More work on cleanup

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Create.java

@@ -23,7 +23,7 @@ package ca.uhn.fhir.rest.annotation;
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
 
-import ca.uhn.fhir.model.api.IResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
 @Retention(RetentionPolicy.RUNTIME)
 
@@ -44,7 +44,7 @@ public @interface Create {
 	 * for client implementations. 
 	 */
 	// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
-	Class<? extends IResource> type() default IResource.class;
+	Class<? extends IBaseResource> type() default IBaseResource.class;
 	
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/TokenClientParam.java

@@ -2,11 +2,10 @@ package ca.uhn.fhir.rest.gclient;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
-import java.util.Arrays;
+import java.util.*;
-import java.util.Collection;
-import java.util.List;
 
 import org.apache.commons.lang3.ObjectUtils;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
 
 import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
 
@@ -20,7 +19,7 @@ import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
  * 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
+ * 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,
@@ -30,14 +29,13 @@ import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
  * #L%
  */
 
-
 /**
  * Token parameter type for use in fluent client interfaces
  */
-public class TokenClientParam extends BaseClientParam  implements IParam {
+public class TokenClientParam extends BaseClientParam implements IParam {
 
 	private static final String[] EMPTY_STRING_LIST = new String[0];
-	
+
 	private String myParamName;
 
 	public TokenClientParam(String theParamName) {
@@ -51,6 +49,21 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 				return new TokenCriterion(getParamName(), null, theCode);
 			}
 
+			@Override
+			public ICriterion<?> codes(Collection<String> theCodes) {
+				return new TokenCriterion(getParamName(), theCodes);
+			}
+
+			@Override
+			public ICriterion<?> codes(String... theCodes) {
+				return new TokenCriterion(getParamName(), convertToList(theCodes));
+			}
+
+			private List<String> convertToList(String[] theValues) {
+				String[] values = ObjectUtils.defaultIfNull(theValues, EMPTY_STRING_LIST);
+				return Arrays.asList(values);
+			}
+
 			@Override
 			public ICriterion<TokenClientParam> identifier(BaseIdentifierDt theIdentifier) {
 				return new TokenCriterion(getParamName(), theIdentifier.getSystemElement().getValueAsString(), theIdentifier.getValueElement().getValue());
@@ -81,33 +94,21 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 				return new TokenCriterion(getParamName(), defaultString(theSystem), theCode);
 			}
 
+			@Override
+			public ICriterion<?> systemAndValues(String theSystem, Collection<String> theValues) {
+				return new TokenCriterion(getParamName(), defaultString(theSystem), theValues);
+			}
+
 			@Override
 			public ICriterion<?> systemAndValues(String theSystem, String... theValues) {
 				return new TokenCriterion(getParamName(), defaultString(theSystem), convertToList(theValues));
 			}
 
 			@Override
-			public ICriterion<?> codes(String... theCodes) {
+			public ICriterion<?> codings(IBaseCoding... theCodings) {
-				return new TokenCriterion(getParamName(), convertToList(theCodes));
+				return new TokenCriterion(getParamName(), theCodings);
 			}
-
+		};
-			@Override
-			public ICriterion<?> codes(Collection<String> theCodes) {
-				return new TokenCriterion(getParamName(), theCodes);
-			}
-
-			
-			
-			private List<String> convertToList(String[] theValues) {
-				String[] values = ObjectUtils.defaultIfNull(theValues, EMPTY_STRING_LIST);
-				return Arrays.asList(values);
-			}
-
-			@Override
-			public ICriterion<?> systemAndValues(String theSystem, Collection<String> theValues) {
-				return new TokenCriterion(getParamName(), defaultString(theSystem), theValues);
-			}
-};
 	}
 
 	@Override
@@ -124,7 +125,7 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 	 * </p>
 	 */
 	public ICriterion<TokenClientParam> hasSystemWithAnyCode(String theSystem) {
-		return new TokenCriterion(getParamName(), theSystem, (String)null);
+		return new TokenCriterion(getParamName(), theSystem, (String) null);
 	}
 
 	public interface IMatches {
@@ -132,28 +133,52 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 		 * Creates a search criterion that matches against the given code, with no code system specified
 		 * 
 		 * @param theIdentifier
-		 *            The identifier
+		 *           The identifier
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> code(String theIdentifier);
 
-
 		/**
-		 * Creates a search criterion that matches a given system with a collection of possible 
+		 * Creates a search criterion that matches a given system with a collection of possible
 		 * codes (this will be used to form a comma-separated OR query) with any system value.
-		 * The URL form of this method will create a parameter like 
+		 * The URL form of this method will create a parameter like
 		 * <code>parameter=code1,code2</code>
 		 * 
-		 * @param theCodes The codes
+		 * @param theCodes
+		 *           The codes
 		 */
 		ICriterion<?> codes(Collection<String> theCodes);
 
+		/**
+		 * Creates a search criterion that matches a given system with a collection of possible
+		 * codes (this will be used to form a comma-separated OR query) with any system value.
+		 * The URL form of this method will create a parameter like
+		 * <code>parameter=code1,code2</code>
+		 * 
+		 * @param theCodes
+		 *           The codes
+		 */
+		ICriterion<?> codes(String... theCodes);
+
+		/**
+		 * Creates a search criterion that matches a given system with a collection of possible
+		 * codes (this will be used to form a comma-separated OR query) with the given
+		 * <code>Coding.system</code> and <code>Coding.value</code> values.
+		 * <p>
+		 * The URL form of this method will create a parameter like
+		 * <code>parameter=system1|code1,system2|code2</code>
+		 * </p>
+		 * 
+		 * @param theCodings
+		 *           The codings
+		 */
+		ICriterion<?> codings(IBaseCoding... theCodings);
 
