tok.hasMoreTokens()) {
 				String nextString = tok.nextToken();
-				if (nextString.startsWith("_history")) {
+				if (nextString.startsWith(PARAM_HISTORY)) {
 					if (tok.hasMoreTokens()) {
 						versionId = new IdDt(tok.nextToken());
 					} else {
@@ -271,7 +301,7 @@ public abstract class RestfulServer extends HttpServlet {
 			List<IResource> result = resourceMethod.invokeServer(resourceBinding.getResourceProvider(), id, versionId, params);
 			switch (resourceMethod.getReturnType()) {
 			case BUNDLE:
-				streamResponseAsBundle(response, result, responseEncoding, fhirServerBase, completeUrl);
+				streamResponseAsBundle(response, result, responseEncoding, fhirServerBase, completeUrl, prettyPrint, requestIsBrowser);
 				break;
 			case RESOURCE:
 				if (result.size() == 0) {
@@ -279,7 +309,7 @@ public abstract class RestfulServer extends HttpServlet {
 				} else if (result.size() > 1) {
 					throw new InternalErrorException("Method returned multiple resources");
 				}
-				streamResponseAsResource(response, result.get(0), resourceBinding, responseEncoding);
+				streamResponseAsResource(response, result.get(0), responseEncoding, prettyPrint, requestIsBrowser);
 				break;
 			}
 			// resourceMethod.get
@@ -344,16 +374,25 @@ public abstract class RestfulServer extends HttpServlet {
 		}
 	}
 
-	private void streamResponseAsBundle(HttpServletResponse theHttpResponse, List<IResource> theResult, EncodingUtil theResponseEncoding, String theFhirServerBase, String theCompleteUrl) throws IOException {
+	private void streamResponseAsBundle(HttpServletResponse theHttpResponse, List<IResource> theResult, EncodingUtil theResponseEncoding, String theServerBase, String theCompleteUrl,
+			boolean thePrettyPrint, boolean theRequestIsBrowser) throws IOException {
+		assert theServerBase.endsWith("/");
+		
 		theHttpResponse.setStatus(200);
-		theHttpResponse.setContentType(theResponseEncoding.getBundleContentType());
+		
+		if (theRequestIsBrowser && myUseBrowserFriendlyContentTypes) {
+			theHttpResponse.setContentType(theResponseEncoding.getBrowserFriendlyBundleContentType());
+		} else {
+			theHttpResponse.setContentType(theResponseEncoding.getBundleContentType());
+		}
+		
 		theHttpResponse.setCharacterEncoding("UTF-8");
 
 		Bundle bundle = new Bundle();
 		bundle.getAuthorName().setValue(getClass().getCanonicalName());
 		bundle.getBundleId().setValue(UUID.randomUUID().toString());
 		bundle.getPublished().setToCurrentTimeInLocalTimeZone();
-		bundle.getLinkBase().setValue(theFhirServerBase);
+		bundle.getLinkBase().setValue(theServerBase);
 		bundle.getLinkSelf().setValue(theCompleteUrl);
 
 		for (IResource next : theResult) {
@@ -361,23 +400,55 @@ public abstract class RestfulServer extends HttpServlet {
 			bundle.getEntries().add(entry);
 
 			entry.setResource(next);
+
+			RuntimeResourceDefinition def = myFhirContext.getResourceDefinition(next);
+
+			if (next.getId() != null && StringUtils.isNotBlank(next.getId().getValue())) {
+				entry.getEntryId().setValue(next.getId().getValue());
+				entry.getTitle().setValue(def.getName() + " " + next.getId().getValue());
+
+				StringBuilder b = new StringBuilder();
+				b.append(theServerBase);
+				b.append(def.getName());
+				b.append('/');
+				b.append(next.getId().getValue());
+				boolean haveQ = false;
+				if (thePrettyPrint) {
+					b.append('?').append(PARAM_PRETTY).append("=true");
+					haveQ = true;
+				}
+				if (theResponseEncoding == EncodingUtil.JSON) {
+					if (!haveQ) {
+						b.append('?');
+						haveQ = true;
+					} else {
+						b.append('&');
+					}
+					b.append(Constants.PARAM_FORMAT).append("=json");
+				}
+				entry.getLinkSelf().setValue(b.toString());
+			}
 		}
 
 		bundle.getTotalResults().setValue(theResult.size());
 
