Work on narrative generator

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

@@ -60,9 +60,11 @@ public class RuntimeChildAny extends RuntimeChildChoiceDefinition {
 				if (o1res && o2res) {
 					return theO1.getSimpleName().compareTo(theO2.getSimpleName());
 				} else if (o1res) {
-					return 1;
-				}else {
 					return -1;
+				} else if (o1res == false && o2res == false) {
+					return 0;
+				}else {
+					return 1;
 				}
 			}});
 		

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

@@ -221,7 +221,12 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		RuntimeResourceDefinition def = theContext.getResourceDefinition(theResource);
 
 		if (theResource.getId() != null && StringUtils.isNotBlank(theResource.getId().getValue())) {
+			String title = ResourceMetadataKeyEnum.TITLE.get(theResource);
+			if (title != null) {
+				entry.getTitle().setValue(title);
+			} else {
 				entry.getTitle().setValue(def.getName() + " " + theResource.getId().getValue());
+			}
 
 			StringBuilder b = new StringBuilder();
 			b.append(theServerBase);

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

@@ -25,6 +25,8 @@ import static org.apache.commons.lang3.StringUtils.*;
 import java.util.Date;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
+
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -129,6 +131,26 @@ public abstract class ResourceMetadataKeyEnum<T> {
 		}
 	};
 
+	/**
+	 * If present and populated with a string (as an instance of {@link String}),
+	 * this value contains the title for this resource, as supplied in any bundles containing the
+	 * resource.  
+	 * <p>
+	 * Values for this key are of type <b>{@link String}</b>
+	 * </p>
+	 */
+	public static final ResourceMetadataKeyEnum<String> TITLE = new ResourceMetadataKeyEnum<String>("TITLE") {
+		@Override
+		public String get(IResource theResource) {
+			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), TITLE);
+		}
+
+		@Override
+		public void put(IResource theResource, String theObject) {
+			theResource.getResourceMetadata().put(TITLE, theObject);
+		}
+	};
+	
 	
 	/**
 	 * The value for this key is the bundle entry <b>Updated</b> time. This is
@@ -182,7 +204,6 @@ public abstract class ResourceMetadataKeyEnum<T> {
 	}
 
 	
-
 	@Override
 	public boolean equals(Object obj) {
 		if (this == obj)
@@ -200,6 +221,8 @@ public abstract class ResourceMetadataKeyEnum<T> {
 		return true;
 	}
 
+
+
 	public abstract T get(IResource theResource);
 
 	@Override
@@ -210,6 +233,10 @@ public abstract class ResourceMetadataKeyEnum<T> {
 		return result;
 	}
 
+	private String name() {
+		return myValue;
+	}
+
 	public abstract void put(IResource theResource, T theObject);
 
 	@Override
@@ -217,10 +244,6 @@ public abstract class ResourceMetadataKeyEnum<T> {
 		return myValue;
 	}
 
-	private String name() {
-		return myValue;
-	}
-
 	private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
 		Object retValObj = theResourceMetadata.get(theKey);
 		if (retValObj == null) {
@@ -259,4 +282,18 @@ public abstract class ResourceMetadataKeyEnum<T> {
 			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected " + InstantDt.class.getCanonicalName());
 		}
 		
+		private static String getStringFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<String> theKey) {
+			Object retValObj = theResourceMetadata.get(theKey);
+			if (retValObj == null) {
+				return null;
+			} else if (retValObj instanceof String) {
+				if (StringUtils.isBlank(((String) retValObj))) {
+					return null;
+				} else {
+					return (String) retValObj;
+				}
+			}
+			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected " + String.class.getCanonicalName());
+		}
+		
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/CodingDt.java

@@ -408,8 +408,10 @@ public class CodingDt
 	public String getValueAsQueryToken() {
 		if (org.apache.commons.lang3.StringUtils.isNotBlank(getSystem().getValueAsString())) {
 			return getSystem().getValueAsString() + '|' + getCode().getValueAsString();
-		} else {
+		} else if (getSystem().getValue()==null) {
 			return getCode().getValueAsString();
+		} else {
+			return '|' + getCode().getValueAsString();
 		}
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/IdentifierDt.java

@@ -414,6 +414,8 @@ public class IdentifierDt
 	public String getValueAsQueryToken() {
 		if (org.apache.commons.lang3.StringUtils.isNotBlank(getSystem().getValueAsString())) {
 			return getSystem().getValueAsString() + '|' + getValue().getValueAsString();
+		} else if (getSystem().getValue() == null) {
+			return getValue().getValueAsString();
 		} else {
 			return '|' + getValue().getValueAsString();
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/BaseThymeleafNarrativeGenerator.java

@@ -69,17 +69,100 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	private boolean myIgnoreMissingTemplates = true;
 
 	private TemplateEngine myProfileTemplateEngine;
-	private HashMap<String, String> myProfileToNarrativeName;
+	private TemplateEngine myTitleTemplateEngine;
-	private HashMap<Class<?>, String> myClassToNarrativeName;
+	private HashMap<String, String> myProfileToName;
+	private HashMap<Class<?>, String> myClassToName;
 	private HashMap<String, String> myNameToNarrativeTemplate;
 	private boolean myApplyDefaultDatatypeTemplates = true;
 	private volatile boolean myInitialized;
 
