Merge branch 'master' of github.com:jamesagnew/hapi-fhir

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

@@ -454,6 +454,7 @@ public class FhirContext {
 	 * 
 	 * @deprecated Support for DEV resources will be removed, you should use DSTU2 resources instead 
 	 */
+	@Deprecated
 	public static FhirContext forDev() {
 		return new FhirContext(FhirVersionEnum.DEV);
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseIdentifiableElement.java

@@ -36,6 +36,7 @@ public abstract class BaseIdentifiableElement extends BaseElement implements IId
 	 * @deprecated Use {@link #getElementSpecificId()} instead. This method will be removed because it is easily
 	 *             confused with other ID methods (such as patient#getIdentifier)
 	 */
+	@Deprecated
 	@Override
 	public IdDt getId() {
 		if (myElementSpecificId == null) {
@@ -54,6 +55,7 @@ public abstract class BaseIdentifiableElement extends BaseElement implements IId
 	 * @deprecated Use {@link #setElementSpecificId(String)} instead. This method will be removed because it is easily
 	 *             confused with other ID methods (such as patient#getIdentifier)
 	 */
+	@Deprecated
 	@Override
 	public void setId(IdDt theId) {
 		if (theId == null) {
@@ -68,6 +70,7 @@ public abstract class BaseIdentifiableElement extends BaseElement implements IId
 	 *             confused with other ID methods (such as patient#getIdentifier)
 	 */
 	@Override
+	@Deprecated
 	public void setId(String theId) {
 		myElementSpecificId = theId;
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Bundle.java

@@ -68,6 +68,7 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	 * @deprecated Tags wil become immutable in a future release of HAPI, so
 	 *             {@link #addCategory(String, String, String)} should be used instead
 	 */
+	@Deprecated
 	public Tag addCategory() {
 		Tag retVal = new Tag();
 		getCategories().add(retVal);

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BundleEntry.java

@@ -67,6 +67,7 @@ public class BundleEntry extends BaseBundle {
 	 * @deprecated Tags wil become immutable in a future release of HAPI, so
 	 *             {@link #addCategory(String, String, String)} should be used instead
 	 */
+	@Deprecated
 	public Tag addCategory() {
 		Tag retVal = new Tag();
 		getCategories().add(retVal);
@@ -146,6 +147,7 @@ public class BundleEntry extends BaseBundle {
 	 *             if this entry represents a deleted resource, use {@link #setDeletedResourceId(IdDt)}.
 	 */
 	@Override
+	@Deprecated
 	public IdDt getId() {
 		return super.getId();
 	}
@@ -160,6 +162,7 @@ public class BundleEntry extends BaseBundle {
 	/**
 	 * @deprecated Use resource ID to determine base URL
 	 */
+	@Deprecated
 	public StringDt getLinkBase() {
 		if (myLinkBase == null) {
 			myLinkBase = new StringDt();
@@ -220,6 +223,7 @@ public class BundleEntry extends BaseBundle {
 	 *             DSTU2, it is recommended that you migrate code away from using this method and over to using resource
 	 *             metadata instead.
 	 */
+	@Deprecated
 	public InstantDt getUpdated() {
 		if (myUpdated == null) {
 			myUpdated = new InstantDt();
@@ -283,6 +287,7 @@ public class BundleEntry extends BaseBundle {
 	 * @deprecated Bundle entries no longer have an ID in DSTU2, as ID is explicitly stated in the resource itself.
 	 */
 	@Override
+	@Deprecated
 	public void setId(IdDt theId) {
 		super.setId(theId);
 	}
@@ -294,6 +299,7 @@ public class BundleEntry extends BaseBundle {
 	/**
 	 * @deprecated Use resource ID to determine base URL
 	 */
+	@Deprecated
 	public void setLinkBase(StringDt theLinkBase) {
 		myLinkBase = theLinkBase;
 	}
@@ -329,6 +335,7 @@ public class BundleEntry extends BaseBundle {
 	 *             DSTU2, it is recommended that you migrate code away from using this method and over to using resource
 	 *             metadata instead.
 	 */
+	@Deprecated
 	public void setUpdated(InstantDt theUpdated) {
 		Validate.notNull(theUpdated, "Updated may not be null");
 		myUpdated = theUpdated;

