Bring DSTU3 structs up to FHIR R3

Squashed commit of the following:

commit 65b70d3
Author: James <[email protected]>
Date:   Tue Apr 18 07:44:08 2017 -0400

    More work on bringing structs up to date

commit 1df2de0
Author: James <[email protected]>
Date:   Tue Apr 18 07:12:45 2017 -0400

    Working

commit 9a51323
Author: James <[email protected]>
Date:   Mon Apr 17 22:18:24 2017 -0400

    Updates to STU3

commit 40aebba
Author: James <[email protected]>
Date:   Mon Apr 17 18:30:26 2017 -0400

    Fix regression caused by #610

Author: jamesagnew

examples/src/main/java/example/ConverterExamples.java

@@ -2,8 +2,8 @@
 
 import org.hl7.fhir.convertors.NullVersionConverterAdvisor;
 import org.hl7.fhir.convertors.VersionConvertorAdvisor;
-import org.hl7.fhir.convertors.VersionConvertor_10_20;
-import org.hl7.fhir.convertors.VersionConvertor_14_20;
+import org.hl7.fhir.convertors.VersionConvertor_10_30;
+import org.hl7.fhir.convertors.VersionConvertor_14_30;
 import org.hl7.fhir.exceptions.FHIRException;
 
 public class ConverterExamples {
@@ -13,7 +13,7 @@ public void c1020() throws FHIRException {
 	//START SNIPPET: 1020
 		// Create a converter
 		VersionConvertorAdvisor advisor = new NullVersionConverterAdvisor();
-		VersionConvertor_10_20 converter = new VersionConvertor_10_20(advisor);
+		VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
 
 		// Create an input resource to convert
 		org.hl7.fhir.instance.model.Observation input = new org.hl7.fhir.instance.model.Observation();
@@ -33,7 +33,7 @@ public void c1420() throws FHIRException {
 		input.setTitle("My title");
 
 		// Convert the resource
-		org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_20.convertQuestionnaire(input);
+		org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
 		String context = output.getTitle();
 	//END SNIPPET: 1420
 	}

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

@@ -82,6 +82,7 @@ public class FhirContext {
 	private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<String, Class<? extends IBaseResource>>();
 	private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
 	private boolean myInitialized;
+	private boolean myInitializing = false;
 	private HapiLocalizer myLocalizer = new HapiLocalizer();
 	private volatile Map<String, BaseRuntimeElementDefinition<?>> myNameToElementDefinition = Collections.emptyMap();
 	private volatile Map<String, RuntimeResourceDefinition> myNameToResourceDefinition = Collections.emptyMap();
@@ -94,6 +95,7 @@ public class FhirContext {
 	private volatile IRestfulClientFactory myRestfulClientFactory;
 	private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
 	private IContextValidationSupport<?, ?, ?, ?, ?, ?> myValidationSupport;
+
 	private final IFhirVersion myVersion;
 
 	private Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> myVersionToNameToResourceType = Collections.emptyMap();
@@ -384,15 +386,6 @@ public RuntimeResourceDefinition getResourceDefinition(String theResourceName) {
 		return retVal;
 	}
 
-	/**
-	 * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
-	 * for extending the core library.
-	 */
-	public RuntimeResourceDefinition getResourceDefinitionById(String theId) {
-		validateInitialized();
-		return myIdToResourceDefinition.get(theId);
-	}
-
 	// /**
 	// * Return an unmodifiable collection containing all known resource definitions
 	// */
@@ -407,6 +400,15 @@ public RuntimeResourceDefinition getResourceDefinitionById(String theId) {
 	// return Collections.unmodifiableCollection(myIdToResourceDefinition.values());
 	// }
 
+	/**
+	 * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
+	 * for extending the core library.
+	 */
+	public RuntimeResourceDefinition getResourceDefinitionById(String theId) {
+		validateInitialized();
+		return myIdToResourceDefinition.get(theId);
+	}
+
 	/**
 	 * Returns the scanned runtime models. This is an advanced feature which is generally only needed for extending the
 	 * core library.
@@ -842,12 +844,13 @@ private List<Class<? extends IElement>> toElementList(Collection<Class<? extends
 		}
 		return resTypes;
 	}
-
+	
 	private void validateInitialized() {
 		// See #610
 		if (!myInitialized) {
 			synchronized (this) {
-				if (!myInitialized) {
+				if (!myInitialized && !myInitializing) {
+					myInitializing = true;
 					scanResourceTypes(toElementList(myResourceTypesToScan));
 				}
 			}

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

@@ -1817,6 +1817,20 @@ public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource
 				 * See #327 
 				 */
 				List<? extends IBase> preProcessedValue = preProcessValues(myDef, theResource, Collections.singletonList(myValue), myChildElem);
+
+//				// Check for undeclared extensions on the declared extension
+//				// (grrrrrr....)
+//				if (myValue instanceof ISupportsUndeclaredExtensions) {
+//					ISupportsUndeclaredExtensions value = (ISupportsUndeclaredExtensions)myValue;
+//					List<ExtensionDt> exts = value.getUndeclaredExtensions();
+//					if (exts.size() > 0) {
+//						ArrayList<IBase> newValueList = new ArrayList<IBase>();
+//						newValueList.addAll(preProcessedValue);
+//						newValueList.addAll(exts);
+//						preProcessedValue = newValueList;
+//					}
+//				}
+				
 				myValue = preProcessedValue.get(0);
 
 				BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertorAdvisor.java

@@ -1,38 +1,17 @@
-package org.hl7.fhir.convertors;
-
-/*
- * #%L
- * HAPI FHIR - Converter
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-import org.hl7.fhir.dstu3.model.CodeSystem;
-import org.hl7.fhir.dstu3.model.ValueSet;
-import org.hl7.fhir.exceptions.FHIRException;
-
-public interface VersionConvertorAdvisor {
-  boolean ignoreEntry(org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent src);
-
-  // called ?
-  org.hl7.fhir.instance.model.Resource convert(org.hl7.fhir.dstu3.model.Resource resource) throws FHIRException;
-
-  // called when an r2 value set has a codeSystem in it
-  void handleCodeSystem(CodeSystem tgtcs, ValueSet source);
-
-  CodeSystem getCodeSystem(ValueSet src);
-}
+package org.hl7.fhir.convertors;
+
+import org.hl7.fhir.dstu3.model.CodeSystem;
+import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.exceptions.FHIRException;
+
+public interface VersionConvertorAdvisor {
+  boolean ignoreEntry(org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent src);
+
+  // called ?
+  org.hl7.fhir.instance.model.Resource convert(org.hl7.fhir.dstu3.model.Resource resource) throws FHIRException;
+
+  // called when an r2 value set has a codeSystem in it
+  void handleCodeSystem(CodeSystem tgtcs, ValueSet source);
+
+  CodeSystem getCodeSystem(ValueSet src);
+}