Fixing unit tests

hapi-fhir-base/pom.xml

@@ -266,6 +266,10 @@
 			var pre = pres[j];
 			if (pre.innerHTML.match(/\/\*/)) {
 				pre.className = 'brush: java';
+			} else if (pre.innerHTML.match(/^\/\//)) {
+				pre.className = 'brush: java';
+			} else if (pre.innerHTML.match(/^\{/)) {
+				pre.className = 'brush: jscript';
 			} else if (pre.innerHTML.match(/^\#/)) {
 				pre.className = 'brush: bash';
 			} else if (pre.innerHTML.match(/\&lt\;\//)) {

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;

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

@@ -26,6 +26,13 @@ public abstract class BaseRuntimeElementDefinition<T extends IElement> {
 		assert theImplementingClass != null;
 
 		myName = theName;
+		
+		// TODO: remove this and fix for the model
+		if (myName.endsWith("Dt")) {
+			myName = myName.substring(0, myName.length() - 2);
+		}
+			
+		
 		myImplementingClass = theImplementingClass;
 	}
 

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 import java.lang.reflect.Field;
 import java.lang.reflect.ParameterizedType;
@@ -35,6 +35,7 @@ import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.api.annotation.Extension;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu.composite.AttachmentDt;
 import ca.uhn.fhir.model.dstu.composite.ContainedDt;
 import ca.uhn.fhir.model.dstu.composite.NarrativeDt;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
@@ -128,6 +129,7 @@ class ModelScanner {
 		toScan.add(DateDt.class);
 		toScan.add(CodeDt.class);
 		toScan.add(DecimalDt.class);
+		toScan.add(AttachmentDt.class);
 		
 		do {
 			for (Class<? extends IElement> nextClass : toScan) {

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.lang.reflect.Field;
 import java.util.Collections;

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

@@ -19,16 +19,14 @@ import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 
 public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildDefinition {
 
-	
 	private Map<String, BaseRuntimeElementDefinition<?>> myAttributeNameToDefinition;
-	private Map<Class<? extends IElement>,String> myDatatypeToAttributeName;
+	private Map<Class<? extends IElement>, String> myDatatypeToAttributeName;
-	private Map<Class<? extends IElement>,BaseRuntimeElementDefinition<?>> myDatatypeToDefinition;
+	private Map<Class<? extends IElement>, BaseRuntimeElementDefinition<?>> myDatatypeToDefinition;
 
 	public RuntimeChildUndeclaredExtensionDefinition() {
 		// nothing
 	}
 
-	
 	@Override
 	public BaseRuntimeElementDefinition<?> getChildByName(String theName) {
 		return myAttributeNameToDefinition.get(theName);
@@ -49,12 +47,15 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		return myDatatypeToDefinition.get(theType);
 	}
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuntimeChildUndeclaredExtensionDefinition.class);
+
 	@Override
 	void sealAndInitialize(Map<Class<? extends IElement>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
-		Map<String, BaseRuntimeElementDefinition<?>> datatypeAttributeNameToDefinition=new HashMap<String, BaseRuntimeElementDefinition<?>>();
+		Map<String, BaseRuntimeElementDefinition<?>> datatypeAttributeNameToDefinition = new HashMap<String, BaseRuntimeElementDefinition<?>>();
 		myDatatypeToAttributeName = new HashMap<Class<? extends IElement>, String>();
 
 		for (BaseRuntimeElementDefinition<?> next : theClassToElementDefinitions.values()) {
+			ourLog.info(next.getName());
 			if (next instanceof IRuntimeDatatypeDefinition) {
 				if (!((IRuntimeDatatypeDefinition) next).isSpecialization()) {
 					String attrName = "value" + WordUtils.capitalize(next.getName());
@@ -65,7 +66,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 			}
 		}
 
-		myAttributeNameToDefinition=datatypeAttributeNameToDefinition;
+		myAttributeNameToDefinition = datatypeAttributeNameToDefinition;
 
 		myDatatypeToDefinition = new HashMap<Class<? extends IElement>, BaseRuntimeElementDefinition<?>>();
 
@@ -86,46 +87,43 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		myDatatypeToDefinition.put(ResourceReferenceDt.class, def);
 	}
 
-
 	@Override
 	public IAccessor getAccessor() {
 		return new IAccessor() {
 			@Override
 			public List<? extends IElement> getValues(Object theTarget) {
-				ExtensionDt target = (ExtensionDt)theTarget;
+				ExtensionDt target = (ExtensionDt) theTarget;
 				if (target.getValue() != null) {
 					return Collections.singletonList(target.getValue());
 				}
 				return target.getUndeclaredExtensions();
-			}};
 			}
-
+		};
+	}
 
 	@Override
 	public IMutator getMutator() {
 		return new IMutator() {
 			@Override
 			public void addValue(Object theTarget, IElement theValue) {
-				ExtensionDt target = (ExtensionDt)theTarget;
+				ExtensionDt target = (ExtensionDt) theTarget;
 				if (theValue instanceof IDatatype) {
 					target.setValue((IDatatype) theTarget);
-				}else {
+				} else {
 					target.getUndeclaredExtensions().add((ExtensionDt) theValue);
 				}
-			}};
 			}
-
+		};
+	}
 
 	@Override
 	public int getMax() {
 		return 1;
 	}
 
-
 	@Override
 	public int getMin() {
 		return 0;
 	}
 
-
 }

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 import ca.uhn.fhir.model.api.ICompositeDatatype;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 import java.util.Map;
 

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.join;
 
 import java.util.Collections;
 import java.util.Comparator;

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

@@ -68,7 +68,7 @@ public class AttachmentDt
 		shortDefinition="Human language of the content (BCP-47)",
 		formalDefinition="The human language of the content. The value can be any valid value according to BCP 47"
 	)
-	private CodeDt myLanguageElement;
+	private CodeDt myLanguage;
 	
 	@Child(name="data", type=Base64BinaryDt.class, order=2, min=0, max=1)	
 	@Description(
@@ -108,7 +108,7 @@ public class AttachmentDt
 
 	@Override
 	public boolean isEmpty() {
-		return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(  myContentType,  myLanguageElement,  myData,  myUrl,  mySize,  myHash,  myTitle);
+		return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(  myContentType,  myLanguage,  myData,  myUrl,  mySize,  myHash,  myTitle);
 	}
 	
 	@Override
@@ -118,7 +118,7 @@ public class AttachmentDt
 
 	@Override
 	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
-		return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myContentType, myLanguageElement, myData, myUrl, mySize, myHash, myTitle);
+		return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myContentType, myLanguage, myData, myUrl, mySize, myHash, myTitle);
 	}
 
 	/**
@@ -175,11 +175,11 @@ public class AttachmentDt
      * The human language of the content. The value can be any valid value according to BCP 47
      * </p> 
 	 */
-	public CodeDt getLanguageElement() {  
+	public CodeDt getLanguage() {  
-		if (myLanguageElement == null) {
+		if (myLanguage == null) {
-			myLanguageElement = new CodeDt();
+			myLanguage = new CodeDt();
 		}
-		return myLanguageElement;
+		return myLanguage;
 	}
 
 	/**
@@ -190,8 +190,8 @@ public class AttachmentDt
      * The human language of the content. The value can be any valid value according to BCP 47
      * </p> 
 	 */
-	public AttachmentDt setLanguageElement(CodeDt theValue) {
+	public AttachmentDt setLanguage(CodeDt theValue) {
-		myLanguageElement = theValue;
+		myLanguage = theValue;
 		return this;
 	}
 
@@ -203,8 +203,8 @@ public class AttachmentDt
      * The human language of the content. The value can be any valid value according to BCP 47
      * </p> 
 	 */
-	public AttachmentDt setLanguageElement( String theCode) {
+	public AttachmentDt setLanguage( String theCode) {
-		myLanguageElement = new CodeDt(theCode); 
+		myLanguage = new CodeDt(theCode); 
 		return this; 
 	}
 

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

@@ -180,19 +180,6 @@ public class QuantityDt
      * <p>
      * <b>Definition:</b>
      * The value of the measured amount. The value includes an implicit precision in the presentation of the value
-     * </p> 
-	 */
-	public QuantityDt setValue( long theValue) {
-		myValue = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>value</b> (Numerical value (with implicit precision))
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The value of the measured amount. The value includes an implicit precision in the presentation of the value
      * </p> 
 	 */
 	public QuantityDt setValue( double theValue) {
@@ -213,6 +200,19 @@ public class QuantityDt
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>value</b> (Numerical value (with implicit precision))
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The value of the measured amount. The value includes an implicit precision in the presentation of the value
+     * </p> 
+	 */
+	public QuantityDt setValue( long theValue) {
+		myValue = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>comparator</b> (< | <= | >= | > - how to understand the value).

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

@@ -239,19 +239,6 @@ public class SampledDataDt
      * <p>
      * <b>Definition:</b>
      * The length of time between sampling times, measured in milliseconds
-     * </p> 
-	 */
-	public SampledDataDt setPeriod( long theValue) {
-		myPeriod = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>period</b> (Number of milliseconds between samples)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The length of time between sampling times, measured in milliseconds
      * </p> 
 	 */
 	public SampledDataDt setPeriod( double theValue) {
@@ -272,6 +259,19 @@ public class SampledDataDt
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>period</b> (Number of milliseconds between samples)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The length of time between sampling times, measured in milliseconds
+     * </p> 
+	 */
+	public SampledDataDt setPeriod( long theValue) {
+		myPeriod = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>factor</b> (Multiply data by this before adding to origin).
@@ -309,19 +309,6 @@ public class SampledDataDt
      * <p>
      * <b>Definition:</b>
      * A correction factor that is applied to the sampled data points before they are added to the origin
-     * </p> 
-	 */
-	public SampledDataDt setFactor( long theValue) {
-		myFactor = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>factor</b> (Multiply data by this before adding to origin)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A correction factor that is applied to the sampled data points before they are added to the origin
      * </p> 
 	 */
 	public SampledDataDt setFactor( double theValue) {
@@ -342,6 +329,19 @@ public class SampledDataDt
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>factor</b> (Multiply data by this before adding to origin)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * A correction factor that is applied to the sampled data points before they are added to the origin
+     * </p> 
+	 */
+	public SampledDataDt setFactor( long theValue) {
+		myFactor = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>lowerLimit</b> (Lower limit of detection).
@@ -379,19 +379,6 @@ public class SampledDataDt
      * <p>
      * <b>Definition:</b>
      * The lower limit of detection of the measured points. This is needed if any of the data points have the value \"L\" (lower than detection limit)
-     * </p> 
-	 */
-	public SampledDataDt setLowerLimit( long theValue) {
-		myLowerLimit = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>lowerLimit</b> (Lower limit of detection)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The lower limit of detection of the measured points. This is needed if any of the data points have the value \"L\" (lower than detection limit)
      * </p> 
 	 */
 	public SampledDataDt setLowerLimit( double theValue) {
@@ -412,6 +399,19 @@ public class SampledDataDt
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>lowerLimit</b> (Lower limit of detection)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The lower limit of detection of the measured points. This is needed if any of the data points have the value \"L\" (lower than detection limit)
+     * </p> 
+	 */
+	public SampledDataDt setLowerLimit( long theValue) {
+		myLowerLimit = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>upperLimit</b> (Upper limit of detection).
@@ -449,19 +449,6 @@ public class SampledDataDt
      * <p>
      * <b>Definition:</b>
      * The upper limit of detection of the measured points. This is needed if any of the data points have the value \"U\" (higher than detection limit)
-     * </p> 
-	 */
-	public SampledDataDt setUpperLimit( long theValue) {
-		myUpperLimit = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>upperLimit</b> (Upper limit of detection)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The upper limit of detection of the measured points. This is needed if any of the data points have the value \"U\" (higher than detection limit)
      * </p> 
 	 */
 	public SampledDataDt setUpperLimit( double theValue) {
@@ -482,6 +469,19 @@ public class SampledDataDt
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>upperLimit</b> (Upper limit of detection)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The upper limit of detection of the measured points. This is needed if any of the data points have the value \"U\" (higher than detection limit)
+     * </p> 
+	 */
+	public SampledDataDt setUpperLimit( long theValue) {
+		myUpperLimit = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>dimensions</b> (Number of sample points at each time point).