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IIdentifiableElement.java

@@ -34,6 +34,7 @@ public interface IIdentifiableElement extends IElement {
 	 * @deprecated Use {@link #getElementSpecificId()} instead. This method will be removed because it is easily
 	 *             confused with other ID methods (such as patient#getIdentifier)
 	 */
+	@Deprecated
 	IdDt getId();
 
 	/**
@@ -46,12 +47,14 @@ public interface IIdentifiableElement extends IElement {
 	 * @deprecated Use {@link #setElementSpecificId(String)} instead. This method will be removed because it is easily
 	 *             confused with other ID methods (such as patient#getIdentifier)
 	 */
+	@Deprecated
 	void setId(IdDt theId);
 
 	/**
 	 * @deprecated Use {@link #setElementSpecificId(String)} instead. This method will be removed because it is easily
 	 *             confused with other ID methods (such as patient#getIdentifier)
 	 */
+	@Deprecated
 	void setId(String theId);
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/PathSpecification.java

@@ -31,6 +31,7 @@ package ca.uhn.fhir.model.api;
  * 
  * @deprecated {@link Include} should be used instead
  */
+@Deprecated
 public class PathSpecification extends Include {
 
 	public PathSpecification(String theInclude) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Tag.java

@@ -61,12 +61,14 @@ public class Tag extends BaseElement implements IElement {
 	/**
 	 * @deprecated Tags will become immutable in a future release, so this constructor should not be used.
 	 */
+	@Deprecated
 	public Tag() {
 	}
 
 	/**
 	 * @deprecated There is no reason to create a tag with a term and not a scheme, so this constructor will be removed
 	 */
+	@Deprecated
 	public Tag(String theTerm) {
 		this((String) null, theTerm, null);
 	}
@@ -148,6 +150,7 @@ public class Tag extends BaseElement implements IElement {
 	 * ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
 	 * tag object
 	 */
+	@Deprecated
 	public Tag setLabel(String theLabel) {
 		myLabel = theLabel;
 		return this;
@@ -160,6 +163,7 @@ public class Tag extends BaseElement implements IElement {
 	 * ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
 	 * tag object
 	 */
+	@Deprecated
 	public Tag setScheme(String theScheme) {
 		myScheme = theScheme;
 		return this;
@@ -172,6 +176,7 @@ public class Tag extends BaseElement implements IElement {
 	 * ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
 	 * tag object
 	 */
+	@Deprecated
 	public Tag setTerm(String theTerm) {
 		myTerm = theTerm;
 		return this;

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/TagList.java

@@ -79,6 +79,7 @@ public class TagList implements Set<Tag>, Serializable, IBase {
 	/**
 	 * @deprecated Tags wil become immutable in a future release of HAPI, so {@link #addTag(String, String, String)} should be used instead
 	 */
+	@Deprecated
 	public Tag addTag() {
 		myOrderedTags = null;
 		return addTag(null, null, null);

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

@@ -181,6 +181,7 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String> {
 	/**
 	 * @deprecated Use {@link #getIdPartAsBigDecimal()} instead (this method was deprocated because its name is ambiguous)
 	 */
+	@Deprecated
 	public BigDecimal asBigDecimal() {
 		return getIdPartAsBigDecimal();
 	}

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

@@ -28,6 +28,7 @@ import java.lang.annotation.Target;
 /**
  * @deprecated IdDt can now hold both an ID and a version ID, so a single parameter with the {@link IdParam} annotation may be used 
  */
+@Deprecated
 @Retention(RetentionPolicy.RUNTIME)
 @Target(ElementType.PARAMETER)
 public @interface VersionIdParam {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/MethodOutcome.java

@@ -97,6 +97,7 @@ public class MethodOutcome {
 	/**
 	 * @deprecated Use the constructor which accepts a single IdDt parameter, and include the logical ID and version ID in that IdDt instance
 	 */
+	@Deprecated
 	public MethodOutcome(IdDt theId, IdDt theVersionId) {
 		myId = theId;
 		myVersionId = theVersionId;
@@ -105,6 +106,7 @@ public class MethodOutcome {
 	/**
 	 * @deprecated Use the constructor which accepts a single IdDt parameter, and include the logical ID and version ID in that IdDt instance
 	 */
+	@Deprecated
 	public MethodOutcome(IdDt theId, IdDt theVersionId, BaseOperationOutcome theBaseOperationOutcome) {
 		myId = theId;
 		myVersionId = theVersionId;
@@ -127,6 +129,7 @@ public class MethodOutcome {
 	/**
 	 * @deprecated {@link MethodOutcome#getId()} should return the complete ID including version if it is available
 	 */
+	@Deprecated
 	public IdDt getVersionId() {
 		return myVersionId;
 	}
@@ -173,6 +176,7 @@ public class MethodOutcome {
 	/**
 	 * @deprecated Put the ID and version ID into the same IdDt instance and pass it to {@link #setId(IdDt)}
 	 */
+	@Deprecated
 	public void setVersionId(IdDt theVersionId) {
 		myVersionId = theVersionId;
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/HttpBasicAuthInterceptor.java

