Enhanced elements (#1192)

Squashed merge: Add elements exclude mode

* Start working on elements enhancement

* Work on elements projection

* Work on elements filter

* Feature is now working

* Just some cleanup

* Address compile issues

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

@@ -30,11 +30,13 @@ import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.hl7.fhir.instance.model.api.*;
 
 import java.io.*;
 import java.lang.reflect.Modifier;
 import java.util.*;
+import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -47,11 +49,9 @@ public abstract class BaseParser implements IParser {
 	private ContainedResources myContainedResources;
 	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private FhirContext myContext;
-	private Set<String> myDontEncodeElements;
+	private List<ElementsPath> myDontEncodeElements;
-	private boolean myDontEncodeElementsIncludesStars;
+	private List<ElementsPath> myEncodeElements;
-	private Set<String> myEncodeElements;
 	private Set<String> myEncodeElementsAppliesToResourceTypes;
-	private boolean myEncodeElementsIncludesStars;
 	private IIdType myEncodeForceResourceId;
 	private IParserErrorHandler myErrorHandler;
 	private boolean myOmitResourceId;
@@ -65,20 +65,19 @@ public abstract class BaseParser implements IParser {
 
 	/**
 	 * Constructor
-	 *
-	 * @param theParserErrorHandler
 	 */
 	public BaseParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
 		myContext = theContext;
 		myErrorHandler = theParserErrorHandler;
 	}
 
-	protected Iterable<CompositeChildElement> compositeChildIterator(IBase theCompositeElement, final boolean theContainedResource, final boolean theSubResource, final CompositeChildElement theParent) {
+	protected Iterable<CompositeChildElement> compositeChildIterator(IBase theCompositeElement, final boolean theContainedResource, final CompositeChildElement theParent, EncodeContext theEncodeContext) {
 
 		BaseRuntimeElementCompositeDefinition<?> elementDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theCompositeElement.getClass());
 		final List<BaseRuntimeChildDefinition> children = elementDef.getChildrenAndExtension();
 
 		return new Iterable<BaseParser.CompositeChildElement>() {
+
 			@Override
 			public Iterator<CompositeChildElement> iterator() {
 
@@ -106,7 +105,7 @@ public abstract class BaseParser implements IParser {
 								return false;
 							}
 
-							myNext = new CompositeChildElement(theParent, myChildrenIter.next(), theSubResource);
+							myNext = new CompositeChildElement(theParent, myChildrenIter.next(), theEncodeContext);
 
 							/*
 							 * There are lots of reasons we might skip encoding a particular child
@@ -181,8 +180,6 @@ public abstract class BaseParser implements IParser {
 					theContained.getExistingIdToContainedResource().put(nextId, next);
 				}
 			}
-		} else {
-			// no resources to contain
 		}
 
 		List<IBaseReference> allReferences = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
@@ -279,7 +276,7 @@ public abstract class BaseParser implements IParser {
 		return ref.getValue();
 	}
 
-	protected abstract void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException, DataFormatException;
+	protected abstract void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext) throws IOException, DataFormatException;
 
 	protected abstract <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) throws DataFormatException;
 
@@ -296,15 +293,27 @@ public abstract class BaseParser implements IParser {
 
 	@Override
 	public final void encodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException, DataFormatException {
+		EncodeContext encodeContext = new EncodeContext();
+
+		encodeResourceToWriter(theResource, theWriter, encodeContext);
+	}
+
+	protected void encodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext) throws IOException {
 		Validate.notNull(theResource, "theResource can not be null");
 		Validate.notNull(theWriter, "theWriter can not be null");
+		Validate.notNull(theEncodeContext, "theEncodeContext can not be null");
 
 		if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
 			throw new IllegalArgumentException(
 				"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
 		}
 
-		doEncodeResourceToWriter(theResource, theWriter);
+		String resourceName = myContext.getResourceDefinition(theResource).getName();
+		theEncodeContext.pushPath(resourceName, true);
+
+		doEncodeResourceToWriter(theResource, theWriter, theEncodeContext);
+
+		theEncodeContext.popPath();
 	}
 
 	private void filterCodingsWithNoCodeOrSystem(List<? extends IBaseCoding> tagList) {
@@ -392,43 +401,32 @@ public abstract class BaseParser implements IParser {
 		return myDontStripVersionsFromReferencesAtPaths;
 	}
 
-	/**
-	 * See {@link #setEncodeElements(Set)}
-	 */
-	@Override
-	public Set<String> getEncodeElements() {
-		return myEncodeElements;
-	}
-
 	@Override
 	public void setEncodeElements(Set<String> theEncodeElements) {
-		myEncodeElementsIncludesStars = false;
+
 		if (theEncodeElements == null || theEncodeElements.isEmpty()) {
 			myEncodeElements = null;
-		} else {
-			myEncodeElements = theEncodeElements;
-			for (String next : theEncodeElements) {
-				if (next.startsWith("*.")) {
-					myEncodeElementsIncludesStars = true;
-				}
-			}
-		}
-	}
-
-	/**
-	 * See {@link #setEncodeElementsAppliesToResourceTypes(Set)}
-	 */
-	@Override
-	public Set<String> getEncodeElementsAppliesToResourceTypes() {
-		return myEncodeElementsAppliesToResourceTypes;
-	}
-
-	@Override
-	public void setEncodeElementsAppliesToResourceTypes(Set<String> theEncodeElementsAppliesToResourceTypes) {
-		if (theEncodeElementsAppliesToResourceTypes == null || theEncodeElementsAppliesToResourceTypes.isEmpty()) {
 			myEncodeElementsAppliesToResourceTypes = null;
 		} else {
-			myEncodeElementsAppliesToResourceTypes = theEncodeElementsAppliesToResourceTypes;
+			myEncodeElements = theEncodeElements
+				.stream()
+				.map(ElementsPath::new)
+				.collect(Collectors.toList());
+
+			myEncodeElementsAppliesToResourceTypes = new HashSet<>();
+			for (String next : myEncodeElements.stream().map(t -> t.getPath().get(0).getName()).collect(Collectors.toList())) {
+				if (next.startsWith("*")) {
+					myEncodeElementsAppliesToResourceTypes = null;
+					break;
+				}
+				int dotIdx = next.indexOf('.');
+				if (dotIdx == -1) {
+					myEncodeElementsAppliesToResourceTypes.add(next);
+				} else {
+					myEncodeElementsAppliesToResourceTypes.add(next.substring(0, dotIdx));
+				}
+			}
+
 		}
 	}
 