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

@@ -376,19 +376,6 @@ public class ScheduleDt
      * <p>
      * <b>Definition:</b>
      * How long each repetition should last
-     * </p> 
-	 */
-	public Repeat setDuration( long theValue) {
-		myDuration = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>duration</b> (Repeating or event-related duration)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * How long each repetition should last
      * </p> 
 	 */
 	public Repeat setDuration( double theValue) {
@@ -409,6 +396,19 @@ public class ScheduleDt
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>duration</b> (Repeating or event-related duration)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * How long each repetition should last
+     * </p> 
+	 */
+	public Repeat setDuration( long theValue) {
+		myDuration = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>units</b> (s | min | h | d | wk | mo | a - unit of time (UCUM)).

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

@@ -1753,19 +1753,6 @@ public class Claim extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * 
-     * </p> 
-	 */
-	public Service setFee( long theValue) {
-		myFee = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>fee</b> (Professional fee)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * 
      * </p> 
 	 */
 	public Service setFee( double theValue) {
@@ -1786,6 +1773,19 @@ public class Claim extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>fee</b> (Professional fee)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * 
+     * </p> 
+	 */
+	public Service setFee( long theValue) {
+		myFee = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>location</b> (Service Location).
@@ -1991,19 +1991,6 @@ public class Claim extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * The amount to reimbuse for a laboratory service.
-     * </p> 
-	 */
-	public ServiceLab setFee( long theValue) {
-		myFee = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>fee</b> (Lab fee)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The amount to reimbuse for a laboratory service.
      * </p> 
 	 */
 	public ServiceLab setFee( double theValue) {
@@ -2024,6 +2011,19 @@ public class Claim extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>fee</b> (Lab fee)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The amount to reimbuse for a laboratory service.
+     * </p> 
+	 */
+	public ServiceLab setFee( long theValue) {
+		myFee = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 
 	}

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

@@ -996,24 +996,6 @@ public class GVFVariant extends BaseResource implements IResource {
      * Frequency of the variant
      * </p> 
      *
-     * @return Returns a reference to this object, to allow for simple chaining.
-	 */
-	public GVFVariant addVariantFreq( long theValue) {
-		if (myVariantFreq == null) {
-			myVariantFreq = new java.util.ArrayList<DecimalDt>();
-		}
-		myVariantFreq.add(new DecimalDt(theValue));
-		return this; 
-	}
-
-	/**
-	 * Adds a new value for <b>variantFreq</b> (Variant frequency)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Frequency of the variant
-     * </p> 
-     *
      * @return Returns a reference to this object, to allow for simple chaining.
 	 */
 	public GVFVariant addVariantFreq( double theValue) {
@@ -1042,6 +1024,24 @@ public class GVFVariant extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Adds a new value for <b>variantFreq</b> (Variant frequency)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Frequency of the variant
+     * </p> 
+     *
+     * @return Returns a reference to this object, to allow for simple chaining.
+	 */
+	public GVFVariant addVariantFreq( long theValue) {
+		if (myVariantFreq == null) {
+			myVariantFreq = new java.util.ArrayList<DecimalDt>();
+		}
+		myVariantFreq.add(new DecimalDt(theValue));
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>variantEffect</b> (Variant effect).

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

@@ -763,19 +763,6 @@ public class GeneExpression extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * Expression level of the gene in RPKM
-     * </p> 
-	 */
-	public RnaSeq setExpression( long theValue) {
-		myExpression = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>expression</b> (Expression level of the gene in RPKM)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Expression level of the gene in RPKM
      * </p> 
 	 */
 	public RnaSeq setExpression( double theValue) {
@@ -796,6 +783,19 @@ public class GeneExpression extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>expression</b> (Expression level of the gene in RPKM)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Expression level of the gene in RPKM
+     * </p> 
+	 */
+	public RnaSeq setExpression( long theValue) {
+		myExpression = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>isoform</b> (Isoform of the gene).
@@ -981,19 +981,6 @@ public class GeneExpression extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * Expression level of the isoform in RPKM
-     * </p> 
-	 */
-	public RnaSeqIsoform setExpression( long theValue) {
-		myExpression = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>expression</b> (Expression level of the isoform in RPKM)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Expression level of the isoform in RPKM
      * </p> 
 	 */
 	public RnaSeqIsoform setExpression( double theValue) {
@@ -1014,6 +1001,19 @@ public class GeneExpression extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>expression</b> (Expression level of the isoform in RPKM)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Expression level of the isoform in RPKM
+     * </p> 
+	 */
+	public RnaSeqIsoform setExpression( long theValue) {
+		myExpression = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 
 	}

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

@@ -828,19 +828,6 @@ public class Location extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * Longitude. The value domain and the interpretation are the same as for the text of the longitude element in KML (see notes below)
-     * </p> 
-	 */
-	public Position setLongitude( long theValue) {
-		myLongitude = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>longitude</b> (Longitude as expressed in KML)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Longitude. The value domain and the interpretation are the same as for the text of the longitude element in KML (see notes below)
      * </p> 
 	 */
 	public Position setLongitude( double theValue) {
@@ -861,6 +848,19 @@ public class Location extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>longitude</b> (Longitude as expressed in KML)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Longitude. The value domain and the interpretation are the same as for the text of the longitude element in KML (see notes below)
+     * </p> 
+	 */
+	public Position setLongitude( long theValue) {
+		myLongitude = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>latitude</b> (Latitude as expressed in KML).
@@ -898,19 +898,6 @@ public class Location extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * Latitude. The value domain and the interpretation are the same as for the text of the latitude element in KML (see notes below)
-     * </p> 
-	 */
-	public Position setLatitude( long theValue) {
-		myLatitude = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>latitude</b> (Latitude as expressed in KML)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Latitude. The value domain and the interpretation are the same as for the text of the latitude element in KML (see notes below)
      * </p> 
 	 */
 	public Position setLatitude( double theValue) {
@@ -931,6 +918,19 @@ public class Location extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>latitude</b> (Latitude as expressed in KML)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Latitude. The value domain and the interpretation are the same as for the text of the latitude element in KML (see notes below)
+     * </p> 
+	 */
+	public Position setLatitude( long theValue) {
+		myLatitude = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>altitude</b> (Altitude as expressed in KML).
@@ -968,19 +968,6 @@ public class Location extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * Altitude. The value domain and the interpretation are the same as for the text of the altitude element in KML (see notes below)
-     * </p> 
-	 */
-	public Position setAltitude( long theValue) {
-		myAltitude = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>altitude</b> (Altitude as expressed in KML)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Altitude. The value domain and the interpretation are the same as for the text of the altitude element in KML (see notes below)
      * </p> 
 	 */
 	public Position setAltitude( double theValue) {
@@ -1001,6 +988,19 @@ public class Location extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>altitude</b> (Altitude as expressed in KML)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Altitude. The value domain and the interpretation are the same as for the text of the altitude element in KML (see notes below)
+     * </p> 
+	 */
+	public Position setAltitude( long theValue) {
+		myAltitude = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 
 	}

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

@@ -956,19 +956,6 @@ public class Microarray extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * Intensity(expression) of the gene
-     * </p> 
-	 */
-	public Sample setIntensity( long theValue) {
-		myIntensity = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>intensity</b> (Intensity)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Intensity(expression) of the gene
      * </p> 
 	 */
 	public Sample setIntensity( double theValue) {
@@ -989,6 +976,19 @@ public class Microarray extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>intensity</b> (Intensity)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Intensity(expression) of the gene
+     * </p> 
+	 */
+	public Sample setIntensity( long theValue) {
+		myIntensity = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>isControl</b> (Control).