 		PrintWriter writer = theHttpResponse.getWriter();
-		getNewParser(theResponseEncoding).encodeBundleToWriter(bundle, writer);
+		getNewParser(theResponseEncoding, thePrettyPrint).encodeBundleToWriter(bundle, writer);
 		writer.close();
 	}
 
-	private void streamResponseAsResource(HttpServletResponse theHttpResponse, IResource theResource, ResourceBinding theResourceBinding, EncodingUtil theResponseEncoding) throws IOException {
+	private void streamResponseAsResource(HttpServletResponse theHttpResponse, IResource theResource, EncodingUtil theResponseEncoding, boolean thePrettyPrint, boolean theRequestIsBrowser) throws IOException {
 
 		theHttpResponse.setStatus(200);
-		theHttpResponse.setContentType(theResponseEncoding.getResourceContentType());
+		if (theRequestIsBrowser && myUseBrowserFriendlyContentTypes) {
+			theHttpResponse.setContentType(theResponseEncoding.getBrowserFriendlyBundleContentType());
+		} else {
+			theHttpResponse.setContentType(theResponseEncoding.getBundleContentType());
+		}
 		theHttpResponse.setCharacterEncoding("UTF-8");
 
 		PrintWriter writer = theHttpResponse.getWriter();
-		getNewParser(theResponseEncoding).encodeResourceToWriter(theResource, writer);
+		getNewParser(theResponseEncoding, thePrettyPrint).encodeResourceToWriter(theResource, writer);
 		writer.close();
 
 	}

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

@@ -10,7 +10,6 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import ch.qos.logback.core.joran.action.ParamAction;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.model.api.PathSpecification;
 import ca.uhn.fhir.rest.annotation.Include;
@@ -89,7 +88,7 @@ public class Util {
 					}
 					Class<? extends Collection<PathSpecification>> instantiableCollectionType = (Class<? extends Collection<PathSpecification>>) CollectionBinder.getInstantiableCollectionType(innerCollectionType, "Method '" + method.getName() + "'");
 					
-					param = new IncludeParameter(instantiableCollectionType);
+					param = new IncludeParameter((Include) nextAnnotation, instantiableCollectionType);
 				} else {
 					continue;
 				}

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

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.rest.server.provider;
 
-import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -22,13 +21,11 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.annotation.Metadata;
 import ca.uhn.fhir.rest.method.BaseMethodBinding;
-import ca.uhn.fhir.rest.method.ReadMethodBinding;
 import ca.uhn.fhir.rest.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.param.IParameter;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.ResourceBinding;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.util.DatatypeUtil;
 import ca.uhn.fhir.util.ExtensionConstants;
 import ca.uhn.fhir.util.VersionUtil;
 

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

@@ -19,6 +19,8 @@ public class ElementUtil {
 				if (!isEmpty((List<? extends IElement>) next)) {
 					return false;
 				}
+			} else if (next instanceof String && (!((String)next).isEmpty())) {
+				return false;
 			} else if (next != null && !((IElement) next).isEmpty()) {
 				return false;
 			}

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

@@ -94,7 +94,7 @@ public class PrettyPrintWriterWrapper implements XMLStreamWriter {
 	@Override
 	public void writeStartElement(String thePrefix, String theLocalName, String theNamespaceURI) throws XMLStreamException {
 		indentAndAdd();
-		myTarget.writeStartElement(thePrefix, theNamespaceURI, theLocalName);
+		myTarget.writeStartElement(thePrefix, theLocalName, theNamespaceURI);
 	}
 
 	@Override

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

@@ -138,8 +138,11 @@ public Class<? extends IResource> getResourceType() {
 
 //START SNIPPET: pathSpec
 @Search()
-public List<DiagnosticReport> getDiagnosticReport( @Required(name=DiagnosticReport.SP_IDENTIFIER) IdentifierDt theIdentifier,
+public List<DiagnosticReport> getDiagnosticReport( 
-                                                   @Include Set<PathSpecification> theIncludes ) {
+               @Required(name=DiagnosticReport.SP_IDENTIFIER) 
+               IdentifierDt theIdentifier,
+               @Include(allow= {"DiagnosticReport.subject"}) 
+               Set<PathSpecification> theIncludes ) {
   List<DiagnosticReport> retVal = new ArrayList<DiagnosticReport>();
  