@@ -448,7 +446,7 @@ public abstract class BaseParser implements IParser {
 	}
 
 	protected List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> getExtensionMetadataKeys(IResource resource) {
-		List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys = new ArrayList<Map.Entry<ResourceMetadataKeyEnum<?>, Object>>();
+		List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys = new ArrayList<>();
 		for (Map.Entry<ResourceMetadataKeyEnum<?>, Object> entry : resource.getResourceMetadata().entrySet()) {
 			if (entry.getKey() instanceof ResourceMetadataKeyEnum.ExtensionResourceMetadataKey) {
 				extensionMetadataKeys.add(entry);
@@ -466,9 +464,9 @@ public abstract class BaseParser implements IParser {
 		return url;
 	}
 
-	protected TagList getMetaTagsForEncoding(IResource theIResource) {
+	protected TagList getMetaTagsForEncoding(IResource theIResource, EncodeContext theEncodeContext) {
 		TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(theIResource);
-		if (shouldAddSubsettedTag()) {
+		if (shouldAddSubsettedTag(theEncodeContext)) {
 			tags = new TagList(tags);
 			tags.add(new Tag(getSubsettedCodeSystem(), Constants.TAG_SUBSETTED_CODE, subsetDescription()));
 		}
@@ -709,7 +707,7 @@ public abstract class BaseParser implements IParser {
 	}
 
 	protected List<? extends IBase> preProcessValues(BaseRuntimeChildDefinition theMetaChildUncast, IBaseResource theResource, List<? extends IBase> theValues,
-																	 CompositeChildElement theCompositeChildElement) {
+																	 CompositeChildElement theCompositeChildElement, EncodeContext theEncodeContext) {
 		if (myContext.getVersion().getVersion().isRi()) {
 
 			/*
@@ -754,7 +752,7 @@ public abstract class BaseParser implements IParser {
 					}
 				}
 
-				if (shouldAddSubsettedTag()) {
+				if (shouldAddSubsettedTag(theEncodeContext)) {
 					IBaseCoding coding = metaValue.addTag();
 					coding.setCode(Constants.TAG_SUBSETTED_CODE);
 					coding.setSystem(getSubsettedCodeSystem());
@@ -806,16 +804,13 @@ public abstract class BaseParser implements IParser {
 
 	@Override
 	public void setDontEncodeElements(Set<String> theDontEncodeElements) {
-		myDontEncodeElementsIncludesStars = false;
 		if (theDontEncodeElements == null || theDontEncodeElements.isEmpty()) {
 			myDontEncodeElements = null;
 		} else {
-			myDontEncodeElements = theDontEncodeElements;
+			myDontEncodeElements = theDontEncodeElements
-			for (String next : theDontEncodeElements) {
+				.stream()
-				if (next.startsWith("*.")) {
+				.map(ElementsPath::new)
-					myDontEncodeElementsIncludesStars = true;
+				.collect(Collectors.toList());
-				}
-			}
 		}
 	}
 
@@ -885,22 +880,39 @@ public abstract class BaseParser implements IParser {
 		return this;
 	}
 
-	protected boolean shouldAddSubsettedTag() {
+	protected boolean shouldAddSubsettedTag(EncodeContext theEncodeContext) {
-		return isSummaryMode() || isSuppressNarratives() || getEncodeElements() != null;
+		if (isSummaryMode()) {
+			return true;
+		}
+		if (isSuppressNarratives()) {
+			return true;
+		}
+		if (myEncodeElements != null) {
+			if (isEncodeElementsAppliesToChildResourcesOnly() && theEncodeContext.getResourcePath().size() < 2) {
+				return false;
 			}
 
-	protected boolean shouldEncodeResourceId(IBaseResource theResource, boolean theSubResource) {
+			String currentResourceName = theEncodeContext.getResourcePath().get(theEncodeContext.getResourcePath().size() - 1).getName();
+			if (myEncodeElementsAppliesToResourceTypes == null || myEncodeElementsAppliesToResourceTypes.contains(currentResourceName)) {
+				return true;
+			}
+		}
+
+		return false;
+	}
+
+	protected boolean shouldEncodeResourceId(IBaseResource theResource, EncodeContext theEncodeContext) {
 		boolean retVal = true;
 		if (isOmitResourceId()) {
 			retVal = false;
 		} else {
 			if (myDontEncodeElements != null) {
 				String resourceName = myContext.getResourceDefinition(theResource).getName();
-				if (myDontEncodeElements.contains(resourceName + ".id")) {
+				if (myDontEncodeElements.stream().anyMatch(t -> t.startsWithPath(resourceName + ".id"))) {
 					retVal = false;
-				} else if (myDontEncodeElements.contains("*.id")) {
+				} else if (myDontEncodeElements.stream().anyMatch(t -> t.startsWithPath("*.id"))) {
 					retVal = false;
-				} else if (theSubResource == false && myDontEncodeElements.contains("id")) {
+				} else if (theEncodeContext.getResourcePath().size() == 1 && myDontEncodeElements.stream().anyMatch(t -> t.startsWithPath("id"))) {
 					retVal = false;
 				}
 			}
@@ -914,9 +926,11 @@ public abstract class BaseParser implements IParser {
 	protected boolean shouldEncodeResourceMeta(IResource theResource) {
 		if (myDontEncodeElements != null) {
 			String resourceName = myContext.getResourceDefinition(theResource).getName();
-			if (myDontEncodeElements.contains(resourceName + ".meta")) {
+			if (myDontEncodeElements.stream().anyMatch(t -> t.startsWithPath(resourceName + ".meta"))) {
 				return false;
-			} else return !myDontEncodeElements.contains("*.meta");
+			} else {
+				return myDontEncodeElements.stream().anyMatch(t -> t.startsWithPath("*.meta"));
+			}
 		}
 		return true;
 	}
@@ -965,13 +979,13 @@ public abstract class BaseParser implements IParser {
 		private final BaseRuntimeChildDefinition myDef;
 		private final CompositeChildElement myParent;
 		private final RuntimeResourceDefinition myResDef;
-		private final boolean mySubResource;
+		private final EncodeContext myEncodeContext;
 
-		public CompositeChildElement(CompositeChildElement theParent, BaseRuntimeChildDefinition theDef, boolean theSubResource) {
+		public CompositeChildElement(CompositeChildElement theParent, BaseRuntimeChildDefinition theDef, EncodeContext theEncodeContext) {
 			myDef = theDef;
 			myParent = theParent;
 			myResDef = null;
-			mySubResource = theSubResource;
+			myEncodeContext = theEncodeContext;
 
 			if (ourLog.isTraceEnabled()) {
 				if (theParent != null) {
@@ -986,11 +1000,11 @@ public abstract class BaseParser implements IParser {
 
 		}
 
-		public CompositeChildElement(RuntimeResourceDefinition theResDef, boolean theSubResource) {
+		public CompositeChildElement(RuntimeResourceDefinition theResDef, EncodeContext theEncodeContext) {
 			myResDef = theResDef;
 			myDef = null;
 			myParent = null;
-			mySubResource = theSubResource;
+			myEncodeContext = theEncodeContext;
 		}
 
 		private void addParent(CompositeChildElement theParent, StringBuilder theB) {
@@ -1038,71 +1052,75 @@ public abstract class BaseParser implements IParser {
 			}
 		}
 