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

@@ -1,939 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-package ca.uhn.fhir.model.dstu.resource;
-
-
-import java.util.Date;
-import java.util.List;
-
-import ca.uhn.fhir.model.api.BaseElement;
-import ca.uhn.fhir.model.api.BaseResource;
-import ca.uhn.fhir.model.api.IElement;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.IResourceBlock;
-import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
-import ca.uhn.fhir.model.api.annotation.Block;
-import ca.uhn.fhir.model.api.annotation.Child;
-import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.model.api.annotation.ResourceDef;
-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.valueset.IdentifierUseEnum;
-import ca.uhn.fhir.model.dstu.valueset.MaritalStatusCodesEnum;
-import ca.uhn.fhir.model.primitive.BooleanDt;
-import ca.uhn.fhir.model.primitive.BoundCodeableConceptDt;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
-
-
-/**
- * HAPI/FHIR <b>Person</b> Resource
- * (Person involved in healthcare)
- *
- * <p>
- * <b>Definition:</b>
- * A person who is involved in the healthcare process
- * </p> 
- *
- * <p>
- * <b>Requirements:</b>
- * Need to track persons potentially across multiple roles
- * </p> 
- *
- * <p>
- * <b>Profile Definition:</b>
- * <a href="http://hl7.org/fhir/profiles/Person">http://hl7.org/fhir/profiles/Person</a> 
- * </p>
- *
- */
-@ResourceDef(name="Person", profile="http://hl7.org/fhir/profiles/Person", id="person")
-public class Person extends BaseResource implements IResource {
-
-	/**
-	 * Search parameter constant for <b>identifier</b>
-	 * <p>
-	 * Description: <b>A patient Identifier</b><br/>
-	 * Type: <b>token</b><br/>
-	 * Path: <b>identifier</b><br/>
-	 * </p>
-	 */
-	public static final String SP_IDENTIFIER = "identifier";
-
-	/**
-	 * Search parameter constant for <b>name</b>
-	 * <p>
-	 * Description: <b>a portion of name in any name part</b><br/>
-	 * Type: <b>string</b><br/>
-	 * Path: <b>name</b><br/>
-	 * </p>
-	 */
-	public static final String SP_NAME = "name";
-
-	/**
-	 * Search parameter constant for <b>phonetic</b>
-	 * <p>
-	 * Description: <b>a portion of name using some kind of phonetic matching algorithm</b><br/>
-	 * Type: <b>string</b><br/>
-	 * Path: <b>phonetic</b><br/>
-	 * </p>
-	 */
-	public static final String SP_PHONETIC = "phonetic";
-
-	/**
-	 * Search parameter constant for <b>telecom</b>
-	 * <p>
-	 * Description: <b>the value in any kind of contact</b><br/>
-	 * Type: <b>string</b><br/>
-	 * Path: <b>telecom</b><br/>
-	 * </p>
-	 */
-	public static final String SP_TELECOM = "telecom";
-
-	/**
-	 * Search parameter constant for <b>address</b>
-	 * <p>
-	 * Description: <b>an address in any kind of address/part</b><br/>
-	 * Type: <b>string</b><br/>
-	 * Path: <b>address</b><br/>
-	 * </p>
-	 */
-	public static final String SP_ADDRESS = "address";
-
-	/**
-	 * Search parameter constant for <b>gender</b>
-	 * <p>
-	 * Description: <b>gender of the person</b><br/>
-	 * Type: <b>token</b><br/>
-	 * Path: <b>gender</b><br/>
-	 * </p>
-	 */
-	public static final String SP_GENDER = "gender";
-
-	/**
-	 * Search parameter constant for <b>language</b>
-	 * <p>
-	 * Description: <b>language code (irrespective of use value)</b><br/>
-	 * Type: <b>token</b><br/>
-	 * Path: <b>language</b><br/>
-	 * </p>
-	 */
-	public static final String SP_LANGUAGE = "language";
-
-	/**
-	 * Search parameter constant for <b>birthdate</b>
-	 * <p>
-	 * Description: <b>the patient's date of birth</b><br/>
-	 * Type: <b>date</b><br/>
-	 * Path: <b>birthdate</b><br/>
-	 * </p>
-	 */
-	public static final String SP_BIRTHDATE = "birthdate";
-
-
-	@Child(name="identifier", type=IdentifierDt.class, order=0, min=0, max=Child.MAX_UNLIMITED)	
-	@Description(
-		shortDefinition="A Human identifier for this person",
-		formalDefinition="Identifier for a person within a particular scope."
-	)
-	private java.util.List<IdentifierDt> myIdentifier;
-	
-	@Child(name="name", type=HumanNameDt.class, order=1, min=0, max=Child.MAX_UNLIMITED)	
-	@Description(
-		shortDefinition="A name associated with the person",
-		formalDefinition="A name associated with the person"
-	)
-	private java.util.List<HumanNameDt> myName;
-	
-	@Child(name="telecom", type=ContactDt.class, order=2, min=0, max=Child.MAX_UNLIMITED)	
-	@Description(
-		shortDefinition="A contact detail for the person",
-		formalDefinition="A contact detail for the person, e.g. a telephone number or an email address."
-	)
-	private java.util.List<ContactDt> myTelecom;
-	
-	@Child(name="gender", type=CodingDt.class, order=3, min=0, max=1)	
-	@Description(
-		shortDefinition="Administrative Gender",
-		formalDefinition="Administrative Gender"
-	)
-	private CodingDt myGender;
-	
-	@Child(name="birthDate", type=DateTimeDt.class, order=4, min=0, max=1)	
-	@Description(
-		shortDefinition="The birth date for the person",
-		formalDefinition="The birth date for the person."
-	)
-	private DateTimeDt myBirthDate;
-	
-	@Child(name="deceased", type=BooleanDt.class, order=5, min=0, max=1)	
-	@Description(
-		shortDefinition="Indicates if the Person is deceased or not",
-		formalDefinition="Indicates if the Person is deceased or not"
-	)
-	private BooleanDt myDeceased;
-	
-	@Child(name="address", type=AddressDt.class, order=6, min=0, max=Child.MAX_UNLIMITED)	
-	@Description(
-		shortDefinition="One or more addresses for the person",
-		formalDefinition="One or more addresses for the person"
-	)
-	private java.util.List<AddressDt> myAddress;
-	
-	@Child(name="maritalStatus", type=CodeableConceptDt.class, order=7, min=0, max=1)	
-	@Description(
-		shortDefinition="Marital (civil) status of the person",
-		formalDefinition="This field contains the patient's marital (civil) status."
-	)
-	private BoundCodeableConceptDt<MaritalStatusCodesEnum> myMaritalStatus;
-	
-	@Child(name="language", order=8, min=0, max=Child.MAX_UNLIMITED)	
-	@Description(
-		shortDefinition="The person's  proficiency level of a language",
-		formalDefinition="A language spoken by the person, with proficiency"
-	)
-	private java.util.List<Language> myLanguageElement;
-	
-
-	@Override
-	public boolean isEmpty() {
-		return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(  myIdentifier,  myName,  myTelecom,  myGender,  myBirthDate,  myDeceased,  myAddress,  myMaritalStatus,  myLanguageElement);
-	}
-	
-	@Override
-	public java.util.List<IElement> getAllPopulatedChildElements() {
-		return getAllPopulatedChildElementsOfType(null);
-	}
-
-	@Override
-	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
-		return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myIdentifier, myName, myTelecom, myGender, myBirthDate, myDeceased, myAddress, myMaritalStatus, myLanguageElement);
-	}
-
-	/**
-	 * Gets the value(s) for <b>identifier</b> (A Human identifier for this person).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Identifier for a person within a particular scope.
-     * </p> 
-	 */
-	public java.util.List<IdentifierDt> getIdentifier() {  
-		if (myIdentifier == null) {
-			myIdentifier = new java.util.ArrayList<IdentifierDt>();
-		}
-		return myIdentifier;
-	}
-
-	/**
-	 * Sets the value(s) for <b>identifier</b> (A Human identifier for this person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Identifier for a person within a particular scope.
-     * </p> 
-	 */
-	public Person setIdentifier(java.util.List<IdentifierDt> theValue) {
-		myIdentifier = theValue;
-		return this;
-	}
-
-	/**
-	 * Adds and returns a new value for <b>identifier</b> (A Human identifier for this person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Identifier for a person within a particular scope.
-     * </p> 
-	 */
-	public IdentifierDt addIdentifier() {
-		IdentifierDt newType = new IdentifierDt();
-		getIdentifier().add(newType);
-		return newType; 
-	}
-
-	/**
-	 * Gets the first repetition for <b>identifier</b> (A Human identifier for this person),
-	 * creating it if it does not already exist.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Identifier for a person within a particular scope.
-     * </p> 
-	 */
-	public IdentifierDt getIdentifierFirstRep() {
-		if (getIdentifier().isEmpty()) {
-			return addIdentifier();
-		}
-		return getIdentifier().get(0); 
-	}
- 	/**
-	 * Adds a new value for <b>identifier</b> (A Human identifier for this person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Identifier for a person within a particular scope.
-     * </p> 
-     *
-     * @return Returns a reference to this object, to allow for simple chaining.
-	 */
-	public Person addIdentifier( IdentifierUseEnum theUse,  String theSystem,  String theValue,  String theLabel) {
-		if (myIdentifier == null) {
-			myIdentifier = new java.util.ArrayList<IdentifierDt>();
-		}
-		myIdentifier.add(new IdentifierDt(theUse, theSystem, theValue, theLabel));
-		return this; 
-	}
-
-	/**
-	 * Adds a new value for <b>identifier</b> (A Human identifier for this person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Identifier for a person within a particular scope.
-     * </p> 
-     *
-     * @return Returns a reference to this object, to allow for simple chaining.
-	 */
-	public Person addIdentifier( String theSystem,  String theValue) {
-		if (myIdentifier == null) {
-			myIdentifier = new java.util.ArrayList<IdentifierDt>();
-		}
-		myIdentifier.add(new IdentifierDt(theSystem, theValue));
-		return this; 
-	}
-
- 
-	/**
-	 * Gets the value(s) for <b>name</b> (A name associated with the person).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A name associated with the person
-     * </p> 
-	 */
-	public java.util.List<HumanNameDt> getName() {  
-		if (myName == null) {
-			myName = new java.util.ArrayList<HumanNameDt>();
-		}
-		return myName;
-	}
-
-	/**
-	 * Sets the value(s) for <b>name</b> (A name associated with the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A name associated with the person
-     * </p> 
-	 */
-	public Person setName(java.util.List<HumanNameDt> theValue) {
-		myName = theValue;
-		return this;
-	}
-
-	/**
-	 * Adds and returns a new value for <b>name</b> (A name associated with the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A name associated with the person
-     * </p> 
-	 */
-	public HumanNameDt addName() {
-		HumanNameDt newType = new HumanNameDt();
-		getName().add(newType);
-		return newType; 
-	}
-
-	/**
-	 * Gets the first repetition for <b>name</b> (A name associated with the person),
-	 * creating it if it does not already exist.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A name associated with the person
-     * </p> 
-	 */
-	public HumanNameDt getNameFirstRep() {
-		if (getName().isEmpty()) {
-			return addName();
-		}
-		return getName().get(0); 
-	}
-  
-	/**
-	 * Gets the value(s) for <b>telecom</b> (A contact detail for the person).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A contact detail for the person, e.g. a telephone number or an email address.
-     * </p> 
-	 */
-	public java.util.List<ContactDt> getTelecom() {  
-		if (myTelecom == null) {
-			myTelecom = new java.util.ArrayList<ContactDt>();
-		}
-		return myTelecom;
-	}
-
-	/**
-	 * Sets the value(s) for <b>telecom</b> (A contact detail for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A contact detail for the person, e.g. a telephone number or an email address.
-     * </p> 
-	 */
-	public Person setTelecom(java.util.List<ContactDt> theValue) {
-		myTelecom = theValue;
-		return this;
-	}
-
-	/**
-	 * Adds and returns a new value for <b>telecom</b> (A contact detail for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A contact detail for the person, e.g. a telephone number or an email address.
-     * </p> 
-	 */
-	public ContactDt addTelecom() {
-		ContactDt newType = new ContactDt();
-		getTelecom().add(newType);
-		return newType; 
-	}
-
-	/**
-	 * Gets the first repetition for <b>telecom</b> (A contact detail for the person),
-	 * creating it if it does not already exist.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A contact detail for the person, e.g. a telephone number or an email address.
-     * </p> 
-	 */
-	public ContactDt getTelecomFirstRep() {
-		if (getTelecom().isEmpty()) {
-			return addTelecom();
-		}
-		return getTelecom().get(0); 
-	}
-  
-	/**
-	 * Gets the value(s) for <b>gender</b> (Administrative Gender).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Administrative Gender
-     * </p> 
-	 */
-	public CodingDt getGender() {  
-		if (myGender == null) {
-			myGender = new CodingDt();
-		}
-		return myGender;
-	}
-
-	/**
-	 * Sets the value(s) for <b>gender</b> (Administrative Gender)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Administrative Gender
-     * </p> 
-	 */
-	public Person setGender(CodingDt theValue) {
-		myGender = theValue;
-		return this;
-	}
-
-  
-	/**
-	 * Gets the value(s) for <b>birthDate</b> (The birth date for the person).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The birth date for the person.
-     * </p> 
-	 */
-	public DateTimeDt getBirthDate() {  
-		if (myBirthDate == null) {
-			myBirthDate = new DateTimeDt();
-		}
-		return myBirthDate;
-	}
-
-	/**
-	 * Sets the value(s) for <b>birthDate</b> (The birth date for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The birth date for the person.
-     * </p> 
-	 */
-	public Person setBirthDate(DateTimeDt theValue) {
-		myBirthDate = theValue;
-		return this;
-	}
-
- 	/**
-	 * Sets the value for <b>birthDate</b> (The birth date for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The birth date for the person.
-     * </p> 
-	 */
-	public Person setBirthDate( Date theDate,  TemporalPrecisionEnum thePrecision) {
-		myBirthDate = new DateTimeDt(theDate, thePrecision); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>birthDate</b> (The birth date for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The birth date for the person.
-     * </p> 
-	 */
-	public Person setBirthDateWithSecondsPrecision( Date theDate) {
-		myBirthDate = new DateTimeDt(theDate); 
-		return this; 
-	}
-
- 
-	/**
-	 * Gets the value(s) for <b>deceased</b> (Indicates if the Person is deceased or not).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Indicates if the Person is deceased or not
-     * </p> 
-	 */
-	public BooleanDt getDeceased() {  
-		if (myDeceased == null) {
-			myDeceased = new BooleanDt();
-		}
-		return myDeceased;
-	}
-
-	/**
-	 * Sets the value(s) for <b>deceased</b> (Indicates if the Person is deceased or not)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Indicates if the Person is deceased or not
-     * </p> 
-	 */
-	public Person setDeceased(BooleanDt theValue) {
-		myDeceased = theValue;
-		return this;
-	}
-
- 	/**
-	 * Sets the value for <b>deceased</b> (Indicates if the Person is deceased or not)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Indicates if the Person is deceased or not
-     * </p> 
-	 */
-	public Person setDeceased( boolean theBoolean) {
-		myDeceased = new BooleanDt(theBoolean); 
-		return this; 
-	}
-
- 
-	/**
-	 * Gets the value(s) for <b>address</b> (One or more addresses for the person).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * One or more addresses for the person
-     * </p> 
-	 */
-	public java.util.List<AddressDt> getAddress() {  
-		if (myAddress == null) {
-			myAddress = new java.util.ArrayList<AddressDt>();
-		}
-		return myAddress;
-	}
-
-	/**
-	 * Sets the value(s) for <b>address</b> (One or more addresses for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * One or more addresses for the person
-     * </p> 
-	 */
-	public Person setAddress(java.util.List<AddressDt> theValue) {
-		myAddress = theValue;
-		return this;
-	}
-
-	/**
-	 * Adds and returns a new value for <b>address</b> (One or more addresses for the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * One or more addresses for the person
-     * </p> 
-	 */
-	public AddressDt addAddress() {
-		AddressDt newType = new AddressDt();
-		getAddress().add(newType);
-		return newType; 
-	}
-
-	/**
-	 * Gets the first repetition for <b>address</b> (One or more addresses for the person),
-	 * creating it if it does not already exist.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * One or more addresses for the person
-     * </p> 
-	 */
-	public AddressDt getAddressFirstRep() {
-		if (getAddress().isEmpty()) {
-			return addAddress();
-		}
-		return getAddress().get(0); 
-	}
-  
-	/**
-	 * Gets the value(s) for <b>maritalStatus</b> (Marital (civil) status of the person).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * This field contains the patient's marital (civil) status.
-     * </p> 
-	 */
-	public BoundCodeableConceptDt<MaritalStatusCodesEnum> getMaritalStatus() {  
-		if (myMaritalStatus == null) {
-			myMaritalStatus = new BoundCodeableConceptDt<MaritalStatusCodesEnum>(MaritalStatusCodesEnum.VALUESET_BINDER);
-		}
-		return myMaritalStatus;
-	}
-
-	/**
-	 * Sets the value(s) for <b>maritalStatus</b> (Marital (civil) status of the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * This field contains the patient's marital (civil) status.
-     * </p> 
-	 */
-	public Person setMaritalStatus(BoundCodeableConceptDt<MaritalStatusCodesEnum> theValue) {
-		myMaritalStatus = theValue;
-		return this;
-	}
-
-	/**
-	 * Sets the value(s) for <b>maritalStatus</b> (Marital (civil) status of the person)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * This field contains the patient's marital (civil) status.
-     * </p> 
-	 */
-	public Person setMaritalStatus(MaritalStatusCodesEnum theValue) {
-		getMaritalStatus().setValueAsEnum(theValue);
-		return this;
-	}
-
-  
-	/**
-	 * Gets the value(s) for <b>language</b> (The person's  proficiency level of a language).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A language spoken by the person, with proficiency
-     * </p> 
-	 */
-	public java.util.List<Language> getLanguageElement() {  
-		if (myLanguageElement == null) {
-			myLanguageElement = new java.util.ArrayList<Language>();
-		}
-		return myLanguageElement;
-	}
-
-	/**
-	 * Sets the value(s) for <b>language</b> (The person's  proficiency level of a language)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A language spoken by the person, with proficiency
-     * </p> 
-	 */
-	public Person setLanguageElement(java.util.List<Language> theValue) {
-		myLanguageElement = theValue;
-		return this;
-	}
-
-	/**
-	 * Adds and returns a new value for <b>language</b> (The person's  proficiency level of a language)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A language spoken by the person, with proficiency
-     * </p> 
-	 */
-	public Language addLanguageElement() {
-		Language newType = new Language();
-		getLanguageElement().add(newType);
-		return newType; 
-	}
-
-	/**
-	 * Gets the first repetition for <b>language</b> (The person's  proficiency level of a language),
-	 * creating it if it does not already exist.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A language spoken by the person, with proficiency
-     * </p> 
-	 */
-	public Language getLanguageElementFirstRep() {
-		if (getLanguageElement().isEmpty()) {
-			return addLanguageElement();
-		}
-		return getLanguageElement().get(0); 
-	}
-  
-	/**
-	 * Block class for child element: <b>Person.language</b> (The person's  proficiency level of a language)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A language spoken by the person, with proficiency
-     * </p> 
-	 */
-	@Block(name="Person.language")	
-	public static class Language extends BaseElement implements IResourceBlock {
-	
-	@Child(name="language", type=CodeableConceptDt.class, order=0, min=1, max=1)	
-	@Description(
-		shortDefinition="Language with optional region",
-		formalDefinition="The ISO-639-1 alpha 2 code in lower case for the language, optionally followed by a hyphen and the ISO-3166-1 alpha 2 code for the region in upper case. E.g. \"en\" for English, or \"en-US\" for American English versus \"en-EN\" for England English"
-	)
-	private CodeableConceptDt myLanguageElement;
-	
-	@Child(name="mode", type=CodeableConceptDt.class, order=1, min=0, max=1)	
-	@Description(
-		shortDefinition="Language method of expression",
-		formalDefinition="A value representing the person's method of expression of this language. Examples: expressed spoken, expressed written, expressed signed, received spoken, received written, received signed"
-	)
-	private CodeableConceptDt myMode;
-	
-	@Child(name="proficiencyLevel", type=CodeableConceptDt.class, order=2, min=0, max=1)	
-	@Description(
-		shortDefinition="Proficiency level of the language",
-		formalDefinition="A code that describes how well the language is spoken"
-	)
-	private CodeableConceptDt myProficiencyLevel;
-	
-	@Child(name="preference", type=BooleanDt.class, order=3, min=0, max=1)	
-	@Description(
-		shortDefinition="Language preference indicator",
-		formalDefinition="Indicates whether or not the Person prefers this language (over other languages he masters up a certain level)"
-	)
-	private BooleanDt myPreference;
-	
-
-	@Override
-	public boolean isEmpty() {
-		return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(  myLanguageElement,  myMode,  myProficiencyLevel,  myPreference);
-	}
-	
-	@Override
-	public java.util.List<IElement> getAllPopulatedChildElements() {
-		return getAllPopulatedChildElementsOfType(null);
-	}
-
-	@Override
-	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
-		return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myLanguageElement, myMode, myProficiencyLevel, myPreference);
-	}
-
-	/**
-	 * Gets the value(s) for <b>language</b> (Language with optional region).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The ISO-639-1 alpha 2 code in lower case for the language, optionally followed by a hyphen and the ISO-3166-1 alpha 2 code for the region in upper case. E.g. \"en\" for English, or \"en-US\" for American English versus \"en-EN\" for England English
-     * </p> 
-	 */
-	public CodeableConceptDt getLanguageElement() {  
-		if (myLanguageElement == null) {
-			myLanguageElement = new CodeableConceptDt();
-		}
-		return myLanguageElement;
-	}
-
-	/**
-	 * Sets the value(s) for <b>language</b> (Language with optional region)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The ISO-639-1 alpha 2 code in lower case for the language, optionally followed by a hyphen and the ISO-3166-1 alpha 2 code for the region in upper case. E.g. \"en\" for English, or \"en-US\" for American English versus \"en-EN\" for England English
-     * </p> 
-	 */
-	public Language setLanguageElement(CodeableConceptDt theValue) {
-		myLanguageElement = theValue;
-		return this;
-	}
-
-  
-	/**
-	 * Gets the value(s) for <b>mode</b> (Language method of expression).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A value representing the person's method of expression of this language. Examples: expressed spoken, expressed written, expressed signed, received spoken, received written, received signed
-     * </p> 
-	 */
-	public CodeableConceptDt getMode() {  
-		if (myMode == null) {
-			myMode = new CodeableConceptDt();
-		}
-		return myMode;
-	}
-
-	/**
-	 * Sets the value(s) for <b>mode</b> (Language method of expression)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A value representing the person's method of expression of this language. Examples: expressed spoken, expressed written, expressed signed, received spoken, received written, received signed
-     * </p> 
-	 */
-	public Language setMode(CodeableConceptDt theValue) {
-		myMode = theValue;
-		return this;
-	}
-
-  
-	/**
-	 * Gets the value(s) for <b>proficiencyLevel</b> (Proficiency level of the language).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A code that describes how well the language is spoken
-     * </p> 
-	 */
-	public CodeableConceptDt getProficiencyLevel() {  
-		if (myProficiencyLevel == null) {
-			myProficiencyLevel = new CodeableConceptDt();
-		}
-		return myProficiencyLevel;
-	}
-
-	/**
-	 * Sets the value(s) for <b>proficiencyLevel</b> (Proficiency level of the language)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * A code that describes how well the language is spoken
-     * </p> 
-	 */
-	public Language setProficiencyLevel(CodeableConceptDt theValue) {
-		myProficiencyLevel = theValue;
-		return this;
-	}
-
-  
-	/**
-	 * Gets the value(s) for <b>preference</b> (Language preference indicator).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Indicates whether or not the Person prefers this language (over other languages he masters up a certain level)
-     * </p> 
-	 */
-	public BooleanDt getPreference() {  
-		if (myPreference == null) {
-			myPreference = new BooleanDt();
-		}
-		return myPreference;
-	}
-
-	/**
-	 * Sets the value(s) for <b>preference</b> (Language preference indicator)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Indicates whether or not the Person prefers this language (over other languages he masters up a certain level)
-     * </p> 
-	 */
-	public Language setPreference(BooleanDt theValue) {
-		myPreference = theValue;
-		return this;
-	}
-
- 	/**
-	 * Sets the value for <b>preference</b> (Language preference indicator)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * Indicates whether or not the Person prefers this language (over other languages he masters up a certain level)
-     * </p> 
-	 */
-	public Language setPreference( boolean theBoolean) {
-		myPreference = new BooleanDt(theBoolean); 
-		return this; 
-	}
-
- 
-
-	}
-
-
-
-
-}