 		/**
 		 * Creates a search criterion that matches against the given identifier (system and code if both are present, or whatever is present)
 		 * 
 		 * @param theIdentifier
-		 *            The identifier
+		 *           The identifier
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> identifier(BaseIdentifierDt theIdentifier);
@@ -162,7 +187,7 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 		 * Creates a search criterion that matches against the given identifier, with no system specified
 		 * 
 		 * @param theIdentifier
-		 *            The identifier
+		 *           The identifier
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> identifier(String theIdentifier);
@@ -172,7 +197,7 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 		 * In the query URL that is generated, identifiers will be joined with a ',' to create an OR query.
 		 * 
 		 * @param theIdentifiers
-		 *            The identifier
+		 *           The identifier
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> identifiers(BaseIdentifierDt... theIdentifiers);
@@ -182,18 +207,18 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 		 * In the query URL that is generated, identifiers will be joined with a ',' to create an OR query.
 		 * 
 		 * @param theIdentifiers
-		 *            The identifier
+		 *           The identifier
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> identifiers(List<BaseIdentifierDt> theIdentifiers);
-		
+
 		/**
 		 * Creates a search criterion that matches against the given code system and code
 		 * 
 		 * @param theSystem
-		 *            The code system (should be a URI)
+		 *           The code system (should be a URI)
 		 * @param theCode
-		 *            The code
+		 *           The code
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> systemAndCode(String theSystem, String theCode);
@@ -202,41 +227,34 @@ public class TokenClientParam extends BaseClientParam  implements IParam {
 		 * Creates a search criterion that matches against the given system and identifier
 		 * 
 		 * @param theSystem
-		 *            The code system (should be a URI)
+		 *           The code system (should be a URI)
 		 * @param theIdentifier
-		 *            The identifier
+		 *           The identifier
 		 * @return A criterion
 		 */
 		ICriterion<TokenClientParam> systemAndIdentifier(String theSystem, String theIdentifier);
 
 		/**
-		 * Creates a search criterion that matches a given system with a collection of possible 
+		 * Creates a search criterion that matches a given system with a collection of possible
 		 * values (this will be used to form a comma-separated OR query)
 		 * 
-		 * @param theSystem The system, which will be used with each value
+		 * @param theSystem
-		 * @param theValues The values
+		 *           The system, which will be used with each value
-		 */
+		 * @param theValues
-		ICriterion<?> systemAndValues(String theSystem, String... theValues);
+		 *           The values
-
-		/**
-		 * Creates a search criterion that matches a given system with a collection of possible 
-		 * values (this will be used to form a comma-separated OR query)
-		 * 
-		 * @param theSystem The system, which will be used with each value
-		 * @param theValues The values
 		 */
 		public ICriterion<?> systemAndValues(String theSystem, Collection<String> theValues);
 
-
 		/**
-		 * Creates a search criterion that matches a given system with a collection of possible 
+		 * Creates a search criterion that matches a given system with a collection of possible
-		 * codes (this will be used to form a comma-separated OR query) with any system value.
+		 * values (this will be used to form a comma-separated OR query)
-		 * The URL form of this method will create a parameter like 
-		 * <code>parameter=code1,code2</code>
 		 * 
-		 * @param theCodes The codes
+		 * @param theSystem
+		 *           The system, which will be used with each value
+		 * @param theValues
+		 *           The values
 		 */
-		ICriterion<?> codes(String...theCodes);
+		ICriterion<?> systemAndValues(String theSystem, String... theValues);
 
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/TokenCriterion.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.rest.gclient;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.Collection;
@@ -27,6 +28,7 @@ import java.util.Collection;
 import java.util.List;
 
 import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
@@ -89,6 +91,23 @@ class TokenCriterion implements ICriterion<TokenClientParam>, ICriterionInternal
 		this(theParamName, null, theCodes);
 	}
 
+	public TokenCriterion(String theParamName, IBaseCoding... theCodings) {
+		myName=theParamName;
+		StringBuilder b = new StringBuilder();
+		if (theCodings != null) {
+		for (IBaseCoding next : theCodings) {
+			if (isBlank(next.getSystem()) && isBlank(next.getCode())) {
+				continue;
+			}
+			if (b.length() > 0) {
+				b.append(',');
+			}
+			b.append(toValue(next.getSystem(), next.getCode()));
+		}
+		}
+		myValue = b.toString();
+	}
+
 	@Override
 	public String getParameterValue(FhirContext theContext) {
 		return myValue;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java

@@ -26,6 +26,7 @@ import java.lang.reflect.Method;
 import java.util.*;
 
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.context.*;
 import ca.uhn.fhir.model.api.*;
@@ -39,19 +40,10 @@ import ca.uhn.fhir.util.UrlUtil;
 
 public class ParameterUtil {
 
-	private static final Set<Class<?>> BINDABLE_INTEGER_TYPES;
 	private static final String LABEL = "label=\"";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ParameterUtil.class);
-
 	private static final String SCHEME = "scheme=\"";
 
