Lots more JPA work, and getting sorting in`

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

@@ -166,4 +166,26 @@ public class Bundle extends BaseBundle /*implements IElement*/ {
 		return retVal;
 	}
 
+	/**
+	 * Returns the number of entries in this bundle
+	 */
+	public int size() {
+		return getEntries().size();
+	}
+
+	/**
+	 * Returns a list containing all resources of the given type from this bundle
+	 */
+	public <T extends IResource> List<T> getResources(Class<T> theClass) {
+		ArrayList<T> retVal = new ArrayList<T>();
+		for (BundleEntry next : getEntries()) {
+			if (next.getResource()!=null && theClass.isAssignableFrom(next.getResource().getClass())) {
+				@SuppressWarnings("unchecked")
+				T resource = (T) next.getResource();
+				retVal.add(resource);
+			}
+		}
+		return retVal;
+	}
+
 }

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

@@ -45,7 +45,7 @@ public interface IQueryParameterAnd {
 	 *    for information on the <b>token</b> format
 	 * </p>
 	 */
-	public List<QualifiedParamList> getValuesAsQueryTokens();
+	public List<IQueryParameterOr> getValuesAsQueryTokens();
 
 	
 }

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

@@ -20,32 +20,33 @@ package ca.uhn.fhir.model.api;
  * #L%
  */
 
+import java.util.List;
+
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 
 public interface IQueryParameterOr {
 
 	/**
-	 * Sets the value of this type using the <b>token</b> format. This 
+	 * Sets the value of this type using the <b>token</b> format. This format is used in HTTP queries as a parameter
-	 * format is used in HTTP queries as a parameter format.
+	 * format.
 	 * <p>
-	 * See FHIR specification 
+	 * See FHIR specification <a href="http://www.hl7.org/implement/standards/fhir/search.html#ptypes">2.2.2 Search
-	 *    <a href="http://www.hl7.org/implement/standards/fhir/search.html#ptypes">2.2.2 Search SearchParameter Types</a>
+	 * SearchParameter Types</a> for information on the <b>token</b> format
-	 *    for information on the <b>token</b> format
 	 * </p>
 	 */
 	public void setValuesAsQueryTokens(QualifiedParamList theParameters);
 
+	// public void setValuesAsQueryTokens(List<IQueryParameterType> theParameters);
+
 	/**
-	 * Returns the value of this type using the <b>token</b> format. This 
+	 * Returns the value of this type using the <b>token</b> format. This format is used in HTTP queries as a parameter
-	 * format is used in HTTP queries as a parameter format.
+	 * format.
 	 * 
 	 * <p>
-	 * See FHIR specification 
+	 * See FHIR specification <a href="http://www.hl7.org/implement/standards/fhir/search.html#ptypes">2.2.2 Search
-	 *    <a href="http://www.hl7.org/implement/standards/fhir/search.html#ptypes">2.2.2 Search SearchParameter Types</a>
+	 * SearchParameter Types</a> for information on the <b>token</b> format
-	 *    for information on the <b>token</b> format
 	 * </p>
 	 */
-	public QualifiedParamList getValuesAsQueryTokens();
+	public List<IQueryParameterType> getValuesAsQueryTokens();
-
 
 }

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

@@ -175,8 +175,7 @@ public class ResourceReferenceDt
      * </p> 
 	 */
 	public ResourceReferenceDt setReference( String theString) {
-		myReference = new StringDt(theString); 
+		return setReference(new StringDt(theString)); 
-		return this; 
 	}
 
  

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.parser;
 import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
+import java.io.ObjectInputStream.GetField;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -39,6 +40,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildDeclaredExtensionDefinition;
+import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
 import ca.uhn.fhir.context.RuntimeElemContainedResources;
 import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
 import ca.uhn.fhir.context.RuntimePrimitiveDatatypeNarrativeDefinition;
@@ -663,7 +665,7 @@ class ParserState<T> {
 			case RESOURCE_REF: {
 				ResourceReferenceDt newChildInstance = new ResourceReferenceDt();
 				myDefinition.getMutator().addValue(myParentInstance, newChildInstance);
-				ResourceReferenceState newState = new ResourceReferenceState(getPreResourceState(), newChildInstance);
+				ResourceReferenceState newState = new ResourceReferenceState(getPreResourceState(), (RuntimeResourceReferenceDefinition)target, newChildInstance);
 				push(newState);
 				return;
 			}
@@ -767,7 +769,7 @@ class ParserState<T> {
 				ResourceReferenceDt newChildInstance = new ResourceReferenceDt();
 				getPreResourceState().getResourceReferences().add(newChildInstance);
 				child.getMutator().addValue(myInstance, newChildInstance);
-				ResourceReferenceState newState = new ResourceReferenceState(getPreResourceState(), newChildInstance);
+				ResourceReferenceState newState = new ResourceReferenceState(getPreResourceState(), resourceRefTarget, newChildInstance);
 				push(newState);
 				return;
 			}
@@ -873,7 +875,7 @@ class ParserState<T> {
 			case RESOURCE_REF: {
 				ResourceReferenceDt newChildInstance = new ResourceReferenceDt();
 				myExtension.setValue(newChildInstance);
-				ResourceReferenceState newState = new ResourceReferenceState(getPreResourceState(), newChildInstance);
+				ResourceReferenceState newState = new ResourceReferenceState(getPreResourceState(), null, newChildInstance);
 				push(newState);
 				return;
 			}
@@ -1125,7 +1127,7 @@ class ParserState<T> {
 		private ResourceReferenceDt myInstance;
 		private ResourceReferenceSubState mySubState;
 
-		public ResourceReferenceState(PreResourceState thePreResourceState, ResourceReferenceDt theInstance) {
+		public ResourceReferenceState(PreResourceState thePreResourceState, RuntimeResourceReferenceDefinition theTarget, ResourceReferenceDt theInstance) {
 			super(thePreResourceState);
 			myInstance = theInstance;
 			mySubState = ResourceReferenceSubState.INITIAL;
@@ -1144,6 +1146,25 @@ class ParserState<T> {
 			case INITIAL:
 				throw new DataFormatException("Unexpected attribute: " + theValue);
 			case REFERENCE:
+				int lastSlash = theValue.lastIndexOf('/');
+				if (lastSlash==-1) {
+					myInstance.setResourceId(theValue);
+				} else if (lastSlash==0) {
+					myInstance.setResourceId(theValue.substring(1));
+				}else {
+					int secondLastSlash=theValue.lastIndexOf('/', lastSlash-1);
+					String resourceTypeName;
+					if (secondLastSlash==-1) {
+						resourceTypeName=theValue.substring(0,lastSlash);
+					}else {
+						resourceTypeName=theValue.substring(secondLastSlash+1,lastSlash);
+					}
+					myInstance.setResourceId(theValue.substring(lastSlash+1));
+					RuntimeResourceDefinition def = myContext.getResourceDefinition(resourceTypeName);
+					if(def!=null) {
+						myInstance.setResourceType(def.getImplementingClass());
+					}
+				}
 				myInstance.setReference(theValue);
 				break;
 			}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SortSpec.java

@@ -21,35 +21,23 @@ package ca.uhn.fhir.rest.api;
  */
 
 /**
- * Represents values for <a
+ * Represents values for <a href="http://hl7.org/implement/standards/fhir/search.html#sort">sorting</a> resources
- * href="http://hl7.org/implement/standards/fhir/search.html#sort">sorting</a>
+ * returned by a server.
- * resources returned by a server.
  */
 public class SortSpec {
 
-	private String myFieldName;
 	private SortSpec myChain;
+	private String myFieldName;
+	private SortOrderEnum myOrder;
 
 	/**
-	 * Gets the chained sort specification, or <code>null</code> if none. If
+	 * Gets the chained sort specification, or <code>null</code> if none. If multiple sort parameters are chained
-	 * multiple sort parameters are chained (indicating a sub-sort), the second
+	 * (indicating a sub-sort), the second level sort is chained via this property.
-	 * level sort is chained via this property.
 	 */
 	public SortSpec getChain() {
 		return myChain;
 	}
 
-	/**
-	 * Sets the chained sort specification, or <code>null</code> if none. If
-	 * multiple sort parameters are chained (indicating a sub-sort), the second
-	 * level sort is chained via this property.
-	 */
-	public void setChain(SortSpec theChain) {
-		myChain = theChain;
-	}
-
-	private SortOrderEnum myOrder;
-
 	/**
 	 * Returns the actual name of the field to sort by
 	 */
@@ -58,16 +46,22 @@ public class SortSpec {
 	}
 
 	/**
-	 * Returns the sort order specified by this parameter, or <code>null</code>
+	 * Returns the sort order specified by this parameter, or <code>null</code> if none is explicitly defined (which
-	 * if none is explicitly defined (which means {@link SortOrderEnum#ASC}
+	 * means {@link SortOrderEnum#ASC} according to the <a
-	 * according to the <a
+	 * href="http://hl7.org/implement/standards/fhir/search.html#sort">FHIR specification</a>)
-	 * href="http://hl7.org/implement/standards/fhir/search.html#sort">FHIR
-	 * specification</a>)
 	 */
 	public SortOrderEnum getOrder() {
 		return myOrder;
 	}
 
+	/**
+	 * Sets the chained sort specification, or <code>null</code> if none. If multiple sort parameters are chained
+	 * (indicating a sub-sort), the second level sort is chained via this property.
+	 */
+	public void setChain(SortSpec theChain) {
+		myChain = theChain;
+	}
+
 	/**
 	 * Sets the actual name of the field to sort by
 	 */
@@ -76,11 +70,9 @@ public class SortSpec {
 	}
 
 	/**
-	 * Sets the sort order specified by this parameter, or <code>null</code> if
+	 * Sets the sort order specified by this parameter, or <code>null</code> if none is explicitly defined (which means
-	 * none is explicitly defined (which means {@link SortOrderEnum#ASC}
+	 * {@link SortOrderEnum#ASC} according to the <a
-	 * according to the <a
+	 * href="http://hl7.org/implement/standards/fhir/search.html#sort">FHIR specification</a>)
-	 * href="http://hl7.org/implement/standards/fhir/search.html#sort">FHIR
-	 * specification</a>)
 	 */
 	public void setOrder(SortOrderEnum theOrder) {
 		myOrder = theOrder;

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

@@ -154,17 +154,26 @@ public abstract class BaseClient {
 			}
 
 			if (response.getStatusLine().getStatusCode() < 200 || response.getStatusLine().getStatusCode() > 299) {
-				BaseServerResponseException exception = BaseServerResponseException.newInstance(response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase());
+				String body=null;
-
 				try {
-					String body = IOUtils.toString(reader);
+					body = IOUtils.toString(reader);
-					exception.setResponseBody(body);
 				} catch (Exception e) {
 					ourLog.debug("Failed to read input stream", e);
 				} finally {
 					IOUtils.closeQuietly(reader);
 				}
 				
+				String message = "HTTP " + response.getStatusLine().getStatusCode()+" " +response.getStatusLine().getReasonPhrase();
+				if (Constants.CT_TEXT.equals(mimeType)) {
+					message = message+": " + body;
+				}
+				
+				BaseServerResponseException exception = BaseServerResponseException.newInstance(response.getStatusLine().getStatusCode(), message);
+
+				if(body!=null) {
+					exception.setResponseBody(body);
+				}
+
 				throw exception;
 			}
 

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

@@ -431,6 +431,12 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			params.get(parameterName).add(parameterValue);
 		}
 
+		@Override
+		public IQuery prettyPrint() {
+			setPrettyPrint(true);
+			return this;
+		}
+
 	}
 
 	private class QueryInternal implements IUntypedQuery {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IQuery.java

@@ -46,4 +46,6 @@ public interface IQuery {
 	 */
 	IQuery andLogRequestAndResponse(boolean theLogRequestAndResponse);
 
+	IQuery prettyPrint();
+	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ReferenceParam.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.rest.gclient;
 
+import ca.uhn.fhir.model.primitive.IdDt;
+
 /*
  * #%L
  * HAPI FHIR Library
@@ -38,6 +40,14 @@ public class ReferenceParam implements IParam {
 		return new ReferenceChainCriterion(getParamName(), theICriterion);
 	}
 
+	/**
+	 * Match the referenced resource if the resource has the given ID (this can be
+	 * the logical ID or the absolute URL of the resource)
+	 */
+	public ICriterion hasId(IdDt theId) {
+		return new StringCriterion(getParamName(), theId.getValueAsString());
+	}
+
 	/**
 	 * Match the referenced resource if the resource has the given ID (this can be
 	 * the logical ID or the absolute URL of the resource)
@@ -48,24 +58,24 @@ public class ReferenceParam implements IParam {
 
 	private static class ReferenceChainCriterion implements ICriterion, ICriterionInternal {
 
-		private ICriterionInternal myWrappedCriterion;
 		private String myParamName;
+		private ICriterionInternal myWrappedCriterion;
 
 		public ReferenceChainCriterion(String theParamName, ICriterion theWrappedCriterion) {
 			myParamName = theParamName;
 			myWrappedCriterion = (ICriterionInternal) theWrappedCriterion;
 		}
 
-		@Override
-		public String getParameterValue() {
-			return myWrappedCriterion.getParameterValue();
-		}
-
 		@Override
 		public String getParameterName() {
 			return myParamName + "." + myWrappedCriterion.getParameterName();
 		}
 
+		@Override
+		public String getParameterValue() {
+			return myWrappedCriterion.getParameterValue();
+		}
+
 	}
 
 }

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

@@ -23,6 +23,10 @@ package ca.uhn.fhir.rest.method;
 import java.util.ArrayList;
 import java.util.StringTokenizer;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+
 public class QualifiedParamList extends ArrayList<String> {
 
 	private static final long serialVersionUID = 1L;
@@ -37,6 +41,15 @@ public class QualifiedParamList extends ArrayList<String> {
 		super(theCapacity);
 	}
 
+	public QualifiedParamList(FhirContext theContext, IQueryParameterOr theNextOr) {
+		for (IQueryParameterType next : theNextOr.getValuesAsQueryTokens()) {
+			if (myQualifier==null) {
+				myQualifier=next.getQueryParameterQualifier(theContext);
+			}
+			add(next.getValueAsQueryToken());
+		}
+	}
+
 	public String getQualifier() {
 		return myQualifier;
 	}

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

@@ -159,6 +159,8 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 					return false;
 
 				}
+			} else {
+				methodParamsTemp.add(name);
 			}
 		}
 		if (myQueryName != null) {
@@ -181,11 +183,17 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 				methodParamsTemp.add(next);
 			}
 		}
-		boolean retVal = methodParamsTemp.containsAll(theRequest.getParameters().keySet());
+		Set<String> keySet = theRequest.getParameters().keySet();
+		for (String next : keySet) {
+			if (next.startsWith("_")) {
+				continue;
+			}
+			if (!methodParamsTemp.contains(next)) {
+				return false;
+			}
+		}
 
-		ourLog.trace("Method {} matches: {}", getMethod().getName(), retVal);
+		return true;
-
-		return retVal;
 	}
 
 	public void setResourceType(Class<?> resourceType) {

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

@@ -26,6 +26,7 @@ import java.util.Iterator;
 import java.util.List;
 
 import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.dstu.composite.CodingDt;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 
@@ -97,10 +98,10 @@ public class CodingListParam implements IQueryParameterOr, Iterable<CodingDt> {
 	}
 
 	@Override
-	public QualifiedParamList getValuesAsQueryTokens() {
+	public List<IQueryParameterType> getValuesAsQueryTokens() {
-		QualifiedParamList retVal = new QualifiedParamList();
+		ArrayList<IQueryParameterType> retVal = new ArrayList<IQueryParameterType>();
 		for (CodingDt next : myCodings) {
-			retVal.add(next.getValueAsQueryToken());
+			retVal.add(next);
 		}
 		return retVal;
 	}