-		private boolean checkIfParentShouldBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
+		private boolean checkIfParentShouldBeEncodedAndBuildPath() {
-			Set<String> encodeElements = myEncodeElements;
+			List<ElementsPath> encodeElements = myEncodeElements;
-			if (encodeElements != null && encodeElements.isEmpty() == false) {
+
-				if (isEncodeElementsAppliesToChildResourcesOnly() && !mySubResource) {
+			String currentResourceName = myEncodeContext.getResourcePath().get(myEncodeContext.getResourcePath().size() - 1).getName();
+			if (myEncodeElementsAppliesToResourceTypes != null && !myEncodeElementsAppliesToResourceTypes.contains(currentResourceName)) {
 				encodeElements = null;
 			}
-			}
-			return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, encodeElements, true);
-		}
 
-		private boolean checkIfParentShouldNotBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
+			boolean retVal = checkIfPathMatchesForEncoding(encodeElements, true);
-			return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, null, myDontEncodeElements, false);
-		}
 
-		private boolean checkIfPathMatchesForEncoding(StringBuilder thePathBuilder, boolean theStarPass, Set<String> theResourceTypes, Set<String> theElements, boolean theCheckingForWhitelist) {
+			/*
-			if (myResDef != null) {
+			 * We force the meta tag to be encoded even if it's not specified as an element in the
-				if (theResourceTypes != null) {
+			 * elements filter, specifically because we'll need it in order to automatically add
-					if (!theResourceTypes.contains(myResDef.getName())) {
+			 * the SUBSETTED tag
-						return true;
+			 */
-					}
-				}
-				if (theStarPass) {
-					thePathBuilder.append('*');
-				} else {
-					thePathBuilder.append(myResDef.getName());
-				}
-				if (theElements == null) {
-					return true;
-				}
-				return theElements.contains(thePathBuilder.toString());
-			} else if (myParent != null) {
-				boolean parentCheck;
-				if (theCheckingForWhitelist) {
-					parentCheck = myParent.checkIfParentShouldBeEncodedAndBuildPath(thePathBuilder, theStarPass);
-				} else {
-					parentCheck = myParent.checkIfParentShouldNotBeEncodedAndBuildPath(thePathBuilder, theStarPass);
-				}
-				if (parentCheck) {
-					return true;
-				}
-
-				if (myDef != null) {
-					if (myDef.getMin() > 0) {
-						if (theElements.contains("*.(mandatory)")) {
-							return true;
-						}
-					}
-
-					thePathBuilder.append('.');
-					thePathBuilder.append(myDef.getElementName());
-					String currentPath = thePathBuilder.toString();
-					boolean retVal = theElements.contains(currentPath);
-					int dotIdx = currentPath.indexOf('.');
 			if (!retVal) {
-						if (dotIdx != -1 && theElements.contains(currentPath.substring(dotIdx + 1))) {
+				if ("meta".equals(myEncodeContext.getLeafResourcePathFirstField()) && shouldAddSubsettedTag(myEncodeContext)) {
-							if (!myParent.isSubResource()) {
+					// The next element is a child of the <meta> element
-								return true;
+					retVal = true;
-							}
+				} else if ("meta".equals(myDef.getElementName()) && shouldAddSubsettedTag(myEncodeContext)) {
+					// The next element is the <meta> element
+					retVal = true;
 				}
 			}
+
 			return retVal;
 		}
+
+		private boolean checkIfParentShouldNotBeEncodedAndBuildPath() {
+			return checkIfPathMatchesForEncoding(myDontEncodeElements, false);
 		}
 
-			return false;
+		private boolean checkIfPathMatchesForEncoding(List<ElementsPath> theElements, boolean theCheckingForEncodeElements) {
+
+			boolean retVal = false;
+			myEncodeContext.pushPath(myDef.getElementName(), false);
+
+			if (theCheckingForEncodeElements && isEncodeElementsAppliesToChildResourcesOnly() && myEncodeContext.getResourcePath().size() < 2) {
+				retVal = true;
+			} else if (theElements == null) {
+				retVal = true;
+			} else {
+				EncodeContextPath currentResourcePath = myEncodeContext.getCurrentResourcePath();
+				ourLog.trace("Current resource path: {}", currentResourcePath);
+				for (ElementsPath next : theElements) {
+
+					if (next.startsWith(currentResourcePath)) {
+						if (theCheckingForEncodeElements || next.getPath().size() == currentResourcePath.getPath().size()) {
+							retVal = true;
+							break;
+						}
+					}
+
+					if (next.getPath().get(next.getPath().size() - 1).getName().equals("(mandatory)")) {
+						if (myDef.getMin() > 0) {
+							retVal = true;
+							break;
+						}
+						if (currentResourcePath.getPath().size() > next.getPath().size()) {
+							retVal = true;
+							break;
+						}
+					}
+
+				}
+			}
+
+			myEncodeContext.popPath();
+			return retVal;
 		}
 
 		public BaseRuntimeChildDefinition getDef() {
@@ -1113,38 +1131,189 @@ public abstract class BaseParser implements IParser {
 			return myParent;
 		}
 
-		public RuntimeResourceDefinition getResDef() {
-			return myResDef;
-		}
-
-		private boolean isSubResource() {
-			return mySubResource;
-		}
-
 		public boolean shouldBeEncoded() {
 			boolean retVal = true;
 			if (myEncodeElements != null) {
-				retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), false);
+				retVal = checkIfParentShouldBeEncodedAndBuildPath();
-				if (retVal == false && myEncodeElementsIncludesStars) {
-					retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), true);
-				}
 			}
 			if (retVal && myDontEncodeElements != null) {
-				retVal = !checkIfParentShouldNotBeEncodedAndBuildPath(new StringBuilder(), false);
+				retVal = !checkIfParentShouldNotBeEncodedAndBuildPath();
-				if (retVal && myDontEncodeElementsIncludesStars) {
-					retVal = !checkIfParentShouldNotBeEncodedAndBuildPath(new StringBuilder(), true);
 			}
-			}
-			// if (retVal == false && myEncodeElements.contains("*.(mandatory)")) {
-			// if (myDef.getMin() > 0) {
-			// retVal = true;
-			// }
-			// }
 