+	private HashMap<String, String> myNameToTitleTemplate;
+
 	@Override
 	public NarrativeDt generateNarrative(IResource theResource) {
 		return generateNarrative(null, theResource);
 	}
 
+	@Override
+	public String generateTitle(IResource theResource) {
+		return generateTitle(null, theResource);
+	}
+
+	@Override
+	public String generateTitle(String theProfile, IResource theResource) {
+		if (!myInitialized) {
+			initialize();
+		}
+
+		String name = null;
+		if (StringUtils.isNotBlank(theProfile)) {
+			name = myProfileToName.get(theProfile);
+		}
+		if (name == null) {
+			name = myClassToName.get(theResource.getClass());
+		}
+
+		if (name == null) {
+			if (myIgnoreMissingTemplates) {
+				ourLog.debug("No title template available for profile: {}", theProfile);
+				return null;
+			} else {
+				throw new DataFormatException("No title template for class " + theResource.getClass().getCanonicalName());
+			}
+		}
+
+		try {
+			Context context = new Context();
+			context.setVariable("resource", theResource);
+
+			String result = myTitleTemplateEngine.process(name, context);
+			StringBuilder b = new StringBuilder();
+			boolean inTag = false;
+			for (int i = 0; i < result.length(); i++) {
+				char nextChar = result.charAt(i);
+				char prevChar = i > 0 ? result.charAt(i - 1) : '\n';
+				if (nextChar == '<') {
+					inTag = true;
+					continue;
+				} else if (inTag) {
+					if (nextChar == '>') {
+						inTag = false;
+					}
+					continue;
+				} else if (nextChar <= ' ') {
+					if (prevChar <= ' ' || prevChar == '>') {
+						continue;
+					} else {
+						b.append(' ');
+					}
+				} else {
+					b.append(nextChar);
+				}
+			}
+			
+			while (b.length() > 0 && b.charAt(b.length()-1) == ' ') {
+				b.setLength(b.length() - 1);
+			}
+			
+			result = b.toString();
+			if (result.startsWith("<") && result.contains(">")) {
+				result = result.substring(result.indexOf('>') + 1);
+			}
+			if (result.endsWith(">") && result.contains("<")) {
+				result = result.substring(0, result.lastIndexOf('<'));
+			}
+
+			return result;
+		} catch (Exception e) {
+			if (myIgnoreFailures) {
+				ourLog.error("Failed to generate narrative", e);
+				return "No title available - Error: " + e.getMessage();
+			} else {
+				throw new DataFormatException(e);
+			}
+		}
+	}
+
 	@Override
 	public NarrativeDt generateNarrative(String theProfile, IResource theResource) {
 		if (!myInitialized) {
@@ -88,10 +171,10 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 
 		String name = null;
 		if (StringUtils.isNotBlank(theProfile)) {
-			name = myProfileToNarrativeName.get(theProfile);
+			name = myProfileToName.get(theProfile);
 		}
 		if (name == null) {
-			name = myClassToNarrativeName.get(theResource.getClass());
+			name = myClassToName.get(theResource.getClass());
 		}
 
 		if (name == null) {
@@ -131,9 +214,10 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 		if (myInitialized) {
 			return;
 		}
-		myProfileToNarrativeName = new HashMap<String, String>();
+		myProfileToName = new HashMap<String, String>();
-		myClassToNarrativeName = new HashMap<Class<?>, String>();
+		myClassToName = new HashMap<Class<?>, String>();
 		myNameToNarrativeTemplate = new HashMap<String, String>();
+		myNameToTitleTemplate = new HashMap<String, String>();
 
 		List<String> propFileName = getPropertyFile();
 
@@ -160,6 +244,15 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 			myProfileTemplateEngine.setDialect(dialect);
 			myProfileTemplateEngine.initialize();
 		}
+		{
+			myTitleTemplateEngine = new TemplateEngine();
+			TemplateResolver resolver = new TemplateResolver();
+			resolver.setResourceResolver(new TitleResourceResolver());
+			myTitleTemplateEngine.setTemplateResolver(resolver);
+			StandardDialect dialect = new StandardDialect();
+			myTitleTemplateEngine.setDialect(dialect);
+			myTitleTemplateEngine.initialize();
+		}
 
 		myInitialized = true;
 	}
@@ -167,12 +260,9 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	protected abstract List<String> getPropertyFile();
 
 	/**
-	 * If set to <code>true</code> (which is the default), most whitespace will
+	 * If set to <code>true</code> (which is the default), most whitespace will be trimmed from the generated narrative before it is returned.
-	 * be trimmed from the generated narrative before it is returned.
 	 * <p>
-	 * Note that in order to preserve formatting, not all whitespace is trimmed.
+	 * Note that in order to preserve formatting, not all whitespace is trimmed. Repeated whitespace characters (e.g. "\n       \n       ") will be trimmed to a single space.
-	 * Repeated whitespace characters (e.g. "\n       \n       ") will be
-	 * trimmed to a single space.
 	 * </p>
 	 */
 	public boolean isCleanWhitespace() {
@@ -180,30 +270,24 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	}
 
