Update to final STU3 ballot definitions

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java

@@ -79,7 +79,7 @@ private ValueSet doExpand(ValueSet theSource) {
 
 		HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
 
-		ValueSetExpansionOutcome outcome = workerContext.expand(theSource);
+		ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
 
 		ValueSet retVal = outcome.getValueset();
 		retVal.setStatus(ConformanceResourceStatus.ACTIVE);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java

@@ -271,7 +271,7 @@ public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
 			ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
 
 			HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
-			ValueSetExpansionOutcome outcome = worker.expand(source);
+			ValueSetExpansionOutcome outcome = worker.expand(source, null);
 			for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
 				retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
 			}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -771,7 +771,7 @@ public void testSearchCodeInValueSetThatImportsInvalidCodeSystem() {
 		try {
 			myObservationDao.search(params);
 		} catch(InvalidRequestException e) {
-			assertEquals("Unable to expand imported value set \"http://example.com/my_value_set\" - Error was: Unable to find imported value set http://non_existant_VS", e.getMessage());
+			assertEquals("Unable to expand imported value set: Unable to find imported value set http://non_existant_VS", e.getMessage());
 		}
 
 		// Now let's update 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/HapiWorkerContext.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.dstu3.hapi.validation;
 
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -19,6 +21,7 @@
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.ConceptMap;
+import org.hl7.fhir.dstu3.model.ExpansionProfile;
 import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.ResourceType;
@@ -34,6 +37,7 @@
 import org.hl7.fhir.dstu3.utils.INarrativeGenerator;
 import org.hl7.fhir.dstu3.utils.IWorkerContext;
 import org.hl7.fhir.dstu3.validation.IResourceValidator;
+import org.hl7.fhir.exceptions.TerminologyServiceException;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -44,6 +48,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
 	private final FhirContext myCtx;
 	private Map<String, Resource> myFetchedResourceCache = new HashMap<String, Resource>();
 	private IValidationSupport myValidationSupport;
+	private ExpansionProfile myExpansionProfile;
 
 	public HapiWorkerContext(FhirContext theCtx, IValidationSupport theValidationSupport) {
 		Validate.notNull(theCtx, "theCtx must not be null");
@@ -57,33 +62,6 @@ public List<StructureDefinition> allStructures() {
 		return myValidationSupport.fetchAllStructureDefinitions(myCtx);
 	}
 
-	@Override
-	public ValueSetExpansionOutcome expand(ValueSet theSource) {
-		ValueSetExpansionOutcome vso;
-		try {
-			vso = getExpander().expand(theSource);
-		} catch (InvalidRequestException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new InternalErrorException(e);
-		}
-		if (vso.getError() != null) {
-			throw new InvalidRequestException(vso.getError());
-		} else {
-			return vso;
-		}
-	}
-
-	@Override
-	public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc) {
-		return myValidationSupport.expandValueSet(myCtx, theInc);
-	}
-
-	@Override
-	public ValueSetExpansionOutcome expandVS(ValueSet theSource, boolean theCacheOk) {
-		throw new UnsupportedOperationException();
-	}
-
 	@Override
 	public CodeSystem fetchCodeSystem(String theSystem) {
 		if (myValidationSupport == null) {
@@ -275,7 +253,7 @@ public ValidationResult validateCode(String theSystem, String theCode, String th
 		// }
 
 		if (expandedValueSet == null) {
-			expandedValueSet = expand(theVs);
+			expandedValueSet = expand(theVs, null);
 		}
 
 		for (ValueSetExpansionContainsComponent next : expandedValueSet.getValueset().getExpansion().getContains()) {
@@ -335,4 +313,46 @@ public boolean hasCache() {
 		throw new UnsupportedOperationException();
 	}
 