 			return retVal;
 		}
 	}
 
+	protected class EncodeContextPath {
+		private final List<EncodeContextPathElement> myPath;
+
+		public EncodeContextPath() {
+			myPath = new ArrayList<>(10);
+		}
+
+		public EncodeContextPath(List<EncodeContextPathElement> thePath) {
+			myPath = thePath;
+		}
+
+		@Override
+		public String toString() {
+			return myPath.toString();
+		}
+
+		protected List<EncodeContextPathElement> getPath() {
+			return myPath;
+		}
+
+		public EncodeContextPath getCurrentResourcePath() {
+			EncodeContextPath retVal = null;
+			for (int i = myPath.size() - 1; i >= 0; i--) {
+				if (myPath.get(i).isResource()) {
+					retVal = new EncodeContextPath(myPath.subList(i, myPath.size()));
+					break;
+				}
+			}
+			Validate.isTrue(retVal != null);
+			return retVal;
+		}
+	}
+
+	protected class ElementsPath extends EncodeContextPath {
+
+		protected ElementsPath(String thePath) {
+			StringTokenizer tok = new StringTokenizer(thePath, ".");
+			boolean first = true;
+			while (tok.hasMoreTokens()) {
+				String next = tok.nextToken();
+				if (first && next.equals("*")) {
+					getPath().add(new EncodeContextPathElement("*", true));
+				} else if (isNotBlank(next)) {
+					getPath().add(new EncodeContextPathElement(next, Character.isUpperCase(next.charAt(0))));
+				}
+				first = false;
+			}
+		}
+
+		public boolean startsWith(EncodeContextPath theCurrentResourcePath) {
+			for (int i = 0; i < getPath().size(); i++) {
+				if (theCurrentResourcePath.getPath().size() == i) {
+					return true;
+				}
+				EncodeContextPathElement expected = getPath().get(i);
+				EncodeContextPathElement actual = theCurrentResourcePath.getPath().get(i);
+				if (!expected.matches(actual)) {
+					return false;
+				}
+			}
+			return true;
+		}
+
+		public boolean startsWithPath(String thePath) {
+			return startsWith(new ElementsPath(thePath));
+		}
+	}
+
+
+	/**
+	 * EncodeContext is a shared state object that is passed around the
+	 * encode process
+	 */
+	protected class EncodeContext extends EncodeContextPath {
+		private final ArrayList<EncodeContextPathElement> myResourcePath = new ArrayList<>(10);
+
+		protected ArrayList<EncodeContextPathElement> getResourcePath() {
+			return myResourcePath;
+		}
+
+		public String getLeafResourcePathFirstField() {
+			String retVal = null;
+			for (int i = getPath().size() - 1; i >= 0; i--) {
+				if (getPath().get(i).isResource()) {
+					break;
+				} else {
+					retVal = getPath().get(i).getName();
+				}
+			}
+			return retVal;
+		}
+
+
+		/**
+		 * Add an element at the end of the path
+		 */
+		protected void pushPath(String thePathElement, boolean theResource) {
+			assert isNotBlank(thePathElement);
+			assert !thePathElement.contains(".");
+			assert theResource ^ Character.isLowerCase(thePathElement.charAt(0));
+
+			EncodeContextPathElement element = new EncodeContextPathElement(thePathElement, theResource);
+			getPath().add(element);
+			if (theResource) {
+				myResourcePath.add(element);
+			}
+		}
+
+		/**
+		 * Remove the element at the end of the path
+		 */
+		public void popPath() {
+			EncodeContextPathElement removed = getPath().remove(getPath().size() - 1);
+			if (removed.isResource()) {
+				myResourcePath.remove(myResourcePath.size() - 1);
+			}
+		}
+
+
+	}
+
+	protected class EncodeContextPathElement {
+		private final String myName;
+		private final boolean myResource;
+
+		public EncodeContextPathElement(String theName, boolean theResource) {
+			Validate.notBlank(theName);
+			myName = theName;
+			myResource = theResource;
+		}
+
+
+		public boolean matches(EncodeContextPathElement theOther) {
+			if (myResource != theOther.isResource()) {
+				return false;
+			}
+			if (myName.equals(theOther.getName())) {
+				return true;
+			}
+			if (myName.equals("*")) {
+				return true;
+			}
+			return false;
+		}
+
+		@Override
+		public int hashCode() {
+			return new HashCodeBuilder(17, 37)
+				.append(myName)
+				.append(myResource)
+				.toHashCode();
+		}
+
+		@Override
+		public String toString() {
+			if (myResource) {
+				return myName + "(res)";
+			}
+			return myName;
+		}
+
+		public String getName() {
+			return myName;
+		}
+
+		public boolean isResource() {
+			return myResource;
+		}
+	}
+
 	static class ContainedResources {
 		private long myNextContainedId = 1;
 
@@ -1242,7 +1411,6 @@ public abstract class BaseParser implements IParser {
 				for (IBaseResource nextResource : getResourceList()) {
 					if (getResourceToIdMap().get(nextResource) != null) {
 						ids.add(getResourceToIdMap().get(nextResource).getValue());
-						continue;
 					}
 				}
 
@@ -1274,24 +1442,24 @@ public abstract class BaseParser implements IParser {
 		return new ArrayList<>(securityLabels);
 	}
 
-	static boolean hasExtensions(IBase theElement) {
+	static boolean hasNoExtensions(IBase theElement) {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
 			ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theElement;
 			if (res.getUndeclaredExtensions().size() > 0 || res.getUndeclaredModifierExtensions().size() > 0) {
-				return true;
+				return false;
 			}
 		}
 		if (theElement instanceof IBaseHasExtensions) {
 			IBaseHasExtensions res = (IBaseHasExtensions) theElement;
 			if (res.hasExtension()) {
-				return true;
+				return false;
 			}
 		}
 		if (theElement instanceof IBaseHasModifierExtensions) {
 			IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) theElement;
-			return res.hasModifierExtension();
+			return !res.hasModifierExtension();
 		}
-		return false;
+		return true;
 	}
 
 }

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

@@ -51,16 +51,6 @@ public interface IParser {
 
 	void encodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException, DataFormatException;
 
-	/**
-	 * See {@link #setEncodeElements(Set)}
-	 */
-	Set<String> getEncodeElements();
-
-	/**
-	 * See {@link #setEncodeElementsAppliesToResourceTypes(Set)}
-	 */
-	Set<String> getEncodeElementsAppliesToResourceTypes();
-
 	/**
 	 * If not set to null (as is the default) this ID will be used as the ID in any
 	 * resources encoded by this parser
@@ -258,14 +248,6 @@ public interface IParser {
 	 */
 	boolean isEncodeElementsAppliesToChildResourcesOnly();
 
-	/**
-	 * If provided, tells the parse which resource types to apply {@link #setEncodeElements(Set) encode elements} to. Any
-	 * resource types not specified here will be encoded completely, with no elements excluded.
-	 * 
-	 * @param theEncodeElementsAppliesToResourceTypes
-	 */
-	void setEncodeElementsAppliesToResourceTypes(Set<String> theEncodeElementsAppliesToResourceTypes);
-
 	/**
 	 * When encoding, force this resource ID to be encoded as the resource ID
 	 */

