Work on multitype extensions

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

@@ -216,18 +216,6 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
 			orderToElementDef = newOrderToExtensionDef;
 		}
 		
-		// while (orderToElementDef.size() > 0 && orderToElementDef.firstKey() <
-		// 0) {
-		// BaseRuntimeDeclaredChildDefinition elementDef =
-		// orderToElementDef.remove(orderToElementDef.firstKey());
-		// if (elementDef.getElementName().equals("identifier")) {
-		// orderToElementDef.put(theIdentifierOrder, elementDef);
-		// } else {
-		// throw new ConfigurationException("Don't know how to handle element: "
-		// + elementDef.getElementName());
-		// }
-		// }
-
 		TreeSet<Integer> orders = new TreeSet<Integer>();
 		orders.addAll(orderToElementDef.keySet());
 		orders.addAll(orderToExtensionDef.keySet());
@@ -372,7 +360,7 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
 				def = new RuntimeChildDirectResource(nextField, childAnnotation, descriptionAnnotation, elementName);
 			} else {
 				childIsChoiceType |= choiceTypes.size() > 1;
-				if (childIsChoiceType && !BaseResourceReferenceDt.class.isAssignableFrom(nextElementType) && !IBaseReference.class.isAssignableFrom(nextElementType)) {
+				if (extensionAttr == null && childIsChoiceType && !BaseResourceReferenceDt.class.isAssignableFrom(nextElementType) && !IBaseReference.class.isAssignableFrom(nextElementType)) {
 					def = new RuntimeChildChoiceDefinition(nextField, elementName, childAnnotation, descriptionAnnotation, choiceTypes);
 				} else if (extensionAttr != null) {
 					/*

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

@@ -38,6 +38,9 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
 	private String myReferenceSuffix;
 	private List<Class<? extends IBaseResource>> myResourceTypes;
 
+	/**
+	 * Constructor
+	 */
 	public RuntimeChildChoiceDefinition(Field theField, String theElementName, Child theChildAnnotation, Description theDescriptionAnnotation, List<Class<? extends IBase>> theChoiceTypes) {
 		super(theField, theChildAnnotation, theDescriptionAnnotation, theElementName);
 
@@ -45,6 +48,8 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
 	}
 
 	/**
+	 * Constructor
+	 * 
 	 * For extension, if myChoiceTypes will be set some other way
 	 */
 	RuntimeChildChoiceDefinition(Field theField, String theElementName, Child theChildAnnotation, Description theDescriptionAnnotation) {

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

@@ -22,32 +22,26 @@ package ca.uhn.fhir.context;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.lang.reflect.Field;
-import java.util.ArrayList;
+import java.lang.reflect.Modifier;
-import java.util.Collections;
+import java.util.*;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
 
 import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 
-import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.api.annotation.Extension;
 
-public class RuntimeChildDeclaredExtensionDefinition extends BaseRuntimeDeclaredChildDefinition {
+public class RuntimeChildDeclaredExtensionDefinition extends RuntimeChildChoiceDefinition {
 
-	private BaseRuntimeElementDefinition<?> myChildDef;
-	private Class<? extends IBase> myChildType;
-	private String myDatatypeChildName;
 	private boolean myDefinedLocally;
 	private String myExtensionUrl;
 	private boolean myModifier;
 	private Map<String, RuntimeChildDeclaredExtensionDefinition> myUrlToChildExtension;
 	private volatile Object myInstanceConstructorArguments;
 	private Class<?> myEnumerationType;
+	private Class<? extends IBase> myChildType;
+	private RuntimeResourceBlockDefinition myChildResourceBlock;
 
 	/**
 	 * @param theBoundTypeBinder
@@ -56,15 +50,25 @@ public class RuntimeChildDeclaredExtensionDefinition extends BaseRuntimeDeclared
 	 * @param theDefinedLocally
 	 *            See {@link Extension#definedLocally()}
 	 */
+	@SuppressWarnings("unchecked")
 	RuntimeChildDeclaredExtensionDefinition(Field theField, Child theChild, Description theDescriptionAnnotation, Extension theExtension, String theElementName, String theExtensionUrl, Class<? extends IBase> theChildType, Object theBoundTypeBinder)
 			throws ConfigurationException {
-		super(theField, theChild, theDescriptionAnnotation, theElementName);
+		super(theField, theElementName, theChild, theDescriptionAnnotation);
 		assert isNotBlank(theExtensionUrl);
 		myExtensionUrl = theExtensionUrl;
 		myChildType = theChildType;
 		myDefinedLocally = theExtension.definedLocally();
 		myModifier = theExtension.isModifier();
 		myInstanceConstructorArguments = theBoundTypeBinder;
+		
+		List<Class<? extends IBase>> choiceTypes = new ArrayList<Class<? extends IBase>>();
+		for (Class<? extends IElement> next : theChild.type()) {
+			choiceTypes.add(next);
+		}
+		if (Modifier.isAbstract(theField.getType().getModifiers()) == false) {
+			choiceTypes.add((Class<? extends IBase>) theField.getType());
+		}
+		setChoiceTypes(choiceTypes);
 	}
 