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

@@ -25,6 +25,7 @@ import java.util.Date;
 import java.util.List;
 
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
@@ -156,13 +157,13 @@ public class DateRangeParam implements IQueryParameterAnd {
 	}
 
 	@Override
-	public List<QualifiedParamList> getValuesAsQueryTokens() {
+	public List<IQueryParameterOr> getValuesAsQueryTokens() {
-		ArrayList<QualifiedParamList> retVal = new ArrayList<QualifiedParamList>();
+		ArrayList<IQueryParameterOr> retVal = new ArrayList<IQueryParameterOr>();
 		if (myLowerBound != null) {
-			retVal.add(QualifiedParamList.singleton(myLowerBound.getValueAsQueryToken()));
+			retVal.add(ParameterUtil.singleton(myLowerBound));
 		}
 		if (myUpperBound != null) {
-			retVal.add(QualifiedParamList.singleton(myUpperBound.getValueAsQueryToken()));
+			retVal.add(ParameterUtil.singleton(myUpperBound));
 		}
 		return retVal;
 	}

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

@@ -23,13 +23,14 @@ package ca.uhn.fhir.rest.param;
 import java.util.List;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 interface IParamBinder {
 	
-	List<QualifiedParamList> encode(FhirContext theContext, Object theString) throws InternalErrorException;
+	List<IQueryParameterOr> encode(FhirContext theContext, Object theString) throws InternalErrorException;
 
 	Object parse(List<QualifiedParamList> theList) throws InternalErrorException, InvalidRequestException;
 

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

@@ -24,6 +24,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 
@@ -39,10 +40,10 @@ public class IdentifierListParam implements IQueryParameterOr {
 	}
 
 	@Override
-	public QualifiedParamList getValuesAsQueryTokens() {
+	public List<IQueryParameterType> getValuesAsQueryTokens() {
-		QualifiedParamList retVal = new QualifiedParamList();
+		ArrayList<IQueryParameterType> retVal = new ArrayList<IQueryParameterType>();
 		for (IdentifierDt next : myIdentifiers) {
-			retVal.add(next.getValueAsQueryToken());
+			retVal.add(next);
 		}
 		return retVal;
 	}

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

@@ -41,6 +41,8 @@ import javax.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.time.DateUtils;
 
 import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.PathSpecification;
 import ca.uhn.fhir.model.api.TagList;
@@ -56,7 +58,9 @@ import ca.uhn.fhir.rest.annotation.RequiredParam;
 import ca.uhn.fhir.rest.annotation.ResourceParam;
 import ca.uhn.fhir.rest.annotation.ServerBase;
 import ca.uhn.fhir.rest.annotation.Since;
+import ca.uhn.fhir.rest.annotation.Sort;
 import ca.uhn.fhir.rest.annotation.VersionIdParam;
+import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.util.ReflectionUtil;
 
 public class ParameterUtil {
@@ -135,6 +139,7 @@ public class ParameterUtil {
 	public static Set<Class<?>> getBindableInstantTypes() {
 		return BINDABLE_TIME_TYPES;
 	}
+
 	public static Set<Class<?>> getBindableIntegerTypes() {
 		return BINDABLE_INTEGER_TYPES;
 	}
@@ -218,6 +223,8 @@ public class ParameterUtil {
 						param = new SinceParameter();
 					} else if (nextAnnotation instanceof Count) {
 						param = new CountParameter();
+					} else if (nextAnnotation instanceof Sort) {
+						param = new SortParameter();
 					} else {
 						continue;
 					}
@@ -227,7 +234,7 @@ public class ParameterUtil {
 			}
 
 			if (param == null) {
-				throw new ConfigurationException("Parameter #" + paramIndex + " of method '" + theMethod.getName() + "' on type '" + theMethod.getDeclaringClass().getCanonicalName()
+				throw new ConfigurationException("Parameter #" + ((paramIndex+1))+"/" + (parameterTypes.length) + " of method '" + theMethod.getName() + "' on type '" + theMethod.getDeclaringClass().getCanonicalName()
 						+ "' has no recognized FHIR interface parameter annotations. Don't know how to handle this parameter");
 			}
 
@@ -290,4 +297,25 @@ public class ParameterUtil {
 		return null;
 	}
 
+	public static IQueryParameterOr singleton(final IQueryParameterType theParam) {
+		return new IQueryParameterOr() {
+
+			@Override
+			public void setValuesAsQueryTokens(QualifiedParamList theParameters) {
+				if (theParameters.isEmpty()) {
+					return;
+				}
+				if (theParameters.size() > 1) {
+					throw new IllegalArgumentException("Type " + theParam.getClass().getCanonicalName() + " does not support multiple values");
+				}
+				theParam.setValueAsQueryToken(theParameters.getQualifier(), theParameters.get(0));
+			}
+
+			@Override
+			public List<IQueryParameterType> getValuesAsQueryTokens() {
+				return Collections.singletonList(theParam);
+			}
+		};
+	}
+
 }

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

@@ -24,6 +24,7 @@ import java.util.List;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -36,8 +37,8 @@ final class QueryParameterAndBinder implements IParamBinder {
 	}
 
 	@Override
-	public List<QualifiedParamList> encode(FhirContext theContext, Object theString) throws InternalErrorException {
+	public List<IQueryParameterOr> encode(FhirContext theContext, Object theString) throws InternalErrorException {
-		List<QualifiedParamList> retVal = ((IQueryParameterAnd) theString).getValuesAsQueryTokens();
+		List<IQueryParameterOr> retVal = ((IQueryParameterAnd) theString).getValuesAsQueryTokens();
 		return retVal;
 	}
 

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

@@ -37,8 +37,8 @@ final class QueryParameterOrBinder implements IParamBinder {
 	}
 
 	@Override
-	public List<QualifiedParamList> encode(FhirContext theContext, Object theString) throws InternalErrorException {
+	public List<IQueryParameterOr> encode(FhirContext theContext, Object theString) throws InternalErrorException {
-		QualifiedParamList retVal = ((IQueryParameterOr) theString).getValuesAsQueryTokens();
+		IQueryParameterOr retVal = ((IQueryParameterOr) theString);
 		return Collections.singletonList(retVal);
 	}
 

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

@@ -24,6 +24,7 @@ import java.util.Collections;
 import java.util.List;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -37,11 +38,9 @@ final class QueryParameterTypeBinder implements IParamBinder {
 	}
 
 	@Override
-	public List<QualifiedParamList> encode(FhirContext theContext, Object theString) throws InternalErrorException {
+	public List<IQueryParameterOr> encode(FhirContext theContext, Object theString) throws InternalErrorException {
 		IQueryParameterType param = (IQueryParameterType) theString;
-		String retVal = param.getValueAsQueryToken();
+		return Collections.singletonList(ParameterUtil.singleton(param));
-		String qualifier=param.getQueryParameterQualifier(theContext);
-		return Collections.singletonList(QualifiedParamList.singleton(qualifier, retVal));
 	}
 
 	@Override

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
+import static org.apache.commons.lang3.StringUtils.*;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
@@ -27,7 +28,7 @@ import ca.uhn.fhir.model.api.IResource;
 public class ReferenceParam implements IQueryParameterType {
 
 	private String myChain;
-	private Class<? extends IResource> myType;
+	private String myResourceType;
 	private String myValue;
 
 	public ReferenceParam() {
@@ -42,8 +43,8 @@ public class ReferenceParam implements IQueryParameterType {
 		setChain(theChain);
 	}
 
-	public ReferenceParam(Class<? extends IResource> theType, String theChain, String theValue) {
+	public ReferenceParam(String theResourceType, String theChain, String theValue) {
-		setType(theType);
+		setResourceType(theResourceType);
 		setValueAsQueryToken(null, theValue);
 		setChain(theChain);
 	}
@@ -52,8 +53,25 @@ public class ReferenceParam implements IQueryParameterType {
 		return myChain;
 	}
 
-	public Class<? extends IResource> getType() {
+	@Override
-		return myType;
+	public String getQueryParameterQualifier(FhirContext theContext) {
+		StringBuilder b = new StringBuilder();
+		if (isNotBlank(myResourceType)) {
+			b.append(':');
+			b.append(myResourceType);
+		}
+		if (isNotBlank(myChain)) {
+			b.append('.');
+			b.append(myChain);
+		}
+		if (b.length() != 0) {
+			return b.toString();
+		}
+		return null;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
 	}
 
 	@Override
@@ -65,21 +83,39 @@ public class ReferenceParam implements IQueryParameterType {
 		myChain = theChain;
 	}
 
-	public void setType(Class<? extends IResource> theType) {
+	public Class<? extends IResource> getResourceType(FhirContext theCtx) {
-		myType = theType;
+		if (isBlank(myResourceType)) {
+			return null;
+		}
+		return theCtx.getResourceDefinition(myResourceType).getImplementingClass();
+	}
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
 	}
 
 	@Override
 	public void setValueAsQueryToken(String theQualifier, String theValue) {
+		String q = theQualifier;
+		if (isNotBlank(q)) {
+			if (q.startsWith(":")) {
+				int nextIdx = q.indexOf('.');
+				if (nextIdx != -1) {
+					myResourceType = q.substring(1, nextIdx);
+					myChain = q.substring(nextIdx + 1);
+				} else {
+					myResourceType = q.substring(1);
+				}
+			} else if (q.startsWith(".")) {
+				myChain = q.substring(1);
+			}
+		}
+
 		myValue = theValue;
 	}
 
-	@Override
+	public String getValue() {
-	public String getQueryParameterQualifier(FhirContext theContext) {
+		return myValue;
-		if (myType != null) {
-			return ":" + theContext.getResourceDefinition(myType).getName();
-		}
-		return null;
 	}
 
 }

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
@@ -63,7 +64,14 @@ public class SearchParameter extends BaseQueryParameter {
 	 */
 	@Override
 	public List<QualifiedParamList> encode(FhirContext theContext, Object theObject) throws InternalErrorException {
-		return myParamBinder.encode(theContext, theObject);
+		ArrayList<QualifiedParamList> retVal = new ArrayList<QualifiedParamList>();
+
+		List<IQueryParameterOr> val = myParamBinder.encode(theContext, theObject);
+		for (IQueryParameterOr nextOr : val) {
+			retVal.add(new QualifiedParamList(theContext, nextOr));
+		}
+
+		return retVal;
 	}
 
 	public String getDescription() {
@@ -150,6 +158,8 @@ public class SearchParameter extends BaseQueryParameter {
 			myParamType = SearchParamTypeEnum.TOKEN;
 		} else if (QuantityDt.class.isAssignableFrom(type)) {
 			myParamType = SearchParamTypeEnum.QUANTITY;
+		} else if (ReferenceParam.class.isAssignableFrom(type)) {
+			myParamType = SearchParamTypeEnum.REFERENCE;
 		} else {
 			throw new ConfigurationException("Unknown search parameter type: " + type);
 		}

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

@@ -20,7 +20,10 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
+import static org.apache.commons.lang3.StringUtils.*;
+
 import java.lang.reflect.Method;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
@@ -55,27 +58,68 @@ public class SortParameter implements IParameter {
 
 		if (ss.getFieldName() != null) {
 			if (!theTargetQueryArguments.containsKey(name)) {
-				// TODO: implement
+				theTargetQueryArguments.put(name, new ArrayList<String>());
 			}
+			theTargetQueryArguments.get(name).add(ss.getFieldName());
 		}
 
 	}
 
 	@Override
 	public Object translateQueryParametersIntoServerArgument(Request theRequest, Object theRequestContents) throws InternalErrorException, InvalidRequestException {
-		// TODO Auto-generated method stub
+		if (!theRequest.getParameters().containsKey(Constants.PARAM_SORT)) {
+			if (!theRequest.getParameters().containsKey(Constants.PARAM_SORT_ASC)) {
+				if (!theRequest.getParameters().containsKey(Constants.PARAM_SORT_DESC)) {
 					return null;
 				}
+			}
+		}
+
+		SortSpec outerSpec = null;
+		SortSpec innerSpec = null;
+		for (String nextParamName : theRequest.getParameters().keySet()) {
+			SortOrderEnum order;
+			if (Constants.PARAM_SORT.equals(nextParamName)) {
+				order = null;
+			} else if (Constants.PARAM_SORT_ASC.equals(nextParamName)) {
+				order = SortOrderEnum.ASC;
+			} else if (Constants.PARAM_SORT_DESC.equals(nextParamName)) {
+				order = SortOrderEnum.DESC;
+			} else {
+				continue;
+			}
+
+			String[] values = theRequest.getParameters().get(nextParamName);
+			if (values != null) {
+				for (String nextValue : values) {
+					if (isNotBlank(nextValue)) {
+						SortSpec spec = new SortSpec();
+						spec.setOrder(order);
+						spec.setFieldName(nextValue);
+						if (innerSpec == null) {
+							outerSpec = spec;
+							innerSpec = spec;
+						} else {
+							innerSpec.setChain(spec);
+							innerSpec = spec;
+						}
+					}
+				}
+			}
+		}
+
+		return outerSpec;
+	}
 
 	@Override
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
-		if (theOuterCollectionType != null) {
+		if (theOuterCollectionType != null || theInnerCollectionType!=null) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + "' is annotated with @" + Sort.class.getName() + " but can not be of collection type");
+			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + Sort.class.getName() + " but can not be of collection type");
-		}
-		if (!ParameterUtil.getBindableInstantTypes().contains(theParameterType)) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + "' is annotated with @" + Sort.class.getName() + " but is an invalid type, must be: " + SortSpec.class.getCanonicalName());
 		}
+		if (!theParameterType.equals(SortSpec.class)) {
+			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '"+theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + Sort.class.getName() + " but is an invalid type, must be: " + SortSpec.class.getCanonicalName());
 		}
 
+	}
 
 }

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

@@ -24,6 +24,7 @@ import java.util.Collections;
 import java.util.List;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -33,9 +34,9 @@ final class StringBinder implements IParamBinder {
 	}
 
 	@Override
-	public List<QualifiedParamList> encode(FhirContext theContext, Object theString) throws InternalErrorException {
+	public List<IQueryParameterOr> encode(FhirContext theContext, Object theString) throws InternalErrorException {
 		String retVal = ((String) theString);
-		return Collections.singletonList(QualifiedParamList.singleton(retVal));
+		return Collections.singletonList(ParameterUtil.singleton(new StringParam(retVal)));
 	}
 
 	@Override

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

@@ -360,7 +360,10 @@ public class RestfulServer extends HttpServlet {
 
 	private void findResourceMethods(Object theProvider, Class<?> clazz) {
 		for (Method m : clazz.getDeclaredMethods()) {
-			if (Modifier.isPublic(m.getModifiers()) && !Modifier.isStatic(m.getModifiers())) {
+			if (!Modifier.isPublic(m.getModifiers())) {
+				ourLog.debug("Ignoring non-public method: {}",m);
+			} else {
+				if (!Modifier.isStatic(m.getModifiers())) {
 					ourLog.debug("Scanning public method: {}#{}", theProvider.getClass(), m.getName());
 
 					BaseMethodBinding<?> foundMethodBinding = BaseMethodBinding.bindMethod(m, myFhirContext, theProvider);
@@ -389,6 +392,7 @@ public class RestfulServer extends HttpServlet {
 				}
 			}
 		}
+	}
 
 	private void findSystemMethods(Object theSystemProvider) {
 		Class<?> clazz = theSystemProvider.getClass();
@@ -535,7 +539,7 @@ public class RestfulServer extends HttpServlet {
 			} else {
 				resourceBinding = myResourceNameToProvider.get(resourceName);
 				if (resourceBinding == null) {
-					throw new ResourceNotFoundException("Unknown resource type '" + resourceName + "' - Server knows how to handle: " + myResourceNameToProvider.keySet());
+					throw new InvalidRequestException("Unknown resource type '" + resourceName + "' - Server knows how to handle: " + myResourceNameToProvider.keySet());
 				}
 			}
 