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

@@ -140,21 +140,21 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		return retVal;
 	}
 
-	public void doEncodeResourceToJsonLikeWriter(IBaseResource theResource, JsonLikeWriter theEventWriter) throws IOException {
+	public void doEncodeResourceToJsonLikeWriter(IBaseResource theResource, JsonLikeWriter theEventWriter, EncodeContext theEncodeContext) throws IOException {
 		if (myPrettyPrint) {
 			theEventWriter.setPrettyPrint(myPrettyPrint);
 		}
 		theEventWriter.init();
 
 		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
-		encodeResourceToJsonStreamWriter(resDef, theResource, theEventWriter, null, false, false);
+		encodeResourceToJsonStreamWriter(resDef, theResource, theEventWriter, null, false,  theEncodeContext);
 		theEventWriter.flush();
 	}
 
 	@Override
-	protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException {
+	protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext) throws IOException {
 		JsonLikeWriter eventWriter = createJsonWriter(theWriter);
-		doEncodeResourceToJsonLikeWriter(theResource, eventWriter);
+		doEncodeResourceToJsonLikeWriter(theResource, eventWriter, theEncodeContext);
 	}
 
 	@Override
@@ -192,8 +192,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBase theNextValue,
-																 BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource, boolean theSubResource, CompositeChildElement theChildElem,
+																 BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource, CompositeChildElement theChildElem,
-																 boolean theForceEmpty) throws IOException {
+																 boolean theForceEmpty, EncodeContext theEncodeContext) throws IOException {
 
 		switch (theChildDef.getChildType()) {
 			case ID_DATATYPE: {
@@ -265,7 +265,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				} else {
 					theEventWriter.beginObject();
 				}
-				encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theChildElem);
+				encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theChildElem, theEncodeContext);
 				theEventWriter.endObject();
 				break;
 			}
@@ -283,7 +283,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 					for (IBaseResource next : containedResources) {
 						IIdType resourceId = getContainedResources().getResourceId(next);
-						encodeResourceToJsonStreamWriter(theResDef, next, theEventWriter, null, true, false, fixContainedResourceId(resourceId.getValue()));
+						encodeResourceToJsonStreamWriter(theResDef, next, theEventWriter, null, true, fixContainedResourceId(resourceId.getValue()), theEncodeContext);
 					}
 
 					theEventWriter.endArray();
@@ -311,7 +311,11 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			case RESOURCE:
 				IBaseResource resource = (IBaseResource) theNextValue;
 				RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
-				encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, false, true);
+
+				theEncodeContext.pushPath(def.getName(), true);
+				encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, false, theEncodeContext);
+				theEncodeContext.popPath();
+
 				break;
 			case UNDECL_EXT:
 			default:
@@ -321,7 +325,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theElement, JsonLikeWriter theEventWriter,
-																				 boolean theContainedResource, boolean theSubResource, CompositeChildElement theParent) throws IOException {
+																				 boolean theContainedResource, CompositeChildElement theParent, EncodeContext theEncodeContext) throws IOException {
 
 		{
 			String elementId = getCompositeElementId(theElement);
@@ -331,14 +335,14 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 
 		boolean haveWrittenExtensions = false;
-		for (CompositeChildElement nextChildElem : super.compositeChildIterator(theElement, theContainedResource, theSubResource, theParent)) {
+		for (CompositeChildElement nextChildElem : super.compositeChildIterator(theElement, theContainedResource, theParent, theEncodeContext)) {
 
 			BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
 
 			if (nextChildElem.getDef().getElementName().equals("extension") || nextChildElem.getDef().getElementName().equals("modifierExtension")
 				|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
 				if (!haveWrittenExtensions) {
-					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent);
+					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent, theEncodeContext);
 					haveWrittenExtensions = true;
 				}
 				continue;
@@ -361,7 +365,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 							RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
 							String childName = nextChild.getChildNameByDatatype(child.getDatatype());
 							BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
-							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName, theContainedResource, theSubResource, nextChildElem, false);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName, theContainedResource, nextChildElem, false, theEncodeContext);
 							continue;
 						}
 					}
@@ -369,12 +373,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			} else if (nextChild instanceof RuntimeChildContainedResources) {
 				String childName = nextChild.getValidChildNames().iterator().next();
 				BaseRuntimeElementDefinition<?> child = nextChild.getChildByName(childName);
-				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, null, child, childName, theContainedResource, theSubResource, nextChildElem, false);
+				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, null, child, childName, theContainedResource, nextChildElem, false, theEncodeContext);
 				continue;
 			}
 
 			List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
-			values = super.preProcessValues(nextChild, theResource, values, nextChildElem);
+			values = super.preProcessValues(nextChild, theResource, values, nextChildElem, theEncodeContext);
 
 			if (values == null || values.isEmpty()) {
 				continue;
@@ -407,6 +411,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				}
 
 				String childName = childNameAndDef.getChildName();
+				theEncodeContext.pushPath(childName, false);
+
 				BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
 				boolean primitive = childDef.getChildType() == ChildTypeEnum.PRIMITIVE_DATATYPE;
 
@@ -452,18 +458,19 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					if (nextChild.getMax() > 1 || nextChild.getMax() == Child.MAX_UNLIMITED) {
 						beginArray(theEventWriter, childName);
 						inArray = true;
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource, nextChildElem, force);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, nextChildElem, force, theEncodeContext);
 					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
 						// suppress narratives from contained resources
 					} else {
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource, theSubResource, nextChildElem, false);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource, nextChildElem, false, theEncodeContext);
 					}
 					currentChildName = childName;
 				} else {
-					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource, nextChildElem, force);
+					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, nextChildElem, force, theEncodeContext);
 				}
 
 				valueIdx++;
+				theEncodeContext.popPath();
 			}
 
 			if (inArray) {
@@ -525,7 +532,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 							}
 							theEventWriter.endArray();
 						}
-						writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, heldExts, heldModExts);
+						writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, heldExts, heldModExts, theEncodeContext);
 						if (inArray) {
 							theEventWriter.endObject();
 						}
@@ -541,11 +548,10 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 	}
 
-	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonLikeWriter theEventWriter, boolean theContainedResource, boolean theSubResource,
+	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonLikeWriter theEventWriter, boolean theContainedResource, 																	  CompositeChildElement theParent, EncodeContext theEncodeContext) throws IOException, DataFormatException {
-																	  CompositeChildElement theParent) throws IOException, DataFormatException {
 
 		writeCommentsPreAndPost(theNextValue, theEventWriter);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theParent);
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theParent, theEncodeContext);
 	}
 
 	@Override
@@ -558,27 +564,15 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
 		}
 