@@ -38,6 +38,7 @@ import ca.uhn.fhir.rest.client.api.IBasicClient;
 /**
  * @deprecated Use {@link ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor} instead. Note that BasicAuthInterceptor class is a HAPI client interceptor instead of being a commons-httpclient interceptor, so you register it to your client instance once it's created using {@link IGenericClient#registerInterceptor(IClientInterceptor)} or {@link IBasicClient#registerInterceptor(IClientInterceptor)} instead 
  */
+@Deprecated
 public class HttpBasicAuthInterceptor  implements HttpRequestInterceptor {
 
 	private String myUsername;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/IGenericClient.java

@@ -66,6 +66,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @deprecated Use {@link #create() fluent method instead}. This method will be removed.
 	 * 
 	 */
+	@Deprecated
 	MethodOutcome create(IResource theResource);
 
 	/**
@@ -83,6 +84,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @return An outcome
 	 * @deprecated Use {@link #delete()} instead
 	 */
+	@Deprecated
 	MethodOutcome delete(Class<? extends IResource> theType, IdDt theId);
 
 	/**
@@ -95,6 +97,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @return An outcome
 	 * @deprecated Use {@link #delete()} instead
 	 */
+	@Deprecated
 	MethodOutcome delete(Class<? extends IResource> theType, String theId);
 
 	/**
@@ -125,6 +128,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @return A bundle containing returned resources
 	 * @deprecated As of 0.9, use the fluent {@link #history()} method instead
 	 */
+	@Deprecated
 	<T extends IResource> Bundle history(Class<T> theType, IdDt theId, DateTimeDt theSince, Integer theLimit);
 
 	/**
@@ -145,6 +149,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @return A bundle containing returned resources
 	 * @deprecated As of 0.9, use the fluent {@link #history()} method instead
 	 */
+	@Deprecated
 	<T extends IResource> Bundle history(Class<T> theType, String theId, DateTimeDt theSince, Integer theLimit);
 
 	/**
@@ -268,6 +273,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @deprecated Use {@link #transaction()}
 	 * 
 	 */
+	@Deprecated
 	List<IResource> transaction(List<IResource> theResources);
 
 	/**
@@ -341,6 +347,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * @return The resource
 	 * @deprecated Deprecated in 0.7 - IdDt can contain an ID and a version, so this class doesn't make a lot of sense
 	 */
+	@Deprecated
 	<T extends IResource> T vread(Class<T> theType, IdDt theId, IdDt theVersionId);
 
 	/**

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link CompositeClientParam} instead. That class is identical to this one but was renamed to reduce
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class CompositeParam<A extends IParam, B extends IParam> extends CompositeClientParam<A,B> {
 
 	public CompositeParam(String theParamName) {

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link DateClientParam} instead. That class is identical to this one but was renamed to reduct
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class DateParam extends DateClientParam {
 
 	public DateParam(String theParamName) {

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

@@ -35,6 +35,7 @@ public interface IClientExecutable<T extends IClientExecutable<?,?>, Y> {
 	 * 
 	 * @deprecated Use the client logging interceptor to log requests and responses instead. See <a href="http://jamesagnew.github.io/hapi-fhir/doc_rest_client.html#req_resp_logging">here</a> for more information.
 	 */
+	@Deprecated
 	T andLogRequestAndResponse(boolean theLogRequestAndResponse);
 
 	T prettyPrint();