 	@Override
@@ -82,57 +86,49 @@ public class RuntimeChildDeclaredExtensionDefinition extends BaseRuntimeDeclared
 	}
 
 	@Override
-	public BaseRuntimeElementDefinition<?> getChildByName(String theName) {
+	public String getChildNameByDatatype(Class<? extends IBase> theDatatype) {
-		if (myDatatypeChildName != null) {
+		String retVal = super.getChildNameByDatatype(theDatatype);
-			if (myDatatypeChildName.equals(theName)) {
+		if (retVal == null) {
-				return myChildDef;
+			if (myModifier) {
+				return "modifierExtension";
 			}else {
-				return null;
+				return "extension";
 			}
-		} else {
-			return null;
 		}
+		return retVal;
 	}
 
 	@Override
-	public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IBase> theType) {
+	public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IBase> theDatatype) {
-		if (myChildType.equals(theType)) {
+		if (myChildResourceBlock != null) {
-			return myChildDef;
+			if (myChildResourceBlock.getImplementingClass().equals(theDatatype)) {
+				return myChildResourceBlock;
 			}
-		return null;
+		}
+		return super.getChildElementDefinitionByDatatype(theDatatype);
 	}
 
 	public RuntimeChildDeclaredExtensionDefinition getChildExtensionForUrl(String theUrl) {
 		return myUrlToChildExtension.get(theUrl);
 	}
 
-	@Override
+//	@Override
-	public String getChildNameByDatatype(Class<? extends IBase> theDatatype) {
+//	public String getChildNameByDatatype(Class<? extends IBase> theDatatype) {
-		if (myChildType.equals(theDatatype) && myDatatypeChildName != null) {
+//		String retVal = super.getChildNameByDatatype(theDatatype);
-			return myDatatypeChildName;
+//		if (retVal )
-		} else {
+//		if (myChildType.equals(theDatatype) && myDatatypeChildName != null) {
-			return "extension";
+//			return myDatatypeChildName;
-		}
+//		} else {
-	}
+//			return "extension";
+//		}
+//	}
 
-	public Class<? extends IBase> getChildType() {
-		return myChildType;
-	}
 
 	@Override
 	public String getExtensionUrl() {
 		return myExtensionUrl;
 	}
 
-	@Override
-	public BaseRuntimeElementDefinition<?> getSingleChildOrThrow() {
-		return myChildDef;
-	}
-
-	@Override
-	public Set<String> getValidChildNames() {
-		return Collections.emptySet();
-	}
 
 	public boolean isDefinedLocally() {
 		return myDefinedLocally;
@@ -143,15 +139,6 @@ public class RuntimeChildDeclaredExtensionDefinition extends BaseRuntimeDeclared
 		return myModifier;
 	}
 
-	public IBase newInstance() {
-		try {
-			return myChildType.newInstance();
-		} catch (InstantiationException e) {
-			throw new ConfigurationException("Failed to instantiate type:" + myChildType.getName(), e);
-		} catch (IllegalAccessException e) {
-			throw new ConfigurationException("Failed to instantiate type:" + myChildType.getName(), e);
-		}
-	}
 
 	@Override
 	void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
@@ -164,29 +151,22 @@ public class RuntimeChildDeclaredExtensionDefinition extends BaseRuntimeDeclared
 		 * built-in types, e.g. custom structures or custom extensions
 		 */
 		if (elementDef == null) {
+			if (Modifier.isAbstract(myChildType.getModifiers()) == false) {
 				elementDef = theContext.getElementDefinition(myChildType);
 			}
-		
-		if (elementDef instanceof RuntimePrimitiveDatatypeDefinition || elementDef instanceof RuntimeCompositeDatatypeDefinition) {
-			myDatatypeChildName = "value" + elementDef.getName().substring(0, 1).toUpperCase() + elementDef.getName().substring(1);
-			if ("valueResourceReference".equals(myDatatypeChildName)) {
-				// Per one of the examples here: http://hl7.org/implement/standards/fhir/extensibility.html#extension
-				myDatatypeChildName = "valueResource";
-				List<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
-				types.add(IResource.class);
-				myChildDef = findResourceReferenceDefinition(theClassToElementDefinitions);
-			} else {
-				myChildDef = elementDef;
 		}
-		} else {
+		
+		if (elementDef instanceof RuntimeResourceBlockDefinition) {
 			RuntimeResourceBlockDefinition extDef = ((RuntimeResourceBlockDefinition) elementDef);
 			for (RuntimeChildDeclaredExtensionDefinition next : extDef.getExtensions()) {
 				myUrlToChildExtension.put(next.getExtensionUrl(), next);
 			}
-			myChildDef = extDef;
+			myChildResourceBlock = (RuntimeResourceBlockDefinition)elementDef;
 		}
 
 		myUrlToChildExtension = Collections.unmodifiableMap(myUrlToChildExtension);
+		
+		super.sealAndInitialize(theContext, theClassToElementDefinitions);
 	}
 