-	static {
-		HashSet<Class<?>> intTypes = new HashSet<Class<?>>();
-		intTypes.add(IntegerDt.class);
-		intTypes.add(Integer.class);
-		BINDABLE_INTEGER_TYPES = Collections.unmodifiableSet(intTypes);
-
-	}
 
 	@SuppressWarnings("unchecked")
 	public static <T extends IIdType> T convertIdToType(IIdType value, Class<T> theIdParamType) {
@@ -213,23 +205,20 @@ public class ParameterUtil {
 	}
 
 	public static Object fromInteger(Class<?> theType, IntegerDt theArgument) {
-		if (theType.equals(IntegerDt.class)) {
-			if (theArgument == null) {
-				return null;
-			}
-			return theArgument;
-		}
 		if (theType.equals(Integer.class)) {
 			if (theArgument == null) {
 				return null;
 			}
 			return theArgument.getValue();
 		}
-		throw new IllegalArgumentException("Invalid Integer type:" + theType);
+		IPrimitiveType<?> retVal = (IPrimitiveType<?>) ReflectionUtil.newInstance(theType);
+		retVal.setValueAsString(theArgument.getValueAsString());
+		return retVal;
 	}
 
-	public static Set<Class<?>> getBindableIntegerTypes() {
+	public static boolean isBindableIntegerType(Class<?> theClass) {
-		return BINDABLE_INTEGER_TYPES;
+		return Integer.class.isAssignableFrom(theClass)
+				|| IPrimitiveType.class.isAssignableFrom(theClass);
 	}
 
 	public static int nonEscapedIndexOf(String theString, char theCharacter) {
@@ -422,6 +411,10 @@ public class ParameterUtil {
 		if (theArgument instanceof Integer) {
 			return new IntegerDt((Integer) theArgument);
 		}
+		if (theArgument instanceof IPrimitiveType) {
+			IPrimitiveType<?> pt = (IPrimitiveType<?>)theArgument;
+			return new IntegerDt(pt.getValueAsString());
+		}
 		return null;
 	}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/CountParameter.java

@@ -31,6 +31,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.primitive.IntegerDt;
+import ca.uhn.fhir.rest.annotation.Count;
 import ca.uhn.fhir.rest.annotation.Since;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.ParameterUtil;
@@ -52,12 +53,12 @@ public class CountParameter implements IParameter {
 	@Override
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
 		if (theOuterCollectionType != null) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + Since.class.getName()
+			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + Count.class.getName()
 					+ " but can not be of collection type");
 		}
-		if (!ParameterUtil.getBindableIntegerTypes().contains(theParameterType)) {
+		if (!ParameterUtil.isBindableIntegerType(theParameterType)) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + Since.class.getName()
+			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName() + "' is annotated with @" + Count.class.getName()
-					+ " but type '" + theParameterType + "' is an invalid type, must be one of: " + ParameterUtil.getBindableIntegerTypes());
+					+ " but type '" + theParameterType + "' is an invalid type, must be Integer or IntegerType");
 		}
 	}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/TransactionMethodBinding.java

@@ -59,8 +59,14 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 	@Override
 	public BaseHttpClientInvocation invokeClient(Object[] theArgs) throws InternalErrorException {
 		FhirContext context = getContext();
+		Object arg = theArgs[myTransactionParamIndex];
+		
+		if (arg instanceof IBaseBundle) {
+			return createTransactionInvocation((IBaseBundle) arg, context);
+		}
+		
 		@SuppressWarnings("unchecked")
-		List<IBaseResource> resources = (List<IBaseResource>) theArgs[myTransactionParamIndex];
+		List<IBaseResource> resources = (List<IBaseResource>) arg;
 		return createTransactionInvocation(resources, context);
 	}
 

hapi-fhir-jacoco/pom.xml

@@ -139,11 +139,6 @@
 			<artifactId>jetty-util</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>xmlunit</groupId>
-			<artifactId>xmlunit</artifactId>
-			<scope>test</scope>
-		</dependency>
 		
 		<dependency>
 			<groupId>net.sf.json-lib</groupId>
@@ -290,6 +285,19 @@
 							</fileSets>
 						</configuration>
 					</execution>
+<execution>
+            <id>post-integration-test</id>
+					<phase>install</phase>
+            <goals>
+					<goal>report</goal>
+            </goals>
+            <configuration>
+					<dataFile>${project.build.directory}/jacoco.exec</dataFile>
+               <outputDirectory>${project.reporting.outputDirectory}/jacoco-report</outputDirectory>
+            </configuration>
+        </execution>
+
+
 				</executions>
 			</plugin>
 			<plugin>

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/CountParameter.java

@@ -28,6 +28,7 @@ import org.apache.commons.lang3.StringUtils;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.annotation.Count;
 import ca.uhn.fhir.rest.annotation.Since;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -60,10 +61,10 @@ public class CountParameter implements IParameter {
 	@Override
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
 		if (theOuterCollectionType != null) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + Since.class.getName() + " but can not be of collection type");
+			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + Count.class.getName() + " but can not be of collection type");
 		}
-		if (!ParameterUtil.getBindableIntegerTypes().contains(theParameterType)) {
+		if (!ParameterUtil.isBindableIntegerType(theParameterType)) {
-			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + Since.class.getName() + " but type '" + theParameterType + "' is an invalid type, must be one of: " + ParameterUtil.getBindableIntegerTypes());
+			throw new ConfigurationException("Method '" + theMethod.getName() + "' in type '" +theMethod.getDeclaringClass().getCanonicalName()+ "' is annotated with @" + Count.class.getName() + " but type '" + theParameterType + "' is an invalid type, must be one of Integer or IntegerType");
 		}
 		myType = theParameterType;
 	}

