..and still...

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

@@ -3,8 +3,10 @@ package ca.uhn.fhir.context;
 import static org.apache.commons.lang3.StringUtils.*;
 
 import java.lang.reflect.Field;
+import java.lang.reflect.ParameterizedType;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -67,7 +69,7 @@ class ModelScanner {
 			toScan.clear();
 			toScan.addAll(myScanAlso);
 			myScanAlso.clear();
-		} while (!myScanAlso.isEmpty());
+		} while (!toScan.isEmpty());
 
 		for (BaseRuntimeElementDefinition<?> next : myClassToElementDefinitions.values()) {
 			next.sealAndInitialize(myClassToElementDefinitions);
@@ -130,17 +132,10 @@ class ModelScanner {
 			throw new ConfigurationException("Resource type @" + ResourceDef.class.getSimpleName() + " annotation contains no resource name: " + theClass.getCanonicalName());
 		}
 
-		if (myNameToResourceDefinitions.containsKey(resourceName)) {
-			if (!myNameToResourceDefinitions.get(resourceName).getImplementingClass().equals(theClass)) {
-				throw new ConfigurationException("Detected duplicate element name '" + resourceName + "' in types '" + theClass.getCanonicalName() + "' and '" + myNameToResourceDefinitions.get(resourceName).getImplementingClass() + "'");
-			}
-			return resourceName;
-		}
-
 		RuntimeCompositeDatatypeDefinition resourceDef = new RuntimeCompositeDatatypeDefinition(resourceName, theClass);
 		myClassToElementDefinitions.put(theClass, resourceDef);
 
-		scanCompositeElementForChildren(theClass, resourceDef);
+		scanCompositeElementForChildren(theClass, resourceDef, null);
 
 		return resourceName;
 	}
@@ -153,13 +148,6 @@ class ModelScanner {
 			throw new ConfigurationException("Resource type @" + ResourceDef.class.getSimpleName() + " annotation contains no resource name: " + theClass.getCanonicalName());
 		}
 
-		if (myNameToResourceDefinitions.containsKey(resourceName)) {
-			if (!myNameToResourceDefinitions.get(resourceName).getImplementingClass().equals(theClass)) {
-				throw new ConfigurationException("Detected duplicate element name '" + resourceName + "' in types '" + theClass.getCanonicalName() + "' and '" + myNameToResourceDefinitions.get(resourceName).getImplementingClass() + "'");
-			}
-			return resourceName;
-		}
-
 		RuntimePrimitiveDatatypeDefinition resourceDef = new RuntimePrimitiveDatatypeDefinition(resourceName, theClass);
 		myClassToElementDefinitions.put(theClass, resourceDef);
 
@@ -185,13 +173,13 @@ class ModelScanner {
 		myClassToElementDefinitions.put(theClass, resourceDef);
 		myNameToResourceDefinitions.put(resourceName, resourceDef);
 
-		scanCompositeElementForChildren(theClass, resourceDef);
+		scanCompositeElementForChildren(theClass, resourceDef, resourceDefinition.identifierOrder());
 
 		return resourceName;
 	}
 
 	@SuppressWarnings("unchecked")
-	private void scanCompositeElementForChildren(Class<? extends ICompositeElement> theClass, BaseRuntimeElementCompositeDefinition<?> theDefinition) {
+	private void scanCompositeElementForChildren(Class<? extends ICompositeElement> theClass, BaseRuntimeElementCompositeDefinition<?> theDefinition, Integer theIdentifierOrder) {
 		Set<String> elementNames = new HashSet<String>();
 		TreeMap<Integer, BaseRuntimeChildDefinition> orderToElementDef = new TreeMap<Integer, BaseRuntimeChildDefinition>();
 
@@ -210,7 +198,14 @@ class ModelScanner {
 			scanCompositeElementForChildren(next, theDefinition, elementNames, orderToElementDef);
 		}
 