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

@@ -392,19 +392,6 @@ public class Remittance extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * The percent of the service fee which would be elegible for coverage
-     * </p> 
-	 */
-	public Service setRate( long theValue) {
-		myRate = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>rate</b> (Benefit Rate %)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The percent of the service fee which would be elegible for coverage
      * </p> 
 	 */
 	public Service setRate( double theValue) {
@@ -425,6 +412,19 @@ public class Remittance extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>rate</b> (Benefit Rate %)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The percent of the service fee which would be elegible for coverage
+     * </p> 
+	 */
+	public Service setRate( long theValue) {
+		myRate = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>benefit</b> (Benefit amount).
@@ -462,19 +462,6 @@ public class Remittance extends BaseResource implements IResource {
      * <p>
      * <b>Definition:</b>
      * The amount payable for a submitted service (includes both professional and lab fees.)
-     * </p> 
-	 */
-	public Service setBenefit( long theValue) {
-		myBenefit = new DecimalDt(theValue); 
-		return this; 
-	}
-
-	/**
-	 * Sets the value for <b>benefit</b> (Benefit amount)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * The amount payable for a submitted service (includes both professional and lab fees.)
      * </p> 
 	 */
 	public Service setBenefit( double theValue) {
@@ -495,6 +482,19 @@ public class Remittance extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Sets the value for <b>benefit</b> (Benefit amount)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The amount payable for a submitted service (includes both professional and lab fees.)
+     * </p> 
+	 */
+	public Service setBenefit( long theValue) {
+		myBenefit = new DecimalDt(theValue); 
+		return this; 
+	}
+
  