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link NumberClientParam} instead. That class is identical to this one but was renamed to reduct
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class NumberParam extends NumberClientParam {
 
 	public NumberParam(String theParamName) {

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link QuantityClientParam} instead. That class is identical to this one but was renamed to reduct
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class QuantityParam extends QuantityClientParam {
 
 	public QuantityParam(String theParamName) {

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link ReferenceClientParam} instead. That class is identical to this one but was renamed to reduct
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class ReferenceParam extends ReferenceClientParam {
 
 	public ReferenceParam(String theParamName) {

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link StringClientParam} instead. That class is identical to this one but was renamed to reduct
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class StringParam extends StringClientParam {
 
 	public StringParam(String theParamName) {

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

@@ -25,6 +25,7 @@ package ca.uhn.fhir.rest.gclient;
  * @deprecated Use {@link TokenClientParam} instead. That class is identical to this one but was renamed to reduct
  *             confusing duplicate names in the API. This class will be removed in a future release.
  */
+@Deprecated
 public class TokenParam extends TokenClientParam {
 
 	public TokenParam(String theParamName) {

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

@@ -27,6 +27,7 @@ import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
 /**
  * @deprecated Use {@link DateParam} instead (this class is identical, but was renamed to be less confusing)
  */
+@Deprecated
 public class QualifiedDateParam extends DateParam {
 	/**
 	 * Constructor

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/ResourceNotFoundException.java

@@ -57,6 +57,7 @@ public class ResourceNotFoundException extends BaseServerResponseException {
 	/**
 	 * @deprecated This doesn't make sense, since an identifier is not a resource ID and shouldn't generate a 404 if it isn't found - Should be removed
 	 */
+	@Deprecated
 	public ResourceNotFoundException(Class<? extends IResource> theClass, BaseIdentifierDt theId) {
 		super(STATUS_CODE, "Resource of type " + theClass.getSimpleName() + " with ID " + theId + " is not known");
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/ResourceVersionNotSpecifiedException.java

@@ -21,13 +21,13 @@ package ca.uhn.fhir.rest.server.exceptions;
  */
 
 import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
-import ca.uhn.fhir.rest.annotation.Update;
 import ca.uhn.fhir.rest.server.Constants;
 
 /**
  * @deprecated Use {@link PreconditionFailedException} instead - This exception is
  * strangely named and will be removed at some point.
  */
+@Deprecated
 public class ResourceVersionNotSpecifiedException extends BaseServerResponseException {
 	public static final int STATUS_CODE = Constants.STATUS_HTTP_412_PRECONDITION_FAILED;
 	private static final long serialVersionUID = 1L;

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

@@ -6,6 +6,7 @@ import static org.junit.Assert.*;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Observable;
 
 import net.sf.json.JSON;
 import net.sf.json.JSONSerializer;
@@ -26,9 +27,9 @@ import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
-import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.Binary;
 import ca.uhn.fhir.model.dstu2.resource.MedicationPrescription;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.resource.QuestionnaireAnswers;
 import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
@@ -53,11 +54,48 @@ public class JsonParserTest {
 		assertEquals("{\"resourceType\":\"Binary\",\"id\":\"11\",\"meta\":{\"versionId\":\"22\"},\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}", val);
 	}
 
+	/**
+	 * see #144 and #146
+	 */
+	@Test
+	public void testParseContained() {
+
+		FhirContext c = FhirContext.forDstu2();
+		IParser parser = c.newJsonParser().setPrettyPrint(true);
+
+		Observation o = new Observation();
+		o.getCode().setText("obs text");
+
+		Patient p = new Patient();
+		p.addName().addFamily("patient family");
+		o.getSubject().setResource(p);
+		
+		String enc = parser.encodeResourceToString(o);
+		ourLog.info(enc);
+		
+		//@formatter:off
+		assertThat(enc, stringContainsInOrder(
+			"\"resourceType\":\"Observation\"",
+			"\"contained\":[",
+			"\"resourceType\":\"Patient\",",
+			"\"id\":\"1\"",
+			"\"reference\":\"#1\""
+			));
+		//@formatter:on
+		
+		o = parser.parseResource(Observation.class, enc);
+		assertEquals("obs text", o.getCode().getText());
+		
+		assertNotNull(o.getSubject().getResource());
+		p = (Patient) o.getSubject().getResource();
+		assertEquals("patient family", p.getNameFirstRep().getFamilyAsSingleString());
+	}
+
 	@Test
 	public void testEncodeAndParseMetaProfileAndTags() {
 		Patient p = new Patient();
 		p.addName().addFamily("FAMILY");
-		
+
 		List<IdDt> profiles = new ArrayList<IdDt>();
 		profiles.add(new IdDt("http://foo/Profile1"));
 		profiles.add(new IdDt("http://foo/Profile2"));
@@ -67,10 +105,10 @@ public class JsonParserTest {
 		tagList.addTag("scheme1", "term1", "label1");
 		tagList.addTag("scheme2", "term2", "label2");
 		ResourceMetadataKeyEnum.TAG_LIST.put(p, tagList);
-		
+
 		String enc = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
 		ourLog.info(enc);
-		
+
 		//@formatter:off
 		assertThat(enc, stringContainsInOrder("\"meta\":{", 
 				"\"profile\":[", 
@@ -91,39 +129,38 @@ public class JsonParserTest {
 				"]", 
 				"},"));
 		//@formatter:on
-		
+
 		Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, enc);
 		List<IdDt> gotLabels = ResourceMetadataKeyEnum.PROFILES.get(parsed);
-		
+
-		assertEquals(2,gotLabels.size());
+		assertEquals(2, gotLabels.size());
 