 	/**
-	 * If set to <code>true</code>, which is the default, if any failure occurs
+	 * If set to <code>true</code>, which is the default, if any failure occurs during narrative generation the generator will suppress any generated exceptions, and simply return a default narrative
-	 * during narrative generation the generator will suppress any generated
+	 * indicating that no narrative is available.
-	 * exceptions, and simply return a default narrative indicating that no
-	 * narrative is available.
 	 */
 	public boolean isIgnoreFailures() {
 		return myIgnoreFailures;
 	}
 
 	/**
-	 * If set to true, will return an empty narrative block for any profiles
+	 * If set to true, will return an empty narrative block for any profiles where no template is available
-	 * where no template is available
 	 */
 	public boolean isIgnoreMissingTemplates() {
 		return myIgnoreMissingTemplates;
 	}
 
 	/**
-	 * If set to <code>true</code> (which is the default), most whitespace will
+	 * If set to <code>true</code> (which is the default), most whitespace will be trimmed from the generated narrative before it is returned.
-	 * be trimmed from the generated narrative before it is returned.
 	 * <p>
-	 * Note that in order to preserve formatting, not all whitespace is trimmed.
+	 * Note that in order to preserve formatting, not all whitespace is trimmed. Repeated whitespace characters (e.g. "\n       \n       ") will be trimmed to a single space.
-	 * Repeated whitespace characters (e.g. "\n       \n       ") will be
-	 * trimmed to a single space.
 	 * </p>
 	 */
 	public void setCleanWhitespace(boolean theCleanWhitespace) {
@@ -211,18 +295,15 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	}
 
 	/**
-	 * If set to <code>true</code>, which is the default, if any failure occurs
+	 * If set to <code>true</code>, which is the default, if any failure occurs during narrative generation the generator will suppress any generated exceptions, and simply return a default narrative
-	 * during narrative generation the generator will suppress any generated
+	 * indicating that no narrative is available.
-	 * exceptions, and simply return a default narrative indicating that no
-	 * narrative is available.
 	 */
 	public void setIgnoreFailures(boolean theIgnoreFailures) {
 		myIgnoreFailures = theIgnoreFailures;
 	}
 
 	/**
-	 * If set to true, will return an empty narrative block for any profiles
+	 * If set to true, will return an empty narrative block for any profiles where no template is available
-	 * where no template is available
 	 */
 	public void setIgnoreMissingTemplates(boolean theIgnoreMissingTemplates) {
 		myIgnoreMissingTemplates = theIgnoreMissingTemplates;
@@ -245,13 +326,22 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 
 				String narrativePropName = name + ".narrative";
 				String narrativeName = file.getProperty(narrativePropName);
-				if (isBlank(narrativeName)) {
+				String titlePropName = name + ".title";
-					throw new ConfigurationException("Found property '" + nextKey + "' but no corresponding property '" + narrativePropName + "' in file " + propFileName);
+				String titleName = file.getProperty(titlePropName);
+				if (isBlank(narrativeName) && isBlank(titleName)) {
+					throw new ConfigurationException("Found property '" + nextKey + "' but no corresponding property '" + narrativePropName + "' or '" + titlePropName + "' in file " + propFileName);
 				}
 
+				myProfileToName.put(file.getProperty(nextKey), name);
+
+				if (StringUtils.isNotBlank(narrativeName)) {
 					String narrative = IOUtils.toString(loadResource(narrativeName));
-				myProfileToNarrativeName.put(file.getProperty(nextKey), name);
 					myNameToNarrativeTemplate.put(name, narrative);
+				}
+				if (StringUtils.isNotBlank(titleName)) {
+					String title = IOUtils.toString(loadResource(titleName));
+					myNameToTitleTemplate.put(name, title);
+				}
 
 			} else if (nextKey.endsWith(".class")) {
 
@@ -262,9 +352,9 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 
 				String className = file.getProperty(nextKey);
 
-				Class<?> dtClass;
+				Class<?> clazz;
 				try {
-					dtClass = Class.forName(className);
+					clazz = Class.forName(className);
 				} catch (ClassNotFoundException e) {
 					ourLog.warn("Unknown datatype class '{}' identified in narrative file {}", name, propFileName);
 					continue;
@@ -272,16 +362,27 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 
 				String narrativePropName = name + ".narrative";
 				String narrativeName = file.getProperty(narrativePropName);
-				if (isBlank(narrativeName)) {
+				String titlePropName = name + ".title";
-					throw new ConfigurationException("Found property '" + nextKey + "' but no corresponding property '" + narrativePropName + "' in file " + propFileName);
+				String titleName = file.getProperty(titlePropName);
+				if (isBlank(narrativeName) && isBlank(titleName)) {
+					throw new ConfigurationException("Found property '" + nextKey + "' but no corresponding property '" + narrativePropName + "' or '" + titlePropName + "' in file " + propFileName);
 				}
 