 
 	}

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

@@ -717,24 +717,6 @@ public class Test extends BaseResource implements IResource {
      * 
      * </p> 
      *
-     * @return Returns a reference to this object, to allow for simple chaining.
-	 */
-	public Test addDecimalErr( long theValue) {
-		if (myDecimalErr == null) {
-			myDecimalErr = new java.util.ArrayList<DecimalDt>();
-		}
-		myDecimalErr.add(new DecimalDt(theValue));
-		return this; 
-	}
-
-	/**
-	 * Adds a new value for <b>decimalErr</b> (Decimals with invalid content)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * 
-     * </p> 
-     *
      * @return Returns a reference to this object, to allow for simple chaining.
 	 */
 	public Test addDecimalErr( double theValue) {
@@ -763,6 +745,24 @@ public class Test extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Adds a new value for <b>decimalErr</b> (Decimals with invalid content)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * 
+     * </p> 
+     *
+     * @return Returns a reference to this object, to allow for simple chaining.
+	 */
+	public Test addDecimalErr( long theValue) {
+		if (myDecimalErr == null) {
+			myDecimalErr = new java.util.ArrayList<DecimalDt>();
+		}
+		myDecimalErr.add(new DecimalDt(theValue));
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>decimalCorr</b> (Decimals with correct content).
@@ -831,24 +831,6 @@ public class Test extends BaseResource implements IResource {
      * 
      * </p> 
      *
-     * @return Returns a reference to this object, to allow for simple chaining.
-	 */
-	public Test addDecimalCorr( long theValue) {
-		if (myDecimalCorr == null) {
-			myDecimalCorr = new java.util.ArrayList<DecimalDt>();
-		}
-		myDecimalCorr.add(new DecimalDt(theValue));
-		return this; 
-	}
-
-	/**
-	 * Adds a new value for <b>decimalCorr</b> (Decimals with correct content)
-	 *
-     * <p>
-     * <b>Definition:</b>
-     * 
-     * </p> 
-     *
      * @return Returns a reference to this object, to allow for simple chaining.
 	 */
 	public Test addDecimalCorr( double theValue) {
@@ -877,6 +859,24 @@ public class Test extends BaseResource implements IResource {
 		return this; 
 	}
 
+	/**
+	 * Adds a new value for <b>decimalCorr</b> (Decimals with correct content)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * 
+     * </p> 
+     *
+     * @return Returns a reference to this object, to allow for simple chaining.
+	 */
+	public Test addDecimalCorr( long theValue) {
+		if (myDecimalCorr == null) {
+			myDecimalCorr = new java.util.ArrayList<DecimalDt>();
+		}
+		myDecimalCorr.add(new DecimalDt(theValue));
+		return this; 
+	}
+
  
 	/**
 	 * Gets the value(s) for <b>b64Err</b> (Binaries with invalid content).

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

@@ -1,6 +1,10 @@
 package ca.uhn.fhir.model.primitive;
 
-import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.*;
+import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.DAY;
+import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.MILLI;
+import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.MONTH;
+import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.SECOND;
+import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.YEAR;
 
 import java.text.ParseException;
 import java.util.Calendar;

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.model.primitive;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
 
 import java.util.Collection;
 import java.util.HashSet;

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.model.primitive;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
 import ca.uhn.fhir.model.api.BasePrimitive;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.api.annotation.SimpleSetter;

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.parser;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.ArrayList;
 import java.util.HashMap;

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.parser;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.Reader;
 import java.io.StringWriter;

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.rest.method;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.lang.reflect.Method;
 import java.util.Collections;

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

@@ -34,7 +34,7 @@ new FhirContextIntro().encodeMsg();
 FhirContext ctx = new FhirContext(Patient.class, Observation.class);
 //START SNIPPET: encodeMsg
 
-/*
+/**
  * FHIR model types in HAPI are simple POJOs. To create a new
  * one, invoke the default constructor and then
  * start populating values.
@@ -53,10 +53,7 @@ name.addFamily("Tester");
 name.addGiven("John");
 name.addGiven("Q");
 
-/*
+// We can now use a parser to encode this resource into a string.
- * We can now use a parser to encode this resource into
- * a string.
- */
 String encoded = ctx.newXmlParser().encodeResourceToString(patient);
 System.out.println(encoded);
 //END SNIPPET: encodeMsg
@@ -75,9 +72,7 @@ System.out.println(encoded);
 FhirContext ctx = new FhirContext(Patient.class, Observation.class);
 
 //START SNIPPET: parseMsg
-/*
+// The following is an example Patient resource
- * The following is an example Patient resource
- */
 String msgString = "<Patient xmlns=\"http://hl7.org/fhir\">" 
   + "<text><status value=\"generated\" /><div xmlns=\"http://www.w3.org/1999/xhtml\">John Cardinal</div></text>"
   + "<identifier><system value=\"http://orionhealth.com/mrn\" /><value value=\"PRP1660\" /></identifier>"
@@ -86,26 +81,20 @@ String msgString = "<Patient xmlns=\"http://hl7.org/fhir\">"
   + "<address><use value=\"home\" /><line value=\"2222 Home Street\" /></address><active value=\"true\" />"
   + "</Patient>";
 
-/* 
+// The hapi context object is used to create a new XML parser
- * The hapi context object is used to create a new XML parser
+// instance. The parser can then be used to parse (or unmarshall) the 
- * instance. The parser can then be used to parse (or unmarshall) the 
+// string message into a Patient object 
- * string message into a Patient object 
- */
 IParser parser = ctx.newXmlParser();
 Patient patient = parser.parseResource(Patient.class, msgString);
 
-/*
+// The patient object has accessor methods to retrieve all of the
- * The patient object has accessor methods to retrieve all of the
+// data which has been parsed into the instance. All of the
- * data which has been parsed into the instance. All of the
+// FHIR datatypes are represented by classes which end in "Dt". 
- * FHIR datatypes are represented by classes which end in "Dt". 
- */
 StringDt patientId = patient.getIdentifier().get(0).getValue();
 StringDt familyName = patient.getName().get(0).getFamily().get(0);
 CodeDt gender = patient.getGender().getCoding().get(0).getCode();
 
-/*
+// The various datatype classes have accessors called getValue()
- * The various datatype classes have accessors called getValue()
- */
 System.out.println(patientId.getValue()); // PRP1660
 System.out.println(familyName.getValue()); // Cardinal
 System.out.println(gender.getValue()); // M

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

@@ -25,10 +25,8 @@ obs.setIssued(new InstantDt(new Date()));
 obs.setIssued(new Date(), TemporalPrecisionEnum.MILLI);
 obs.setIssuedWithMillisPrecision(new Date());
 
-/* 
+// The InstantDt also lets you work with the instant as a Java Date
- * The InstantDt also lets you work with the instant as a Java Date
+// object or as a FHIR String.
- * object or as a FHIR String.
- */
 Date date = obs.getIssued().getValue(); // A date object
 String dateString = obs.getIssued().getValueAsString(); // "2014-03-08T12:59:58.068-05:00"
 // END SNIPPET: datatypes
@@ -43,18 +41,14 @@ public void nonNull() {
 // START SNIPPET: nonNull
 Observation observation = new Observation();
 
-/*
+// None of these calls will return null, but instead create their respective
- * None of these calls will return null, but instead create their respective
+// child elements.
- * child elements.
- */
 IdentifierDt identifierDt = observation.getIdentifier();
 PeriodDt periodDt         = observation.getIdentifier().getPeriod();
 DateTimeDt activeDt       = observation.getIdentifier().getPeriod().getStart();
 
-/*
+// DateTimeDt is a FHIR primitive however, so the following will return null
- * DateTimeDt is a FHIR primitive however, so the following will return null
+// unless a value has been placed there.
- * unless a value has been placed there.
- */
 Date active = observation.getIdentifier().getPeriod().getStart().getValue();
 // END SNIPPET: nonNull
 

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

@@ -25,6 +25,7 @@
 
 		<menu name="Welcome">
 			<item name="Welcome" href="index.html" />
+			<item name="Download" href="./download.html" />
 		</menu>
 
 		<menu name="Documentation">

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

@@ -46,7 +46,7 @@
 			
 			<p>
 				To get started with HAPI FHIR, first download a copy and add it
-				to your project. See the <a href="doc_download.html">Download Page</a>
+				to your project. See the <a href="./download.html">Download Page</a>
 				for instructions.
 			</p>			
 			

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

@@ -26,12 +26,30 @@
 			
 		</section>
 
-		<section name="Why HAPI FHIR?">
+		<section name="What is HAPI FHIR?">
 			<p>
 				HAPI FHIR is a simple-but-powerful library for adding FHIR messaging to your application. It
 				is pure Java (1.6+ compatible), and licensed under the business-friendly Apache Software
 				License, version 2.0.
 			</p>
+			
+			<subsection name="Multiple Usage Patterns">
+				<p>
+					HAPI is designed with one main intent: providing a flexible way of adding
+					FHIR capability to applications. We at <a href="http://www.uhn.ca">University Health Network</a> 
+					developed HAPI-FHIR to allow us to 
+					build up our own unified FHIR RESTful server which exposes data backed by
+					a number of systems and repositories, so it is designed to be flexible
+					above all else. 
+				</p>
+				<p>
+					The library is designed to support several main usage patterns:
+					<img src="images/hapi-usage.png" alt="HAPI Usage Patterns"/>  
+				</p>
+			</subsection>
+						
+			<subsection name="The Data Model">
+			
 				<p>
 					The HAPI API makes it very easy to create FHIR resources:
 				</p>
@@ -44,7 +62,11 @@ patient.addName().addFamily("Smith").addGiven("John").addGiven("Q").addSuffix("J
 patient.setGender(AdministrativeGenderCodesEnum.M);]]></source>
 			
 				<p>
-				This library supports both XML and JSON encoding natively:
+					Both XML and JSON encoding are suported natively using a simple API
+					to pick between them. XML support is built on top of the lightning-fast 
+					<a href="http://docs.oracle.com/javase/tutorial/jaxp/stax/why.html">STaX/JSR 173</a> 
+					API, and JSON support is provided using the new
+					<a href="https://jcp.org/en/jsr/detail?id=353">javax.json/JSR-353</a> API. 
 				</p>
 	
 				<source><![CDATA[FhirContext ctx = new FhirContext();
@@ -75,6 +97,8 @@ String jsonEncoded = ctx.newJsonParser().encodeResourceToString(patient);
 				<source><![CDATA[MyClientInterface client = ctx.newRestfulClient(MyClientInterface.class, "http://foo/fhir");
 IdentifierDt searchParam = new IdentifierDt("urn:someidentifiers", "7000135");
 List<Patient> clients = client.findPatientsByIdentifier(searchParam);]]></source>
+
+			</subsection>
 		</section>
 
 	</body>

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

@@ -30,7 +30,7 @@ public class CustomThymeleafNarrativeGeneratorTest {
 		String actual = narrative.getDiv().getValueAsString();
 		ourLog.info(actual);
 
-		assertThat(actual, containsString("<h1>Name</h1><div> given <b>FAM1 </b></div><h1>Address</h1><div><span>line1 </span><br/><span>line2 </span><br/></div></div>"));
+		assertThat(actual, containsString("<h1>Name</h1><div class=\"nameElement\"> given <b>FAM1 </b></div><h1>Address</h1><div><span>line1 </span><br/><span>line2 </span><br/></div></div>"));
 		