 		IdDt label = (IdDt) gotLabels.get(0);
 		assertEquals("http://foo/Profile1", label.getValue());
 		label = (IdDt) gotLabels.get(1);
 		assertEquals("http://foo/Profile2", label.getValue());
-		
+
 		tagList = ResourceMetadataKeyEnum.TAG_LIST.get(parsed);
 		assertEquals(2, tagList.size());
-		
+
 		assertEquals(new Tag("scheme1", "term1", "label1"), tagList.get(0));
 		assertEquals(new Tag("scheme2", "term2", "label2"), tagList.get(1));
 	}
 
-	
 	@Test
 	public void testEncodeAndParseSecurityLabels() {
 		Patient p = new Patient();
 		p.addName().addFamily("FAMILY");
-		
+
 		List<BaseCodingDt> labels = new ArrayList<BaseCodingDt>();
 		labels.add(new CodingDt().setSystem("SYSTEM1").setCode("CODE1").setDisplay("DISPLAY1").setPrimary(true).setVersion("VERSION1"));
 		labels.add(new CodingDt().setSystem("SYSTEM2").setCode("CODE2").setDisplay("DISPLAY2").setPrimary(false).setVersion("VERSION2"));
-		
+
 		ResourceMetadataKeyEnum.SECURITY_LABELS.put(p, labels);
 
 		String enc = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
 		ourLog.info(enc);
-		
+
 		//@formatter:off
 		assertEquals("{\n" + 
 			"    \"resourceType\":\"Patient\",\n" + 
@@ -154,11 +191,11 @@ public class JsonParserTest {
 			"    ]\n" + 
 			"}", enc.trim());
 		//@formatter:on
-		
+
 		Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, enc);
 		List<BaseCodingDt> gotLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(parsed);
-		
+
-		assertEquals(2,gotLabels.size());
+		assertEquals(2, gotLabels.size());
 
 		CodingDt label = (CodingDt) gotLabels.get(0);
 		assertEquals("SYSTEM1", label.getSystem());
@@ -175,7 +212,6 @@ public class JsonParserTest {
 		assertEquals("VERSION2", label.getVersion());
 	}
 
-	
 	/**
 	 * Fixing #89
 	 */
@@ -183,9 +219,9 @@ public class JsonParserTest {
 	public void testEncodeBundleWithDeletedEntry() throws ConfigurationException, DataFormatException, IOException {
 		Bundle b = ourCtx.newXmlParser().parseBundle(IOUtils.toString(JsonParserTest.class.getResourceAsStream("/xml-bundle.xml")));
 		String val = ourCtx.newJsonParser().encodeBundleToString(b);
-		
+
 		ourLog.info(val);
-		
+
 		//@formatter:off
 		assertThat(val, containsString("\"deleted\":{" + 
 				"\"type\":\"Patient\"," + 
@@ -236,39 +272,12 @@ public class JsonParserTest {
 		ourLog.info(output);
 