-		doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter);
+		EncodeContext encodeContext = new EncodeContext();
+		String resourceName = myContext.getResourceDefinition(theResource).getName();
+		encodeContext.pushPath(resourceName, true);
+		doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter, encodeContext);
 	}
 
 	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, String theObjectNameOrNull,
-																 boolean theContainedResource, boolean theSubResource) throws IOException {
+																 boolean theContainedResource, EncodeContext theEncodeContext) throws IOException {
 		IIdType resourceId = null;
-		// if (theResource instanceof IResource) {
-		// IResource res = (IResource) theResource;
-		// if (StringUtils.isNotBlank(res.getId().getIdPart())) {
-		// if (theContainedResource) {
-		// resourceId = res.getId().getIdPart();
-		// } else if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
-		// resourceId = res.getId().getIdPart();
-		// }
-		// }
-		// } else if (theResource instanceof IAnyResource) {
-		// IAnyResource res = (IAnyResource) theResource;
-		// if (/* theContainedResource && */StringUtils.isNotBlank(res.getIdElement().getIdPart())) {
-		// resourceId = res.getIdElement().getIdPart();
-		// }
-		// }
 
 		if (StringUtils.isNotBlank(theResource.getIdElement().getIdPart())) {
 			resourceId = theResource.getIdElement();
@@ -588,18 +582,18 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 
 		if (!theContainedResource) {
-			if (super.shouldEncodeResourceId(theResource, theSubResource) == false) {
+			if (!super.shouldEncodeResourceId(theResource, theEncodeContext)) {
 				resourceId = null;
-			} else if (!theSubResource && getEncodeForceResourceId() != null) {
+			} else if (theEncodeContext.getResourcePath().size() == 1 && getEncodeForceResourceId() != null) {
 				resourceId = getEncodeForceResourceId();
 			}
 		}
 
-		encodeResourceToJsonStreamWriter(theResDef, theResource, theEventWriter, theObjectNameOrNull, theContainedResource, theSubResource, resourceId);
+		encodeResourceToJsonStreamWriter(theResDef, theResource, theEventWriter, theObjectNameOrNull, theContainedResource, resourceId, theEncodeContext);
 	}
 
 	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, String theObjectNameOrNull,
-																 boolean theContainedResource, boolean theSubResource, IIdType theResourceId) throws IOException {
+																 boolean theContainedResource, IIdType theResourceId, EncodeContext theEncodeContext) throws IOException {
 		if (!theContainedResource) {
 			super.containResourcesForEncoding(theResource);
 		}
@@ -630,7 +624,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					writeCommentsPreAndPost(theResourceId, theEventWriter);
 				}
 				if (haveExtension) {
-					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
 				}
 				theEventWriter.endObject();
 			}
@@ -644,7 +638,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
 			profiles = super.getProfileTagsForEncoding(resource, profiles);
 
-			TagList tags = getMetaTagsForEncoding(resource);
+			TagList tags = getMetaTagsForEncoding(resource, theEncodeContext);
 			InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
 			IdDt resourceId = resource.getId();
 			String versionIdPart = resourceId.getVersionIdPart();
@@ -672,7 +666,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					beginArray(theEventWriter, "security");
 					for (BaseCodingDt securityLabel : securityLabels) {
 						theEventWriter.beginObject();
-						encodeCompositeElementChildrenToStreamWriter(resDef, resource, securityLabel, theEventWriter, theContainedResource, theSubResource, null);
+						theEncodeContext.pushPath("security", false);
+						encodeCompositeElementChildrenToStreamWriter(resDef, resource, securityLabel, theEventWriter, theContainedResource, null, theEncodeContext);
+						theEncodeContext.popPath();
 						theEventWriter.endObject();
 					}
 					theEventWriter.endArray();
@@ -693,23 +689,23 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					theEventWriter.endArray();
 				}
 
-				addExtensionMetadata(theResDef, theResource, theContainedResource, theSubResource, extensionMetadataKeys, resDef, theEventWriter);
+				addExtensionMetadata(theResDef, theResource, theContainedResource, extensionMetadataKeys, resDef, theEventWriter, theEncodeContext);
 
 				theEventWriter.endObject(); // end meta
 			}
 		}
 
-		encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
+		encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef, theEncodeContext), theEncodeContext);
 
 		theEventWriter.endObject();
 	}
 
 
 	private void addExtensionMetadata(RuntimeResourceDefinition theResDef, IBaseResource theResource,
-												 boolean theContainedResource, boolean theSubResource,
+												 boolean theContainedResource,
 												 List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys,
 												 RuntimeResourceDefinition resDef,
-												 JsonLikeWriter theEventWriter) throws IOException {
+												 JsonLikeWriter theEventWriter, EncodeContext theEncodeContext) throws IOException {
 		if (extensionMetadataKeys.isEmpty()) {
 			return;
 		}
@@ -718,7 +714,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		for (Map.Entry<ResourceMetadataKeyEnum<?>, Object> entry : extensionMetadataKeys) {
 			metaResource.addUndeclaredExtension((ExtensionDt) entry.getValue());
 		}
-		encodeCompositeElementToStreamWriter(theResDef, theResource, metaResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
+		encodeCompositeElementToStreamWriter(theResDef, theResource, metaResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef, theEncodeContext), theEncodeContext);
 	}
 
 	/**
@@ -726,7 +722,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	 * called _name): resource extensions, and extension extensions
 	 */
 	private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef,
-																		 IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
+																		 IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent, EncodeContext theEncodeContext) throws IOException {
 		List<HeldExtension> extensions = new ArrayList<>(0);
 		List<HeldExtension> modifierExtensions = new ArrayList<>(0);
 
@@ -739,7 +735,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 
 		// Write the extensions
-		writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+		writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
 	}
 
 	private void extractDeclaredExtensions(IBase theResource, BaseRuntimeElementDefinition<?> resDef, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions,
@@ -1260,18 +1256,18 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void writeExtensionsAsDirectChild(IBaseResource theResource, JsonLikeWriter theEventWriter, RuntimeResourceDefinition resDef, List<HeldExtension> extensions,
-															List<HeldExtension> modifierExtensions) throws IOException {
+															List<HeldExtension> modifierExtensions, EncodeContext theEncodeContext) throws IOException {
 		if (extensions.isEmpty() == false) {
 			beginArray(theEventWriter, "extension");
 			for (HeldExtension next : extensions) {
-				next.write(resDef, theResource, theEventWriter);
+				next.write(resDef, theResource, theEventWriter, theEncodeContext);
 			}
 			theEventWriter.endArray();
 		}
 		if (modifierExtensions.isEmpty() == false) {
 			beginArray(theEventWriter, "modifierExtension");
 			for (HeldExtension next : modifierExtensions) {
-				next.write(resDef, theResource, theEventWriter);
+				next.write(resDef, theResource, theEventWriter, theEncodeContext);
 			}
 			theEventWriter.endArray();
 		}
@@ -1334,7 +1330,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			return url1.compareTo(url2);
 		}
 