@@ -614,7 +618,7 @@ public class RestfulServer extends HttpServlet {
 				resourceMethod = resourceBinding.getMethod(r);
 			}
 			if (null == resourceMethod) {
-				throw new ResourceNotFoundException("No resource method available for the supplied parameters " + params);
+				throw new InvalidRequestException("No resource method available for the supplied parameters " + params);
 			}
 
 			resourceMethod.invokeServer(this, r, theResponse);

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.server.provider;
  * #L%
  */
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
@@ -89,7 +90,7 @@ public class ServerConformanceProvider {
 			resource.getProfile().setId(new IdDt(def.getResourceProfile()));
 
 			Map<String, Conformance.RestResourceSearchParam> nameToSearchParam = new HashMap<String, Conformance.RestResourceSearchParam>();
-			for (BaseMethodBinding nextMethodBinding : next.getMethodBindings()) {
+			for (BaseMethodBinding<?> nextMethodBinding : next.getMethodBindings()) {
 				RestfulOperationTypeEnum resOp = nextMethodBinding.getResourceOperationType();
 				if (resOp != null) {
 					if (resourceOps.contains(resOp) == false) {
@@ -108,19 +109,34 @@ public class ServerConformanceProvider {
 
 				if (nextMethodBinding instanceof SearchMethodBinding) {
 					List<IParameter> params = ((SearchMethodBinding) nextMethodBinding).getParameters();
-					// TODO: this would probably work best if we sorted these by
+					List<SearchParameter> searchParameters = new ArrayList<SearchParameter>(); 
-					// required first, then optional
+					for (IParameter nextParameter : params) {
+						if ((nextParameter instanceof SearchParameter)) {
+							searchParameters.add((SearchParameter) nextParameter);
+						}
+					}
+					Collections.sort(searchParameters, new Comparator<SearchParameter>() {
+						@Override
+						public int compare(SearchParameter theO1, SearchParameter theO2) {
+							if (theO1.isRequired() == theO2.isRequired()) {
+								return 0;
+							}
+							if (theO1.isRequired()) {
+								return 1;
+							}
+							return -1;
+						}
+					});
+					if (searchParameters.isEmpty()) {
+						continue;
+					}
+					boolean allOptional = searchParameters.get(0).isRequired()==false; 
 							
 					RestResourceSearchParam searchParam = null;
 					ExtensionDt searchParamChain = null;
-					for (IParameter nextParameterObj : params) {
+					for (SearchParameter nextParameter : searchParameters) {
-						if (!(nextParameterObj instanceof SearchParameter)) {
-							continue;
-						}
 
-						SearchParameter nextParameter = (SearchParameter) nextParameterObj;
+						if (searchParam == null || allOptional) {
-
-						if (searchParam == null) {
 							if (!nameToSearchParam.containsKey(nextParameter.getName())) {
 								RestResourceSearchParam param = resource.addSearchParam();
 								param.setName(nextParameter.getName());

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

@@ -59,6 +59,7 @@ import ca.uhn.fhir.rest.client.api.IRestfulClient;
 import ca.uhn.fhir.rest.param.CodingListParam;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.QualifiedDateParam;
+import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -90,6 +91,34 @@ public List<Patient> findPatients(
 }
 //END SNIPPET: underlyingReq
 
+//START SNIPPET: reference
+@Search
+public List<Patient> findPatients(
+		@RequiredParam(name=Patient.SP_PROVIDER) ReferenceParam theProvider
+		) {
+
+// May be populated with the resource type (e.g. "Patient") if the client requested one
+String type = theProvider.getResourceType(); 
+
+// May be populated with the chain (e.g. "name") if the client requested one
+String chain = theProvider.getChain();
+
+/* The actual parameter value. This will be the resource ID if no chain was provided,
+ * but refers to the value of a specific property noted by the chain if one was given.
+ * For example, the following request: 
+ * http://example.com/fhir/Patient?provider:Organization.name=FooOrg
+ * has a type of "Organization" and a chain of "name", meaning that
+ * the returned patients should have a provider which is an Organization
+ * with a name matching "FooOrg".
+ */
+String value = theProvider.getValue();
+
+List<Patient> retVal=new ArrayList<Patient>(); // populate this
+return retVal;
+
+}
+//END SNIPPET: reference
+
 
 //START SNIPPET: read
 @Read()
@@ -557,7 +586,7 @@ private interface IPatientClient extends IBasicClient
   // Only one method is shown here, but many methods may be 
   // added to the same client interface!
 }
-//START SNIPPET: clientReadInterface
+//END SNIPPET: clientReadInterface
 
 public void clientRead() {
 //START SNIPPET: clientReadTags

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

@@ -693,6 +693,49 @@
 
 			</subsection>
 
+			<subsection name="Search Parameters: Resource Reference">
+
+				<p>
+					Many search parameters refer to resource references. For instance, the Patient
+					parameter "provider" refers to the resource marked as the managing organization
+					for patients.
+				</p>
+				<p>
+					Reference parameters use the 
+					<a href="./apidocs/ca/uhn/fhir/rest/param/ReferenceParam.html">ReferenceParam</a> 
+					type. Reference param objects being passed into server methods will have three properties
+					populated:
+				</p>
+				<ul>
+					<li>
+						<b>The resource type (optional):</b> This is the type of resource
+						being targeted, if the client specifies one in the URL.
+					</li>
+					<li>
+						<b>The chain property (optional):</b> This is the name of the 
+						property on the target resource to search for
+					</li>
+					<li>
+						<b>The value (required):</b> This is the actual value to search for. If
+						a chain property has not been specified, this is the ID of the resource.
+					</li>
+				</ul>
+
+				<macro name="snippet">
+					<param name="id" value="reference" />
+					<param name="file" value="src/site/example/java/example/RestfulPatientResourceProviderMore.java" />
+				</macro>
+
+				<p>
+					Example URLs to invoke this method:
+					<br />
+					Resource by ID: <code>http://fhir.example.com/Patient?provider=1234</code>
+					<br />
+					Resource by chained parameter value: <code>http://fhir.example.com/Patient?provider:Organization.name=FooOrg</code>
+				</p>
+
+			</subsection>
+
 			<subsection name="Combining Multiple Parameters">
 
 				<p>

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/dstu/composite/ResourceReferenceDtTest.java

@@ -0,0 +1,100 @@
+package ca.uhn.fhir.model.dstu.composite;
+
+import static org.junit.Assert.*;
+
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu.resource.Observation;
+import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+
+public class ResourceReferenceDtTest {
+
+	private static FhirContext ourCtx;
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceReferenceDtTest.class);
+
+	@Test
+	public void testParseValueAbsolute() {
+		Patient patient = new Patient();
+		ResourceReferenceDt rr = new ResourceReferenceDt();
+		rr.setReference("http://foo/fhir/Organization/123");
+		patient.setManagingOrganization(rr);
+
+		Patient actual = parseAndEncode(patient);
+		rr = actual.getManagingOrganization();
+		assertEquals(Organization.class, rr.getResourceType());
+		assertEquals("123", rr.getResourceId());
+
+	}
+
+	@Test
+	public void testParseValueMissingType1() {
+		Patient patient = new Patient();
+		ResourceReferenceDt rr = new ResourceReferenceDt();
+		rr.setReference("/123");
+		patient.setManagingOrganization(rr);
+
+		Patient actual = parseAndEncode(patient);
+		rr = actual.getManagingOrganization();
+		assertEquals(null, rr.getResourceType());
+		assertEquals("123", rr.getResourceId());
+
+	}
+
+	@Test
+	public void testParseValueMissingType2() {
+		Patient patient = new Patient();
+		ResourceReferenceDt rr = new ResourceReferenceDt();
+		rr.setReference("123");
+		patient.setManagingOrganization(rr);
+
+		Patient actual = parseAndEncode(patient);
+		rr = actual.getManagingOrganization();
+		assertEquals(null, rr.getResourceType());
+		assertEquals("123", rr.getResourceId());
+
+	}
+
+	@Test
+	public void testParseValueRelative1() {
+		Patient patient = new Patient();
+		ResourceReferenceDt rr = new ResourceReferenceDt();
+		rr.setReference("Organization/123");
+		patient.setManagingOrganization(rr);
+
+		Patient actual = parseAndEncode(patient);
+		rr = actual.getManagingOrganization();
+		assertEquals(Organization.class, rr.getResourceType());
+		assertEquals("123", rr.getResourceId());
+
+	}
+
+	@Test
+	public void testParseValueRelative2() {
+		Patient patient = new Patient();
+		ResourceReferenceDt rr = new ResourceReferenceDt();
+		rr.setReference("/Organization/123");
+		patient.setManagingOrganization(rr);
+
+		Patient actual = parseAndEncode(patient);
+		rr = actual.getManagingOrganization();
+		assertEquals(Organization.class, rr.getResourceType());
+		assertEquals("123", rr.getResourceId());
+
+	}
+
+	private Patient parseAndEncode(Patient patient) {
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(patient);
+		ourLog.info("\n" + encoded);
+		return ourCtx.newXmlParser().parseResource(Patient.class, encoded);
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		ourCtx = new FhirContext();
+	}
+
+}

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

@@ -0,0 +1,129 @@
+package ca.uhn.fhir.rest.client;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.io.StringReader;
+import java.nio.charset.Charset;
+import java.util.List;
+
+import org.apache.commons.io.input.ReaderInputStream;
+import org.apache.http.HttpResponse;
+import org.apache.http.ProtocolVersion;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.message.BasicHeader;
+import org.apache.http.message.BasicStatusLine;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.dstu.resource.Conformance;
+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.IBasicClient;
+import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.Constants;
+
+public class ReferenceClientTest {
+
+	private FhirContext ctx;
+	private HttpClient httpClient;
+	private HttpResponse httpResponse;
+
+	// atom-document-large.xml
+
+	@Before
+	public void before() {
+		ctx = new FhirContext(Patient.class, Conformance.class);
+
+		httpClient = mock(HttpClient.class, new ReturnsDeepStubs());
+		ctx.getRestfulClientFactory().setHttpClient(httpClient);
+
+		httpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
+	}
+
+	@Test
+	public void testWithParam() throws Exception {
+		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")));
+
+		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
+		client.search(new ReferenceParam("123"));
+
+		assertEquals(HttpGet.class, capt.getValue().getClass());
+		HttpGet get = (HttpGet) capt.getValue();
+		assertEquals("http://foo/Patient?provider=123", get.getURI().toString());
+	}
+
+	@Test
+	public void testWithParamAndChain() throws Exception {
+		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")));
+
+		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
+		client.search(new ReferenceParam("chain", "123"));
+
+		assertEquals(HttpGet.class, capt.getValue().getClass());
+		HttpGet get = (HttpGet) capt.getValue();
+		assertEquals("http://foo/Patient?provider.chain=123", get.getURI().toString());
+	}
+	
+	@Test
+	public void testWithParamAndTypeAndChain() throws Exception {
+		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")));
+
+		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
+		client.search(new ReferenceParam("Organization", "chain", "123"));
+
+		assertEquals(HttpGet.class, capt.getValue().getClass());
+		HttpGet get = (HttpGet) capt.getValue();
+		assertEquals("http://foo/Patient?provider%3AOrganization.chain=123", get.getURI().toString());
+	}
+	
+	@Test
+	public void testWithParamAndType() throws Exception {
+		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")));
+
+		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
+		client.search(new ReferenceParam("Organization", null, "123"));
+
+		assertEquals(HttpGet.class, capt.getValue().getClass());
+		HttpGet get = (HttpGet) capt.getValue();
+		assertEquals("http://foo/Patient?provider%3AOrganization=123", get.getURI().toString());
+	}
+
+	private String createBundle() {
+		return ctx.newXmlParser().encodeBundleToString(new Bundle());
+	}
+
+
+	private interface IClient extends IBasicClient {
+
+		@Search(type=Patient.class)
+		public List<Patient> search(@RequiredParam(name=Patient.SP_PROVIDER) ReferenceParam theString);
+
+	}
+
+}

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

@@ -0,0 +1,165 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.apache.commons.lang3.StringUtils.*;
+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.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.BundleEntry;
+import ca.uhn.fhir.model.api.IResource;
+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.param.ReferenceParam;
+import ca.uhn.fhir.testutil.RandomServerPortProvider;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class ReferenceParameterTest {
+
+	private static CloseableHttpClient ourClient;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ReferenceParameterTest.class);
+	private static int ourPort;
+	private static Server ourServer;
+	private static FhirContext ourCtx;
+
+	
+
+
+	@Test
+	public void testSearchWithValue() throws Exception {
+		{
+			HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?" + Patient.SP_PROVIDER+"=123");
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			List<BundleEntry> entries = new FhirContext().newXmlParser().parseBundle(responseContent).getEntries();
+			assertEquals(1, entries.size());
+			Patient p = (Patient) entries.get(0).getResource();
+			assertEquals("0123",p.getName().get(0).getFamilyFirstRep().getValue());
+			assertEquals("1",p.getName().get(1).getFamilyFirstRep().getValue());
+			assertEquals("2",p.getName().get(2).getFamilyFirstRep().getValue());
+		}
+	}
+	
+	@Test
+	public void testSearchWithValueAndType() throws Exception {
+		{
+			HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?" + Patient.SP_PROVIDER+":Organization=123");
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			List<BundleEntry> entries = new FhirContext().newXmlParser().parseBundle(responseContent).getEntries();
+			assertEquals(1, entries.size());
+			Patient p = (Patient) entries.get(0).getResource();
+			assertEquals("0123",p.getName().get(0).getFamilyFirstRep().getValue());
+			assertEquals("1Organization",p.getName().get(1).getFamilyFirstRep().getValue());
+			assertEquals("2",p.getName().get(2).getFamilyFirstRep().getValue());
+		}
+	}
+	@Test
+	public void testSearchWithValueAndTypeAndChain() throws Exception {
+		{
+			HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?" + Patient.SP_PROVIDER+":Organization.name=123");
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			List<BundleEntry> entries = new FhirContext().newXmlParser().parseBundle(responseContent).getEntries();
+			assertEquals(1, entries.size());
+			Patient p = (Patient) entries.get(0).getResource();
+			assertEquals("0123",p.getName().get(0).getFamilyFirstRep().getValue());
+			assertEquals("1Organization",p.getName().get(1).getFamilyFirstRep().getValue());
+			assertEquals("2name",p.getName().get(2).getFamilyFirstRep().getValue());
+		}
+	}
+	
+	@Test
+	public void testSearchWithValueAndChain() throws Exception {
+		{
+			HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?" + Patient.SP_PROVIDER+".name=123");
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			List<BundleEntry> entries = new FhirContext().newXmlParser().parseBundle(responseContent).getEntries();
+			assertEquals(1, entries.size());
+			Patient p = (Patient) entries.get(0).getResource();
+			assertEquals("0123",p.getName().get(0).getFamilyFirstRep().getValue());
+			assertEquals("1",p.getName().get(1).getFamilyFirstRep().getValue());
+			assertEquals("2name",p.getName().get(2).getFamilyFirstRep().getValue());
+		}
+	}
+	
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = RandomServerPortProvider.findFreePort();
+		ourServer = new Server(ourPort);
+
+		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer();
+		servlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+		ourCtx = servlet.getFhirContext();
+	}
+
+	/**
+	 * Created by dsotnikov on 2/25/2014.
+	 */
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		@Search
+		public List<Patient> findPatient(@RequiredParam(name = Patient.SP_PROVIDER) ReferenceParam theParam) {
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+
+			Patient p = new Patient();
+			p.addName().addFamily("0"+theParam.getValueAsQueryToken());
+			p.addName().addFamily("1"+defaultString(theParam.getResourceType()));
+			p.addName().addFamily("2"+defaultString(theParam.getChain()));
+			retVal.add(p);
+			
+			return retVal;
+		}
+
+		
+		
+		
+		@Override
+		public Class<? extends IResource> getResourceType() {
+			return Patient.class;
+		}
+
+	}
+
+}