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/CustomTypeTest.java

@@ -15,19 +15,15 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.junit.AfterClass;
+import org.junit.*;
-import org.junit.BeforeClass;
-import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.api.AddProfileTagEnum;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.BundleEntry;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Tag;
-import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.*;
-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.resource.Patient;
 import ca.uhn.fhir.model.dstu.resource.Profile;
 import ca.uhn.fhir.model.primitive.StringDt;
@@ -38,9 +34,6 @@ import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.util.PortUtil;
 import ca.uhn.fhir.util.TestUtil;
 
-/**
- * Created by dsotnikov on 2/25/2014.
- */
 public class CustomTypeTest {
 
 	private static CloseableHttpClient ourClient;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/BinaryClientTest.java

@@ -15,12 +15,12 @@ import org.apache.http.client.methods.*;
 import org.apache.http.message.BasicHeader;
 import org.apache.http.message.BasicStatusLine;
 import org.hl7.fhir.r4.model.Binary;
+import org.hl7.fhir.r4.model.IdType;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
 import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.primitive.IdType;
 import ca.uhn.fhir.rest.annotation.*;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.MethodOutcome;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/ClientIntegrationTest.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.rest.client;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 import java.util.Collections;
 import java.util.List;
@@ -14,18 +14,15 @@ import org.apache.http.impl.client.HttpClientBuilder;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.junit.After;
+import org.hl7.fhir.r4.model.Patient;
-import org.junit.AfterClass;
+import org.junit.*;
-import org.junit.Before;
-import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.annotation.RequiredParam;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.client.api.IBasicClient;
+import ca.uhn.fhir.rest.client.impl.HttpBasicAuthInterceptor;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.PortUtil;
@@ -36,7 +33,7 @@ public class ClientIntegrationTest {
 	private int myPort;
 	private Server myServer;
 	private MyPatientResourceProvider myPatientProvider;
-	private static FhirContext ourCtx = FhirContext.forDstu1();
+	private static FhirContext ourCtx = FhirContext.forR4();
 
 	@Before
 	public void before() {
@@ -60,7 +57,7 @@ public class ClientIntegrationTest {
 
 		myServer.start();
 
-		FhirContext ctx = FhirContext.forDstu1();
+		FhirContext ctx = FhirContext.forR4();
 
 		HttpClientBuilder builder = HttpClientBuilder.create();
 		// PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
@@ -74,7 +71,7 @@ public class ClientIntegrationTest {
 
 		List<Patient> actualPatients = client.searchForPatients(new StringDt("AAAABBBB"));
 		assertEquals(1, actualPatients.size());
-		assertEquals("AAAABBBB", actualPatients.get(0).getNameFirstRep().getFamilyAsSingleString());
+		assertEquals("AAAABBBB", actualPatients.get(0).getNameFirstRep().getFamily());
 
 		assertEquals("Basic Zm9vYmFyOmJvb2JlYXI=", myPatientProvider.getAuthorizationHeader());
 	}
@@ -92,7 +89,7 @@ public class ClientIntegrationTest {
 		}
 
 		@Override
-		public Class<? extends IResource> getResourceType() {
+		public Class<Patient> getResourceType() {
 			return Patient.class;
 		}
 
@@ -105,7 +102,7 @@ public class ClientIntegrationTest {
 
 			Patient retVal = new Patient();
 			retVal.setId("1");
-			retVal.addName().addFamily(theFooParam.getValue());
+			retVal.addName().setFamily(theFooParam.getValue());
 			return Collections.singletonList(retVal);
 		}
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationDstu1Test.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.rest.client;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.*;
 
@@ -15,9 +15,9 @@ import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.message.BasicHeader;
 import org.apache.http.message.BasicStatusLine;
-import org.junit.AfterClass;
+import org.hl7.fhir.r4.model.CapabilityStatement;
-import org.junit.Before;
+import org.hl7.fhir.r4.model.Patient;
-import org.junit.Test;
+import org.junit.*;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Matchers;
 import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
@@ -25,11 +25,11 @@ import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.dstu.resource.Conformance;
-import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
-import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ClientServerValidationDstu1Test {
@@ -45,13 +45,13 @@ public class ClientServerValidationDstu1Test {
 		myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
 		myFirstResponse = true;
 
-		myCtx = FhirContext.forDstu1();
+		myCtx = FhirContext.forR4();
 		myCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
 	}
 
 	@Test
 	public void testServerReturnsAppropriateVersionDstu() throws Exception {
-		Conformance conf = new Conformance();
+		CapabilityStatement conf = new CapabilityStatement();
 		conf.setFhirVersion("0.0.8");
 		final String confResource = myCtx.newXmlParser().encodeResourceToString(conf);
 
@@ -88,7 +88,7 @@ public class ClientServerValidationDstu1Test {
 
 	@Test
 	public void testServerReturnsWrongVersionDstu() throws Exception {
-		Conformance conf = new Conformance();
+		CapabilityStatement conf = new CapabilityStatement();
 		conf.setFhirVersion("0.4.0");
 		String msg = myCtx.newXmlParser().encodeResourceToString(conf);
 