-		private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
+		private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName, EncodeContext theEncodeContext) throws IOException {
 			if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
 				final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
 				final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
@@ -1350,15 +1346,15 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				}
 				if (haveContent) {
 					beginObject(theEventWriter, '_' + childName);
-					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
 					theEventWriter.endObject();
 				}
 			}
 		}
 
-		public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter) throws IOException {
+		public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, EncodeContext theEncodeContext) throws IOException {
 			if (myUndeclaredExtension != null) {
-				writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension);
+				writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension, theEncodeContext);
 			} else {
 				theEventWriter.beginObject();
 
@@ -1372,7 +1368,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				 *
 				 * See #327
 				 */
-				List<? extends IBase> preProcessedValue = preProcessValues(myDef, theResource, Collections.singletonList(myValue), myChildElem);
+				List<? extends IBase> preProcessedValue = preProcessValues(myDef, theResource, Collections.singletonList(myValue), myChildElem, theEncodeContext);
 
 				// // Check for undeclared extensions on the declared extension
 				// // (grrrrrr....)
@@ -1391,18 +1387,18 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 				BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());
 				if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) {
-					extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null);
+					extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null, theEncodeContext);
 				} else {
 					String childName = myDef.getChildNameByDatatype(myValue.getClass());
-					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, false, myParent, false);
+					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false,  myParent, false, theEncodeContext);
-					managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
+					managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName, theEncodeContext);
 				}
 
 				theEventWriter.endObject();
 			}
 		}
 
-		private void writeUndeclaredExtension(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBaseExtension<?, ?> ext) throws IOException {
+		private void writeUndeclaredExtension(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBaseExtension<?, ?> ext, EncodeContext theEncodeContext) throws IOException {
 			IBase value = ext.getValue();
 			final String extensionUrl = getExtensionUrl(ext.getUrl());
 
@@ -1429,7 +1425,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				}
 
 				for (Object next : ext.getExtension()) {
-					writeUndeclaredExtension(theResDef, theResource, theEventWriter, (IBaseExtension<?, ?>) next);
+					writeUndeclaredExtension(theResDef, theResource, theEventWriter, (IBaseExtension<?, ?>) next, theEncodeContext);
 				}
 				theEventWriter.endArray();
 			} else {
@@ -1438,7 +1434,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				 * Pre-process value - This is called in case the value is a reference
 				 * since we might modify the text
 				 */
-				value = JsonParser.super.preProcessValues(myDef, theResource, Collections.singletonList(value), myChildElem).get(0);
+				value = JsonParser.super.preProcessValues(myDef, theResource, Collections.singletonList(value), myChildElem, theEncodeContext).get(0);
 
 				RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
 				String childName = extDef.getChildNameByDatatype(value.getClass());
@@ -1449,8 +1445,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				if (childDef == null) {
 					throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
 				}
-				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, false, myParent, false);
+				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, myParent,false, theEncodeContext);
-				managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
+				managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName, theEncodeContext);
 			}
 
 			// theEventWriter.name(myUndeclaredExtension.get);

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

@@ -20,28 +20,32 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
+import ca.uhn.fhir.context.*;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import ca.uhn.fhir.model.api.*;
-
+import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import java.io.Reader;
+import ca.uhn.fhir.model.primitive.IdDt;
-import java.io.StringReader;
+import ca.uhn.fhir.model.primitive.InstantDt;
-import java.io.Writer;
+import ca.uhn.fhir.model.primitive.XhtmlDt;
-import java.util.*;
+import ca.uhn.fhir.narrative.INarrativeGenerator;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.util.ElementUtil;
+import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
+import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
+import ca.uhn.fhir.util.XmlUtil;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.*;
 
 import javax.xml.namespace.QName;
 import javax.xml.stream.*;
 import javax.xml.stream.events.*;
+import java.io.Reader;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
 
-import org.apache.commons.lang3.StringUtils;
+import static org.apache.commons.lang3.StringUtils.isBlank;
-import org.hl7.fhir.instance.model.api.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import ca.uhn.fhir.context.*;
-import ca.uhn.fhir.model.api.*;
-import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import ca.uhn.fhir.model.primitive.*;
-import ca.uhn.fhir.narrative.INarrativeGenerator;
-import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.util.*;
 
 /**
  * This class is the FHIR XML parser/encoder. Users should not interact with this class directly, but should use
@@ -52,14 +56,13 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 	static final String ATOM_NS = "http://www.w3.org/2005/Atom";
 	static final String FHIR_NS = "http://hl7.org/fhir";
 	static final String OPENSEARCH_NS = "http://a9.com/-/spec/opensearch/1.1/";
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
 	static final String RESREF_DISPLAY = "display";
 	static final String RESREF_REFERENCE = "reference";
 	static final String TOMBSTONES_NS = "http://purl.org/atompub/tombstones/1.0";
 	static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
 
 	// private static final Set<String> RESOURCE_NAMESPACES;
-
 	private FhirContext myContext;
 	private boolean myPrettyPrint;
 
@@ -101,12 +104,12 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 	}
 
 	@Override
-	public void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws DataFormatException {
+	public void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext) throws DataFormatException {
 		XMLStreamWriter eventWriter;
 		try {
 			eventWriter = createXmlWriter(theWriter);
 
-			encodeResourceToXmlStreamWriter(theResource, eventWriter, false, false);
+			encodeResourceToXmlStreamWriter(theResource, eventWriter, false, theEncodeContext);
 			eventWriter.flush();
 		} catch (XMLStreamException e) {
 			throw new ConfigurationException("Failed to initialize STaX event factory", e);
@@ -123,7 +126,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 		ourLog.trace("Entering XML parsing loop with state: {}", parserState);
 
 		try {
-			List<String> heldComments = new ArrayList<String>(1);
+			List<String> heldComments = new ArrayList<>(1);
 
 			while (streamReader.hasNext()) {
 				XMLEvent nextEvent = streamReader.nextEvent();
@@ -167,10 +170,8 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 								heldComments.clear();
 							}
 
-						@SuppressWarnings("unchecked")
+							for (Iterator<Attribute> attributes = elem.getAttributes(); attributes.hasNext(); ) {
-						Iterator<Attribute> attributes = elem.getAttributes();
+								Attribute next = attributes.next();
-						for (Iterator<Attribute> iter = attributes; iter.hasNext();) {
-							Attribute next = iter.next();
 								parserState.attributeValue(next.getName().getLocalPart(), next.getValue());
 							}
 