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

@@ -96,7 +96,9 @@ public class ResourceMethodTest {
 		inputParams.add("lastName");
 		inputParams.add("mrn");
 
-		assertEquals(true, rm.incomingServerRequestMatchesMethod(Request.withResourceAndParams("Patient", RequestType.GET, inputParams))); // True
+		Request params = Request.withResourceAndParams("Patient", RequestType.GET, inputParams);
+		boolean actual = rm.incomingServerRequestMatchesMethod(params);
+		assertTrue( actual); // True
 	}
 
 	@Test

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

@@ -13,6 +13,8 @@ import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu.resource.Conformance;
 import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.StringDt;
+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.method.BaseMethodBinding;
@@ -20,9 +22,9 @@ import ca.uhn.fhir.rest.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.param.SearchParameter;
 import ca.uhn.fhir.rest.server.provider.ServerConformanceProvider;
 
-public class DocumentationTest {
+public class ServerConformanceProviderTest {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DocumentationTest.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerConformanceProviderTest.class);
 
 	@Test
 	public void testSearchParameterDocumentation() throws Exception {
@@ -55,6 +57,39 @@ public class DocumentationTest {
 		assertThat(conf, containsString("<type value=\"token\"/>"));
 	}
 
+	
+	@Test
+	public void testMultiOptionalDocumentation() throws Exception {
+
+		RestfulServer rs = new RestfulServer();
+		rs.setProviders(new MultiOptionalProvider());
+
+		ServerConformanceProvider sc = new ServerConformanceProvider(rs);
+		rs.setServerConformanceProvider(sc);
+
+		rs.init(null);
+		
+		boolean found=false;
+		Collection<ResourceBinding> resourceBindings = rs.getResourceBindings();
+		for (ResourceBinding resourceBinding : resourceBindings) {
+			if (resourceBinding.getResourceName().equals("Patient")) {
+				List<BaseMethodBinding<?>> methodBindings = resourceBinding.getMethodBindings();
+				SearchMethodBinding binding = (SearchMethodBinding) methodBindings.get(0);
+				SearchParameter param = (SearchParameter) binding.getParameters().iterator().next();
+				assertEquals("The patient's identifier", param.getDescription());
+				found=true;
+			}
+		}
+		assertTrue(found);
+		Conformance conformance = sc.getServerConformance();
+		String conf = new FhirContext().newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance);
+		ourLog.info(conf);
+
+		assertThat(conf, containsString("<documentation value=\"The patient's identifier (MRN or other card number)\"/>"));
+		assertThat(conf, containsString("<type value=\"token\"/>"));
+	}
+
+	
 	/**
 	 * Created by dsotnikov on 2/25/2014.
 	 */
@@ -70,4 +105,22 @@ public class DocumentationTest {
 
 	}
 	
+	
+	/**
+	 * Created by dsotnikov on 2/25/2014.
+	 */
+	@SuppressWarnings("unused")
+	public static class MultiOptionalProvider {
+
+		@Search(type = Patient.class)
+		public Patient findPatient(
+				@Description(shortDefinition = "The patient's identifier") 
+				@OptionalParam(name = Patient.SP_IDENTIFIER) IdentifierDt theIdentifier,
+				@Description(shortDefinition = "The patient's name") 
+				@OptionalParam(name=Patient.SP_NAME) StringDt theName) {
+			return null;
+		}
+
+	}
+
 }

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

@@ -0,0 +1,177 @@
+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.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.annotation.Sort;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.testutil.RandomServerPortProvider;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class SortTest {
+
+	private static CloseableHttpClient ourClient;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SortTest.class);
+	private static int ourPort;
+	private static Server ourServer;
+
+	@Test
+	public void testNoSort() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = new FhirContext().newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(1, p.getName().size());
+		assertEquals("Hello", p.getNameFirstRep().getFamilyFirstRep().getValue());
+	}
+	
+	@Test
+	public void testSingleSort() throws Exception {
+		{
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_sort=given");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = new FhirContext().newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(2, p.getName().size());
+		assertEquals("Hello", p.getNameFirstRep().getFamilyFirstRep().getValue());
+		assertEquals("given|null", p.getName().get(1).getFamilyFirstRep().getValue());
+		}
+		{
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_sort:asc=given");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = new FhirContext().newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(2, p.getName().size());
+		assertEquals("Hello", p.getNameFirstRep().getFamilyFirstRep().getValue());
+		assertEquals("given|ASC", p.getName().get(1).getFamilyFirstRep().getValue());
+		}
+		{
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_sort:desc=given");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = new FhirContext().newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(2, p.getName().size());
+		assertEquals("Hello", p.getNameFirstRep().getFamilyFirstRep().getValue());
+		assertEquals("given|DESC", p.getName().get(1).getFamilyFirstRep().getValue());
+		}
+
+	}
+
+	@Test
+	public void testSortChain() throws Exception {
+		{
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_sort=given&_sort=family&_sort=name");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = new FhirContext().newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(4, p.getName().size());
+		assertEquals("Hello", p.getNameFirstRep().getFamilyFirstRep().getValue());
+		assertEquals("given|null", p.getName().get(1).getFamilyFirstRep().getValue());
+		assertEquals("family|null", p.getName().get(2).getFamilyFirstRep().getValue());
+		assertEquals("name|null", p.getName().get(3).getFamilyFirstRep().getValue());
+		}
+		
+
+	}
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = RandomServerPortProvider.findFreePort();
+		ourServer = new Server(ourPort);
+
+		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer();
+		servlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	/**
+	 * Created by dsotnikov on 2/25/2014.
+	 */
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		@Search
+		public List<Patient> findPatient(@RequiredParam(name = Patient.SP_NAME) StringDt theName, @Sort SortSpec theSort) {
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+
+			Patient p = new Patient();
+			p.addName().addFamily().setValue(theName.getValue());
+			SortSpec sort = theSort;
+			while (sort != null) {
+				p.addName().addFamily().setValue(sort.getFieldName() + "|" + sort.getOrder());
+				sort = sort.getChain();
+			}
+
+			retVal.add(p);
+
+			return retVal;
+		}
+
+		@Override
+		public Class<? extends IResource> getResourceType() {
+			return Patient.class;
+		}
+
+	}
+
+}

hapi-fhir-jpaserver-base/.classpath

@@ -1,151 +1,152 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-  <classpathentry kind="src" path="src/test/java" output="target/test-classes" including="**/*.java"/>
+	<classpathentry including="**/*.java" kind="src" output="target/test-classes" path="src/test/java"/>
-  <classpathentry kind="src" path="src/test/resources" output="target/test-classes" excluding="**/*.java"/>
+	<classpathentry excluding="**/*.java" kind="src" output="target/test-classes" path="src/test/resources"/>
-  <classpathentry kind="src" path="src/main/java" including="**/*.java"/>
+	<classpathentry including="**/*.java" kind="src" path="src/main/java"/>
-  <classpathentry kind="src" path="src/main/resources" excluding="**/*.java"/>
+	<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
-  <classpathentry kind="output" path="target/classes"/>
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-      <attribute value="jar:file:/Users/james/.m2/repository/junit/junit/4.11/junit-4.11-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/junit/junit/4.11/junit-4.11-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/slf4j/slf4j-api/1.7.6/slf4j-api-1.7.6.jar" sourcepath="M2_REPO/org/slf4j/slf4j-api/1.7.6/slf4j-api-1.7.6-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/slf4j/slf4j-api/1.7.6/slf4j-api-1.7.6.jar" sourcepath="M2_REPO/org/slf4j/slf4j-api/1.7.6/slf4j-api-1.7.6-sources.jar">
 		<attributes>
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+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/slf4j/slf4j-api/1.7.6/slf4j-api-1.7.6-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
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+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-aop/4.0.1.RELEASE/spring-aop-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-aop/4.0.1.RELEASE/spring-aop-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-aop/4.0.1.RELEASE/spring-aop-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-aop/4.0.1.RELEASE/spring-aop-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-beans/4.0.1.RELEASE/spring-beans-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-beans/4.0.1.RELEASE/spring-beans-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-beans/4.0.1.RELEASE/spring-beans-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-beans/4.0.1.RELEASE/spring-beans-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-beans/4.0.1.RELEASE/spring-beans-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-beans/4.0.1.RELEASE/spring-beans-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-context/4.0.1.RELEASE/spring-context-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-context/4.0.1.RELEASE/spring-context-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-context/4.0.1.RELEASE/spring-context-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-context/4.0.1.RELEASE/spring-context-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-context/4.0.1.RELEASE/spring-context-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-context/4.0.1.RELEASE/spring-context-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-context-support/4.0.1.RELEASE/spring-context-support-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-context-support/4.0.1.RELEASE/spring-context-support-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-context-support/4.0.1.RELEASE/spring-context-support-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-context-support/4.0.1.RELEASE/spring-context-support-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-context-support/4.0.1.RELEASE/spring-context-support-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-context-support/4.0.1.RELEASE/spring-context-support-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-core/4.0.1.RELEASE/spring-core-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-core/4.0.1.RELEASE/spring-core-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-core/4.0.1.RELEASE/spring-core-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-core/4.0.1.RELEASE/spring-core-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-core/4.0.1.RELEASE/spring-core-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-core/4.0.1.RELEASE/spring-core-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-expression/4.0.1.RELEASE/spring-expression-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-expression/4.0.1.RELEASE/spring-expression-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-expression/4.0.1.RELEASE/spring-expression-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-expression/4.0.1.RELEASE/spring-expression-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-expression/4.0.1.RELEASE/spring-expression-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-expression/4.0.1.RELEASE/spring-expression-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-jdbc/4.0.1.RELEASE/spring-jdbc-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-jdbc/4.0.1.RELEASE/spring-jdbc-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-jdbc/4.0.1.RELEASE/spring-jdbc-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-jdbc/4.0.1.RELEASE/spring-jdbc-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-jdbc/4.0.1.RELEASE/spring-jdbc-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-jdbc/4.0.1.RELEASE/spring-jdbc-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/springframework/spring-tx/4.0.1.RELEASE/spring-tx-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-tx/4.0.1.RELEASE/spring-tx-4.0.1.RELEASE-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/springframework/spring-tx/4.0.1.RELEASE/spring-tx-4.0.1.RELEASE.jar" sourcepath="M2_REPO/org/springframework/spring-tx/4.0.1.RELEASE/spring-tx-4.0.1.RELEASE-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/springframework/spring-tx/4.0.1.RELEASE/spring-tx-4.0.1.RELEASE-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/springframework/spring-tx/4.0.1.RELEASE/spring-tx-4.0.1.RELEASE-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
-  <classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/stax2-api/3.1.1/stax2-api-3.1.1.jar" sourcepath="M2_REPO/org/codehaus/woodstox/stax2-api/3.1.1/stax2-api-3.1.1-sources.jar"/>
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/codehaus/woodstox/stax2-api/3.1.1/stax2-api-3.1.1.jar" sourcepath="M2_REPO/org/codehaus/woodstox/stax2-api/3.1.1/stax2-api-3.1.1-sources.jar"/>
-  <classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0.jar" sourcepath="M2_REPO/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-sources.jar">
+	<classpathentry exported="true" kind="var" path="M2_REPO/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0.jar" sourcepath="M2_REPO/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-sources.jar">
 		<attributes>
-      <attribute value="jar:file:/Users/james/.m2/repository/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-javadoc.jar!/" name="javadoc_location"/>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-javadoc.jar!/"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="output" path="bin"/>
 </classpath>

hapi-fhir-jpaserver-base/.gitignore

@@ -1 +1,2 @@
 target/
+/bin

hapi-fhir-jpaserver-base/pom.xml

@@ -175,6 +175,59 @@
 					<skip>true</skip>
 				</configuration>
 			</plugin>
+		
+<plugin>
+				<groupId>de.juplo</groupId>
+				<artifactId>hibernate4-maven-plugin</artifactId>
+				<version>1.0.1</version>
+				<configuration>
+					<force>true</force>
+					<target>SCRIPT</target>
+					<skip>false</skip>
+				</configuration>
+				<executions>
+					<execution>
+						<id>o10g</id>
+						<goals>
+							<goal>export</goal>
+						</goals>
+						<configuration>
+							<hibernateDialect>org.hibernate.dialect.Oracle10gDialect</hibernateDialect>
+							<outputFile>${project.build.directory}/schema_oracle_10g.sql</outputFile>
+						</configuration>
+					</execution>
+					<execution>
+						<id>derby</id>
+						<goals>
+							<goal>export</goal>
+						</goals>
+						<configuration>
+							<hibernateDialect>org.hibernate.dialect.DerbyTenSevenDialect</hibernateDialect>
+							<outputFile>${project.build.directory}/schema_derby.sql</outputFile>
+						</configuration>
+					</execution>
+					<execution>
+						<id>hsql</id>
+						<goals>
+							<goal>export</goal>
+						</goals>
+						<configuration>
+							<hibernateDialect>org.hibernate.dialect.HSQLDialect</hibernateDialect>
+							<outputFile>${project.build.directory}/schema_hsql.sql</outputFile>
+						</configuration>
+					</execution>
+					<execution>
+						<id>mysql5</id>
+						<goals>
+							<goal>export</goal>
+						</goals>
+						<configuration>
+							<hibernateDialect>org.hibernate.dialect.MySQL5Dialect</hibernateDialect>
+							<outputFile>${project.build.directory}/schema_mysql_5.sql</outputFile>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>		
 		</plugins>
 	</build>
 

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

@@ -56,8 +56,10 @@ 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.composite.AddressDt;
 import ca.uhn.fhir.model.dstu.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu.composite.CodingDt;
+import ca.uhn.fhir.model.dstu.composite.ContactDt;
 import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
 import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu.composite.QuantityDt;
@@ -96,6 +98,312 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 
 	private Class<X> myTableType;
 