+				myClassToName.put(clazz, name);
+
+				if (StringUtils.isNotBlank(narrativeName)) {
 					String narrative = IOUtils.toString(loadResource(narrativeName));
-				myClassToNarrativeName.put(dtClass, name);
 					myNameToNarrativeTemplate.put(name, narrative);
+				}
+				if (StringUtils.isNotBlank(titleName)) {
+					String title = IOUtils.toString(loadResource(titleName));
+					myNameToTitleTemplate.put(name, title);
+				}
 
 			} else if (nextKey.endsWith(".narrative")) {
 				continue;
+			} else if (nextKey.endsWith(".title")) {
+				continue;
 			} else {
 				throw new ConfigurationException("Invalid property name: " + nextKey);
 			}
@@ -379,14 +480,13 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 			final IStandardExpression expression = expressionParser.parseExpression(configuration, theArguments, attributeValue);
 			final Object value = expression.execute(configuration, theArguments);
 
-
 			theElement.removeAttribute(theAttributeName);
 			theElement.clearChildren();
 
 			Context context = new Context();
 			context.setVariable("resource", value);
 
-			String name = myClassToNarrativeName.get(value.getClass());
+			String name = myClassToName.get(value.getClass());
 			if (name == null) {
 				if (myIgnoreMissingTemplates) {
 					ourLog.debug("No narrative template available for type: {}", value.getClass());
@@ -438,4 +538,21 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 			return new ReaderInputStream(new StringReader(template));
 		}
 	}
+
+	private final class TitleResourceResolver implements IResourceResolver {
+		@Override
+		public String getName() {
+			return getClass().getCanonicalName();
+		}
+
+		@Override
+		public InputStream getResourceAsStream(TemplateProcessingParameters theTemplateProcessingParameters, String theName) {
+			String template = myNameToTitleTemplate.get(theName);
+			if (template == null) {
+				ourLog.info("No narative template for resource profile: {}", theName);
+				return new ReaderInputStream(new StringReader(""));
+			}
+			return new ReaderInputStream(new StringReader(template));
+		}
+	}
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGenerator.java

@@ -64,4 +64,6 @@ public class DefaultThymeleafNarrativeGenerator extends BaseThymeleafNarrativeGe
 		return myUseHapiServerConformanceNarrative;
 	}
 
+
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/INarrativeGenerator.java

@@ -30,4 +30,8 @@ public interface INarrativeGenerator {
 
 	NarrativeDt generateNarrative(IResource theResource);
 
+	String generateTitle(IResource theResource);
+
+	String generateTitle(String theProfile, IResource theResource);
+
 }

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

@@ -222,6 +222,7 @@ public class JsonParser extends BaseParser implements IParser {
 		eventWriter.writeEnd(); // entry array
 
 		eventWriter.writeEnd();
+		eventWriter.flush();
 		eventWriter.close();
 	}
 
@@ -506,6 +507,7 @@ public class JsonParser extends BaseParser implements IParser {
 		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
 		encodeResourceToJsonStreamWriter(resDef, theResource, eventWriter, null,false);
 		eventWriter.flush();
+		eventWriter.close();
 	}
 
 	@Override
@@ -536,6 +538,7 @@ public class JsonParser extends BaseParser implements IParser {
 
 		eventWriter.writeEnd();
 		eventWriter.flush();
+		eventWriter.close();
 	}
 
 	/**

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

@@ -417,6 +417,9 @@ class ParserState<T> {
 			if (myEntry.getUpdated().isEmpty() == false) {
 				ResourceMetadataKeyEnum.UPDATED.put(myEntry.getResource(), myEntry.getUpdated());
 			}
+			
+			ResourceMetadataKeyEnum.TITLE.put(myEntry.getResource(), myEntry.getTitle().getValue());
+			
 			if (myEntry.getCategories().isEmpty() == false) {
 				TagList tagList = new TagList();
 				for (Tag next : myEntry.getCategories()) {
@@ -608,7 +611,6 @@ class ParserState<T> {
 			myPreResourceState = thePreResourceState;
 		}
 
-		@SuppressWarnings("unused")
 		public void attributeValue(String theName, String theValue) throws DataFormatException {
 			// ignore by default
 		}
@@ -617,7 +619,6 @@ class ParserState<T> {
 			// ignore by default
 		}
 
-		@SuppressWarnings("unused")
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			// ignore by default
 		}
@@ -657,7 +658,7 @@ class ParserState<T> {
 			myStack = theState;
 		}
 
-		public void string(@SuppressWarnings("unused") String theData) {
+		public void string(String theData) {
 			// ignore by default
 		}
 
@@ -665,7 +666,7 @@ class ParserState<T> {
 			// allow an implementor to override
 		}
 
-		public void xmlEvent(@SuppressWarnings("unused") XMLEvent theNextEvent) {
+		public void xmlEvent(XMLEvent theNextEvent) {
 			// ignore
 		}
 

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

@@ -64,4 +64,10 @@ public class IdentifierListParam implements IQueryParameterOr {
 		}
 	}
 
+	public void addIdentifier(IdentifierDt theIdentifierDt) {
+		if (theIdentifierDt != null && theIdentifierDt.isEmpty() == false) {
+			getIdentifiers().add(theIdentifierDt);
+		}
+	}
+
 }