-		dealwithnegative
+		while (orderToElementDef.firstKey() < 0) {
+			BaseRuntimeChildDefinition elementDef = orderToElementDef.remove(orderToElementDef.firstKey());
+			if (elementDef.getElementName().equals("identifier")) {
+				orderToElementDef.put(theIdentifierOrder, elementDef);
+			}else {
+				throw new ConfigurationException("Don't know how to handle element: " + elementDef.getElementName());
+			}
+		}
 		
 		for (int i = 0; i < orderToElementDef.size(); i++) {
 			if (!orderToElementDef.containsKey(i)) {
@@ -222,6 +217,7 @@ class ModelScanner {
 
 	}
 
+	@SuppressWarnings("unchecked")
 	private void scanCompositeElementForChildren(Class<? extends ICompositeElement> theClass, BaseRuntimeElementCompositeDefinition<?> theDefinition, Set<String> elementNames, TreeMap<Integer, BaseRuntimeChildDefinition> orderToElementDef) {
 		for (Field next : theClass.getDeclaredFields()) {
 			
@@ -292,12 +288,25 @@ class ModelScanner {
 				if (resRefAnnotation != null) {
 					throw new ConfigurationException("Field '" + elementName + "' in type '" + theClass.getCanonicalName() + "' is not a resource reference but has a @" + ChildResource.class.getSimpleName() + " annotation");
 				}
-				if (!IDatatype.class.isAssignableFrom(next.getType())) {
+
-					throw new ConfigurationException("Field '" + elementName + "' in type '" + theClass.getCanonicalName() + "' is not a resource reference and is not an instance of type " + IDatatype.class.getName());
+				Class<? extends IDatatype> nextDatatype;
+
+				if (IDatatype.class.isAssignableFrom(next.getType())) {
+					nextDatatype = (Class<? extends IDatatype>) next.getType();
+				} else {
+					if (Collection.class.isAssignableFrom(next.getType())) {
+						Class<?> type = (Class<?>) ((ParameterizedType) next.getType().getGenericSuperclass()).getActualTypeArguments()[0];
+						if (IDatatype.class.isAssignableFrom(type)) {
+							nextDatatype=(Class<? extends IDatatype>) type;
+						}else {
+							throw new ConfigurationException("Field '" + elementName + "' in type '" + theClass.getCanonicalName() + "' is not a resource reference and is not an instance of type " + IDatatype.class.getName());
+						}
+					}else {
+						throw new ConfigurationException("Field '" + elementName + "' in type '" + theClass.getCanonicalName() + "' is not a resource reference and is not an instance of type " + IDatatype.class.getName());
+					}
 				}
 
-				@SuppressWarnings("unchecked")
+				
-				Class<? extends IDatatype> nextDatatype = (Class<? extends IDatatype>) next.getType();
 				myScanAlso.add(nextDatatype);
 
 				BaseRuntimeChildDatatypeDefinition def;

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

@@ -32,4 +32,53 @@ public class IdentifierDt extends BaseCompositeDatatype {
 	@ChildResource(types= {Organization.class})
 	private ResourceReference myAssigner;
 
+	public CodeDt<IdentifierUseEnum> getUse() {
+		return myUse;
+	}
+
+	public void setUse(CodeDt<IdentifierUseEnum> theUse) {
+		myUse = theUse;
+	}
+
+	public StringDt getLabel() {
+		return myLabel;
+	}
+
+	public void setLabel(StringDt theLabel) {
+		myLabel = theLabel;
+	}
+
+	public UriDt getSystem() {
+		return mySystem;
+	}
+
+	public void setSystem(UriDt theSystem) {
+		mySystem = theSystem;
+	}
+
+	public StringDt getValue() {
+		return myValue;
+	}
+
+	public void setValue(StringDt theValue) {
+		myValue = theValue;
+	}
+
+	public PeriodDt getPeriod() {
+		return myPeriod;
+	}
+
+	public void setPeriod(PeriodDt thePeriod) {
+		myPeriod = thePeriod;
+	}
+
+	public ResourceReference getAssigner() {
+		return myAssigner;
+	}
+
+	public void setAssigner(ResourceReference theAssigner) {
+		myAssigner = theAssigner;
+	}
+
+	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/datatype/PeriodDt.java