+	@Transactional(propagation = Propagation.REQUIRED, readOnly = true)
+	@Override
+	public MethodOutcome create(T theResource) {
+
+		final X entity = toEntity(theResource);
+
+		entity.setPublished(new Date());
+		entity.setUpdated(entity.getPublished());
+
+		final List<ResourceIndexedSearchParamString> stringParams = extractSearchParamStrings(entity, theResource);
+		final List<ResourceIndexedSearchParamToken> tokenParams = extractSearchParamTokens(entity, theResource);
+		final List<ResourceIndexedSearchParamNumber> numberParams = extractSearchParamNumber(entity, theResource);
+		final List<ResourceIndexedSearchParamDate> dateParams = extractSearchParamDates(entity, theResource);
+		final List<ResourceLink> links = extractResourceLinks(entity, theResource);
+
+		ourLog.info("Saving links: {}", links);
+
+		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
+		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		template.setReadOnly(false);
+		template.execute(new TransactionCallback<X>() {
+			@Override
+			public X doInTransaction(TransactionStatus theStatus) {
+				myEntityManager.persist(entity);
+				for (ResourceIndexedSearchParamString next : stringParams) {
+					myEntityManager.persist(next);
+				}
+				for (ResourceIndexedSearchParamToken next : tokenParams) {
+					myEntityManager.persist(next);
+				}
+				for (ResourceIndexedSearchParamNumber next : numberParams) {
+					myEntityManager.persist(next);
+				}
+				for (ResourceIndexedSearchParamDate next : dateParams) {
+					myEntityManager.persist(next);
+				}
+				for (ResourceLink next : links) {
+					myEntityManager.persist(next);
+				}
+				return entity;
+			}
+		});
+
+		MethodOutcome outcome = toMethodOutcome(entity);
+		return outcome;
+	}
+
+	public Class<T> getResourceType() {
+		return myResourceType;
+	}
+
+	@Override
+	public Class<X> getTableType() {
+		return myTableType;
+	}
+
+	@Transactional(propagation = Propagation.REQUIRED)
+	@Override
+	public List<T> history(IdDt theId) {
+		ArrayList<T> retVal = new ArrayList<T>();
+
+		String resourceType = myCtx.getResourceDefinition(myResourceType).getName();
+		TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(ResourceHistoryTable.Q_GETALL, ResourceHistoryTable.class);
+		q.setParameter("PID", theId.asLong());
+		q.setParameter("RESTYPE", resourceType);
+
+		// TypedQuery<ResourceHistoryTable> query =
+		// myEntityManager.createQuery(criteriaQuery);
+		List<ResourceHistoryTable> results = q.getResultList();
+		for (ResourceHistoryTable next : results) {
+			retVal.add(toResource(next));
+		}
+
+		try {
+			retVal.add(read(theId));
+		} catch (ResourceNotFoundException e) {
+			// ignore
+		}
+
+		if (retVal.isEmpty()) {
+			throw new ResourceNotFoundException(theId);
+		}
+
+		return retVal;
+	}
+
+	@PostConstruct
+	public void postConstruct() throws Exception {
+		myResourceType = myTableType.newInstance().getResourceType();
+		myCtx = new FhirContext(myResourceType);
+		myResourceName = myCtx.getResourceDefinition(myResourceType).getName();
+	}
+
+	@Transactional(propagation = Propagation.REQUIRED)
+	@Override
+	public T read(IdDt theId) {
+		X entity = readEntity(theId);
+
+		T retVal = toResource(entity);
+		return retVal;
+	}
+
+	@Override
+	public List<T> search(Map<String, IQueryParameterType> theParams) {
+		SearchParameterMap map = new SearchParameterMap();
+		for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
+			map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
+			map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
+		}
+		return search(map);
+	}
+
+	@Override
+	public List<T> search(SearchParameterMap theParams) {
+
+		Set<Long> pids;
+		if (theParams.isEmpty()) {
+			pids = null;
+		} else {
+			pids = searchForIdsWithAndOr(theParams);
+			if (pids.isEmpty()) {
+				return new ArrayList<>();
+			}
+		}
+
+		// Execute the query and make sure we return distinct results
+		{
+			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
+			CriteriaQuery<X> cq = builder.createQuery(myTableType);
+			Root<X> from = cq.from(myTableType);
+			if (!theParams.isEmpty()) {
+				cq.where(from.get("myId").in(pids));
+			}
+			TypedQuery<X> q = myEntityManager.createQuery(cq);
+
+			List<T> retVal = new ArrayList<>();
+			for (X next : q.getResultList()) {
+				T resource = toResource(next);
+				retVal.add(resource);
+			}
+			return retVal;
+		}
+	}
+
+	@Override
+	public List<T> search(String theParameterName, IQueryParameterType theValue) {
+		return search(Collections.singletonMap(theParameterName, theValue));
+	}
+
+	@Override
+	public Set<Long> searchForIds(Map<String, IQueryParameterType> theParams) {
+		Map<String, List<List<IQueryParameterType>>> map = new HashMap<String, List<List<IQueryParameterType>>>();
+		for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
+			map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
+			map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
+		}
+		return searchForIdsWithAndOr(map);
+	}
+
+	@Override
+	public Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue) {
+		return searchForIds(Collections.singletonMap(theParameterName, theValue));
+	}
+
+	@Override
+	public Set<Long> searchForIdsWithAndOr(Map<String, List<List<IQueryParameterType>>> theParams) {
+		Map<String, List<List<IQueryParameterType>>> params = theParams;
+		if (params == null) {
+			params = Collections.emptyMap();
+		}
+
+		RuntimeResourceDefinition resourceDef = myCtx.getResourceDefinition(myResourceType);
+
+		Set<Long> pids = new HashSet<Long>();
+
+		for (Entry<String, List<List<IQueryParameterType>>> nextParamEntry : params.entrySet()) {
+			String nextParamName = nextParamEntry.getKey();
+			RuntimeSearchParam nextParamDef = resourceDef.getSearchParam(nextParamName);
+			if (nextParamDef != null) {
+				if (nextParamDef.getParamType() == SearchParamTypeEnum.TOKEN) {
+					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
+						pids = addPredicateToken(pids, nextAnd);
+						if (pids.isEmpty()) {
+							return new HashSet<Long>();
+						}
+					}
+				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.STRING) {
+					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
+						pids = addPredicateString(pids, nextAnd);
+						if (pids.isEmpty()) {
+							return new HashSet<Long>();
+						}
+					}
+				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.QUANTITY) {
+					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
+						pids = addPredicateQuantity(pids, nextAnd);
+						if (pids.isEmpty()) {
+							return new HashSet<Long>();
+						}
+					}
+				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.DATE) {
+					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
+						pids = addPredicateDate(pids, nextAnd);
+						if (pids.isEmpty()) {
+							return new HashSet<Long>();
+						}
+					}
+				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.REFERENCE) {
+					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
+						pids = addPredicateReference(nextParamName, pids, nextAnd);
+						if (pids.isEmpty()) {
+							return new HashSet<Long>();
+						}
+					}
+				} else {
+					throw new IllegalArgumentException("Don't know how to handle parameter of type: " + nextParamDef.getParamType());
+				}
+			}
+		}
+
+		return pids;
+	}
+
+	@Required
+	public void setTableType(Class<X> theTableType) {
+		myTableType = theTableType;
+	}
+
+	@Transactional(propagation = Propagation.SUPPORTS)
+	@Override
+	public MethodOutcome update(final T theResource, final IdDt theId) {
+
+		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
+		X savedEntity = template.execute(new TransactionCallback<X>() {
+			@Override
+			public X doInTransaction(TransactionStatus theStatus) {
+
+				final X entity = readEntity(theId);
+				entity.setUpdated(entity.getPublished());
+
+				final ResourceHistoryTable historyEntry = entity.toHistory(myCtx);
+
+				final List<ResourceIndexedSearchParamString> stringParams = extractSearchParamStrings(entity, theResource);
+				final List<ResourceIndexedSearchParamToken> tokenParams = extractSearchParamTokens(entity, theResource);
+				final List<ResourceIndexedSearchParamNumber> numberParams = extractSearchParamNumber(entity, theResource);
+				final List<ResourceIndexedSearchParamDate> dateParams = extractSearchParamDates(entity, theResource);
+				final List<ResourceLink> links = extractResourceLinks(entity, theResource);
+
+				populateResourceIntoEntity(theResource, entity);
+				myEntityManager.persist(historyEntry);
+
+				entity.setUpdated(new Date());
+				myEntityManager.persist(entity);
+
+				if (entity.isParamsStringPopulated()) {
+					for (ResourceIndexedSearchParamString next : entity.getParamsString()) {
+						myEntityManager.remove(next);
+					}
+				}
+				for (ResourceIndexedSearchParamString next : stringParams) {
+					myEntityManager.persist(next);
+				}
+				
+				if (entity.isParamsTokenPopulated()) {
+					for (ResourceIndexedSearchParamToken next : entity.getParamsToken()) {
+						myEntityManager.remove(next);
+					}
+				}
+				for (ResourceIndexedSearchParamToken next : tokenParams) {
+					myEntityManager.persist(next);
+				}
+
+				if (entity.isParamsNumberPopulated()) {
+					for (ResourceIndexedSearchParamNumber next : entity.getParamsNumber()) {
+						myEntityManager.remove(next);
+					}
+				}
+				for (ResourceIndexedSearchParamNumber next : numberParams) {
+					myEntityManager.persist(next);
+				}
+				
+				if (entity.isParamsDatePopulated()) {
+					for (ResourceIndexedSearchParamDate next : entity.getParamsDate()) {
+						myEntityManager.remove(next);
+					}
+				}
+				for (ResourceIndexedSearchParamDate next : dateParams) {
+					myEntityManager.persist(next);
+				}
+				
+				if (entity.isHasLinks()) {
+					for (ResourceLink next : entity.getResourceLinks()) {
+						myEntityManager.remove(next);
+					}
+				}
+				for (ResourceLink next : links) {
+					myEntityManager.persist(next);
+				}
+
+				return entity;
+			}
+		});
+
+		return toMethodOutcome(savedEntity);
+	}
+
 	private Set<Long> addPredicateDate(Set<Long> thePids, List<IQueryParameterType> theOrParams) {
 		if (theOrParams == null || theOrParams.isEmpty()) {
 			return thePids;
@@ -266,19 +574,19 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 					Predicate eq = builder.equal(from.get("myTargetResourcePid"), targetPid);
 					codePredicates.add(eq);
 				} else {
-					// TODO: handle chain with resource type
 					String chain = myCtx.getResourceDefinition(myResourceType).getSearchParam(theParamName).getPath();
 					BaseRuntimeChildDefinition def = myCtx.newTerser().getDefinition(myResourceType, chain);
 					if (!(def instanceof RuntimeChildResourceDefinition)) {
 						throw new ConfigurationException("Property " + chain + " of type " + myResourceName + " is not a resource: " + def.getClass());
 					}
 					List<Class<? extends IResource>> resourceTypes;
-					if (ref.getType() == null) {
+					if (isBlank(ref.getResourceType())) {
 						RuntimeChildResourceDefinition resDef = (RuntimeChildResourceDefinition) def;
 						resourceTypes = resDef.getResourceTypes();
 					} else {
 						resourceTypes = new ArrayList<>();
-						resourceTypes.add(ref.getType());
+						RuntimeResourceDefinition resDef = myCtx.getResourceDefinition(ref.getResourceType());
+						resourceTypes.add(resDef.getImplementingClass());
 					}
 					for (Class<? extends IResource> nextType : resourceTypes) {
 						RuntimeResourceDefinition typeDef = myCtx.getResourceDefinition(nextType);
@@ -313,7 +621,10 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 
 		Predicate masterCodePredicate = builder.or(codePredicates.toArray(new Predicate[0]));
 
-		Predicate type = builder.equal(from.get("mySourcePath"), myResourceName + "." + theParamName);
+		RuntimeSearchParam param = myCtx.getResourceDefinition(getResourceType()).getSearchParam(theParamName);
+		String path = param.getPath();
+		
+		Predicate type = builder.equal(from.get("mySourcePath"), path);
 		if (pidsToRetain.size() > 0) {
 			Predicate inPids = (from.get("mySourceResourcePid").in(pidsToRetain));
 			cq.where(builder.and(type, inPids, masterCodePredicate));
@@ -422,53 +733,6 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 		return new HashSet<Long>(q.getResultList());
 	}
 
-	@Transactional(propagation = Propagation.REQUIRED, readOnly = true)
-	@Override
-	public MethodOutcome create(T theResource) {
-
-		final X entity = toEntity(theResource);
-
-		entity.setPublished(new Date());
-		entity.setUpdated(entity.getPublished());
-
-		final List<ResourceIndexedSearchParamString> stringParams = extractSearchParamStrings(entity, theResource);
-		final List<ResourceIndexedSearchParamToken> tokenParams = extractSearchParamTokens(entity, theResource);
-		final List<ResourceIndexedSearchParamNumber> numberParams = extractSearchParamNumber(entity, theResource);
-		final List<ResourceIndexedSearchParamDate> dateParams = extractSearchParamDates(entity, theResource);
-		final List<ResourceLink> links = extractResourceLinks(entity, theResource);
-
-		ourLog.info("Saving links: {}", links);
-
-		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
-		template.setReadOnly(false);
-		template.execute(new TransactionCallback<X>() {
-			@Override
-			public X doInTransaction(TransactionStatus theStatus) {
-				myEntityManager.persist(entity);
-				for (ResourceIndexedSearchParamString next : stringParams) {
-					myEntityManager.persist(next);
-				}
-				for (ResourceIndexedSearchParamToken next : tokenParams) {
-					myEntityManager.persist(next);
-				}
-				for (ResourceIndexedSearchParamNumber next : numberParams) {
-					myEntityManager.persist(next);
-				}
-				for (ResourceIndexedSearchParamDate next : dateParams) {
-					myEntityManager.persist(next);
-				}
-				for (ResourceLink next : links) {
-					myEntityManager.persist(next);
-				}
-				return entity;
-			}
-		});
-
-		MethodOutcome outcome = toMethodOutcome(entity);
-		return outcome;
-	}
-
 	private List<ResourceLink> extractResourceLinks(X theEntity, T theResource) {
 		ArrayList<ResourceLink> retVal = new ArrayList<ResourceLink>();
 
@@ -533,6 +797,8 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 			}
 		}
 
+		theEntity.setHasLinks(retVal.size() > 0);
+
 		return retVal;
 	}
 
@@ -580,6 +846,8 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 			}
 		}
 
+		theEntity.setParamsDatePopulated(retVal.size() > 0);
+
 		return retVal;
 	}
 
@@ -608,8 +876,7 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 
 				if (nextObject instanceof QuantityDt) {
 					QuantityDt nextValue = (QuantityDt) nextObject;
-					ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue().getValue(), nextValue.getSystem().getValueAsString(),
+					ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue().getValue(), nextValue.getSystem().getValueAsString(), nextValue.getUnits().getValue());
-							nextValue.getUnits().getValue());
 					nextEntity.setResource(theEntity, def.getName());
 					retVal.add(nextEntity);
 				} else {
@@ -622,6 +889,8 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 			}
 		}
 
+		theEntity.setParamsNumberPopulated(retVal.size() > 0);
+
 		return retVal;
 	}
 
@@ -657,10 +926,12 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 					ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, normalizeString(nextValue.getValueAsString()), nextValue.getValueAsString());
 					nextEntity.setResource(theEntity, def.getName());
 					retVal.add(nextEntity);
-				} else if (nextObject instanceof HumanNameDt) {
+				} else {
+					if (nextObject instanceof HumanNameDt) {
 						ArrayList<StringDt> allNames = new ArrayList<>();
-					allNames.addAll(((HumanNameDt) nextObject).getFamily());
+						HumanNameDt nextHumanName = (HumanNameDt) nextObject;
-					allNames.addAll(((HumanNameDt) nextObject).getGiven());
+						allNames.addAll(nextHumanName.getFamily());
+						allNames.addAll(nextHumanName.getGiven());
 						for (StringDt nextName : allNames) {
 							if (nextName.isEmpty()) {
 								continue;
@@ -669,6 +940,29 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 							nextEntity.setResource(theEntity, def.getName());
 							retVal.add(nextEntity);
 						}
+					} else if (nextObject instanceof AddressDt) {
+						ArrayList<StringDt> allNames = new ArrayList<>();
+						AddressDt nextAddress = (AddressDt) nextObject;
+						allNames.addAll(nextAddress.getLine());
+						allNames.add(nextAddress.getCity());
+						allNames.add(nextAddress.getState());
+						allNames.add(nextAddress.getCountry());
+						allNames.add(nextAddress.getZip());
+						for (StringDt nextName : allNames) {
+							if (nextName.isEmpty()) {
+								continue;
+							}
+							ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, normalizeString(nextName.getValueAsString()), nextName.getValueAsString());
+							nextEntity.setResource(theEntity, def.getName());
+							retVal.add(nextEntity);
+						}
+					} else if (nextObject instanceof ContactDt) {
+						ContactDt nextContact = (ContactDt) nextObject;
+						if (nextContact.getValue().isEmpty() == false) {
+							ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, normalizeString(nextContact.getValue().getValueAsString()), nextContact.getValue().getValueAsString());
+							nextEntity.setResource(theEntity, def.getName());
+							retVal.add(nextEntity);
+						}
 					} else {
 						if (!multiType) {
 							throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass());
@@ -676,23 +970,13 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 					}
 				}
 			}
+		}
+		
+		theEntity.setParamsStringPopulated(retVal.size() > 0);
 
 		return retVal;
 	}
 
-	private String normalizeString(String theString) {
-		char[] out = new char[theString.length()];
-		theString = Normalizer.normalize(theString, Normalizer.Form.NFD);
-		int j = 0;
-		for (int i = 0, n = theString.length(); i < n; ++i) {
-			char c = theString.charAt(i);
-			if (c <= '\u007F') {
-				out[j++] = c;
-			}
-		}
-		return new String(out).toUpperCase();
-	}
-
 	private List<ResourceIndexedSearchParamToken> extractSearchParamTokens(X theEntity, T theResource) {
 		ArrayList<ResourceIndexedSearchParamToken> retVal = new ArrayList<ResourceIndexedSearchParamToken>();
 