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

@@ -160,6 +160,8 @@ public class SearchParameter extends BaseQueryParameter {
 			myParamType = SearchParamTypeEnum.QUANTITY;
 		} else if (ReferenceParam.class.isAssignableFrom(type)) {
 			myParamType = SearchParamTypeEnum.REFERENCE;
+		} else if (IdentifierListParam.class.isAssignableFrom(type)) {
+			myParamType = SearchParamTypeEnum.TOKEN;
 		} else {
 			throw new ConfigurationException("Unknown search parameter type: " + type);
 		}

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

@@ -45,6 +45,7 @@ import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.exception.ExceptionUtils;
@@ -557,7 +558,7 @@ public class RestfulServer extends HttpServlet {
 				statusCode=((BaseServerResponseException) e).getStatusCode();
 				issue.getDetails().setValue(e.getMessage());
 			} else {
-				ourLog.warn("Failure during REST processing: {}", e.toString());
+				ourLog.error("Failure during REST processing: {}"+ e.toString(), e);
 				issue.getDetails().setValue(e.toString() + "\n\n" + ExceptionUtils.getStackTrace(e));
 			}
 
@@ -779,6 +780,14 @@ public class RestfulServer extends HttpServlet {
 		bundle.getLinkSelf().setValue(theCompleteUrl);
 
 		for (IResource next : theResult) {
+			
+			if (theContext.getNarrativeGenerator() != null) {
+				String title = theContext.getNarrativeGenerator().generateTitle(next);
+				if (StringUtils.isNotBlank(title)) {
+					ResourceMetadataKeyEnum.TITLE.put(next, title);
+				}
+			}
+			
 			bundle.addResource(next, theContext, theServerBase);
 		}
 
@@ -1019,6 +1028,7 @@ public class RestfulServer extends HttpServlet {
 				RestfulServer.getNewParser(theServer.getFhirContext(), theResponseEncoding, thePrettyPrint, theNarrativeMode).encodeBundleToWriter(bundle, writer);
 			}
 		} finally {
+			writer.flush();
 			writer.close();
 		}
 	}
@@ -1093,6 +1103,7 @@ public class RestfulServer extends HttpServlet {
 				RestfulServer.getNewParser(theServer.getFhirContext(), theResponseEncoding, thePrettyPrint, theNarrativeMode).encodeResourceToWriter(theResource, writer);
 			}
 		} finally {
+			writer.flush();
 			writer.close();
 		}
 	}

hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/narratives.properties

@@ -32,6 +32,9 @@ quantity.narrative=classpath:ca/uhn/fhir/narrative/QuantityDt.html
 
 patient.class=ca.uhn.fhir.model.dstu.resource.Patient
 patient.narrative=classpath:ca/uhn/fhir/narrative/Patient.html
+patient.title=classpath:ca/uhn/fhir/narrative/title/Patient.html
+
 
 diagnosticreport.class=ca.uhn.fhir.model.dstu.resource.DiagnosticReport
 diagnosticreport.narrative=classpath:ca/uhn/fhir/narrative/DiagnosticReport.html
+diagnosticreport.title=classpath:ca/uhn/fhir/narrative/title/DiagnosticReport.html

hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/title/DiagnosticReport.html

@@ -0,0 +1,9 @@
+<div>
+	<th:block th:if="${not resource.name.text.empty}" th:text="${resource.name.text.value}"/>
+	<th:block th:if="    ${resource.name.text.empty} and ${not resource.name.codingFirstRep.display.empty}" th:text="${resource.name.codingFirstRep.display}"/>
+	<th:block th:if=    "${resource.name.text.empty} and     ${resource.name.codingFirstRep.display.empty}" th:text="Untitled Diagnostic Report"/>
+	
+	<th:block th:if="${not resource.status.empty}" th:text="' - ' + ${resource.status.value}"/>
+	<th:block th:text="' - ' + ${resource.result.size} + ' observations'"/>
+	
+</div>

hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/title/Patient.html

@@ -0,0 +1,9 @@
+<div>
+	<th:block th:each="prefix : ${resource.nameFirstRep.prefix}" th:text="${prefix.value} + ' '">Dr</th:block>
+	<th:block th:each="givenName : ${resource.nameFirstRep.given}" th:text="${givenName.value} + ' '">John</th:block>
+	<th:block th:each="familyName : ${resource.nameFirstRep.family}" th:text="${#strings.toUpperCase(familyName.value)} + ' '">SMITH</th:block>
+	<th:block th:each="suffix : ${resource.nameFirstRep.suffix}" th:text="${suffix.value} + ' '">Jr</th:block>
+	<th:block th:if="${not resource.identifierFirstRep.empty}">
+		(<th:block th:text="${resource.identifierFirstRep.value.value}">8708660</th:block>)
+	</th:block>
+</div>

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/primitive/CodingDtTest.java