+	@Override
+	public ValueSetExpansionOutcome expand(ValueSet theSource, ExpansionProfile theProfile) {
+		ValueSetExpansionOutcome vso;
+		try {
+			vso = getExpander().expand(theSource, theProfile);
+		} catch (InvalidRequestException e) {
+			throw e;
+		} catch (Exception e) {
+			throw new InternalErrorException(e);
+		}
+		if (vso.getError() != null) {
+			throw new InvalidRequestException(vso.getError());
+		} else {
+			return vso;
+		}
+	}
+
+	@Override
+	public ExpansionProfile getExpansionProfile() {
+		return myExpansionProfile;
+	}
+
+	@Override
+	public void setExpansionProfile(ExpansionProfile theExpProfile) {
+		myExpansionProfile = theExpProfile;
+	}
+
+	@Override
+	public ValueSetExpansionOutcome expandVS(ValueSet theSource, boolean theCacheOk, boolean theHeiarchical) {
+		throw new UnsupportedOperationException();
+	}
+
+	@Override
+	public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc, boolean theHeiarchical) throws TerminologyServiceException {
+		return myValidationSupport.expandValueSet(myCtx, theInc);
+	}
+
+	@Override
+	public void setLogger(ILoggingService theLogger) {
+		throw new UnsupportedOperationException();
+	}
+
 }

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Account.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/ActivityDefinition.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Address.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Age.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/AllergyIntolerance.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 
@@ -301,6 +301,10 @@ public enum AllergyIntoleranceCategory {
          * Substances administered to achieve a physiological effect.
          */
         MEDICATION, 
+        /**
+         * A preparation that is synthesized from living organisms or their products, especially a human or animal protein, such as a hormone or antitoxin, that is used as a diagnostic, preventive, or therapeutic agent. Also called biological drug.  Examples of biological products include: vaccines; blood and blood products for transfusion and/or manufacturing into other products; allergenic extracts, which are used for both diagnosis and treatment (for example, allergy shots); human cells and tissues used for transplantation (for example, tendons, ligaments and bone); gene therapies; cellular therapies; tests to screen potential blood donors for infectious agents such as HIV.
+         */
+        BIOLOGIC, 
         /**
          * Substances that are encountered in the environment.
          */
@@ -316,6 +320,8 @@ public static AllergyIntoleranceCategory fromCode(String codeString) throws FHIR
           return FOOD;
         if ("medication".equals(codeString))
           return MEDICATION;
+        if ("biologic".equals(codeString))
+          return BIOLOGIC;
         if ("environment".equals(codeString))
           return ENVIRONMENT;
         if (Configuration.isAcceptInvalidEnums())
@@ -327,6 +333,7 @@ public String toCode() {
           switch (this) {
             case FOOD: return "food";
             case MEDICATION: return "medication";
+            case BIOLOGIC: return "biologic";
             case ENVIRONMENT: return "environment";
             default: return "?";
           }
@@ -335,6 +342,7 @@ public String getSystem() {
           switch (this) {
             case FOOD: return "http://hl7.org/fhir/allergy-intolerance-category";
             case MEDICATION: return "http://hl7.org/fhir/allergy-intolerance-category";
+            case BIOLOGIC: return "http://hl7.org/fhir/allergy-intolerance-category";
             case ENVIRONMENT: return "http://hl7.org/fhir/allergy-intolerance-category";
             default: return "?";
           }
@@ -343,6 +351,7 @@ public String getDefinition() {
           switch (this) {
             case FOOD: return "Any substance consumed to provide nutritional support for the body.";
             case MEDICATION: return "Substances administered to achieve a physiological effect.";
+            case BIOLOGIC: return "A preparation that is synthesized from living organisms or their products, especially a human or animal protein, such as a hormone or antitoxin, that is used as a diagnostic, preventive, or therapeutic agent. Also called biological drug.  Examples of biological products include: vaccines; blood and blood products for transfusion and/or manufacturing into other products; allergenic extracts, which are used for both diagnosis and treatment (for example, allergy shots); human cells and tissues used for transplantation (for example, tendons, ligaments and bone); gene therapies; cellular therapies; tests to screen potential blood donors for infectious agents such as HIV.";
             case ENVIRONMENT: return "Substances that are encountered in the environment.";
             default: return "?";
           }
@@ -351,6 +360,7 @@ public String getDisplay() {
           switch (this) {
             case FOOD: return "Food";
             case MEDICATION: return "Medication";
+            case BIOLOGIC: return "Biologic";
             case ENVIRONMENT: return "Environment";
             default: return "?";
           }
@@ -366,6 +376,8 @@ public AllergyIntoleranceCategory fromCode(String codeString) throws IllegalArgu
           return AllergyIntoleranceCategory.FOOD;
         if ("medication".equals(codeString))
           return AllergyIntoleranceCategory.MEDICATION;
+        if ("biologic".equals(codeString))
+          return AllergyIntoleranceCategory.BIOLOGIC;
         if ("environment".equals(codeString))
           return AllergyIntoleranceCategory.ENVIRONMENT;
         throw new IllegalArgumentException("Unknown AllergyIntoleranceCategory code '"+codeString+"'");
@@ -380,6 +392,8 @@ public Enumeration<AllergyIntoleranceCategory> fromType(Base code) throws FHIREx
           return new Enumeration<AllergyIntoleranceCategory>(this, AllergyIntoleranceCategory.FOOD);
         if ("medication".equals(codeString))
           return new Enumeration<AllergyIntoleranceCategory>(this, AllergyIntoleranceCategory.MEDICATION);
+        if ("biologic".equals(codeString))
+          return new Enumeration<AllergyIntoleranceCategory>(this, AllergyIntoleranceCategory.BIOLOGIC);
         if ("environment".equals(codeString))
           return new Enumeration<AllergyIntoleranceCategory>(this, AllergyIntoleranceCategory.ENVIRONMENT);
         throw new FHIRException("Unknown AllergyIntoleranceCategory code '"+codeString+"'");
@@ -389,6 +403,8 @@ public String toCode(AllergyIntoleranceCategory code) {
         return "food";
       if (code == AllergyIntoleranceCategory.MEDICATION)
         return "medication";
+      if (code == AllergyIntoleranceCategory.BIOLOGIC)
+        return "biologic";
       if (code == AllergyIntoleranceCategory.ENVIRONMENT)
         return "environment";
       return "?";
@@ -1352,7 +1368,7 @@ public String fhirType() {
      * Category of the identified substance.
      */
     @Child(name = "category", type = {CodeType.class}, order=3, min=0, max=1, modifier=false, summary=true)
-    @Description(shortDefinition="food | medication | environment", formalDefinition="Category of the identified substance." )
+    @Description(shortDefinition="food | medication | biologic | environment", formalDefinition="Category of the identified substance." )
     @ca.uhn.fhir.model.api.annotation.Binding(valueSet="http://hl7.org/fhir/ValueSet/allergy-intolerance-category")
     protected Enumeration<AllergyIntoleranceCategory> category;
 