@@ -753,11 +1037,9 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 			}
 		}
 
-		return retVal;
+		theEntity.setParamsTokenPopulated(retVal.size() > 0);
-	}
 
-	public Class<T> getResourceType() {
+		return retVal;
-		return myResourceType;
 	}
 
 	private Map<Class<? extends IResource>, IFhirResourceDao<?>> getResourceTypeToDao() {
@@ -772,39 +1054,17 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 		return resourceTypeToDao;
 	}
 
-	@Override
+	private String normalizeString(String theString) {
-	public Class<X> getTableType() {
+		char[] out = new char[theString.length()];
-		return myTableType;
+		theString = Normalizer.normalize(theString, Normalizer.Form.NFD);
+		int j = 0;
+		for (int i = 0, n = theString.length(); i < n; ++i) {
+			char c = theString.charAt(i);
+			if (c <= '\u007F') {
+				out[j++] = c;
 			}
-
-	@Transactional(propagation = Propagation.REQUIRED)
-	@Override
-	public List<T> history(IdDt theId) {
-		ArrayList<T> retVal = new ArrayList<T>();
-
-		String resourceType = myCtx.getResourceDefinition(myResourceType).getName();
-		TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(ResourceHistoryTable.Q_GETALL, ResourceHistoryTable.class);
-		q.setParameter("PID", theId.asLong());
-		q.setParameter("RESTYPE", resourceType);
-
-		// TypedQuery<ResourceHistoryTable> query =
-		// myEntityManager.createQuery(criteriaQuery);
-		List<ResourceHistoryTable> results = q.getResultList();
-		for (ResourceHistoryTable next : results) {
-			retVal.add(toResource(next));
 		}
-
+		return new String(out).toUpperCase();
-		try {
-			retVal.add(read(theId));
-		} catch (ResourceNotFoundException e) {
-			// ignore
-		}
-
-		if (retVal.isEmpty()) {
-			throw new ResourceNotFoundException(theId);
-		}
-
-		return retVal;
 	}
 
 	private void populateResourceIntoEntity(T theResource, X retVal) {
@@ -820,22 +1080,6 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 
 	}
 
-	@PostConstruct
-	public void postConstruct() throws Exception {
-		myResourceType = myTableType.newInstance().getResourceType();
-		myCtx = new FhirContext(myResourceType);
-		myResourceName = myCtx.getResourceDefinition(myResourceType).getName();
-	}
-
-	@Transactional(propagation = Propagation.REQUIRED)
-	@Override
-	public T read(IdDt theId) {
-		X entity = readEntity(theId);
-
-		T retVal = toResource(entity);
-		return retVal;
-	}
-
 	private X readEntity(IdDt theId) {
 		X entity = (X) myEntityManager.find(myTableType, theId.asLong());
 		if (entity == null) {
@@ -844,132 +1088,6 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 		return entity;
 	}
 
-	@Override
-	public List<T> search(Map<String, IQueryParameterType> theParams) {
-		SearchParameterMap map = new SearchParameterMap();
-		for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
-			map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
-			map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
-		}
-		return search(map);
-	}
-
-	@Override
-	public List<T> search(String theParameterName, IQueryParameterType theValue) {
-		return search(Collections.singletonMap(theParameterName, theValue));
-	}
-
-	@Override
-	public Set<Long> searchForIds(Map<String, IQueryParameterType> theParams) {
-		Map<String, List<List<IQueryParameterType>>> map = new HashMap<String, List<List<IQueryParameterType>>>();
-		for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
-			map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
-			map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
-		}
-		return searchForIdsWithAndOr(map);
-	}
-
-	@Override
-	public Set<Long> searchForIdsWithAndOr(Map<String, List<List<IQueryParameterType>>> theParams) {
-		Map<String, List<List<IQueryParameterType>>> params = theParams;
-		if (params == null) {
-			params = Collections.emptyMap();
-		}
-
-		RuntimeResourceDefinition resourceDef = myCtx.getResourceDefinition(myResourceType);
-
-		Set<Long> pids = new HashSet<Long>();
-
-		for (Entry<String, List<List<IQueryParameterType>>> nextParamEntry : params.entrySet()) {
-			String nextParamName = nextParamEntry.getKey();
-			RuntimeSearchParam nextParamDef = resourceDef.getSearchParam(nextParamName);
-			if (nextParamDef != null) {
-				if (nextParamDef.getParamType() == SearchParamTypeEnum.TOKEN) {
-					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
-						pids = addPredicateToken(pids, nextAnd);
-						if (pids.isEmpty()) {
-							return new HashSet<Long>();
-						}
-					}
-				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.STRING) {
-					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
-						pids = addPredicateString(pids, nextAnd);
-						if (pids.isEmpty()) {
-							return new HashSet<Long>();
-						}
-					}
-				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.QUANTITY) {
-					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
-						pids = addPredicateQuantity(pids, nextAnd);
-						if (pids.isEmpty()) {
-							return new HashSet<Long>();
-						}
-					}
-				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.DATE) {
-					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
-						pids = addPredicateDate(pids, nextAnd);
-						if (pids.isEmpty()) {
-							return new HashSet<Long>();
-						}
-					}
-				} else if (nextParamDef.getParamType() == SearchParamTypeEnum.REFERENCE) {
-					for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
-						pids = addPredicateReference(nextParamName, pids, nextAnd);
-						if (pids.isEmpty()) {
-							return new HashSet<Long>();
-						}
-					}
-				} else {
-					throw new IllegalArgumentException("Don't know how to handle parameter of type: " + nextParamDef.getParamType());
-				}
-			}
-		}
-
-		return pids;
-	}
-
-	@Override
-	public Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue) {
-		return searchForIds(Collections.singletonMap(theParameterName, theValue));
-	}
-
-	@Override
-	public List<T> search(SearchParameterMap theParams) {
-
-		Set<Long> pids;
-		if (theParams.isEmpty()) {
-			pids = null;
-		} else {
-			pids = searchForIdsWithAndOr(theParams);
-			if (pids.isEmpty()) {
-				return new ArrayList<>();
-			}
-		}
-
-		// Execute the query and make sure we return distinct results
-		{
-			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-			CriteriaQuery<X> cq = builder.createQuery(myTableType);
-			Root<X> from = cq.from(myTableType);
-			if (!theParams.isEmpty()) {
-				cq.where(from.get("myId").in(pids));
-			}
-			TypedQuery<X> q = myEntityManager.createQuery(cq);
-
-			List<T> retVal = new ArrayList<>();
-			for (X next : q.getResultList()) {
-				T resource = toResource(next);
-				retVal.add(resource);
-			}
-			return retVal;
-		}
-	}
-
-	@Required
-	public void setTableType(Class<X> theTableType) {
-		myTableType = theTableType;
-	}
-
 	private X toEntity(T theResource) {
 		X retVal;
 		try {
@@ -1034,27 +1152,4 @@ public class FhirResourceDao<T extends IResource, X extends BaseResourceTable<T>
 		}
 		return retVal;
 	}
-
-	@Transactional(propagation = Propagation.SUPPORTS)
-	@Override
-	public MethodOutcome update(final T theResource, final IdDt theId) {
-		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-		X savedEntity = template.execute(new TransactionCallback<X>() {
-			@Override
-			public X doInTransaction(TransactionStatus theStatus) {
-				final X entity = readEntity(theId);
-				final ResourceHistoryTable existing = entity.toHistory(myCtx);
-
-				populateResourceIntoEntity(theResource, entity);
-				myEntityManager.persist(existing);
-
-				entity.setUpdated(new Date());
-				myEntityManager.persist(entity);
-				return entity;
-			}
-		});
-
-		return toMethodOutcome(savedEntity);
-	}
-
 }

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

@@ -5,15 +5,17 @@ import java.util.HashMap;
 import java.util.List;
 
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.api.IQueryParameterType;
-import ca.uhn.fhir.rest.method.QualifiedParamList;
-import ca.uhn.fhir.rest.param.DateRangeParam;
 
 public class SearchParameterMap extends HashMap<String, List<List<IQueryParameterType>>> {
 
 	private static final long serialVersionUID = 1L;
 
 	public void add(String theName, IQueryParameterType theParam) {
+		if (theParam == null) {
+			return;
+		}
 		if (!containsKey(theName)) {
 			put(theName, new ArrayList<List<IQueryParameterType>>());
 		}
@@ -22,13 +24,19 @@ public class SearchParameterMap extends HashMap<String, List<List<IQueryParamete
 		get(theName).add(list);
 	}
 
-	public void add(String theName, IQueryParameterAnd theBirthdate) {
+	public void add(String theName, IQueryParameterAnd theAnd) {
+		if (theAnd==null) {
+			return;
+		}
 		if (!containsKey(theName)) {
 			put(theName, new ArrayList<List<IQueryParameterType>>());
 		}
 
-		for (QualifiedParamList next : theBirthdate.getValuesAsQueryTokens()) {
+		for (IQueryParameterOr next : theAnd.getValuesAsQueryTokens()) {
-			next.get
+			if (next==null) {
+				continue;
+			}
+			get(theName).add(next.getValuesAsQueryTokens());
 		}
 	}
 

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

@@ -28,17 +28,29 @@ import ca.uhn.fhir.model.primitive.IdDt;
 @DiscriminatorColumn(name = "SVCVER_TYPE", length = 20, discriminatorType = DiscriminatorType.STRING)
 public abstract class BaseResourceTable<T extends IResource> extends BaseHasResource {
 
+	@Column(name = "SP_HAS_LINKS")
+	private boolean myHasLinks;
+
 	@Id
 	@GeneratedValue(strategy = GenerationType.AUTO)
 	@Column(name = "RES_ID")
 	private Long myId;
 
+	@OneToMany(mappedBy = "myTargetResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
+	private Collection<ResourceLink> myIncomingResourceLinks;
+
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
 	private Collection<ResourceIndexedSearchParamDate> myParamsDate;
 
 	@Column(name = "SP_DATE_PRESENT")
 	private boolean myParamsDatePopulated;
 
+	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
+	private Collection<ResourceIndexedSearchParamNumber> myParamsNumber;
+
+	@Column(name = "SP_NUMBER_PRESENT")
+	private boolean myParamsNumberPopulated;
+
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
 	private Collection<ResourceIndexedSearchParamString> myParamsString;
 
@@ -51,6 +63,9 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 	@Column(name = "SP_TOKEN_PRESENT")
 	private boolean myParamsTokenPopulated;
 
+	@OneToMany(mappedBy = "mySourceResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
+	private Collection<ResourceLink> myResourceLinks;
+
 	@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.EAGER, orphanRemoval = true)
 	private Collection<ResourceTag> myTags;
 
@@ -67,14 +82,14 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 		getTags().add(new ResourceTag(this, theTerm, theLabel, theScheme));
 	}
 
-	public Long getIdAsLong() {
-		return myId;
-	}
-
 	public IdDt getId() {
 		return new IdDt(myId);
 	}
 
+	public Long getIdAsLong() {
+		return myId;
+	}
+
 	public Collection<ResourceIndexedSearchParamDate> getParamsDate() {
 		if (myParamsDate == null) {
 			myParamsDate = new ArrayList<>();
@@ -82,6 +97,13 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 		return myParamsDate;
 	}
 
+	public Collection<ResourceIndexedSearchParamNumber> getParamsNumber() {
+		if (myParamsNumber == null) {
+			myParamsNumber = new ArrayList<>();
+		}
+		return myParamsNumber;
+	}
+
 	public Collection<ResourceIndexedSearchParamString> getParamsString() {
 		if (myParamsString == null) {
 			myParamsString = new ArrayList<>();
@@ -96,6 +118,13 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 		return myParamsToken;
 	}
 
+	public Collection<ResourceLink> getResourceLinks() {
+		if (myResourceLinks == null) {
+			myResourceLinks = new ArrayList<>();
+		}
+		return myResourceLinks;
+	}
+
 	public abstract Class<T> getResourceType();
 
 	public Collection<ResourceTag> getTags() {
@@ -109,10 +138,18 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 		return new IdDt(myVersion);
 	}
 
+	public boolean isHasLinks() {
+		return myHasLinks;
+	}
+
 	public boolean isParamsDatePopulated() {
 		return myParamsDatePopulated;
 	}
 
+	public boolean isParamsNumberPopulated() {
+		return myParamsNumberPopulated;
+	}
+
 	public boolean isParamsStringPopulated() {
 		return myParamsStringPopulated;
 	}
@@ -121,6 +158,10 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 		return myParamsTokenPopulated;
 	}
 
+	public void setHasLinks(boolean theHasLinks) {
+		myHasLinks = theHasLinks;
+	}
+
 	public void setId(IdDt theId) {
 		myId = theId.asLong();
 	}
@@ -133,6 +174,10 @@ public abstract class BaseResourceTable<T extends IResource> extends BaseHasReso
 		myParamsDatePopulated = theParamsDatePopulated;
 	}
 
+	public void setParamsNumberPopulated(boolean theParamsNumberPopulated) {
+		myParamsNumberPopulated = theParamsNumberPopulated;
+	}
+
 	public void setParamsString(Collection<ResourceIndexedSearchParamString> theParamsString) {
 		myParamsString = theParamsString;
 	}

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.entity;
 import java.io.Serializable;
 
 import javax.persistence.Entity;
+import javax.persistence.ForeignKey;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
@@ -26,7 +27,7 @@ public class ResourceHistoryTag extends BaseTag implements Serializable {
 			@JoinColumn(name="RES_TYPE", referencedColumnName="RES_TYPE"),
 			@JoinColumn(name="PID", referencedColumnName="PID"),
 			@JoinColumn(name="VERSION", referencedColumnName="VERSION")
-	})
+	}, foreignKey=@ForeignKey(name="FK_HT_RT"))
 	private ResourceHistoryTable myResourceHistory;
 
 	public ResourceHistoryTag() {

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

@@ -4,6 +4,8 @@ import java.util.Date;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.ForeignKey;
+import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
@@ -11,7 +13,7 @@ import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 
 @Entity
-@Table(name = "IDX_SP_DATE")
+@Table(name = "SPIDX_DATE", indexes= {@Index(name="IDX_SP_DATE", columnList="myValueLow,myValueHigh")})
 public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchParam {
 
 	private static final long serialVersionUID = 1L;
@@ -25,7 +27,7 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
 	public Date myValueLow;
 
 	@ManyToOne(optional = false)
-	@JoinColumn(name = "RESOURCE_PID", nullable = false)
+	@JoinColumn(name = "RESOURCE_PID", nullable = false, foreignKey=@ForeignKey(name="FK_ISD_RESOURCE"))
 	private BaseResourceTable<?> myResource;
 
 	@Column(name = "RESOURCE_PID", insertable = false, updatable = false)