@@ -105,7 +105,7 @@ public class ClientServerValidationDstu1Test {
 			myCtx.newRestfulGenericClient("http://foo").read(new UriDt("http://foo/Patient/1"));
 			fail();
 		} catch (FhirClientInappropriateForServerException e) {
-			assertThat(e.toString(), containsString("The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"0.4.0\" which corresponds to DSTU2, but this client is configured to use DSTU1 (via the FhirContext)"));
+			assertThat(e.toString(), containsString("The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"0.4.0\" which corresponds to DSTU2, but this client is configured to use R4 (via the FhirContext)"));
 		}
 	}
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/ExceptionHandlingTest.java

@@ -1,7 +1,8 @@
 package ca.uhn.fhir.rest.client;
 
 import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 import java.io.StringReader;
 import java.nio.charset.Charset;
@@ -14,22 +15,17 @@ import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.message.BasicHeader;
 import org.apache.http.message.BasicStatusLine;
 import org.hamcrest.core.StringContains;
-import org.junit.AfterClass;
+import org.hl7.fhir.r4.model.*;
-import org.junit.Before;
+import org.junit.*;
-import org.junit.BeforeClass;
-import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
-import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
-import ca.uhn.fhir.model.dstu.resource.Patient;
-import ca.uhn.fhir.model.primitive.IdType;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Read;
-import ca.uhn.fhir.rest.client.api.IRestfulClient;
+import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.client.api.*;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.TestUtil;
 
@@ -41,7 +37,7 @@ public class ExceptionHandlingTest {
 
 	@BeforeClass
 	public static void beforeClass() {
-		ourCtx = FhirContext.forDstu1();
+		ourCtx = FhirContext.forR4();
 	}
 
 	@Before
@@ -49,7 +45,7 @@ public class ExceptionHandlingTest {
 
 		myHttpClient = mock(HttpClient.class, new ReturnsDeepStubs());
 		ourCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
-		ourCtx.getRestfulClientFactory().setServerValidationModeEnum(ServerValidationModeEnum.NEVER);
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
 
 		myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
 	}
@@ -68,7 +64,7 @@ public class ExceptionHandlingTest {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
 		try {
-			client.read(Patient.class, new IdType("Patient/1234"));
+			client.read().resource(Patient.class).withId(new IdType("Patient/1234")).execute();
 			fail();
 		} catch (InternalErrorException e) {
 			assertThat(e.getMessage(), StringContains.containsString("HTTP 500 Internal Error"));
@@ -80,7 +76,7 @@ public class ExceptionHandlingTest {
 	@Test
 	public void testFail500WithOperationOutcomeMessage() throws Exception {
 		OperationOutcome oo = new OperationOutcome();
-		oo.getIssueFirstRep().getDetails().setValue("Help I'm a bug");
+		oo.getIssueFirstRep().getDiagnosticsElement().setValue("Help I'm a bug");
 		String msg = ourCtx.newXmlParser().encodeResourceToString(oo);
 		String contentType = Constants.CT_FHIR_XML;
 
@@ -93,7 +89,7 @@ public class ExceptionHandlingTest {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
 		try {
-			client.read(Patient.class, new IdType("Patient/1234"));
+        client.read().resource(Patient.class).withId(new IdType("Patient/1234")).execute();
 			fail();
 		} catch (InternalErrorException e) {
 			assertThat(e.getMessage(), StringContains.containsString("HTTP 500 Internal Error"));
@@ -118,7 +114,7 @@ public class ExceptionHandlingTest {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
 		try {
-			client.read(Patient.class, new IdType("Patient/1234"));
+        client.read().resource(Patient.class).withId(new IdType("Patient/1234")).execute();
 			fail();
 		} catch (InternalErrorException e) {
 			assertEquals("HTTP 500 Internal Error", e.getMessage());
@@ -130,7 +126,7 @@ public class ExceptionHandlingTest {
 	@Test
 	public void testFail500WithOperationOutcomeMessageJson() throws Exception {
 		OperationOutcome oo = new OperationOutcome();
-		oo.getIssueFirstRep().getDetails().setValue("Help I'm a bug");
+		oo.getIssueFirstRep().getDiagnosticsElement().setValue("Help I'm a bug");
 		String msg = ourCtx.newJsonParser().encodeResourceToString(oo);
 		String contentType = Constants.CT_FHIR_JSON;
 
@@ -142,7 +138,7 @@ public class ExceptionHandlingTest {
 
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 		try {
-			client.read(Patient.class, new IdType("Patient/1234"));
+        client.read().resource(Patient.class).withId(new IdType("Patient/1234")).execute();
 			fail();
 		} catch (InternalErrorException e) {
 			assertThat(e.getMessage(), StringContains.containsString("HTTP 500 Internal Error"));
@@ -156,7 +152,7 @@ public class ExceptionHandlingTest {
 	@Test
 	public void testFail500WithOperationOutcomeMessageGeneric() throws Exception {
 		OperationOutcome oo = new OperationOutcome();
-		oo.getIssueFirstRep().getDetails().setValue("Help I'm a bug");
+		oo.getIssueFirstRep().getDiagnosticsElement().setValue("Help I'm a bug");
 		String msg = ourCtx.newJsonParser().encodeResourceToString(oo);
 		String contentType = Constants.CT_FHIR_JSON;
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/HttpProxyTest.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.rest.client;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 import java.io.IOException;
 