 		String enc = ourCtx.newJsonParser().encodeResourceToString(patient);
-		assertThat(enc, Matchers.stringContainsInOrder("{\"resourceType\":\"Patient\",",
+		assertThat(enc, Matchers.stringContainsInOrder("{\"resourceType\":\"Patient\",", "\"extension\":[{\"url\":\"http://example.com/extensions#someext\",\"valueDateTime\":\"2011-01-02T11:13:15\"}",
-				"\"extension\":[{\"url\":\"http://example.com/extensions#someext\",\"valueDateTime\":\"2011-01-02T11:13:15\"}",
+				"{\"url\":\"http://example.com#parent\",\"extension\":[{\"url\":\"http://example.com#child\",\"valueString\":\"value1\"},{\"url\":\"http://example.com#child\",\"valueString\":\"value2\"}]}"));
-				"{\"url\":\"http://example.com#parent\",\"extension\":[{\"url\":\"http://example.com#child\",\"valueString\":\"value1\"},{\"url\":\"http://example.com#child\",\"valueString\":\"value2\"}]}"
+		assertThat(enc, Matchers.stringContainsInOrder("\"modifierExtension\":[" + "{" + "\"url\":\"http://example.com/extensions#modext\"," + "\"valueDate\":\"1995-01-02\"" + "}" + "],"));
-		));
+		assertThat(enc, containsString("\"_given\":[" + "{" + "\"extension\":[" + "{" + "\"url\":\"http://examples.com#givenext\"," + "\"valueString\":\"given\"" + "}" + "]" + "}," + "{" + "\"extension\":[" + "{" + "\"url\":\"http://examples.com#givenext_parent\"," + "\"extension\":[" + "{"
-		assertThat(enc, Matchers.stringContainsInOrder("\"modifierExtension\":[" +
+				+ "\"url\":\"http://examples.com#givenext_child\"," + "\"valueString\":\"CHILD\"" + "}" + "]" + "}" + "]" + "}"));
-				"{" +
+
-				"\"url\":\"http://example.com/extensions#modext\"," +
-				"\"valueDate\":\"1995-01-02\"" +
-				"}" +
-				"],"));
-		assertThat(enc, containsString("\"_given\":[" +
-				"{" +
-				"\"extension\":[" +
-				"{" +
-				"\"url\":\"http://examples.com#givenext\"," +
-				"\"valueString\":\"given\"" +
-				"}" +
-				"]" +
-				"}," +
-				"{" +
-				"\"extension\":[" +
-				"{" +
-				"\"url\":\"http://examples.com#givenext_parent\"," +
-				"\"extension\":[" +
-				"{" +
-				"\"url\":\"http://examples.com#givenext_child\"," +
-				"\"valueString\":\"CHILD\"" +
-				"}" +
-				"]" +
-				"}" +
-				"]" +
-				"}"));
-		
 		/*
 		 * Now parse this back
 		 */
@@ -307,22 +316,20 @@ public class JsonParserTest {
 
 	}
 
-	
-	
 	/**
 	 * #65
 	 */
 	@Test
 	public void testJsonPrimitiveWithExtensionEncoding() {
-		
+
 		QuestionnaireAnswers parsed = new QuestionnaireAnswers();
 		parsed.getGroup().setLinkId("value123");
 		parsed.getGroup().getLinkIdElement().addUndeclaredExtension(false, "http://123", new StringDt("HELLO"));
-	
+
 		String encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(parsed);
 		ourLog.info(encoded);
 		assertThat(encoded, containsString("{\"linkId\":\"value123\",\"_linkId\":{\"extension\":[{\"url\":\"http://123\",\"valueString\":\"HELLO\"}]}}"));
-		
+
 	}
 
 	@Test
@@ -358,10 +365,10 @@ public class JsonParserTest {
 			"   }]\n" + 
 			"}";
 		//@formatter:on
-		
+
 		Bundle b = ourCtx.newJsonParser().parseBundle(bundle);
 		assertEquals(1, b.getEntries().size());
-		
+
 		Patient pt = (Patient) b.getEntries().get(0).getResource();
 		assertEquals("http://foo/fhirBase2/Patient/1/_history/2", pt.getId().getValue());
 		assertEquals("2012-01-02", pt.getBirthDateElement().getValueAsString());
@@ -370,12 +377,12 @@ public class JsonParserTest {
 		assertEquals("POST", ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(pt).getCode());
 		assertEquals("http://foo/Patient?identifier=value", ResourceMetadataKeyEnum.LINK_SEARCH.get(pt));
 		assertEquals("2001-02-22T11:22:33-05:00", ResourceMetadataKeyEnum.UPDATED.get(pt).getValueAsString());
-		
+
 		Bundle toBundle = new Bundle();
 		toBundle.getLinkBase().setValue("http://foo/fhirBase1");
 		toBundle.getTotalResults().setValue(1);
 		toBundle.getLinkSelf().setValue("http://localhost:52788/Binary?_pretty=true");
-		
+
 		toBundle.addResource(pt, ourCtx, "http://foo/fhirBase1");
 		String reEncoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(toBundle);
 