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

@@ -4,12 +4,14 @@ import java.math.BigDecimal;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.ForeignKey;
+import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
 @Entity
-@Table(name = "IDX_SP_NUMBER")
+@Table(name = "SPIDX_NUMBER", indexes= {@Index(name="IDX_SP_NUMBER", columnList="myValue")})
 public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchParam {
 
 	private static final long serialVersionUID = 1L;
@@ -24,7 +26,7 @@ public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchP
 	public BigDecimal myValue;
 
 	@ManyToOne(optional = false)
-	@JoinColumn(name = "RESOURCE_PID", nullable = false)
+	@JoinColumn(name = "RESOURCE_PID", nullable = false, foreignKey=@ForeignKey(name="FK_ISN_RESOURCE"))
 	private BaseResourceTable<?> myResource;
 
 	@Column(name = "RESOURCE_PID", insertable = false, updatable = false)

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

@@ -3,18 +3,20 @@ package ca.uhn.fhir.jpa.entity;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
+import javax.persistence.ForeignKey;
+import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
 @Entity
-@Table(name = "IDX_SP_STRING")
+@Table(name = "SPIDX_STRING", indexes= {@Index(name="IDX_SP_STRING", columnList="myValueNormalized")})
 public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchParam {
 
 	private static final long serialVersionUID = 1L;
 
 	@ManyToOne(optional = false, cascade = {}, fetch = FetchType.LAZY)
-	@JoinColumn(name = "RESOURCE_PID", nullable = false)
+	@JoinColumn(name = "RESOURCE_PID", nullable = false, foreignKey=@ForeignKey(name="FK_ISS_RESOURCE"))
 	private BaseResourceTable<?> myResource;
 
 	@Column(name = "RESOURCE_PID", insertable=false, updatable=false)

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

@@ -2,18 +2,20 @@ package ca.uhn.fhir.jpa.entity;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.ForeignKey;
+import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
 @Entity
-@Table(name = "IDX_SP_TOKEN")
+@Table(name = "SPIDX_TOKEN", indexes= {@Index(name="IDX_SP_STRING", columnList="mySystem,myValue")})
 public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchParam {
 
 	private static final long serialVersionUID = 1L;
 
 	@ManyToOne(optional = false)
-	@JoinColumn(name = "RESOURCE_PID", nullable = false)
+	@JoinColumn(name = "RESOURCE_PID", nullable = false, foreignKey=@ForeignKey(name="FK_IST_RESOURCE"))
 	private BaseResourceTable<?> myResource;
 
 	@Column(name = "RESOURCE_PID", insertable=false, updatable=false)
@@ -33,6 +35,9 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
 		mySystem = theSystem;
 	}
 
+	public ResourceIndexedSearchParamToken() {
+	}
+	
 	public ResourceIndexedSearchParamToken(String theName, String theSystem, String theValue) {
 		setName(theName);
 		setSystem(theSystem);

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.entity;
 
 import javax.persistence.Entity;
+import javax.persistence.ForeignKey;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
@@ -19,7 +20,7 @@ public class ResourceTag extends BaseTag {
 	private Long myId;
 	
 	@ManyToOne(cascade= {})
-	@JoinColumn(name = "RESOURCE_PID", nullable=false)
+	@JoinColumn(name = "RESOURCE_PID", nullable=false, foreignKey=@ForeignKey(name="FK_RESTAG_RESOURCE"))
 	private BaseResourceTable<?> myResource;
 
 	public ResourceTag() {

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

@@ -1,18 +1,14 @@
 package ca.uhn.fhir.jpa.dao;
 
-import static org.junit.Assert.assertEquals;
+import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.hamcrest.core.StringContains;
 import org.junit.AfterClass;
@@ -190,7 +186,7 @@ public class FhirResourceDaoTest {
 		found = ourPatientDao.search(Patient.SP_GENDER, new IdentifierDt(null, "F"));
 		assertEquals(0, found.size());
 
-		Map<String, List<List<IQueryParameterType>>> map = new HashMap<>();
+		SearchParameterMap map = new SearchParameterMap();
 		map.put(Patient.SP_IDENTIFIER, new ArrayList<List<IQueryParameterType>>());
 		map.get(Patient.SP_IDENTIFIER).add(new ArrayList<IQueryParameterType>());
 		map.get(Patient.SP_IDENTIFIER).get(0).add(new IdentifierDt("urn:system", "001testPersistSearchParams"));
@@ -201,7 +197,7 @@ public class FhirResourceDaoTest {
 		assertEquals(1, found.size());
 		assertEquals(id, found.get(0).getId().asLong().longValue());
 
-		map = new HashMap<>();
+		map = new SearchParameterMap();
 		map.put(Patient.SP_IDENTIFIER, new ArrayList<List<IQueryParameterType>>());
 		map.get(Patient.SP_IDENTIFIER).add(new ArrayList<IQueryParameterType>());
 		map.get(Patient.SP_IDENTIFIER).get(0).add(new IdentifierDt("urn:system", "001testPersistSearchParams"));
@@ -358,7 +354,7 @@ public class FhirResourceDaoTest {
 		result = ourObservationDao.search(Observation.SP_SUBJECT, new ReferenceParam(Patient.SP_NAME, "testSearchResourceLinkWithChainWithMultipleTypesYY"));
 		assertEquals(0,result.size());
 
-		result = ourObservationDao.search(Observation.SP_SUBJECT, new ReferenceParam(Patient.class, Patient.SP_NAME, "testSearchResourceLinkWithChainWithMultipleTypes01"));
+		result = ourObservationDao.search(Observation.SP_SUBJECT, new ReferenceParam("Patient", Patient.SP_NAME, "testSearchResourceLinkWithChainWithMultipleTypes01"));
 		assertEquals(1,result.size());
 		assertEquals(obsId01, result.get(0).getId());
 
@@ -505,6 +501,36 @@ public class FhirResourceDaoTest {
 
 	}
 
+	
+	@Test
+	public void testUpdateMaintainsSearchParams() throws InterruptedException {
+		Patient p1 = new Patient();
+		p1.addIdentifier("urn:system", "testUpdateMaintainsSearchParamsAAA");
+		p1.addName().addFamily("Tester").addGiven("testUpdateMaintainsSearchParamsAAA");
+		IdDt p1id = ourPatientDao.create(p1).getId();
+
+		Patient p2 = new Patient();
+		p2.addIdentifier("urn:system", "testUpdateMaintainsSearchParamsBBB");
+		p2.addName().addFamily("Tester").addGiven("testUpdateMaintainsSearchParamsBBB");
+		IdDt p2id = ourPatientDao.create(p2).getId();
+		
+		Set<Long> ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsAAA"));
+		assertEquals(1,ids.size());
+		assertThat(ids, contains(p1id.asLong()));
+		
+		// Update the name
+		p1.getNameFirstRep().getGivenFirstRep().setValue("testUpdateMaintainsSearchParamsBBB");
+		ourPatientDao.update(p1, p1id);
+
+		ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsAAA"));
+		assertEquals(0,ids.size());
+
+		ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsBBB"));
+		assertEquals(2,ids.size());
+
+	}
+
+	
 	@AfterClass
 	public static void afterClass() {
 		ourCtx.close();
@@ -514,7 +540,7 @@ public class FhirResourceDaoTest {
 	@BeforeClass
 	public static void beforeClass() {
 		ourTestStarted = new Date();
-		ourCtx = new ClassPathXmlApplicationContext("fhir-spring-test-config.xml");
+		ourCtx = new ClassPathXmlApplicationContext("fhir-jpabase-spring-test-config.xml");
 		ourPatientDao = ourCtx.getBean("myPatientDao", IFhirResourceDao.class);
 		ourObservationDao = ourCtx.getBean("myObservationDao", IFhirResourceDao.class);
 		ourDiagnosticReportDao = ourCtx.getBean("myDiagnosticReportDao", IFhirResourceDao.class);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/DeviceResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.Device;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/DiagnosticReportResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/LocationResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.Location;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/ObservationResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.Observation;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/OrganizationResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.Organization;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/PatientResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.Patient;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/testentity/QuestionnaireResourceTable.java

@@ -1,8 +1,9 @@
-package ca.uhn.fhir.jpa.entity;
+package ca.uhn.fhir.jpa.testentity;
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
 import ca.uhn.fhir.model.dstu.resource.Questionnaire;
 
 @Entity

hapi-fhir-jpaserver-base/src/test/resources/META-INF/persistence.xml

@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<persistence xmlns="http://java.sun.com/xml/ns/persistence"
+             xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+             xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
+             version="2.0">
+
+	<persistence-unit name="FHIR_UT" transaction-type="RESOURCE_LOCAL">
+		<provider>org.hibernate.ejb.HibernatePersistence</provider>
+		<!-- <class>ca.uhn.fhir.jpa.entity.PatientResourceTable</class>  -->
+		
+		<class>ca.uhn.fhir.jpa.testentity.DeviceResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.DiagnosticReportResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.LocationResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.ObservationResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.OrganizationResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.PatientResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.QuestionnaireResourceTable</class>
+		<class>ca.uhn.fhir.jpa.testentity.QuestionnaireResourceTable</class>
+
+		<class>ca.uhn.fhir.jpa.entity.ResourceHistoryTable</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceHistoryTag</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceLink</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceTag</class>
+		
+		<exclude-unlisted-classes>false</exclude-unlisted-classes>
+		<properties>
+			<property name="hibernate.connection.url" value="jdbc:hsqldb:mem:unit-testing-jpa" />
+			<property name="hibernate.connection.driver_class" value="org.hsqldb.jdbcDriver" />
+			<property name="hibernate.dialect" value="org.hibernate.dialect.DerbyTenSevenDialect" />
+			<property name="hibernate.hbm2ddl.auto" value="update" />
+			<property name="hibernate.connection.username" value="sa" />
+			<property name="hibernate.connection.password" value="" />
+			<property name="hibernate.jdbc.batch_size" value="0" />
+			<property name="hibernate.cache.use_minimal_puts" value="false" />
+			<property name="hibernate.show_sql" value="false" />
+			<property name="hibernate.cache.use_query_cache" value="false" />
+			<property name="hibernate.cache.use_second_level_cache" value="false" />
+			<property name="hibernate.cache.use_structured_entries" value="false" />
+			<property name="hibernate.ejb.naming_strategy" value="ca.uhn.fhir.jpa.util.CustomNamingStrategy" />
+			<!-- 
+			<property name="hibernate.cache.region.factory_class" value="org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory" />
+			 -->
+		</properties>                                                    
+	</persistence-unit>
+
+</persistence>

hapi-fhir-jpaserver-base/src/test/resources/fhir-jpabase-spring-test-config.xml

@@ -14,22 +14,22 @@
 	<context:mbean-server />
 
 	<bean id="myPatientDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.PatientResourceTable"/>
+		<property name="tableType" value="ca.uhn.fhir.jpa.testentity.PatientResourceTable"/>
 	</bean>
 	<bean id="myObservationDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.ObservationResourceTable"/>
+		<property name="tableType" value="ca.uhn.fhir.jpa.testentity.ObservationResourceTable"/>
 	</bean>
 	<bean id="myDiagnosticReportDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.DiagnosticReportResourceTable"/>
+		<property name="tableType" value="ca.uhn.fhir.jpa.testentity.DiagnosticReportResourceTable"/>
 	</bean>
 	<bean id="myDeviceDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.DeviceResourceTable"/>
+		<property name="tableType" value="ca.uhn.fhir.jpa.testentity.DeviceResourceTable"/>
 	</bean>
 	<bean id="myLocationDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.LocationResourceTable"/>
+		<property name="tableType" value="ca.uhn.fhir.jpa.testentity.LocationResourceTable"/>
 	</bean>
 	<bean id="myOrganizationDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.OrganizationResourceTable"/>
+		<property name="tableType" value="ca.uhn.fhir.jpa.testentity.OrganizationResourceTable"/>
 	</bean>
 
 	<bean id="myPersistenceDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" lazy-init="true">

hapi-fhir-jpaserver-test/.classpath

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry excluding="**/*.java" kind="src" output="target/test-classes" path="src/test/resources"/>
+	<classpathentry kind="src" path="target/generated-sources/tinder"/>
 	<classpathentry including="**/*.java" kind="src" path="src/main/java"/>
 	<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
 	<classpathentry kind="var" path="M2_REPO/javax/activation/activation/1.1/activation-1.1.jar" sourcepath="M2_REPO/javax/activation/activation/1.1/activation-1.1-sources.jar"/>

hapi-fhir-jpaserver-test/pom.xml

@@ -80,6 +80,33 @@
 			</plugins>
 		</pluginManagement>
 		<plugins>
+					<plugin>
+				<groupId>ca.uhn.hapi.fhir</groupId>
+				<artifactId>hapi-tinder-plugin</artifactId>
+				<version>0.3</version>
+				<executions>
+					<execution>
+						<id>buildclient</id>
+						<goals>
+							<goal>generate-jparest-server</goal>
+						</goals>
+						<configuration>
+							<packageBase>ca.uhn.test.jpasrv</packageBase>
+							<baseResourceNames>
+								<baseResourceName>device</baseResourceName>
+								<baseResourceName>location</baseResourceName>
+								<baseResourceName>observation</baseResourceName>
+								<baseResourceName>organization</baseResourceName>
+								<baseResourceName>patient</baseResourceName>
+								<baseResourceName>practitioner</baseResourceName>
+								<baseResourceName>questionnaire</baseResourceName>
+								<baseResourceName>valueset</baseResourceName>
+							</baseResourceNames>
+							<buildDatatypes>true</buildDatatypes>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-deploy-plugin</artifactId>

hapi-fhir-jpaserver-test/src/main/java/ca/uhn/fhir/jpa/test/CompleteResourceProviderTest.java