@@ -9,28 +9,18 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.collections.EnumerationUtils;
-import org.apache.http.HttpHost;
-import org.apache.http.auth.AuthScope;
-import org.apache.http.auth.UsernamePasswordCredentials;
-import org.apache.http.client.CredentialsProvider;
-import org.apache.http.impl.client.BasicCredentialsProvider;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.http.impl.client.ProxyAuthenticationStrategy;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.server.handler.ContextHandlerCollection;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.junit.AfterClass;
+import org.hl7.fhir.r4.model.IdType;
-import org.junit.BeforeClass;
+import org.hl7.fhir.r4.model.Patient;
-import org.junit.Test;
+import org.junit.*;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.dstu.resource.Patient;
-import ca.uhn.fhir.model.primitive.IdType;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.PortUtil;
@@ -112,7 +102,7 @@ public class HttpProxyTest {
 			IGenericClient client = ourCtx.newRestfulGenericClient(baseUri);
 
 			IdType id = new IdType("Patient", "123");
-			client.read(Patient.class, id);
+			client.read().resource(Patient.class).withId(id).execute();
 
 			assertEquals("Basic dXNlcm5hbWU6cGFzc3dvcmQ=", myAuthHeader);
 			
@@ -124,13 +114,13 @@ public class HttpProxyTest {
 
 	@BeforeClass
 	public static void beforeClass() throws Exception {
-		ourCtx = FhirContext.forDstu1();
+		ourCtx = FhirContext.forR4();
 	}
 
 	public static class PatientResourceProvider implements IResourceProvider {
 
 		@Override
-		public Class<? extends IResource> getResourceType() {
+		public Class<Patient> getResourceType() {
 			return Patient.class;
 		}
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/ITestClient.java

@@ -3,11 +3,11 @@ package ca.uhn.fhir.rest.client;
 import java.util.Date;
 import java.util.List;
 
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.*;
 
-import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
-import ca.uhn.fhir.model.primitive.*;
 import ca.uhn.fhir.rest.annotation.*;
 import ca.uhn.fhir.rest.annotation.Count;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -29,9 +29,12 @@ public interface ITestClient extends IBasicClient {
 	public List<Patient> getPatientByDob(@RequiredParam(name=Patient.SP_BIRTHDATE) DateParam theBirthDate);
 
 	@Search(type=ExtendedPatient.class)
-	public List<IResource> getPatientByDobWithGenericResourceReturnType(@RequiredParam(name=Patient.SP_BIRTHDATE) DateParam theBirthDate);
+	public List<IBaseResource> getPatientByDobWithGenericResourceReturnType(@RequiredParam(name=Patient.SP_BIRTHDATE) DateParam theBirthDate);
 
-	@Search()
+   @Search(type=ExtendedPatient.class)
+   public List<IAnyResource> getPatientByDobWithGenericResourceReturnType2(@RequiredParam(name=Patient.SP_BIRTHDATE) DateParam theBirthDate);
+
+   @Search()
 	public List<Patient> getPatientMultipleIdentifiers(@RequiredParam(name = "ids") TokenOrListParam theIdentifiers);
 
 	@Search(queryName="someQueryNoParams")
@@ -65,7 +68,7 @@ public interface ITestClient extends IBasicClient {
 	Bundle getHistoryPatientInstance(@IdParam IdType theId);
 
 	@History(type=Patient.class)
-	Bundle getHistoryPatientInstance(@IdParam IdType theId, @Since InstantDt theSince, @Count IntegerDt theCount);
+	Bundle getHistoryPatientInstance(@IdParam IdType theId, @Since InstantType theSince, @Count IntegerType theCount);
 	
 	@History(type=Patient.class)
 	Bundle getHistoryPatientInstance(@IdParam IdType theId, @Since Date theSince, @Count Integer theCount);
@@ -83,7 +86,7 @@ public interface ITestClient extends IBasicClient {
 	 MethodOutcome validatePatient(@ResourceParam Patient thePatient);
 
 	@Search(type=Patient.class)
-	Patient findPatientQuantity(@RequiredParam(name="quantityParam") QuantityParam theQuantityDt);
+	Patient findPatientQuantity(@RequiredParam(name="quantityParam") QuantityParam theQuantityType);
 
 	@Search(compartmentName="compartmentName")
 	public List<Patient> getPatientByCompartmentAndDob(@IdParam IdType theIdType, @RequiredParam(name=Patient.SP_BIRTHDATE) DateParam theBirthDate);

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/IncludedResourceStitchingClientTest.java

@@ -23,8 +23,6 @@ import org.mockito.ArgumentCaptor;
 import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.ExtensionDt;
-import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
@@ -92,99 +90,112 @@ public class IncludedResourceStitchingClientTest {
 		when(httpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(createLinkedBundle()), Charset.forName("UTF-8")));
 
 		IGenericClient client = ctx.newRestfulGenericClient( "http://foo");
-		Bundle bundle = client.search().forResource(IncludeTest.ExtPatient.class).execute();
+		Bundle bundle = client.search().forResource(IncludeTest.ExtPatient.class).returnBundle(Bundle.class).execute();
 
 		assertEquals(HttpGet.class, capt.getValue().getClass());
 		HttpGet get = (HttpGet) capt.getValue();
 		assertEquals("http://foo/Patient", get.getURI().toString());
 		