   // Assume this method exists and loads the report from the DB

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

@@ -300,7 +300,7 @@
 				</p>
 				
 				<p>
-					Invoking a client of thie type involves the following syntax:
+					Invoking a client of this type involves the following syntax:
 				</p>
 				
 				<macro name="snippet">
@@ -328,6 +328,11 @@
 					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
 				</macro>
 				
+				<p>
+					Example URL to invoke this method:<br/>
+					<code>http://fhir.example.com/DiagnosticReport?subject.identifier=7000135&amp;_include=DiagnosticReport.subject</code>
+				</p>
+				
 			</subsection>
 
 		</section>

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

@@ -27,6 +27,8 @@ import ca.uhn.fhir.model.dstu.resource.Observation;
 import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.dstu.resource.Specimen;
 import ca.uhn.fhir.model.dstu.resource.ValueSet;
+import ca.uhn.fhir.model.dstu.valueset.AddressUseEnum;
+import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
 import ca.uhn.fhir.model.dstu.valueset.NarrativeStatusEnum;
 import ca.uhn.fhir.model.primitive.DecimalDt;
 
@@ -44,6 +46,33 @@ public class XmlParserTest {
 		
 	}
 
+	@Test
+	public void testEncodeBoundCode() throws IOException {
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		
+		patient.getGender().setValueAsEnum(AdministrativeGenderCodesEnum.M);
+		
+		String val = new FhirContext().newXmlParser().encodeResourceToString(patient);
+		ourLog.info(val);
+		
+	}
+
+	@Test
+	public void testEncodeBundleResultCount() throws IOException {
+
+		Bundle b = new Bundle();
+		b.getTotalResults().setValue(123);
+		
+		String val = new FhirContext().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 testParseContainedResources() throws IOException {
 		

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

@@ -1,9 +1,9 @@
 package ca.uhn.fhir.rest.server;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 
-import java.io.OutputStreamWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -23,13 +23,15 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.hamcrest.core.IsNot;
+import org.hamcrest.core.StringContains;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
-import org.junit.experimental.theories.Theories;
 
 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.PathSpecification;
 import ca.uhn.fhir.model.dstu.composite.CodingDt;
 import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
@@ -104,12 +106,60 @@ public class ResfulServerMethodTest {
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
 
-		Patient patient = (Patient) bundle.getEntries().get(0).getResource();
+		BundleEntry entry0 = bundle.getEntries().get(0);
+		Patient patient = (Patient) entry0.getResource();
 		assertEquals("include1", patient.getCommunication().get(0).getText().getValue());
 		assertEquals("include2", patient.getAddress().get(0).getLine().get(0).getValue());
 		assertEquals("include3", patient.getAddress().get(1).getLine().get(0).getValue());
 	}
 
+	@Test
+	public void testSearchWithIncludesNone() throws Exception {
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?withIncludes=include1");
+		HttpResponse status = ourClient.execute(httpGet);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		ourLog.info("Response was:\n{}", responseContent);
+
+		// Make sure there is no crash
+		assertEquals(200, status.getStatusLine().getStatusCode());
+	}
+	
+	@Test
+	public void testSearchWithIncludesBad() throws Exception {
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?withIncludes=include1&_include=include2&_include=include4");
+		HttpResponse status = ourClient.execute(httpGet);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		ourLog.info("Response was:\n{}", responseContent);
+
+		assertEquals(400, status.getStatusLine().getStatusCode());
+	}
+
+	@Test
+	public void testEntryLinkSelf() throws Exception {
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?withIncludes=include1&_include=include2&_include=include3");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+		BundleEntry entry0 = bundle.getEntries().get(0);
+		assertEquals("http://localhost:" + ourPort + "/Patient/1", entry0.getLinkSelf().getValue());
+		assertEquals("1", entry0.getEntryId().getValue());
+
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?withIncludes=include1&_include=include2&_include=include3&_format=json");
+		status = ourClient.execute(httpGet);
+		responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		bundle = ourCtx.newJsonParser().parseBundle(responseContent);
+		entry0 = bundle.getEntries().get(0);
+		assertEquals("http://localhost:" + ourPort + "/Patient/1?_format=json", entry0.getLinkSelf().getValue());
+
+	}
+
 	@Test
 	public void testSearchAllProfiles() throws Exception {
 