@@ -2645,17 +2661,17 @@ public ResourceType getResourceType() {
  /**
    * Search parameter: <b>category</b>
    * <p>
-   * Description: <b>food | medication | environment</b><br>
+   * Description: <b>food | medication | biologic | environment</b><br>
    * Type: <b>token</b><br>
    * Path: <b>AllergyIntolerance.category</b><br>
    * </p>
    */
-  @SearchParamDefinition(name="category", path="AllergyIntolerance.category", description="food | medication | environment", type="token" )
+  @SearchParamDefinition(name="category", path="AllergyIntolerance.category", description="food | medication | biologic | environment", type="token" )
   public static final String SP_CATEGORY = "category";
  /**
    * <b>Fluent Client</b> search parameter constant for <b>category</b>
    * <p>
-   * Description: <b>food | medication | environment</b><br>
+   * Description: <b>food | medication | biologic | environment</b><br>
    * Type: <b>token</b><br>
    * Path: <b>AllergyIntolerance.category</b><br>
    * </p>

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Annotation.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Appointment.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/AppointmentResponse.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Attachment.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/AuditEvent.java

@@ -29,7 +29,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
   
 */
 
-// Generated on Wed, Aug 3, 2016 09:39-0400 for FHIR v1.5.0
+// Generated on Thu, Aug 25, 2016 23:04-0400 for FHIR v1.6.0
 
 import java.util.*;