-		assertEquals(4, bundle.size());
+		assertEquals(4, bundle.getEntry().size());
 		
 		ExtPatient p = (ExtPatient) bundle.getEntry().get(0).getResource();
-		ResourceReferenceDt ref = (ResourceReferenceDt) p.getSecondOrg();
+		Reference ref = (Reference) p.getSecondOrg();
-		assertEquals("Organization/o1", ref.getReference().getValue());
+		assertEquals("Organization/o1", ref.getReferenceElement().getValue());
 		assertNotNull(ref.getResource());
 		
 		Organization o1 = (Organization) ref.getResource();
-		assertEquals("o2", o1.getPartOf().getReference().toUnqualifiedVersionless().getIdPart());
+		assertEquals("o2", o1.getPartOf().getReferenceElement().toUnqualifiedVersionless().getIdPart());
 		assertNotNull(o1.getPartOf().getResource());
 		
 	}
 	
 	private String createLinkedBundle() {
-		//@formatter:off
+	  
-		return "<feed xmlns=\"http://www.w3.org/2005/Atom\">\n" + 
+	  Bundle bundle = new Bundle();
-				"   <title/>\n" + 
+	  
-				"   <id>6cfcd90e-877a-40c6-a11c-448006712979</id>\n" + 
+	  Patient p1 = new Patient();
-				"   <link rel=\"self\" href=\"http://localhost:49782/Patient?_query=declaredExtInclude&amp;_pretty=true\"/>\n" + 
+	  p1.addIdentifier().setValue("p1");
-				"   <link rel=\"fhir-base\" href=\"http://localhost:49782\"/>\n" + 
+	  bundle.addEntry().setResource(p1);
-				"   <os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>\n" + 
+
-				"   <author>\n" +
+     Patient p2 = new Patient();
-				"      <name>HAPI FHIR Server</name>\n" + 
+     p2.addIdentifier().setValue("p1");
-				"   </author>\n" + 
+     bundle.addEntry().setResource(p2);
-				"   <entry>\n" + 
+
-				"      <title>Patient p1</title>\n" + 
+     return ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
-				"      <id>http://localhost:49782/Patient/p1</id>\n" + 
+     
-				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
+//		//@formatter:off
-				"      <link rel=\"self\" href=\"http://localhost:49782/Patient/p1\"/>\n" + 
+//		return "<feed xmlns=\"http://www.w3.org/2005/Atom\">\n" + 
-				"      <content type=\"text/xml\">\n" + 
+//				"   <title/>\n" + 
-				"         <Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+//				"   <id>6cfcd90e-877a-40c6-a11c-448006712979</id>\n" + 
-				"            <extension url=\"http://foo#secondOrg\">\n" + 
+//				"   <link rel=\"self\" href=\"http://localhost:49782/Patient?_query=declaredExtInclude&amp;_pretty=true\"/>\n" + 
-				"               <valueResource>\n" + 
+//				"   <link rel=\"fhir-base\" href=\"http://localhost:49782\"/>\n" + 
-				"                  <reference value=\"Organization/o1\"/>\n" + 
+//				"   <os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>\n" + 
-				"               </valueResource>\n" + 
+//				"   <author>\n" +
-				"            </extension>\n" + 
+//				"      <name>HAPI FHIR Server</name>\n" + 
-				"            <identifier>\n" + 
+//				"   </author>\n" + 
-				"               <label value=\"p1\"/>\n" + 
+//				"   <entry>\n" + 
-				"            </identifier>\n" + 
+//				"      <title>Patient p1</title>\n" + 
-				"         </Patient>\n" + 
+//				"      <id>http://localhost:49782/Patient/p1</id>\n" + 
-				"      </content>\n" + 
+//				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
-				"   </entry>\n" + 
+//				"      <link rel=\"self\" href=\"http://localhost:49782/Patient/p1\"/>\n" + 
-				"   <entry>\n" + 
+//				"      <content type=\"text/xml\">\n" + 
-				"      <title>Patient p2</title>\n" + 
+//				"         <Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-				"      <id>http://localhost:49782/Patient/p2</id>\n" + 
+//				"            <extension url=\"http://foo#secondOrg\">\n" + 
-				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
+//				"               <valueResource>\n" + 
-				"      <link rel=\"self\" href=\"http://localhost:49782/Patient/p2\"/>\n" + 
+//				"                  <reference value=\"Organization/o1\"/>\n" + 
-				"      <content type=\"text/xml\">\n" + 
+//				"               </valueResource>\n" + 
-				"         <Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+//				"            </extension>\n" + 
-				"            <extension url=\"http://foo#secondOrg\">\n" + 
+//				"            <identifier>\n" + 
-				"               <valueResource>\n" + 
+//				"               <label value=\"p1\"/>\n" + 
-				"                  <reference value=\"Organization/o1\"/>\n" + 
+//				"            </identifier>\n" + 
-				"               </valueResource>\n" + 
+//				"         </Patient>\n" + 
-				"            </extension>\n" + 
+//				"      </content>\n" + 
-				"            <identifier>\n" + 
+//				"   </entry>\n" + 
-				"               <label value=\"p2\"/>\n" + 
+//				"   <entry>\n" + 
-				"            </identifier>\n" + 
+//				"      <title>Patient p2</title>\n" + 
-				"         </Patient>\n" + 
+//				"      <id>http://localhost:49782/Patient/p2</id>\n" + 
-				"      </content>\n" + 
+//				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
-				"   </entry>\n" + 
+//				"      <link rel=\"self\" href=\"http://localhost:49782/Patient/p2\"/>\n" + 
-				"   <entry>\n" + 
+//				"      <content type=\"text/xml\">\n" + 
-				"      <title>Organization o1</title>\n" + 
+//				"         <Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-				"      <id>http://localhost:49782/Organization/o1</id>\n" + 
+//				"            <extension url=\"http://foo#secondOrg\">\n" + 
-				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
+//				"               <valueResource>\n" + 
-				"      <link rel=\"self\" href=\"http://localhost:49782/Organization/o1\"/>\n" + 
+//				"                  <reference value=\"Organization/o1\"/>\n" + 
-				"      <content type=\"text/xml\">\n" + 
+//				"               </valueResource>\n" + 
-				"         <Organization xmlns=\"http://hl7.org/fhir\">\n" + 
+//				"            </extension>\n" + 
-				"            <name value=\"o1\"/>\n" + 
+//				"            <identifier>\n" + 
-				"            <partOf>\n" + 
+//				"               <label value=\"p2\"/>\n" + 
-				"               <reference value=\"Organization/o2\"/>\n" + 
+//				"            </identifier>\n" + 
-				"            </partOf>\n" + 
+//				"         </Patient>\n" + 
-				"         </Organization>\n" + 
+//				"      </content>\n" + 
-				"      </content>\n" + 
+//				"   </entry>\n" + 
-				"   </entry>\n" + 
+//				"   <entry>\n" + 
-				"   <entry>\n" + 
+//				"      <title>Organization o1</title>\n" + 
-				"      <title>Organization o2</title>\n" + 
+//				"      <id>http://localhost:49782/Organization/o1</id>\n" + 
-				"      <id>http://localhost:49782/Organization/o2</id>\n" + 
+//				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
-				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
+//				"      <link rel=\"self\" href=\"http://localhost:49782/Organization/o1\"/>\n" + 
-				"      <link rel=\"self\" href=\"http://localhost:49782/Organization/o2\"/>\n" + 
+//				"      <content type=\"text/xml\">\n" + 
-				"      <content type=\"text/xml\">\n" + 
+//				"         <Organization xmlns=\"http://hl7.org/fhir\">\n" + 
-				"         <Organization xmlns=\"http://hl7.org/fhir\">\n" + 
+//				"            <name value=\"o1\"/>\n" + 
-				"            <name value=\"o2\"/>\n" + 
+//				"            <partOf>\n" + 
-				"         </Organization>\n" + 
+//				"               <reference value=\"Organization/o2\"/>\n" + 
-				"      </content>\n" + 
+//				"            </partOf>\n" + 
-				"   </entry>\n" + 
+//				"         </Organization>\n" + 
-				"</feed>";
+//				"      </content>\n" + 
-		//@formatter:on
+//				"   </entry>\n" + 
+//				"   <entry>\n" + 
+//				"      <title>Organization o2</title>\n" + 
+//				"      <id>http://localhost:49782/Organization/o2</id>\n" + 
+//				"      <published>2014-08-12T10:22:19-04:00</published>\n" + 
+//				"      <link rel=\"self\" href=\"http://localhost:49782/Organization/o2\"/>\n" + 
+//				"      <content type=\"text/xml\">\n" + 
+//				"         <Organization xmlns=\"http://hl7.org/fhir\">\n" + 
+//				"            <name value=\"o2\"/>\n" + 
+//				"         </Organization>\n" + 
+//				"      </content>\n" + 
+//				"   </entry>\n" + 
+//				"</feed>";
+//		//@formatter:on
 	}
 	