 	}
 }

hapi-fhir-structures-dstu/pom.xml

@@ -89,7 +89,7 @@
 						<baseResourceName>organization</baseResourceName>
 						<baseResourceName>other</baseResourceName>
 						<baseResourceName>patient</baseResourceName>
-						<baseResourceName>person</baseResourceName>
+						<!--<baseResourceName>person</baseResourceName>-->
 						<baseResourceName>practitioner</baseResourceName>
 						<baseResourceName>procedure</baseResourceName>
 						<baseResourceName>profile</baseResourceName>

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

@@ -1,312 +0,0 @@
-
-package ca.uhn.fhir.tinder;
-
-import static org.apache.commons.lang.StringUtils.capitalize;
-import static org.apache.commons.lang.StringUtils.isBlank;
-
-import java.io.File;
-import java.io.FileReader;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.maven.plugin.MojoFailureException;
-
-import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.dstu.resource.Profile;
-import ca.uhn.fhir.model.dstu.resource.Profile.ExtensionDefn;
-import ca.uhn.fhir.model.dstu.resource.Profile.Structure;
-import ca.uhn.fhir.model.dstu.resource.Profile.StructureElement;
-import ca.uhn.fhir.model.dstu.resource.Profile.StructureElementDefinition;
-import ca.uhn.fhir.model.dstu.resource.Profile.StructureElementDefinitionType;
-import ca.uhn.fhir.model.dstu.resource.Profile.StructureSearchParam;
-import ca.uhn.fhir.model.dstu.valueset.DataTypeEnum;
-import ca.uhn.fhir.model.dstu.valueset.SlicingRulesEnum;
-import ca.uhn.fhir.tinder.model.AnyChild;
-import ca.uhn.fhir.tinder.model.BaseElement;
-import ca.uhn.fhir.tinder.model.BaseRootType;
-import ca.uhn.fhir.tinder.model.Child;
-import ca.uhn.fhir.tinder.model.Extension;
-import ca.uhn.fhir.tinder.model.Resource;
-import ca.uhn.fhir.tinder.model.ResourceBlock;
-import ca.uhn.fhir.tinder.model.SearchParameter;
-import ca.uhn.fhir.tinder.model.SimpleChild;
-import ca.uhn.fhir.tinder.model.Slicing;
-
-public class CopyOfProfileParser extends BaseStructureParser {
-
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CopyOfProfileParser.class);
-
-	private ExtensionDefn findExtension(Profile theProfile, String theCode) {
-		for (ExtensionDefn next : theProfile.getExtensionDefn()) {
-			if (theCode.equals(next.getCode().getValue())) {
-				return next;
-			}
-		}
-		return null;
-	}
-
-	@Override
-	protected String getFilenameSuffix() {
-		return "";
-	}
-
-	@Override
-	protected String getTemplate() {
-		return "/vm/resource.vm";
-	}
-
-	public void parseBaseResources(List<String> theBaseResourceNames) throws MojoFailureException {
-		FhirContext fhirContext = new FhirContext(Profile.class);
-
-		for (String nextFileName : theBaseResourceNames) {
-			ourLog.info("Parsing file: {}", nextFileName);
-
-			Profile profile;
-			try {
-				profile = (Profile) fhirContext.newXmlParser().parseResource(IOUtils.toString(new FileReader(nextFileName)));
-			} catch (Exception e) {
-				throw new MojoFailureException("Failed to load or parse file: " + nextFileName, e);
-			}
-
-			try {
-				parseSingleProfile(profile, "");
-			} catch (Exception e) {
-				throw new MojoFailureException("Failed to process file: " + nextFileName, e);
-			}
-		}
-
-		// for (int i = 0; i < theBaseResourceNames.size(); i++) {
-		// theBaseResourceNames.set(i,
-		// theBaseResourceNames.get(i).toLowerCase());
-		// }
-		//
-		// try {
-		//
-		// Bundle bundle =
-		// fhirContext.newXmlParser().parseBundle(IOUtils.toString(getClass().getResourceAsStream("/prof/allprofiles.xml")));
-		// TreeSet<String> allProfiles = new TreeSet<String>();
-		// for (BundleEntry nextResource : bundle.getEntries() ) {
-		// Profile nextProfile = (Profile) nextResource.getResource();
-		// allProfiles.add(nextProfile.getName().getValue());
-		// if
-		// (theBaseResourceNames.contains(nextProfile.getName().getValue().toLowerCase())){
-		// parseSingleProfile(nextProfile,
-		// bundle.getLinkBase().getValueNotNull());
-		// }
-		// }
-		//
-		// ourLog.info("Base profiles found: {}", allProfiles);
-		//
-		// } catch (Exception e) {
-		// throw new MojoFailureException("Failed to load base resources", e);
-		// }
-	}
-
-	public BaseRootType parseSingleProfile(Profile theProfile, String theUrlTOThisProfile) throws Exception {
-		BaseRootType retVal = null;
-		for (Structure nextStructure : theProfile.getStructure()) {
-
-			int elemIdx = 0;
-			boolean extensionsSliced = false;
-			SlicingRulesEnum extensionsSlicingIsOpen = SlicingRulesEnum.OPEN;
-
-			Map<String, BaseElement> elements = new HashMap<String, BaseElement>();
-			for (StructureElement next : nextStructure.getElement()) {
-
-				BaseElement elem;
-				if (elemIdx == 0) {
-					retVal = new Resource();
-					retVal.setProfile(theProfile.getIdentifier().getValue());
-					if (retVal.getProfile() == null) {
-						retVal.setProfile(theUrlTOThisProfile);
-					}
-
-					for (StructureSearchParam nextParam : nextStructure.getSearchParam()) {
-						SearchParameter param = new SearchParameter();
-						param.setName(nextParam.getName().getValue());
-						param.setPath(nextParam.getXpath().getValue());
-						param.setType(nextParam.getType().getValue());
-						param.setDescription(nextParam.getDocumentation().getValue());
-						retVal.getSearchParameters().add(param);
-					}
-
-					addResource(retVal);
-					elem = retVal;
-					// below StringUtils.isBlank(type) || type.startsWith("=")
-				} else {
-					if (next.getDefinition().getType().size() > 0 && next.getDefinition().getType().get(0).getCode().getValue().equals("Extension")) {
-						if (!next.getSlicing().isEmpty()) {
-							if (!"url".equals(next.getSlicing().getDiscriminator().getValue())) {
-								throw new ConfigurationException("Invalid extension slicing discriminator (must be 'url'): " + next.getSlicing().getDiscriminator().getValue());
-							}
-							extensionsSliced = true;
-							if (StringUtils.isNotBlank(next.getSlicing().getRules().getValueAsString())) {
-								extensionsSlicingIsOpen = next.getSlicing().getRules().getValueAsEnum();
-								if (extensionsSlicingIsOpen == null) {
-									throw new ConfigurationException("Invalid extension slicing rules: " + next.getSlicing().getRules().getValueAsString());
-								}
-							}
-							continue;
-						} else {
-							if (!extensionsSliced) {
-								continue;
-							}
-							
-							if (next.getDefinition().getType().size() != 1) {
-								throw new ConfigurationException("Extension definition '" + next.getName().getValue() + "' has multiple type blocks. This is not supported.");
-							}
-							String extUrl = next.getDefinition().getType().get(0).getProfile().getValueAsString();
-							elem = new Extension(next.getName().getValue(), extUrl, "CodeDt");
-						}
-					} else {
-						if (next.getDefinition().getType().isEmpty()) {
-							elem = new ResourceBlock();
-							// } else if (type.startsWith("@")) {
-							// elem = new ResourceBlockCopy();
-						} else if (next.getDefinition().getType().get(0).getCode().getValue().equals("*")) {
-							elem = new AnyChild();
-						} else {
-							elem = new SimpleChild();
-						}
-					}
-				}
-
-				elem.setName(next.getPath().getValue());
-				elem.setElementNameAndDeriveParentElementName(next.getPath().getValue());
-
-				boolean allResourceReferences = next.getDefinition().getType().size() > 0;
-				for (StructureElementDefinitionType nextType : next.getDefinition().getType()) {
-					if (nextType.getCode().getValueAsEnum() != DataTypeEnum.RESOURCEREFERENCE) {
-						allResourceReferences = false;
-					}
-				}
-				elem.setResourceRef(allResourceReferences);
-
-				StructureElementDefinition definition = next.getDefinition();
-
-				BaseElement parentElement = elements.get(elem.getElementParentName());
-				Slicing childIsSliced = parentElement != null ? parentElement.getChildElementNameToSlicing().get(elem.getName()) : null;
-
-				if (next.getSlicing().getDiscriminator().getValue() != null) {
-					Slicing slicing = new Slicing();
-					slicing.setDiscriminator(next.getSlicing().getDiscriminator().getValue());
-					if (parentElement.getChildElementNameToSlicing().get(elem.getName()) != null) {
-						throw new ConfigurationException("Found multiple slicing definitions for path: " + next.getPath().getValue());
-					}
-					parentElement.getChildElementNameToSlicing().put(elem.getName(), slicing);
-					continue;
-				}
-
-				/*
-				 * Profiles come with a number of standard elements which are generally ignored because they are boilerplate, unless the definition is somehow changing their behaviour (e.g. through
-				 * slices)
-				 */
-				if (next.getPath().getValue().endsWith(".contained")) {
-					continue;
-				}
-				if (next.getPath().getValue().endsWith(".text")) {
-					continue;
-				}
-				if (next.getPath().getValue().endsWith(".extension")) {
-					if (childIsSliced != null) {
-						if (!"url".equals(childIsSliced.getDiscriminator())) {
-							throw new ConfigurationException("Extensions must be sliced on 'url' discriminator. Found: " + next.getSlicing().getDiscriminator().getValue());
-						}
-						if (next.getDefinition().getType().size() != 1 || next.getDefinition().getType().get(0).getCode().getValueAsEnum() != DataTypeEnum.EXTENSION) {
-							throw new ConfigurationException("Extension slices must have a single type with a code of 'Extension'");
-						}
-						String name = next.getName().getValue();
-						if (StringUtils.isBlank(name)) {
-							throw new ConfigurationException("Extension slices must have a 'name' defined, none found at path: " + next.getPath());
-						}
-						elem.setName(name);
-						elem.setElementName(name);
-						String profile = next.getDefinition().getType().get(0).getProfile().getValueAsString();
-						if (isBlank(profile)) {
-							throw new ConfigurationException("Extension slice for " + next.getPath().getValue() + " has no profile specified in its type");
-						}
-						if (profile.startsWith("#")) {
-							Profile.ExtensionDefn extension = findExtension(theProfile, profile.substring(1));
-							if (extension == null) {
-								throw new ConfigurationException("Unknown local extension reference: " + profile);
-							}
-							ourLog.info("Element at path {} is using extension {}", next.getPath(), profile);
-							definition = extension.getDefinition();
-							String extensionUrl = theUrlTOThisProfile + profile;
-							elem.setExtensionUrl(extensionUrl);
-						} else {
-							// TODO: implement this
-							throw new ConfigurationException("Extensions specified outside of the given profile are not yet supported");
-						}
-					} else {
-						continue;
-					}
-				}
-				if (next.getPath().getValue().endsWith(".modifierExtension")) {
-					continue;
-				}
-
-				for (StructureElementDefinitionType nextType : definition.getType()) {
-					if (nextType.getCode().getValueAsEnum() == DataTypeEnum.RESOURCEREFERENCE) {
-						if (nextType.getProfile().getValueAsString().startsWith("http://hl7.org/fhir/profiles/")) {
-							elem.getType().add(capitalize(nextType.getProfile().getValueAsString().substring("http://hl7.org/fhir/profiles/".length())));
-						} else {
-							// TODO: implement this.. we need to be able to
-							// reference other profiles
-							throw new ConfigurationException("Profile type not yet supported");
-						}
-					} else {
-						elem.getType().add(capitalize(nextType.getCode().getValue()) + "Dt");
-					}
-
-				}
-
-				elem.setBinding(definition.getBinding().getName().getValue());
-				elem.setShortName(definition.getShort().getValue());
-				elem.setDefinition(definition.getFormal().getValue());
-				elem.setRequirement(definition.getRequirements().getValue());
-				elem.setCardMin(definition.getMin().getValueAsString());
-				elem.setCardMax(definition.getMax().getValue());
-
-				if (elem instanceof Child) {
-					Child child = (Child) elem;
-					elements.put(elem.getName(), elem);
-					if (parentElement == null) {
-						throw new Exception("Can't find element " + elem.getElementParentName() + "  -  Valid values are: " + elements.keySet());
-					}
-					parentElement.addChild(child);
-
-					/*
-					 * Find simple setters
-					 */
-					scanForSimpleSetters(child);
-				} else {
-					BaseRootType res = (BaseRootType) elem;
-					elements.put(res.getName(), res);
-				}
-
-				elemIdx++;
-			}
-
-		}
-
-		return retVal;
-	}
-
-	public static void main(String[] args) throws Exception {
-		String str = IOUtils.toString(Profile.class.getResourceAsStream("/tmp.txt"));
-		str = IOUtils.toString(new FileReader("../hapi-tinder-test/src/test/resources/profile/organization.xml"));
-		Profile prof = new FhirContext(Profile.class).newXmlParser().parseResource(Profile.class, str);
-
-		CopyOfProfileParser pp = new CopyOfProfileParser();
-		pp.parseSingleProfile(prof, "http://foo");
-		pp.markResourcesForImports();
-		pp.writeAll(new File("target/gen/test/resource"), "test");
-
-	}
-
-}