@@ -0,0 +1,41 @@
+package ca.uhn.fhir.model.primitive;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+import ca.uhn.fhir.model.dstu.composite.CodingDt;
+
+public class CodingDtTest {
+
+	@Test
+	public void testTokenWithPipeInValue() {
+		CodingDt dt = new CodingDt();
+		dt.setValueAsQueryToken(null, "a|b|c");
+		
+		assertEquals("a", dt.getSystem().getValueAsString());
+		assertEquals("b|c", dt.getCode().getValue());
+		assertEquals("a|b|c", dt.getValueAsQueryToken());
+	}
+
+	@Test
+	public void testTokenWithPipeInValueAndNoSystem() {
+		CodingDt dt = new CodingDt();
+		dt.setValueAsQueryToken(null, "|b|c");
+		
+		assertEquals("", dt.getSystem().getValueAsString());
+		assertEquals("b|c", dt.getCode().getValue());
+		assertEquals("|b|c", dt.getValueAsQueryToken());
+	}
+
+	@Test
+	public void testTokenNoSystem() {
+		CodingDt dt = new CodingDt();
+		dt.setValueAsQueryToken(null, "c");
+		
+		assertEquals(null, dt.getSystem().getValueAsString());
+		assertEquals("c", dt.getCode().getValue());
+		assertEquals("c", dt.getValueAsQueryToken());
+	}
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/primitive/IdentifierDtTest.java

@@ -28,4 +28,14 @@ public class IdentifierDtTest {
 		assertEquals("|b|c", dt.getValueAsQueryToken());
 	}
 
+	@Test
+	public void testTokenNoSystem() {
+		IdentifierDt dt = new IdentifierDt();
+		dt.setValueAsQueryToken(null, "c");
+		
+		assertEquals(null, dt.getSystem().getValueAsString());
+		assertEquals("c", dt.getValue().getValue());
+		assertEquals("c", dt.getValueAsQueryToken());
+	}
+
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGeneratorTest.java

@@ -46,9 +46,12 @@ public class DefaultThymeleafNarrativeGeneratorTest {
 
 		value.setBirthDate(new Date(), TemporalPrecisionEnum.DAY);
 
-		String output = gen.generateNarrative("http://hl7.org/fhir/profiles/Patient", value).getDiv().getValueAsString();
+		String output = gen.generateNarrative(value).getDiv().getValueAsString();
+		assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> joe john <b>BLOW </b></div>"));
 		
-		ourLog.info(output);
+		String title = gen.generateTitle(value);
+		assertEquals("joe john BLOW (123456)", title);
+		ourLog.info(title);
 	}
 
 	@Test
@@ -105,6 +108,11 @@ public class DefaultThymeleafNarrativeGeneratorTest {
 		ourLog.info(output);
 		assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> Some Diagnostic Report </div>"));
 
+		String title = gen.generateTitle(value);
+		ourLog.info(title);
+		assertEquals("Some Diagnostic Report - final - 2 observations", title);
+
+		
 		// Now try it with the parser
 
 		FhirContext context = new FhirContext();

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

@@ -23,9 +23,8 @@ 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.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;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.testutil.RandomServerPortProvider;
@@ -36,7 +35,6 @@ import ca.uhn.fhir.testutil.RandomServerPortProvider;
 public class SearchTest {
 
 	private static CloseableHttpClient ourClient;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchTest.class);
 	private static int ourPort;
 	private static Server ourServer;
 	private static FhirContext ourCtx = new FhirContext();
@@ -46,12 +44,14 @@ public class SearchTest {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_id=aaa");
 		HttpResponse status = ourClient.execute(httpGet);
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
 		assertEquals(1, bundle.getEntries().size());
 		
 		Patient p = bundle.getResources(Patient.class).get(0);
 		assertEquals("idaaa", p.getNameFirstRep().getFamilyAsSingleString());
+		assertEquals("IDAAA (identifier123)", bundle.getEntries().get(0).getTitle().getValue());
 	}
 
 	@AfterClass
@@ -68,6 +68,8 @@ public class SearchTest {
 
 		ServletHandler proxyHandler = new ServletHandler();
 		RestfulServer servlet = new RestfulServer();
+		servlet.getFhirContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
+		
 		servlet.setResourceProviders(patientProvider);
 		ServletHolder servletHolder = new ServletHolder(servlet);
 		proxyHandler.addServletWithMapping(servletHolder, "/*");
@@ -92,6 +94,7 @@ public class SearchTest {
 
 			Patient patient = new Patient();
 			patient.setId("1");
+			patient.addIdentifier("system", "identifier123");
 			patient.addName().addFamily("id"+theParam.getValue());
 			retVal.add(patient);
 			return retVal;

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

@@ -747,6 +747,9 @@ public abstract class BaseFhirDao {
 			}
 		}
 
+		String title = ResourceMetadataKeyEnum.TITLE.get(theResource);
+		theEntity.setTitle(title);
+		
 	}
 
 	protected ResourceTable toEntity(IResource theResource) {
@@ -784,6 +787,10 @@ public abstract class BaseFhirDao {
 		retVal.getResourceMetadata().put(ResourceMetadataKeyEnum.PUBLISHED, theEntity.getPublished());
 		retVal.getResourceMetadata().put(ResourceMetadataKeyEnum.UPDATED, theEntity.getUpdated());
 		
+		if (theEntity.getTitle()!=null) {
+			ResourceMetadataKeyEnum.TITLE.put(retVal, theEntity.getTitle());
+		}
+		
 		if (theEntity.getDeleted()!=null) {
 			ResourceMetadataKeyEnum.DELETED_AT.put(retVal, new InstantDt(theEntity.getDeleted()));
 		}