 	

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/IncludeTest.java

@@ -404,12 +404,12 @@ public class IncludeTest {
 			Patient p1 = new Patient();
 			p1.setId("p1");
 			p1.addIdentifier().setValue("p1");
-			p1.addUndeclaredExtension(false, "http://foo", new Reference(o1));
+			p1.addExtension(new org.hl7.fhir.r4.model.Extension("http://foo", new Reference(o1)));
 
 			Patient p2 = new Patient();
 			p2.setId("p2");
 			p2.addIdentifier().setValue("p2");
-			p2.addUndeclaredExtension(false, "http://foo", new Reference(o1));
+			p2.addExtension(new org.hl7.fhir.r4.model.Extension( "http://foo", new Reference(o1)));
 
 			return Arrays.asList(p1, p2);
 		}
@@ -419,13 +419,13 @@ public class IncludeTest {
 			ArrayList<Patient> retVal = new ArrayList<Patient>();
 
 			Patient p = new Patient();
-			p.addIdentifier("Mr", "Test");
+			p.addIdentifier().setSystem("Mr").setValue("Test");
 
 			p.setId(theName.getValue());
 
 			if (theIncludes != null) {
 				for (Include next : theIncludes) {
-					p.addName().setFamily().setValue(next.getValue());
+					p.addName().setFamily(next.getValue());
 				}
 			}
 			retVal.add(p);
@@ -434,7 +434,7 @@ public class IncludeTest {
 		}
 
 		@Override
-		public Class<? extends IResource> getResourceType() {
+		public Class<Patient> getResourceType() {
 			return Patient.class;
 		}