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

@@ -51,9 +51,9 @@ public abstract class Child extends BaseElement {
 		if ("Class".equals(elementName)) {
 			elementName = "ClassElement";
 		}
-		if ("Language".equals(elementName)) {
+//		if ("Language".equals(elementName)) {
-			elementName = "LanguageElement";
+//			elementName = "LanguageElement";
-		}
+//		}
 		return elementName;
 	}
 

restful-server-example/.classpath

@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+  <classpathentry kind="src" path="src/main/java" including="**/*.java"/>
+  <classpathentry kind="output" path="target/classes"/>
+  <classpathentry kind="var" path="M2_REPO/javax/json/javax.json-api/1.0/javax.json-api-1.0.jar" sourcepath="M2_REPO/javax/json/javax.json-api/1.0/javax.json-api-1.0-sources.jar"/>
+  <classpathentry kind="var" path="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2.jar" sourcepath="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2-sources.jar"/>
+  <classpathentry kind="var" path="M2_REPO/javax/servlet/javax.servlet-api/3.0.1/javax.servlet-api-3.0.1.jar" sourcepath="M2_REPO/javax/servlet/javax.servlet-api/3.0.1/javax.servlet-api-3.0.1-sources.jar"/>
+  <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+  <classpathentry kind="var" path="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-base/0.1/hapi-fhir-base-0.1.jar" sourcepath="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-base/0.1/hapi-fhir-base-0.1-sources.jar">
+    <attributes>
+      <attribute value="jar:file:/home/t3903uhn/.m2/repository/ca/uhn/hapi/fhir/hapi-fhir-base/0.1/hapi-fhir-base-0.1-javadoc.jar!/" name="javadoc_location"/>
+    </attributes>
+  </classpathentry>
+  <classpathentry kind="var" path="M2_REPO/org/glassfish/javax.json/1.0.4/javax.json-1.0.4.jar" sourcepath="M2_REPO/org/glassfish/javax.json/1.0.4/javax.json-1.0.4-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">
+    <attributes>
+      <attribute value="jar:file:/home/t3903uhn/.m2/repository/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-javadoc.jar!/" name="javadoc_location"/>
+    </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 kind="var" path="M2_REPO/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1.jar" sourcepath="M2_REPO/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1-sources.jar">
+    <attributes>
+      <attribute value="jar:file:/home/t3903uhn/.m2/repository/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1-javadoc.jar!/" name="javadoc_location"/>
+    </attributes>
+  </classpathentry>
+  <classpathentry kind="var" path="M2_REPO/commons-codec/commons-codec/1.9/commons-codec-1.9.jar" sourcepath="M2_REPO/commons-codec/commons-codec/1.9/commons-codec-1.9-sources.jar"/>
+  <classpathentry kind="var" path="M2_REPO/commons-io/commons-io/2.4/commons-io-2.4.jar" sourcepath="M2_REPO/commons-io/commons-io/2.4/commons-io-2.4-sources.jar"/>
+  <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">
+    <attributes>
+      <attribute value="jar:file:/home/t3903uhn/.m2/repository/org/slf4j/slf4j-api/1.7.6/slf4j-api-1.7.6-javadoc.jar!/" name="javadoc_location"/>
+    </attributes>
+  </classpathentry>
+  <classpathentry kind="var" path="M2_REPO/org/apache/httpcomponents/httpclient/4.3.3/httpclient-4.3.3.jar" sourcepath="M2_REPO/org/apache/httpcomponents/httpclient/4.3.3/httpclient-4.3.3-sources.jar"/>
+  <classpathentry kind="var" path="M2_REPO/org/apache/httpcomponents/httpcore/4.3.2/httpcore-4.3.2.jar" sourcepath="M2_REPO/org/apache/httpcomponents/httpcore/4.3.2/httpcore-4.3.2-sources.jar"/>
+  <classpathentry kind="var" path="M2_REPO/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar" sourcepath="M2_REPO/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3-sources.jar"/>
+  <classpathentry kind="var" path="M2_REPO/ch/qos/logback/logback-classic/1.1.1/logback-classic-1.1.1.jar" sourcepath="M2_REPO/ch/qos/logback/logback-classic/1.1.1/logback-classic-1.1.1-sources.jar">
+    <attributes>
+      <attribute value="jar:file:/home/t3903uhn/.m2/repository/ch/qos/logback/logback-classic/1.1.1/logback-classic-1.1.1-javadoc.jar!/" name="javadoc_location"/>
+    </attributes>
+  </classpathentry>
+  <classpathentry kind="var" path="M2_REPO/ch/qos/logback/logback-core/1.1.1/logback-core-1.1.1.jar" sourcepath="M2_REPO/ch/qos/logback/logback-core/1.1.1/logback-core-1.1.1-sources.jar">
+    <attributes>
+      <attribute value="jar:file:/home/t3903uhn/.m2/repository/ch/qos/logback/logback-core/1.1.1/logback-core-1.1.1-javadoc.jar!/" name="javadoc_location"/>
+    </attributes>
+  </classpathentry>
+</classpath>

restful-server-example/.project

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+  <name>restful-server-example</name>
+  <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
+  <projects/>
+  <buildSpec>
+    <buildCommand>
+      <name>org.eclipse.jdt.core.javabuilder</name>
+    </buildCommand>
+  </buildSpec>
+  <natures>
+    <nature>org.eclipse.jdt.core.javanature</nature>
+  </natures>
+</projectDescription>

restful-server-example/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+#Thu Apr 03 09:37:42 EDT 2014
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6

restful-server-example/pom.xml

@@ -0,0 +1,55 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<groupId>ca.uhn.hapi.example</groupId>
+	<artifactId>restful-server-example</artifactId>
+	<version>0.1</version>
+	<packaging>war</packaging>
+
+	<name>Sample RESTful Server</name>
+
+	<dependencies>
+
+		<!-- This dependency includes all neccesary HAPI FHIR classes -->
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>0.1</version>
+		</dependency>
+
+		<!-- HAPI-FHIR uses Logback for logging support. The logback library is 
+			included automatically by Maven as a part of the hapi-fhir-base dependency, 
+			but you also need to include a logging library. Logback is used here, but 
+			log4j would also be fine. -->
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<version>1.1.1</version>
+		</dependency>
+
+		<!-- Needed for JEE/Servlet support -->
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<version>3.0.1</version>
+			<scope>provided</scope>
+		</dependency>
+
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.1</version>
+				<configuration>
+					<source>1.6</source>
+					<target>1.6</target>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+	
+</project>

restful-server-example/src/main/java/ca/uhn/example/rest/ExampleRestfulServlet.java

@@ -0,0 +1,46 @@
+package ca.uhn.example.rest;
+
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.servlet.annotation.WebServlet;
+
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+
+/**
+ * In this example, we are using Servlet 3.0 annotations to define
+ * the URL pattern for this servlet, but we could also
+ * define this in a web.xml file.
+ */
+@WebServlet(urlPatterns= {"/fhir/*"}, displayName="FHIR Server")
+public class ExampleRestfulServlet extends RestfulServer {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Constructor
+	 */
+	public ExampleRestfulServlet() {
+		// Use a narrative generator
+		setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
+	}
+	
+	/**
+	 * Restful servers must provide an implementation of this method, which
+	 * returns all resource providers to be used by this server. In the example
+	 * below, we are creating a RESTful server which is able to serve
+	 * Patient and Observation resources.
+	 */
+	@Override
+	public Collection<IResourceProvider> getResourceProviders() {
+		List<IResourceProvider> retVal = new ArrayList<IResourceProvider>();
+		retVal.add(new RestfulPatientResourceProvider());
+		retVal.add(new RestfulObservationResourceProvider());
+		return retVal;
+	}
+
+}

restful-server-example/src/main/java/ca/uhn/example/rest/RestfulObservationResourceProvider.java

@@ -0,0 +1,88 @@
+package ca.uhn.example.rest;
+
+
+import java.util.Collections;
+import java.util.List;
+
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
+import ca.uhn.fhir.model.dstu.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+
+//START SNIPPET: provider
+/**
+ * All resource providers must implement IResourceProvider
+ */
+public class RestfulObservationResourceProvider implements IResourceProvider {
+
+	/**
+	 * The getResourceType method comes from IResourceProvider, and must
+	 * be overridden to indicate what type of resource this provider
+	 * supplies.
+	 */
+	@Override
+	public Class<Patient> getResourceType() {
+		return Patient.class;
+	}
+	
+	/**
+	 * The "@Read" annotation indicates that this method supports the
+	 * read operation. It takes one argument, the Resource type being returned. 
+	 * 
+	 * @param theId
+	 *    The read operation takes one parameter, which must be of type
+	 *    IdDt and must be annotated with the "@Read.IdParam" annotation.
+	 * @return 
+	 *    Returns a resource matching this identifier, or null if none exists.
+	 */
+	@Read()
+	public Patient getResourceById(@IdParam IdDt theId) {
+		Patient patient = new Patient();
+		patient.addIdentifier();
+		patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+		patient.getIdentifier().get(0).setValue("00002");
+		patient.addName().addFamily("Test");
+		patient.getName().get(0).addGiven("PatientOne");
+		patient.setGender(AdministrativeGenderCodesEnum.F);
+		return patient;
+	}
+
+	/**
+	 * The "@Search" annotation indicates that this method supports the 
+	 * search operation. You may have many different method annotated with 
+	 * this annotation, to support many different search criteria. This
+	 * example searches by family name.
+	 * 
+	 * @param theIdentifier
+	 *    This operation takes one parameter which is the search criteria. It is
+	 *    annotated with the "@Required" annotation. This annotation takes one argument,
+	 *    a string containing the name of the search criteria. The datatype here
+	 *    is StringDt, but there are other possible parameter types depending on the
+	 *    specific search criteria.
+	 * @return
+	 *    This method returns a list of Patients. This list may contain multiple
+	 *    matching resources, or it may also be empty.
+	 */
+	@Search()
+	public List<Patient> getPatient(@RequiredParam(name = Patient.SP_FAMILY) StringDt theFamilyName) {
+		Patient patient = new Patient();
+		patient.addIdentifier();
+		patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
+		patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+		patient.getIdentifier().get(0).setValue("00001");
+		patient.addName();
+		patient.getName().get(0).addFamily("Test");
+		patient.getName().get(0).addGiven("PatientOne");
+		patient.getGender().setText("M");
+		return Collections.singletonList(patient);
+	}
+
+}
+//END SNIPPET: provider

restful-server-example/src/main/java/ca/uhn/example/rest/RestfulPatientResourceProvider.java