 }

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

@@ -1487,7 +1487,8 @@ class ParserState<T> {
 			RuntimeChildDeclaredExtensionDefinition declaredExtension = myDefinition.getChildExtensionForUrl(theUrlAttr);
 			if (declaredExtension != null) {
 				if (myChildInstance == null) {
-					myChildInstance = myDefinition.newInstance();
+					BaseRuntimeElementDefinition<?> child = declaredExtension.getChildByName(theElement.getName().getLocalPart());
+					myChildInstance = child.newInstance();
 					myDefinition.getMutator().addValue(myParentInstance, myChildInstance);
 				}
 				BaseState newState = new DeclaredExtensionState(getPreResourceState(), declaredExtension, myChildInstance);

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

@@ -53,8 +53,6 @@ public class DaoConfig {
 	// ***
 	private long myExpireSearchResultsAfterMillis = DateUtils.MILLIS_PER_HOUR;
 	
-	private int myHardSearchLimit = 1000;
-	
 	private int myHardTagListLimit = 1000;
 	
 	private int myIncludeLimit = 2000;
@@ -325,8 +323,17 @@ public class DaoConfig {
 		myExpireSearchResultsAfterMillis = theExpireSearchResultsAfterMillis;
 	}
 
-	public void setHardSearchLimit(int theHardSearchLimit) {
+	/**
-		myHardSearchLimit = theHardSearchLimit;
+	 * Do not call this method, it exists only for legacy reasons. It
+	 * will be removed in a future version. Configure the page size on your
+	 * paging provider instead.
+	 * 
+	 * @deprecated This method does not do anything. Configure the page size on your
+	 * paging provider instead. Deprecated in HAPI FHIR 2.3 (Jan 2017) 
+	 */
+	@Deprecated
+	public void setHardSearchLimit(@SuppressWarnings("unused") int theHardSearchLimit) {
+		// this method does nothing
 	}
 
 	/**

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -54,7 +54,6 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setAllowExternalReferences(true);
 		retVal.getTreatBaseUrlsAsLocal().add("http://fhirtest.uhn.ca/baseDstu3");
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu3");
-		retVal.setHardSearchLimit(500);
 		return retVal;
 	}
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -919,7 +919,7 @@ public class XmlParserDstu2Test {
 	public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
 		IParser xmlParser = ourCtx.newXmlParser();
 
-		String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
+		String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"), StandardCharsets.UTF_8);
 		MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
 		SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
 		assertEquals("1", q.getValueElement().getValueAsString());
@@ -1869,7 +1869,7 @@ public class XmlParserDstu2Test {
 
 	@Test
 	public void testParseAndEncodeBundle() throws Exception {
-		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
+		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"), StandardCharsets.UTF_8);
 
 		Bundle parsed = ourCtx.newXmlParser().parseBundle(content);
 		assertEquals("Bundle/example/_history/1", parsed.getId().getValue());
@@ -1904,7 +1904,7 @@ public class XmlParserDstu2Test {
 
 	@Test
 	public void testParseAndEncodeBundleNewStyle() throws Exception {
-		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
+		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"), StandardCharsets.UTF_8);
 
 		IParser newXmlParser = ourCtx.newXmlParser();
 		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = newXmlParser.parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, content);
@@ -2411,12 +2411,14 @@ public class XmlParserDstu2Test {
 		// TODO: implement this test, make sure we handle ID and meta correctly in Binary
 	}
 
+	
+	
 	/**
 	 * See #191
 	 */
 	@Test
 	public void testParseBundleWithLinksOfUnknownRelation() throws Exception {
-		String input = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle_orion.xml"));
+		String input = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle_orion.xml"), StandardCharsets.UTF_8);
 		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
 
 		Link link = parsed.getLink().get(0);