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

@@ -431,7 +431,10 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 			ArrayList<Predicate> singleCodePredicates = (new ArrayList<Predicate>());
 			if (StringUtils.isNotBlank(system)) {
 				singleCodePredicates.add(builder.equal(from.get("mySystem"), system));
+			} else if (system == null) {
+				// don't check the system
 			} else {
+				// If the system is "", we only match on null systems
 				singleCodePredicates.add(builder.isNull(from.get("mySystem")));
 			}
 			if (StringUtils.isNotBlank(code)) {

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

@@ -35,6 +35,17 @@ public class SearchParameterMap extends HashMap<String, List<List<IQueryParamete
 		}
 	}
 
+	public void add(String theName, IQueryParameterOr theOr) {
+		if (theOr == null) {
+			return;
+		}
+		if (!containsKey(theName)) {
+			put(theName, new ArrayList<List<IQueryParameterType>>());
+		}
+
+		get(theName).add(theOr.getValuesAsQueryTokens());
+	}
+
 	public void add(String theName, IQueryParameterType theParam) {
 		if (theParam == null) {
 			return;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java

@@ -17,6 +17,8 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 @MappedSuperclass
 public abstract class BaseHasResource {
 
+	private static final int MAX_TITLE_LENGTH = 100;
+
 	@Column(name = "RES_DELETED_AT", nullable = true)
 	@Temporal(TemporalType.TIMESTAMP)
 	private Date myDeleted;
@@ -33,6 +35,9 @@ public abstract class BaseHasResource {
 	@Lob()
 	private byte[] myResource;
 
+	@Column(name = "RES_TITLE", nullable = true, length = MAX_TITLE_LENGTH)
+	private String myTitle;
+
 	@Temporal(TemporalType.TIMESTAMP)
 	@Column(name = "RES_UPDATED", nullable = false)
 	private Date myUpdated;
@@ -61,6 +66,10 @@ public abstract class BaseHasResource {
 
 	public abstract Collection<? extends BaseTag> getTags();
 
+	public String getTitle() {
+		return myTitle;
+	}
+
 	public InstantDt getUpdated() {
 		return new InstantDt(myUpdated);
 	}
@@ -87,6 +96,10 @@ public abstract class BaseHasResource {
 		myResource = theResource;
 	}
 
+	public void setTitle(String theTitle) {
+		myTitle = theTitle;
+	}
+
 	public void setUpdated(Date theUpdated) {
 		myUpdated = theUpdated;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamToken.java

@@ -8,7 +8,10 @@ import org.apache.commons.lang3.StringUtils;
 
 @Entity
 @Table(name = "HFJ_SPIDX_TOKEN" /* , indexes = { @Index(name = "IDX_SP_TOKEN", columnList = "SP_SYSTEM,SP_VALUE") } */)
-@org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_TOKEN", indexes = { @org.hibernate.annotations.Index(name = "IDX_SP_TOKEN", columnNames = { "RES_TYPE", "SP_NAME", "SP_SYSTEM", "SP_VALUE" }) })
+@org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_TOKEN", indexes = { 
+		@org.hibernate.annotations.Index(name = "IDX_SP_TOKEN", columnNames = { "RES_TYPE", "SP_NAME", "SP_SYSTEM", "SP_VALUE" }), 
+		@org.hibernate.annotations.Index(name = "IDX_SP_TOKEN_UNQUAL", columnNames = { "RES_TYPE", "SP_NAME", "SP_VALUE" }) 
+})
 public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchParam {
 
 	private static final long serialVersionUID = 1L;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java

@@ -252,6 +252,7 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		retVal.setResourceType(myResourceType);
 		retVal.setVersion(myVersion);
 
+		retVal.setTitle(getTitle());
 		retVal.setPublished(getPublished());
 		retVal.setUpdated(getUpdated());
 		retVal.setEncoding(getEncoding());

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

@@ -39,7 +39,9 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
+import ca.uhn.fhir.rest.gclient.IQuery;
 import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.IdentifierListParam;
 import ca.uhn.fhir.rest.param.QualifiedDateParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
@@ -122,6 +124,50 @@ public class FhirResourceDaoTest {
 		assertEquals(o1id.toUnqualifiedVersionless(), p1.getManagingOrganization().getReference().toUnqualifiedVersionless());
 	}
 