@@ -0,0 +1,91 @@
+package ca.uhn.example.rest;
+
+
+import java.util.Collections;
+import java.util.List;
+
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
+import ca.uhn.fhir.model.dstu.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+
+//START SNIPPET: provider
+/**
+ * All resource providers must implement IResourceProvider
+ */
+public class RestfulPatientResourceProvider implements IResourceProvider {
+
+	/**
+	 * The getResourceType method comes from IResourceProvider, and must
+	 * be overridden to indicate what type of resource this provider
+	 * supplies.
+	 */
+	@Override
+	public Class<Patient> getResourceType() {
+		return Patient.class;
+	}
+	
+	/**
+	 * The "@Read" annotation indicates that this method supports the
+	 * read operation. Read operations should return a single resource
+	 * instance. 
+	 * 
+	 * @param theId
+	 *    The read operation takes one parameter, which must be of type
+	 *    IdDt and must be annotated with the "@Read.IdParam" annotation.
+	 * @return 
+	 *    Returns a resource matching this identifier, or null if none exists.
+	 */
+	@Read()
+	public Patient getResourceById(@IdParam IdDt theId) {
+		Patient patient = new Patient();
+		patient.addIdentifier();
+		patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+		patient.getIdentifier().get(0).setValue("00002");
+		patient.addName().addFamily("Test");
+		patient.getName().get(0).addGiven("PatientOne");
+		patient.setGender(AdministrativeGenderCodesEnum.F);
+		return patient;
+	}
+
+	/**
+	 * The "@Search" annotation indicates that this method supports the 
+	 * search operation. You may have many different method annotated with 
+	 * this annotation, to support many different search criteria. This
+	 * example searches by family name.
+	 * 
+	 * @param theIdentifier
+	 *    This operation takes one parameter which is the search criteria. It is
+	 *    annotated with the "@Required" annotation. This annotation takes one argument,
+	 *    a string containing the name of the search criteria. The datatype here
+	 *    is StringDt, but there are other possible parameter types depending on the
+	 *    specific search criteria.
+	 * @return
+	 *    This method returns a list of Patients. This list may contain multiple
+	 *    matching resources, or it may also be empty.
+	 */
+	@Search()
+	public List<Patient> getPatient(@RequiredParam(name = Patient.SP_FAMILY) StringDt theFamilyName) {
+		Patient patient = new Patient();
+		patient.addIdentifier();
+		patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
+		patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+		patient.getIdentifier().get(0).setValue("00001");
+		patient.addName();
+		patient.getName().get(0).addFamily(theFamilyName.getValue());
+		patient.getName().get(0).addGiven("PatientOne");
+		patient.getGender().setText("M");
+		return Collections.singletonList(patient);
+	}
+
+}
+//END SNIPPET: provider
+
+

restful-server-example/src/main/webapp/WEB-INF/web-app_3_0.xsd

@@ -0,0 +1,272 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
+            targetNamespace="http://java.sun.com/xml/ns/javaee"
+            xmlns:javaee="http://java.sun.com/xml/ns/javaee"
+            xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+            elementFormDefault="qualified"
+            attributeFormDefault="unqualified"
+            version="3.0">
+  <xsd:annotation>
+    <xsd:documentation>
+
+      DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+      
+      Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
+      
+      The contents of this file are subject to the terms of either the
+      GNU General Public License Version 2 only ("GPL") or the Common
+      Development and Distribution License("CDDL") (collectively, the
+      "License").  You may not use this file except in compliance with
+      the License. You can obtain a copy of the License at
+      https://glassfish.dev.java.net/public/CDDL+GPL.html or
+      glassfish/bootstrap/legal/LICENSE.txt.  See the License for the
+      specific language governing permissions and limitations under the
+      License.
+      
+      When distributing the software, include this License Header
+      Notice in each file and include the License file at
+      glassfish/bootstrap/legal/LICENSE.txt.  Sun designates this
+      particular file as subject to the "Classpath" exception as
+      provided by Sun in the GPL Version 2 section of the License file
+      that accompanied this code.  If applicable, add the following
+      below the License Header, with the fields enclosed by brackets []
+      replaced by your own identifying information:
+      "Portions Copyrighted [year] [name of copyright owner]"
+      
+      Contributor(s):
+      
+      If you wish your version of this file to be governed by only the
+      CDDL or only the GPL Version 2, indicate your decision by adding
+      "[Contributor] elects to include this software in this
+      distribution under the [CDDL or GPL Version 2] license."  If you
+      don't indicate a single choice of license, a recipient has the
+      option to distribute your version of this file under either the
+      CDDL, the GPL Version 2 or to extend the choice of license to its
+      licensees as provided above.  However, if you add GPL Version 2
+      code and therefore, elected the GPL Version 2 license, then the
+      option applies only if the new code is made subject to such
+      option by the copyright holder.
+      
+    </xsd:documentation>
+  </xsd:annotation>
+
+  <xsd:annotation>
+    <xsd:documentation>
+      <![CDATA[[
+      This is the XML Schema for the Servlet 3.0 deployment descriptor.
+      The deployment descriptor must be named "WEB-INF/web.xml" in the
+      web application's war file.  All Servlet deployment descriptors
+      must indicate the web application schema by using the Java EE
+      namespace:
+      
+      http://java.sun.com/xml/ns/javaee 
+      
+      and by indicating the version of the schema by 
+      using the version element as shown below: 
+      
+      <web-app xmlns="http://java.sun.com/xml/ns/javaee"
+      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+      xsi:schemaLocation="..."
+      version="3.0"> 
+      ...
+      </web-app>
+      
+      The instance documents may indicate the published version of
+      the schema using the xsi:schemaLocation attribute for Java EE
+      namespace with the following location:
+      
+      http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd
+      
+      ]]>
+    </xsd:documentation>
+  </xsd:annotation>
+
+  <xsd:annotation>
+    <xsd:documentation>
+
+      The following conventions apply to all Java EE
+      deployment descriptor elements unless indicated otherwise.
+      
+      - In elements that specify a pathname to a file within the
+      same JAR file, relative filenames (i.e., those not
+      starting with "/") are considered relative to the root of
+      the JAR file's namespace.  Absolute filenames (i.e., those
+      starting with "/") also specify names in the root of the
+      JAR file's namespace.  In general, relative names are
+      preferred.  The exception is .war files where absolute
+      names are preferred for consistency with the Servlet API.
+      
+    </xsd:documentation>
+  </xsd:annotation>
+
+  <xsd:include schemaLocation="web-common_3_0.xsd"/>
+
+
+<!-- **************************************************** -->
+
+  <xsd:element name="web-app"
+               type="javaee:web-appType">
+    <xsd:annotation>
+      <xsd:documentation>
+
+        The web-app element is the root of the deployment
+        descriptor for a web application.  Note that the sub-elements
+        of this element can be in the arbitrary order. Because of
+        that, the multiplicity of the elements of distributable,
+        session-config, welcome-file-list, jsp-config, login-config,
+        and locale-encoding-mapping-list was changed from "?" to "*"
+        in this schema.  However, the deployment descriptor instance
+        file must not contain multiple elements of session-config,
+        jsp-config, and login-config. When there are multiple elements of
+        welcome-file-list or locale-encoding-mapping-list, the container
+        must concatenate the element contents.  The multiple occurence
+        of the element distributable is redundant and the container
+        treats that case exactly in the same way when there is only
+        one distributable. 
+        
+      </xsd:documentation>
+    </xsd:annotation>
+    <xsd:unique name="web-common-servlet-name-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The servlet element contains the name of a servlet.
+          The name must be unique within the web application.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:servlet"/>
+      <xsd:field xpath="javaee:servlet-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-filter-name-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The filter element contains the name of a filter.
+          The name must be unique within the web application.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:filter"/>
+      <xsd:field xpath="javaee:filter-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-ejb-local-ref-name-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The ejb-local-ref-name element contains the name of an EJB
+          reference. The EJB reference is an entry in the web
+          application's environment and is relative to the
+          java:comp/env context.  The name must be unique within
+          the web application.
+          
+          It is recommended that name is prefixed with "ejb/".
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:ejb-local-ref"/>
+      <xsd:field xpath="javaee:ejb-ref-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-ejb-ref-name-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The ejb-ref-name element contains the name of an EJB
+          reference. The EJB reference is an entry in the web
+          application's environment and is relative to the
+          java:comp/env context.  The name must be unique within
+          the web application.
+          
+          It is recommended that name is prefixed with "ejb/".
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:ejb-ref"/>
+      <xsd:field xpath="javaee:ejb-ref-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-resource-env-ref-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The resource-env-ref-name element specifies the name of
+          a resource environment reference; its value is the
+          environment entry name used in the web application code.
+          The name is a JNDI name relative to the java:comp/env
+          context and must be unique within a web application.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:resource-env-ref"/>
+      <xsd:field xpath="javaee:resource-env-ref-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-message-destination-ref-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The message-destination-ref-name element specifies the name of
+          a message destination reference; its value is the
+          environment entry name used in the web application code.
+          The name is a JNDI name relative to the java:comp/env
+          context and must be unique within a web application.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:message-destination-ref"/>
+      <xsd:field xpath="javaee:message-destination-ref-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-res-ref-name-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The res-ref-name element specifies the name of a
+          resource manager connection factory reference.  The name
+          is a JNDI name relative to the java:comp/env context.
+          The name must be unique within a web application.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:resource-ref"/>
+      <xsd:field xpath="javaee:res-ref-name"/>
+    </xsd:unique>
+    <xsd:unique name="web-common-env-entry-name-uniqueness">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The env-entry-name element contains the name of a web
+          application's environment entry.  The name is a JNDI
+          name relative to the java:comp/env context.  The name
+          must be unique within a web application.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:env-entry"/>
+      <xsd:field xpath="javaee:env-entry-name"/>
+    </xsd:unique>
+    <xsd:key name="web-common-role-name-key">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          A role-name-key is specified to allow the references
+          from the security-role-refs.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:security-role"/>
+      <xsd:field xpath="javaee:role-name"/>
+    </xsd:key>
+    <xsd:keyref name="web-common-role-name-references"
+                refer="javaee:web-common-role-name-key">
+      <xsd:annotation>
+        <xsd:documentation>
+
+          The keyref indicates the references from
+          security-role-ref to a specified role-name.
+          
+        </xsd:documentation>
+      </xsd:annotation>
+      <xsd:selector xpath="javaee:servlet/javaee:security-role-ref"/>
+      <xsd:field xpath="javaee:role-link"/>
+    </xsd:keyref>
+  </xsd:element>
+
+</xsd:schema>

restful-server-example/src/main/webapp/WEB-INF/web.xml

@@ -0,0 +1,12 @@
+<web-app 
+	xmlns="http://java.sun.com/xml/ns/javaee" 
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+	version="3.0" 
+	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./web-app_3_0.xsd">
+
+	<!-- 
+	Nothing needs to be here, since the servlet class contains
+	annotations describing its mapping.
+	 -->
+
+</web-app>

restful-server-example/target/.gitignore

@@ -0,0 +1 @@
+/classes