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/CustomTypeDstu3Test.java

@@ -10,13 +10,7 @@ import static org.junit.Assert.assertThat;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.DateTimeType;
-import org.hl7.fhir.dstu3.model.Medication;
-import org.hl7.fhir.dstu3.model.MedicationRequest;
-import org.hl7.fhir.dstu3.model.Patient;
-import org.hl7.fhir.dstu3.model.Quantity;
-import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -49,6 +43,63 @@ public class CustomTypeDstu3Test {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@SuppressWarnings("serial")
+	@ResourceDef
+	public static class PatientWithExtensionWithTwoTypes extends Patient {
+		@Child(name = "foo", type = { DateTimeType.class, Period.class }, min = 0, max = 1)
+		@Extension(url = "http://example.com/extension#foo", definedLocally = true, isModifier = false)
+		@Description(shortDefinition = "Some description")
+		private Type foo;
+
+		public Type getFoo() {
+			return foo;
+		}
+
+		public void setFoo(Type theFoo) {
+			foo = theFoo;
+		}
+	}
+
+	@Test
+	public void testExtensionWithTwoTypes() {
+		PatientWithExtensionWithTwoTypes pt = new PatientWithExtensionWithTwoTypes();
+		pt.setFoo(new DateTimeType("2011-01-01T00:00:00Z"));
+		
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pt);
+		ourLog.info(encoded);
+		
+		pt = ourCtx.newXmlParser().parseResource(PatientWithExtensionWithTwoTypes.class, encoded);
+		assertEquals("2011-01-01T00:00:00Z", ((DateTimeType)pt.getFoo()).getValueAsString());
+	}
+
+	@SuppressWarnings("serial")
+	@ResourceDef
+	public static class PatientWithExtensionWithOneTypes extends Patient {
+		@Child(name = "foo", type = { DateTimeType.class }, min = 0, max = 1)
+		@Extension(url = "http://example.com/extension#foo", definedLocally = true, isModifier = false)
+		@Description(shortDefinition = "Some description")
+		private Type foo;
+
+		public Type getFoo() {
+			return foo;
+		}
+
+		public void setFoo(Type theFoo) {
+			foo = theFoo;
+		}
+	}
+
+	@Test
+	public void testExtensionWithOneTypes() {
+		PatientWithExtensionWithOneTypes pt = new PatientWithExtensionWithOneTypes();
+		pt.setFoo(new DateTimeType("2011-01-01T00:00:00Z"));
+		
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pt);
+		ourLog.info(encoded);
+		
+		pt = ourCtx.newXmlParser().parseResource(PatientWithExtensionWithOneTypes.class, encoded);
+		assertEquals("2011-01-01T00:00:00Z", ((DateTimeType)pt.getFoo()).getValueAsString());
+	}
 
 	/**
 	 * See #364
@@ -71,8 +122,7 @@ public class CustomTypeDstu3Test {
 				"<CustomResource xmlns=\"http://hl7.org/fhir\">",
 				"<meta><profile value=\"http://hl7.org/fhir/profiles/custom-resource\"/></meta>",
 				"<baseValueCustomDate><date value=\"2016-05-13\"/></baseValueCustomDate>",
-			"</CustomResource>"
+				"</CustomResource>"));
-		));
 		//@formatter:on
 
 		CustomResource364Dstu3 parsedResource = parser.parseResource(CustomResource364Dstu3.class, xml);
@@ -99,15 +149,13 @@ public class CustomTypeDstu3Test {
 				"<CustomResource xmlns=\"http://hl7.org/fhir\">",
 				"<meta><profile value=\"http://hl7.org/fhir/profiles/custom-resource\"/></meta>",
 				"<baseValueString value=\"2016-05-13\"/>",
-			"</CustomResource>"
+				"</CustomResource>"));
-		));
 		//@formatter:on
 
 		CustomResource364Dstu3 parsedResource = parser.parseResource(CustomResource364Dstu3.class, xml);
 		assertEquals("2016-05-13", ((StringType) parsedResource.getBaseValues()).getValueAsString());
 	}
 
-	
 	@Test
 	public void parseBundleWithResourceDirective() {
 		String input = createBundle(createResource(false), createResource(true));
@@ -148,7 +196,6 @@ public class CustomTypeDstu3Test {
 		assertEquals("185 cm", parsed.getWeight().getValue());
 	}
 
-	
 	@Test
 	public void parseResourceWithNoDirective() {
 		String input = createResource(true);
@@ -411,8 +458,7 @@ public class CustomTypeDstu3Test {
 		b.append("      <given value=\"Mario\"/>\n");
 		b.append("   </name>\n");
 		b.append("</Patient>");
-		String input =
+		String input = b.toString();
-			b.toString();
 		return input;
 	}
 
@@ -596,10 +642,8 @@ public class CustomTypeDstu3Test {
 
 	}
 
-	
 	@ResourceDef()
-	public static class MyMedication extends Medication
+	public static class MyMedication extends Medication {
-	{
 
 		private static final long serialVersionUID = 1L;