+	@Test
+	public void testSearchTokenParam() {
+		Patient patient = new Patient();
+		patient.addIdentifier("urn:system", "testSearchTokenParam001");
+		patient.addName().addFamily("Tester").addGiven("testSearchTokenParam1");
+		ourPatientDao.create(patient);
+
+		patient = new Patient();
+		patient.addIdentifier("urn:system", "testSearchTokenParam002");
+		patient.addName().addFamily("Tester").addGiven("testSearchTokenParam2");
+		ourPatientDao.create(patient);
+
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.add(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testSearchTokenParam001"));
+			IBundleProvider retrieved = ourPatientDao.search(map);
+			assertEquals(1, retrieved.size());
+		}
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.add(Patient.SP_IDENTIFIER, new IdentifierDt(null, "testSearchTokenParam001"));
+			IBundleProvider retrieved = ourPatientDao.search(map);
+			assertEquals(1, retrieved.size());
+		}
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			IdentifierListParam listParam = new IdentifierListParam();
+			listParam.addIdentifier(new IdentifierDt("urn:system", "testSearchTokenParam001"));
+			listParam.addIdentifier(new IdentifierDt("urn:system", "testSearchTokenParam002"));
+			map.add(Patient.SP_IDENTIFIER, listParam);
+			IBundleProvider retrieved = ourPatientDao.search(map);
+			assertEquals(2, retrieved.size());
+		}
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			IdentifierListParam listParam = new IdentifierListParam();
+			listParam.addIdentifier(new IdentifierDt(null, "testSearchTokenParam001"));
+			listParam.addIdentifier(new IdentifierDt("urn:system", "testSearchTokenParam002"));
+			map.add(Patient.SP_IDENTIFIER, listParam);
+			IBundleProvider retrieved = ourPatientDao.search(map);
+			assertEquals(2, retrieved.size());
+		}
+	}
+	
 	@Test
 	public void testIdParam() {
 		Patient patient = new Patient();
@@ -360,6 +406,7 @@ public class FhirResourceDaoTest {
 			Patient patient = new Patient();
 			patient.addIdentifier("urn:system", "001");
 			patient.addName().addFamily("testSearchNameParam01Fam").addGiven("testSearchNameParam01Giv");
+			ResourceMetadataKeyEnum.TITLE.put(patient, "P1TITLE");
 			id1 = ourPatientDao.create(patient).getId();
 		}
 		{
@@ -374,6 +421,7 @@ public class FhirResourceDaoTest {
 		List<Patient> patients = toList(ourPatientDao.search(params));
 		assertEquals(1, patients.size());
 		assertEquals(id1.getIdPart(), patients.get(0).getId().getIdPart());
+		assertEquals("P1TITLE", ResourceMetadataKeyEnum.TITLE.get(patients.get(0)));
 
 		// Given name shouldn't return for family param
 		params = new HashMap<String, IQueryParameterType>();

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/templates/tmpl-home-welcome.html

@@ -1,15 +1,15 @@
 <!DOCTYPE html>
 <html lang="en">
 	<div th:fragment="banner" class="well">
+		<th:block th:if="${serverEntry.key} == 'home'">
 			<p>
 				This is the home for the FHIR test server operated by
-			<a href="http://uhn.ca">University Health Network</a>.
+				<a href="http://uhn.ca">University Health Network</a>. This server
-		</p>
+				(and the testing application you are currently using to access it)
-		<p>
+				is entirely built using
-			<b style="color: red;">This is not a production server!</b> 
+				<a href="https://github.com/jamesagnew/hapi-fhir">HAPI-FHIR</a>, 
-			Do not store any information here that contains personal health information
+				a 100% open-source Java implementation of the
-			or otherwise confidential information. This server will be regularly purged 
+				<a href="http://hl7.org/implement/standards/fhir/">FHIR specification</a>.
-			and reloaded with fixed test data. 
 			</p>
 			<p>
 				Here are some things you might wish to try:
@@ -31,5 +31,22 @@
 					(use the <b>Server</b> menu at the top of the page to see a list of public FHIR servers)
 				</li>
 			</ul>
+		</th:block>
+		<th:block th:if="${serverEntry.key} != 'home'">
+			<p>
+				You are accessing the public FHIR server
+				<b th:text="${baseName}"/>. This server is hosted elsewhere on the internet
+				but is being accessed using 
+			</p>
+		</th:block>
+		<p>
+			<b style="color: red;">
+				<span class="glyphicon glyphicon-warning-sign/> 
+				This is not a production server!
+			</b> 
+			Do not store any information here that contains personal health information
+			or any other confidential information. This server will be regularly purged 
+			and reloaded with fixed test data. 
+		</p>
 	</div>
 </html>

hapi-fhir-testpage-overlay/src/main/webapp/WEB-INF/hapi-fhir-tester-config.xml

@@ -11,6 +11,7 @@
 	<bean class="ca.uhn.fhir.to.TesterConfig">
 		<property name="servers">
 			<list>
+				<value>test, TEST, http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.2/</value>
 				<value>home     , Localhost Server                , http://localhost:8887/fhir/context </value>
 				<value>hi       , Health Intersections            , http://fhir.healthintersections.com.au/open</value>
 				<value>furore   , Spark - Furore Reference Server , http://spark.furore.com/fhir</value>

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

@@ -34,7 +34,7 @@ public class ${className}ResourceProvider extends JpaResourceProvider<${classNam
 #if (${param.type} == 'string' )
 			StringParam the${param.nameCapitalized}, 
 #elseif (${param.type} == 'token' )
-			IdentifierDt the${param.nameCapitalized}, 
+			IdentifierListParam the${param.nameCapitalized}, 
 #elseif (${param.type} == 'date' )
 			DateRangeParam the${param.nameCapitalized}, 
 #elseif (${param.type} == 'quantity' )