@@ -0,0 +1,177 @@
+package ca.uhn.fhir.jpa.test;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.Observation;
+import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu.resource.Questionnaire;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.tester.RestfulServerTesterServlet;
+import ca.uhn.test.jpasrv.ObservationResourceProvider;
+import ca.uhn.test.jpasrv.OrganizationResourceProvider;
+import ca.uhn.test.jpasrv.PatientResourceProvider;
+
+public class CompleteResourceProviderTest {
+
+	private static ClassPathXmlApplicationContext ourAppCtx;
+	private static FhirContext ourCtx;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CompleteResourceProviderTest.class);
+
+	private static Server ourServer;
+	private static IFhirResourceDao<Patient> patientDao;
+	private static IFhirResourceDao<Questionnaire> questionnaireDao;
+	private static IGenericClient ourClient;
+	private static IFhirResourceDao<Observation> observationDao;
+
+	// @Test
+	// public void test01UploadTestResources() throws Exception {
+	//
+	// IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:8888/fhir/context");
+	//
+	// File[] files = new File("src/test/resources/resources").listFiles(new PatternFilenameFilter(".*patient.*"));
+	// for (File file : files) {
+	// ourLog.info("Uploading: {}", file);
+	// Patient patient = ourCtx.newXmlParser().parseResource(Patient.class, new FileReader(file));
+	// client.create(patient);
+	// }
+	//
+	// files = new File("src/test/resources/resources").listFiles(new PatternFilenameFilter(".*questionnaire.*"));
+	// for (File file : files) {
+	// ourLog.info("Uploading: {}", file);
+	// Questionnaire patient = ourCtx.newXmlParser().parseResource(Questionnaire.class, new FileReader(file));
+	// client.create(patient);
+	// }
+	//
+	// }
+
+	@Test
+	public void testSearchByIdentifier() {
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByIdentifier01");
+		p1.addName().addFamily("testSearchByIdentifierFamily01").addGiven("testSearchByIdentifierGiven01");
+		IdDt p1Id = ourClient.create(p1).getId();
+
+		Patient p2 = new Patient();
+		p2.addIdentifier().setSystem("urn:system").setValue("testSearchByIdentifier02");
+		p2.addName().addFamily("testSearchByIdentifierFamily01").addGiven("testSearchByIdentifierGiven02");
+		ourClient.create(p2).getId();
+
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testSearchByIdentifier01")).encodedJson().prettyPrint().execute();
+		assertEquals(1, actual.size());
+		assertEquals(p1Id, actual.getEntries().get(0).getId());
+
+	}
+
+	@Test
+	public void testSearchByResourceChain() {
+		Organization o1 = new Organization();
+		o1.setName("testSearchByResourceChainName01");
+		IdDt o1id = ourClient.create(o1).getId();
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByResourceChain01");
+		p1.addName().addFamily("testSearchByResourceChainFamily01").addGiven("testSearchByResourceChainGiven01");
+		p1.setManagingOrganization(new ResourceReferenceDt(Organization.class, o1id));
+		IdDt p1Id = ourClient.create(p1).getId();
+
+		//@formatter:off
+		Bundle actual = ourClient.search()
+				.forResource(Patient.class)
+				.where(Patient.PROVIDER.hasId(o1id))
+				.encodedJson().prettyPrint().execute();
+		//@formatter:on
+		assertEquals(1, actual.size());
+		assertEquals(p1Id, actual.getEntries().get(0).getId());
+
+	}
+	
+	@Test
+	public void testInsertBadReference() {
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByResourceChain01");
+		p1.addName().addFamily("testSearchByResourceChainFamily01").addGiven("testSearchByResourceChainGiven01");
+		p1.setManagingOrganization(new ResourceReferenceDt(Organization.class, "132312323"));
+		
+		try {
+		ourClient.create(p1).getId();
+		fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Organization/132312323"));
+		}
+
+	}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+		ourAppCtx.stop();
+	}
+
+	@SuppressWarnings("unchecked")
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourAppCtx = new ClassPathXmlApplicationContext("fhir-spring-test-config.xml");
+
+		patientDao = (IFhirResourceDao<Patient>) ourAppCtx.getBean("myPatientDao", IFhirResourceDao.class);
+		PatientResourceProvider patientRp = new PatientResourceProvider();
+		patientRp.setDao(patientDao);
+
+		questionnaireDao = (IFhirResourceDao<Questionnaire>) ourAppCtx.getBean("myQuestionnaireDao", IFhirResourceDao.class);
+		QuestionnaireResourceProvider questionnaireRp = new QuestionnaireResourceProvider();
+		questionnaireRp.setDao(questionnaireDao);
+
+		observationDao = (IFhirResourceDao<Observation>) ourAppCtx.getBean("myObservationDao", IFhirResourceDao.class);
+		ObservationResourceProvider observationRp = new ObservationResourceProvider();
+		observationRp.setDao(observationDao);
+
+		IFhirResourceDao<Organization> organizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDao", IFhirResourceDao.class);
+		OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
+		organizationRp.setDao(organizationDao);
+
+		RestfulServer restServer = new RestfulServer();
+		restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
+
+		int myPort = 8888;
+		ourServer = new Server(myPort);
+
+		ServletContextHandler proxyHandler = new ServletContextHandler();
+		proxyHandler.setContextPath("/");
+
+		RestfulServerTesterServlet testerServlet = new RestfulServerTesterServlet();
+		String serverBase = "http://localhost:" + myPort + "/fhir/context";
+		testerServlet.setServerBase(serverBase);
+		// testerServlet.setServerBase("http://fhir.healthintersections.com.au/open");
+		ServletHolder handler = new ServletHolder();
+		handler.setServlet(testerServlet);
+		proxyHandler.addServlet(handler, "/fhir/tester/*");
+
+		ServletHolder servletHolder = new ServletHolder();
+		servletHolder.setServlet(restServer);
+		proxyHandler.addServlet(servletHolder, "/fhir/context/*");
+
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		ourCtx = restServer.getFhirContext();
+
+		ourClient = ourCtx.newRestfulGenericClient(serverBase);
+	}
+
+}

hapi-fhir-jpaserver-test/src/main/java/ca/uhn/fhir/jpa/test/JpaTestApp.java

@@ -10,6 +10,7 @@ import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.dstu.resource.Questionnaire;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.tester.RestfulServerTesterServlet;
+import ca.uhn.test.jpasrv.PatientResourceProvider;
 
 public class JpaTestApp {
 

hapi-fhir-jpaserver-test/src/main/java/ca/uhn/fhir/jpa/test/PatientResourceProvider.java

@@ -1,46 +0,0 @@
-package ca.uhn.fhir.jpa.test;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ca.uhn.fhir.jpa.dao.BaseJpaResourceProvider;
-import ca.uhn.fhir.model.api.IQueryParameterType;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.model.dstu.resource.Patient;
-import ca.uhn.fhir.model.primitive.StringDt;
-import ca.uhn.fhir.rest.annotation.OptionalParam;
-import ca.uhn.fhir.rest.annotation.RequiredParam;
-import ca.uhn.fhir.rest.annotation.Search;
-
-public class PatientResourceProvider extends BaseJpaResourceProvider<Patient> {
-
-	@Override
-	public Class<? extends IResource> getResourceType() {
-		return Patient.class;
-	}
-	
-	@Search
-	public List<Patient> searchByName(
-			@Description(shortDefinition="Matches the patient's family (last) name")
-			@RequiredParam(name=Patient.SP_NAME) StringDt theFamily,
-			@Description(shortDefinition="Matches the patient's given (first) name")
-			@OptionalParam(name=Patient.SP_GIVEN) StringDt theGiven) {
-		
-		Map<String, IQueryParameterType> params = new HashMap<>();
-		params.put(Patient.SP_NAME, theFamily);
-		params.put(Patient.SP_GIVEN, theGiven);
-		
-		return getDao().search(params);
-	}
-	
-	@Search
-	public List<Patient> searchByGiven(
-			@Description(shortDefinition="Matches the patient's given (first) name")
-			@RequiredParam(name=Patient.SP_GIVEN) StringDt theValue
-			) {
-		return getDao().search(Patient.SP_GIVEN, theValue);
-	}
-
-}

hapi-fhir-jpaserver-test/src/main/resources/fhir-spring-test-config.xml

@@ -14,18 +14,29 @@
 	<context:mbean-server />
 
 	<bean id="myPatientDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.PatientResourceTable"/>
+		<property name="tableType" value="ca.uhn.test.jpasrv.PatientResourceTable"/>
+	</bean>
+	<bean id="myObservationDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
+		<property name="tableType" value="ca.uhn.test.jpasrv.ObservationResourceTable"/>
+	</bean>
+	<bean id="myOrganizationDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
+		<property name="tableType" value="ca.uhn.test.jpasrv.OrganizationResourceTable"/>
+	</bean>
+	<bean id="myLocationDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
+		<property name="tableType" value="ca.uhn.test.jpasrv.LocationResourceTable"/>
 	</bean>
 	<bean id="myQuestionnaireDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
-		<property name="tableType" value="ca.uhn.fhir.jpa.entity.QuestionnaireResourceTable"/>
+		<property name="tableType" value="ca.uhn.test.jpasrv.QuestionnaireResourceTable"/>
 	</bean>
 
 	<bean id="myPersistenceDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" lazy-init="true">
-		<property name="url" value="jdbc:derby:directory:myUnitTestDB;create=true" />
+		<property name="url" value="jdbc:derby:memory:myUnitTestDB;create=true" />
+		<!-- <property name="url" value="jdbc:derby:directory:myUnitTestDB;create=true" />  -->
 	</bean>
 
 	<bean id="myEntityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
 		<property name="dataSource" ref="myPersistenceDataSource" />
+		<property name="persistenceXmlLocation" value="classpath:fhir_jpatest_persistence.xml" />
 		<property name="persistenceUnitName" value="FHIR_UT" />
 		<property name="jpaVendorAdapter">
 			<bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">

hapi-fhir-jpaserver-test/src/main/resources/fhir_jpatest_persistence.xml

@@ -6,8 +6,21 @@
 
 	<persistence-unit name="FHIR_UT" transaction-type="RESOURCE_LOCAL">
 		<provider>org.hibernate.ejb.HibernatePersistence</provider>
-		<!-- <class>ca.uhn.fhir.jpa.entity.PatientResourceTable</class>  -->
+		<class>ca.uhn.test.jpasrv.PatientResourceTable</class>
-		<exclude-unlisted-classes>false</exclude-unlisted-classes>
+		<class>ca.uhn.test.jpasrv.LocationResourceTable</class>
+		<class>ca.uhn.test.jpasrv.ObservationResourceTable</class>
+		<class>ca.uhn.test.jpasrv.OrganizationResourceTable</class>
+		<class>ca.uhn.test.jpasrv.QuestionnaireResourceTable</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceHistoryTable</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceHistoryTag</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceLink</class>
+		<class>ca.uhn.fhir.jpa.entity.ResourceTag</class>
+		
+		<exclude-unlisted-classes>true</exclude-unlisted-classes>
 		<properties>
 			<property name="hibernate.connection.url" value="jdbc:hsqldb:mem:unit-testing-jpa" />
 			<property name="hibernate.connection.driver_class" value="org.hsqldb.jdbcDriver" />

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

@@ -45,7 +45,7 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
 	private String packageBase;
 
 	@Parameter(required = true)
-	private List<String> resources;
+	private List<String> baseResourceNames;
 
 	@Override
 	public void execute() throws MojoExecutionException, MojoFailureException {
@@ -54,14 +54,20 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
 		directoryBase.mkdirs();
 		
 		ResourceGeneratorUsingSpreadsheet gen = new ResourceGeneratorUsingSpreadsheet();
-		gen.setBaseResourceNames(resources);
+		gen.setBaseResourceNames(baseResourceNames);
 
-		gen.setFilenameSuffix("ResourceProvider");
-		gen.setTemplate("/vm/jpa_resource_provider.vm");
 		
 		try {
 			gen.parse();
+			
+			gen.setFilenameSuffix("ResourceProvider");
+			gen.setTemplate("/vm/jpa_resource_provider.vm");
 			gen.writeAll(directoryBase, packageBase);
+			
+			gen.setFilenameSuffix("ResourceTable");
+			gen.setTemplate("/vm/jpa_resource_table.vm");
+			gen.writeAll(directoryBase, packageBase);
+			
 		} catch (Exception e) {
 			throw new MojoFailureException("Failed to generate server",e);
 		}
@@ -114,7 +120,7 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
 
 		TinderJpaRestServerMojo mojo = new TinderJpaRestServerMojo();
 		mojo.packageBase = "ca.uhn.test";
-		mojo.resources =java.util.Collections.singletonList("patient");
+		mojo.baseResourceNames =java.util.Collections.singletonList("patient");
 		mojo.targetDirectory = new File("target/gen");
 		mojo.execute();
 	}

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

@@ -25,6 +25,16 @@ public abstract class BaseRootType extends BaseElement {
 		return mySearchParameters;
 	}
 
+	public List<SearchParameter> getSearchParametersWithoutComposite() {
+		ArrayList<SearchParameter> retVal = new ArrayList<SearchParameter>();
+		for(SearchParameter next:getSearchParameters()) {
+			if(!next.getType().equals("composite")) {
+				retVal.add(next);
+			}
+		}
+		return retVal;
+	}
+
 	@Override
 	public String getTypeSuffix() {
 		return "";

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

@@ -50,6 +50,7 @@ public abstract class BaseStructureParser {
 	private TreeSet<String> myImports = new TreeSet<String>();
 	private Map<String, String> myLocallyDefinedClassNames = new HashMap<String, String>();
 	private List<BaseRootType> myResources = new ArrayList<BaseRootType>();
+	private boolean myImportsResolved;
 
 	public void addResource(BaseRootType theResource) {
 		myResources.add(theResource);
@@ -286,6 +287,7 @@ public abstract class BaseStructureParser {
 		ctx.put("resourceBlockChildren", theResource.getResourceBlockChildren());
 		ctx.put("childExtensionTypes", ObjectUtils.defaultIfNull(myExtensions, new ArrayList<Extension>()));
 		ctx.put("searchParams", (theResource.getSearchParameters()));
+		ctx.put("searchParamsWithoutComposite", (theResource.getSearchParametersWithoutComposite()));
 
 		VelocityEngine v = new VelocityEngine();
 		v.setProperty("resource.loader", "cp");
@@ -319,10 +321,13 @@ public abstract class BaseStructureParser {
 			throw new MojoFailureException(theOutputDirectory + " is not a directory");
 		}
 
+		if (!myImportsResolved) {
 			for (BaseRootType next : myResources) {
 				ourLog.info("Scanning resource for imports {}", next.getName());
 				scanForImportsNames(next);
 			}
+			myImportsResolved = true;
+		}
 
 		for (BaseRootType next : myResources) {
 			ourLog.info("Writing Resource {}", next.getName());
@@ -330,7 +335,8 @@ public abstract class BaseStructureParser {
 			scanForTypeNameConflicts(next);
 			fixResourceReferenceClassNames(next, thePackageBase);
 
-//			File f = new File(theOutputDirectory, (next.getDeclaringClassNameComplete()) /*+ getFilenameSuffix()*/ + ".java");
+			// File f = new File(theOutputDirectory, (next.getDeclaringClassNameComplete()) /*+ getFilenameSuffix()*/ +
+			// ".java");
 			File f = new File(theOutputDirectory, (next.getElementName()) + getFilenameSuffix() + ".java");
 			try {
 				write(next, f, thePackageBase);
@@ -348,9 +354,8 @@ public abstract class BaseStructureParser {
 	// }
 
 	/**
-	 * Example: Encounter has an internal block class named "Location", but it
+	 * Example: Encounter has an internal block class named "Location", but it also has a reference to the Location
-	 * also has a reference to the Location resource type, so we need to use the
+	 * resource type, so we need to use the fully qualified name for that resource reference
-	 * fully qualified name for that resource reference
 	 */
 	private void fixResourceReferenceClassNames(BaseElement theNext, String thePackageBase) {
 		for (BaseElement next : theNext.getChildren()) {

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

@@ -23,8 +23,8 @@ public class ${className}ResourceProvider extends BaseJpaResourceProvider<${clas
 	}
 
 	@Search()
-	List<${className}> search(
+	public List<${className}> search(
-#foreach ( $param in $searchParams ) #{if}(true) #{end} 
+#foreach ( $param in $searchParamsWithoutComposite ) #{if}(true) #{end} 
 
 			@Description(shortDefinition="${param.description}")
 			@OptionalParam(name="${param.name}")
@@ -40,12 +40,14 @@ public class ${className}ResourceProvider extends BaseJpaResourceProvider<${clas
 			QuantityDt the${param.nameCapitalized} #{if}($foreach.hasNext), #{end} 
 #elseif (${param.type} == 'reference' )
 			ReferenceParam the${param.nameCapitalized} #{if}($foreach.hasNext), #{end} 
+#elseif (${param.type} == 'composite' )
+			ReferenceParam the${param.nameCapitalized} #{if}($foreach.hasNext), #{end} 
 #end
 #end	
 	) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 					
-#foreach ( $param in $searchParams ) 
+#foreach ( $param in $searchParamsWithoutComposite ) 
 		paramMap.add("${param.name}", the${param.nameCapitalized});	
 #end
 

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

@@ -3,13 +3,13 @@ package ${packageBase};
 
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
-import ca.uhn.fhir.model.dstu.resource.*;
 
-public class ${className}ResourceTable extends BaseResourceTable<${className}> {
+import ca.uhn.fhir.jpa.entity.BaseResourceTable;
+import ca.uhn.fhir.model.dstu.resource.*;
 
 @Entity
 @DiscriminatorValue("${className}")
-public class PatientResourceTable extends BaseResourceTable<Patient> {
+public class ${className}ResourceTable extends BaseResourceTable<${className}> {
 
 	@Override
 	public Class<${className}> getResourceType() {