@@ -16,4 +16,21 @@ public class PeriodDt extends BaseCompositeDatatype {
 	@Constraint(greaterThan= {"start"})
 	private DateTimeDt myEnd;
 
+	public DateTimeDt getStart() {
+		return myStart;
+	}
+
+	public void setStart(DateTimeDt theStart) {
+		myStart = theStart;
+	}
+
+	public DateTimeDt getEnd() {
+		return myEnd;
+	}
+
+	public void setEnd(DateTimeDt theEnd) {
+		myEnd = theEnd;
+	}
+
+	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/datatype/QuantityDt.java

@@ -4,7 +4,7 @@ import ca.uhn.fhir.model.api.BaseCompositeDatatype;
 import ca.uhn.fhir.model.api.annotation.Constraint;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
-import ca.uhn.fhir.model.enm.QuantityComparator;
+import ca.uhn.fhir.model.enm.QuantityComparatorEnum;
 
 @DatatypeDef(name="Quantity")
 public class QuantityDt extends BaseCompositeDatatype {
@@ -13,7 +13,7 @@ public class QuantityDt extends BaseCompositeDatatype {
 	private DecimalDt myValue;
 	
 	@Child(name="comparator",order=1, min=0, max=1)
-	private QuantityComparator myComparator;
+	private CodeDt<QuantityComparatorEnum> myComparator;
 	
 	@Child(name="units",order=2, min=0, max=1)
 	private StringDt myUnits;
@@ -24,6 +24,46 @@ public class QuantityDt extends BaseCompositeDatatype {
 	
 	@Child(name="code",order=4, min=0, max=1)
 	@Constraint(coRequirements= {"system"})
-	private CodeDt myCode;
+	private CodeDt<?> myCode;
+
+	public DecimalDt getValue() {
+		return myValue;
+	}
+
+	public void setValue(DecimalDt theValue) {
+		myValue = theValue;
+	}
+
+	public CodeDt<QuantityComparatorEnum> getComparator() {
+		return myComparator;
+	}
+
+	public void setComparator(CodeDt<QuantityComparatorEnum> theComparator) {
+		myComparator = theComparator;
+	}
+
+	public StringDt getUnits() {
+		return myUnits;
+	}
+
+	public void setUnits(StringDt theUnits) {
+		myUnits = theUnits;
+	}
+
+	public UriDt getSystem() {
+		return mySystem;
+	}
+
+	public void setSystem(UriDt theSystem) {
+		mySystem = theSystem;
+	}
+
+	public CodeDt<?> getCode() {
+		return myCode;
+	}
+
+	public void setCode(CodeDt<?> theCode) {
+		myCode = theCode;
+	}
 	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/enm/QuantityComparatorEnum.java

@@ -6,7 +6,7 @@ import ca.uhn.fhir.model.api.annotation.EnumeratedCodeValue;
 import ca.uhn.fhir.model.api.annotation.CodeTableDef;
 
 @CodeTableDef(tableId=14, name="quantity-comparator")
-public enum QuantityComparator implements ICodeEnum {
+public enum QuantityComparatorEnum implements ICodeEnum {
 
 	@EnumeratedCodeValue("<")
 	@Description("The actual value is less than the given value.")

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/resource/Group.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.model.resource;
 
-public class Group extends BaseResource {
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+
+@ResourceDef(name="Group", identifierOrder=0)
+public class Group extends BaseResourceWithIdentifier {
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/resource/Organization.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.model.resource;
 
-public class Organization extends BaseResource {
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+
+@ResourceDef(name="Organization", identifierOrder=0)
+public class Organization extends BaseResourceWithIdentifier {
 //TODO: fill in
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/resource/Patient.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.model.resource;
 
-public class Patient extends BaseResource {
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+
+@ResourceDef(name="Patient", identifierOrder=0)
+public class Patient extends BaseResourceWithIdentifier {
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/resource/ValueSet.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.model.resource;
 
-public class ValueSet extends BaseResource {
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+
+@ResourceDef(name="ValueSet", identifierOrder=0)
+public class ValueSet extends BaseResourceWithIdentifier {
 
 }