@@ -216,17 +266,17 @@ public class ResfulServerMethodTest {
 		assertEquals("urn:bbb|bbb", patient.getIdentifier().get(2).getValueAsQueryToken());
 	}
 
-//	@Test
+	// @Test
-//	public void testSearchByComplex() throws Exception {
+	// public void testSearchByComplex() throws Exception {
-//
+	//
-//		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?Patient.identifier=urn:oid:2.16.840.1.113883.3.239.18.148%7C7000135&name=urn:oid:1.3.6.1.4.1.12201.102.5%7C522&date=");
+	// HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?Patient.identifier=urn:oid:2.16.840.1.113883.3.239.18.148%7C7000135&name=urn:oid:1.3.6.1.4.1.12201.102.5%7C522&date=");
-//		HttpResponse status = ourClient.execute(httpGet);
+	// HttpResponse status = ourClient.execute(httpGet);
-//
+	//
-//		String responseContent = IOUtils.toString(status.getEntity().getContent());
+	// String responseContent = IOUtils.toString(status.getEntity().getContent());
-//		ourLog.info("Response was:\n{}", responseContent);
+	// ourLog.info("Response was:\n{}", responseContent);
-//
+	//
-//		assertEquals(200, status.getStatusLine().getStatusCode());
+	// assertEquals(200, status.getStatusLine().getStatusCode());
-//	}
+	// }
 
 	@Test
 	public void testSearchByDob() throws Exception {
@@ -404,6 +454,31 @@ public class ResfulServerMethodTest {
 
 	}
 
+	@Test
+	public void testPrettyPrint() throws Exception {
+
+		// HttpPost httpPost = new HttpPost("http://localhost:" + ourPort +
+		// "/Patient/1");
+		// httpPost.setEntity(new StringEntity("test",
+		// ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertThat(responseContent, StringContains.containsString("<identifier><use"));
+
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_pretty=false");
+		status = ourClient.execute(httpGet);
+		responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertThat(responseContent, StringContains.containsString("<identifier><use"));
+
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_pretty=true");
+		status = ourClient.execute(httpGet);
+		responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertThat(responseContent, IsNot.not(StringContains.containsString("<identifier><use")));
+
+	}
+
 	@Test
 	public void testGetById() throws Exception {
 
@@ -510,6 +585,7 @@ public class ResfulServerMethodTest {
 				patient.getName().get(0).addFamily("Test");
 				patient.getName().get(0).addGiven("PatientOne");
 				patient.getGender().setText("M");
+				patient.getId().setValue("1");
 				idToPatient.put("1", patient);
 			}
 			{
@@ -522,13 +598,15 @@ public class ResfulServerMethodTest {
 				patient.getName().get(0).addFamily("Test");
 				patient.getName().get(0).addGiven("PatientTwo");
 				patient.getGender().setText("F");
+				patient.getId().setValue("2");
 				idToPatient.put("2", patient);
 			}
 			return idToPatient;
 		}
 
 		@Search()
-		public Patient getPatientWithIncludes(@Required(name = "withIncludes") StringDt theString, @Include List<PathSpecification> theIncludes) {
+		public Patient getPatientWithIncludes(@Required(name = "withIncludes") StringDt theString, 
+				@Include(allow= {"include1","include2", "include3"}) List<PathSpecification> theIncludes) {
 			Patient next = getIdToPatient().get("1");
 
 			next.addCommunication().setText(theString.getValue());
@@ -553,11 +631,8 @@ public class ResfulServerMethodTest {
 		}
 
 		@SuppressWarnings("unused")
-		public List<Patient> findDiagnosticReportsByPatient(
+		public List<Patient> findDiagnosticReportsByPatient(@Required(name = "Patient.identifier") IdentifierDt thePatientId, @Required(name = DiagnosticReport.SP_NAME) CodingListParam theNames,
-				@Required(name="Patient.identifier") IdentifierDt thePatientId, 
+				@Optional(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange) throws Exception {
-				@Required(name=DiagnosticReport.SP_NAME) CodingListParam theNames,
-				@Optional(name=DiagnosticReport.SP_DATE) DateRangeParam theDateRange
-				) throws Exception {
 			return Collections.emptyList();
 		}