@@ -394,22 +401,20 @@ public class JsonParserTest {
 
 	}
 
-	
-	
 	@Test
 	public void testParsePatientInBundle() {
-		
+
 		String text = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 		FhirContext ctx = FhirContext.forDstu2();
 		Bundle b = ctx.newJsonParser().parseBundle(text);
-		
+
 		IResource patient = b.getEntries().get(0).getResource();
 		assertEquals(Patient.class, patient.getClass());
-		
+
 		assertNull(ResourceMetadataKeyEnum.TAG_LIST.get(patient));
 		assertNull(ResourceMetadataKeyEnum.PROFILES.get(patient));
 	}
-	
+
 	@Test
 	public void testParseAndEncodeBundle() throws Exception {
 		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-example.json"));
@@ -455,22 +460,25 @@ public class JsonParserTest {
 		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-transaction.json"));
 
 		Bundle parsed = ourCtx.newJsonParser().parseBundle(content);
-//		assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
+		// assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
-//		assertEquals("1", parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.VERSION));
+		// assertEquals("1", parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.VERSION));
-//		assertEquals("1", parsed.getId().getVersionIdPart());
+		// assertEquals("1", parsed.getId().getVersionIdPart());
-//		assertEquals(new InstantDt("2014-08-18T01:43:30Z"), parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
+		// assertEquals(new InstantDt("2014-08-18T01:43:30Z"),
-//		assertEquals("searchset", parsed.getType().getValue());
+		// parsed.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
-//		assertEquals(3, parsed.getTotalResults().getValue().intValue());
+		// assertEquals("searchset", parsed.getType().getValue());
-//		assertEquals("http://example.com/base", parsed.getLinkBase().getValue());
+		// assertEquals(3, parsed.getTotalResults().getValue().intValue());
-//		assertEquals("https://example.com/base/MedicationPrescription?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLinkNext().getValue());
+		// assertEquals("http://example.com/base", parsed.getLinkBase().getValue());
-//		assertEquals("https://example.com/base/MedicationPrescription?patient=347&_include=MedicationPrescription.medication", parsed.getLinkSelf().getValue());
+		// assertEquals("https://example.com/base/MedicationPrescription?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2",
-//
+		// parsed.getLinkNext().getValue());
-//		assertEquals(2, parsed.getEntries().size());
+		// assertEquals("https://example.com/base/MedicationPrescription?patient=347&_include=MedicationPrescription.medication",
-//
+		// parsed.getLinkSelf().getValue());
-//		MedicationPrescription p = (MedicationPrescription) parsed.getEntries().get(0).getResource();
+		//
-//		assertEquals("Patient/347", p.getPatient().getReference().getValue());
+		// assertEquals(2, parsed.getEntries().size());
-//		assertEquals("2014-08-16T05:31:17Z", ResourceMetadataKeyEnum.UPDATED.get(p).getValueAsString());
+		//
-//		assertEquals("http://example.com/base/MedicationPrescription/3123/_history/1", p.getId().getValue());
+		// MedicationPrescription p = (MedicationPrescription) parsed.getEntries().get(0).getResource();
+		// assertEquals("Patient/347", p.getPatient().getReference().getValue());
+		// assertEquals("2014-08-16T05:31:17Z", ResourceMetadataKeyEnum.UPDATED.get(p).getValueAsString());
+		// assertEquals("http://example.com/base/MedicationPrescription/3123/_history/1", p.getId().getValue());
 
 		String reencoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(parsed);
 		ourLog.info(reencoded);
@@ -483,15 +491,15 @@ public class JsonParserTest {
 		String exp = expected.toString().replace("\\r\\n", "\\n"); // .replace("&sect;", "§");
 		String act = actual.toString().replace("\\r\\n", "\\n");
 
-		exp=exp.replace(",\"ifNoneExist\":\"Patient?identifier=234234\"", "");
+		exp = exp.replace(",\"ifNoneExist\":\"Patient?identifier=234234\"", "");
-		
+
 		ourLog.info("Expected: {}", exp);
 		ourLog.info("Actual  : {}", act);
 
 		assertEquals(exp, act);
 
 	}
-	
+
 	@Test
 	public void testParseAndEncodeBundleNewStyle() throws Exception {
 		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-example.json"));
@@ -532,24 +540,22 @@ public class JsonParserTest {
 
 	}
 
-	
-	
 	@Test
 	public void testParseAndEncodeBundleWithDeletedEntry() {
-		
+
 		Patient res = new Patient();
 		res.setId(new IdDt("Patient", "111", "222"));
 		ResourceMetadataKeyEnum.DELETED_AT.put(res, new InstantDt("2011-01-01T12:12:22Z"));
-		
+
 		Bundle bundle = new Bundle();
 		bundle.addResource(res, ourCtx, "http://foo/base");
-		
+
 		String actual = ourCtx.newJsonParser().encodeBundleToString(bundle);
 		ourLog.info(actual);
-		
+
 		String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"deleted\":{\"type\":\"Patient\",\"resourceId\":\"111\",\"versionId\":\"222\",\"instant\":\"2011-01-01T12:12:22Z\"}}]}";
 		assertEquals(expected, actual);
-		
+
 	}
 
 }

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

@@ -1,11 +1,7 @@
 package ca.uhn.fhir.parser;
 
 import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
 
 import java.io.StringReader;
 import java.util.ArrayList;
@@ -37,6 +33,7 @@ import ca.uhn.fhir.model.dstu2.resource.Composition;
 import ca.uhn.fhir.model.dstu2.resource.Encounter;
 import ca.uhn.fhir.model.dstu2.resource.Medication;
 import ca.uhn.fhir.model.dstu2.resource.MedicationPrescription;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
@@ -57,6 +54,44 @@ public class XmlParserTest {
 		XMLUnit.setIgnoreWhitespace(true);
 	}
 
+	/**
+	 * see #144 and #146
+	 */
+	@Test
+	public void testParseContained() {
+
+		FhirContext c = FhirContext.forDstu2();
+		IParser parser = c.newXmlParser().setPrettyPrint(true);
+
+		Observation o = new Observation();
+		o.getCode().setText("obs text");
+
+		Patient p = new Patient();
+		p.addName().addFamily("patient family");
+		o.getSubject().setResource(p);
+		
+		String enc = parser.encodeResourceToString(o);
+		ourLog.info(enc);
+		
+		//@formatter:off
+		assertThat(enc, stringContainsInOrder(
+			"<Observation xmlns=\"http://hl7.org/fhir\">",
+			"<contained>",
+			"<Patient xmlns=\"http://hl7.org/fhir\">",
+			"<id value=\"1\"/>",
+			"</contained>",
+			"<reference value=\"#1\"/>"
+			));
+		//@formatter:on
+		
+		o = parser.parseResource(Observation.class, enc);
+		assertEquals("obs text", o.getCode().getText());
+		
+		assertNotNull(o.getSubject().getResource());
+		p = (Patient) o.getSubject().getResource();
+		assertEquals("patient family", p.getNameFirstRep().getFamilyAsSingleString());
+	}
+
 	/**
 	 * See #113
 	 */

pom.xml

@@ -217,11 +217,30 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.2</version>
+					<version>3.3</version>
 					<configuration>
 						<source>1.6</source>
 						<target>1.6</target>
+						<compilerId>javac-with-errorprone</compilerId>
+						<forceJavacCompilerUse>true</forceJavacCompilerUse>
 					</configuration>
+					<dependencies>
+						<dependency>
+							<groupId>com.google.errorprone</groupId>
+							<artifactId>error_prone_core</artifactId>
+							<version>2.0.1</version>
+						</dependency>
+						<dependency>
+							<groupId>org.codehaus.plexus</groupId>
+							<artifactId>plexus-compiler-javac</artifactId>
+							<version>2.5</version>
+						</dependency>
+						<dependency>
+							<groupId>org.codehaus.plexus</groupId>
+							<artifactId>plexus-compiler-javac-errorprone</artifactId>
+							<version>2.5</version>
+						</dependency>
+					</dependencies>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -374,6 +393,26 @@
 										<ignore></ignore>
 									</action>
 								</pluginExecution>
+								<pluginExecution>
+									<pluginExecutionFilter>
+										<groupId>
+											org.apache.maven.plugins
+										</groupId>
+										<artifactId>
+											maven-compiler-plugin
+										</artifactId>
+										<versionRange>
+											[3.3,)
+										</versionRange>
+										<goals>
+											<goal>compile</goal>
+											<goal>testCompile</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<ignore></ignore>
+									</action>
+								</pluginExecution>
 							</pluginExecutions>
 						</lifecycleMappingMetadata>
 					</configuration>