@@ -215,7 +216,10 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 	}
 
 	private void encodeChildElementToStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, IBase theElement, String childName, BaseRuntimeElementDefinition<?> childDef,
-			String theExtensionUrl, boolean theIncludedResource, boolean theSubResource, CompositeChildElement theParent) throws XMLStreamException, DataFormatException {
+																 String theExtensionUrl, boolean theIncludedResource, CompositeChildElement theParent, EncodeContext theEncodeContext) throws XMLStreamException, DataFormatException {
+		theEncodeContext.pushPath(childName, false);
+		try {
+
 			if (theElement == null || theElement.isEmpty()) {
 				if (isChildContained(childDef, theIncludedResource)) {
 					// We still want to go in..
@@ -230,12 +234,12 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 				case ID_DATATYPE: {
 					IIdType value = IIdType.class.cast(theElement);
 					String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue();
-      if (StringUtils.isNotBlank(encodedValue) || super.hasExtensions(value)) {
+					if (StringUtils.isNotBlank(encodedValue) || !super.hasNoExtensions(value)) {
 						theEventWriter.writeStartElement(childName);
 						if (StringUtils.isNotBlank(encodedValue)) {
 							theEventWriter.writeAttribute("value", encodedValue);
 						}
-        encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource, theSubResource);
+						encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource, theEncodeContext);
 						theEventWriter.writeEndElement();
 					}
 					break;
@@ -243,7 +247,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 				case PRIMITIVE_DATATYPE: {
 					IPrimitiveType<?> pd = IPrimitiveType.class.cast(theElement);
 					String value = pd.getValueAsString();
-			if (value != null || super.hasExtensions(pd)) {
+					if (value != null || !super.hasNoExtensions(pd)) {
 						theEventWriter.writeStartElement(childName);
 						String elementId = getCompositeElementId(theElement);
 						if (isNotBlank(elementId)) {
@@ -252,7 +256,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 						if (value != null) {
 							theEventWriter.writeAttribute("value", value);
 						}
-				encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource,theSubResource);
+						encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource, theEncodeContext);
 						theEventWriter.writeEndElement();
 					}
 					break;
@@ -267,7 +271,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 					if (isNotBlank(theExtensionUrl)) {
 						theEventWriter.writeAttribute("url", theExtensionUrl);
 					}
-			encodeCompositeElementToStreamWriter(theResource, theElement, theEventWriter, theIncludedResource, theSubResource, theParent);
+					encodeCompositeElementToStreamWriter(theResource, theElement, theEventWriter, theIncludedResource, theParent, theEncodeContext);
 					theEventWriter.writeEndElement();
 					break;
 				}
@@ -281,7 +285,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 					for (IBaseResource next : getContainedResources().getContainedResources()) {
 						IIdType resourceId = getContainedResources().getResourceId(next);
 						theEventWriter.writeStartElement("contained");
-				encodeResourceToXmlStreamWriter(next, theEventWriter, true, false, fixContainedResourceId(resourceId.getValue()));
+						encodeResourceToXmlStreamWriter(next, theEventWriter, true, fixContainedResourceId(resourceId.getValue()), theEncodeContext);
 						theEventWriter.writeEndElement();
 					}
 					break;
@@ -289,7 +293,10 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 				case RESOURCE: {
 					theEventWriter.writeStartElement(childName);
 					IBaseResource resource = (IBaseResource) theElement;
-			encodeResourceToXmlStreamWriter(resource, theEventWriter, false, true);
+					String resourceName = myContext.getResourceDefinition(resource).getName();
+					theEncodeContext.pushPath(resourceName, true);
+					encodeResourceToXmlStreamWriter(resource, theEventWriter, false, theEncodeContext);
+					theEncodeContext.popPath();
 					theEventWriter.writeEndElement();
 					break;
 				}
@@ -318,12 +325,16 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 
 			writeCommentsPost(theEventWriter, theElement);
 
+		} finally {
+			theEncodeContext.popPath();
 		}
 
-	private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, boolean theContainedResource, boolean theSubResource, CompositeChildElement theParent)
+	}
+
+	private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement theParent, EncodeContext theEncodeContext)
 		throws XMLStreamException, DataFormatException {
 
-		for (CompositeChildElement nextChildElem : super.compositeChildIterator(theElement, theContainedResource, theSubResource, theParent)) {
+		for (CompositeChildElement nextChildElem : super.compositeChildIterator(theElement, theContainedResource, theParent, theEncodeContext)) {
 
 			BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
 
@@ -353,17 +364,17 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 					RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
 					String childName = nextChild.getChildNameByDatatype(child.getDatatype());
 					BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
-					encodeChildElementToStreamWriter(theResource, theEventWriter, narr, childName, type, null, theContainedResource, theSubResource, nextChildElem);
+					encodeChildElementToStreamWriter(theResource, theEventWriter, narr, childName, type, null, theContainedResource, nextChildElem, theEncodeContext);
 					continue;
 				}
 			}
 
 			if (nextChild instanceof RuntimeChildContainedResources) {
-				encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theContainedResource, theSubResource, nextChildElem);
+				encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theContainedResource, nextChildElem, theEncodeContext);
 			} else {
 
 				List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
-				values = super.preProcessValues(nextChild, theResource, values, nextChildElem);
+				values = super.preProcessValues(nextChild, theResource, values, nextChildElem, theEncodeContext);
 
 				if (values == null || values.isEmpty()) {
 					continue;
@@ -383,7 +394,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 					String extensionUrl = getExtensionUrl(nextChild.getExtensionUrl());
 
 					if (extensionUrl != null && childName.equals("extension") == false) {
-						encodeExtension(theResource, theEventWriter, theContainedResource, theSubResource, nextChildElem, nextChild, nextValue, childName, extensionUrl, childDef);
+						encodeExtension(theResource, theEventWriter, theContainedResource, nextChildElem, nextChild, nextValue, childName, extensionUrl, childDef, theEncodeContext);
 					} else if (nextChild instanceof RuntimeChildExtension) {
 						IBaseExtension<?, ?> extension = (IBaseExtension<?, ?>) nextValue;
 						if ((extension.getValue() == null || extension.getValue().isEmpty())) {
@@ -391,18 +402,19 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 								continue;
 							}
 						}
-						encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, getExtensionUrl(extension.getUrl()), theContainedResource, theSubResource, nextChildElem);
+						encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, getExtensionUrl(extension.getUrl()), theContainedResource, nextChildElem, theEncodeContext);
 					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
 						// suppress narratives from contained resources
 					} else {
-						encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, extensionUrl, theContainedResource, theSubResource, nextChildElem);
+						encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, extensionUrl, theContainedResource, nextChildElem, theEncodeContext);
 					}
+
 				}
 			}
 		}
 	}
 
-	private void encodeExtension(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, boolean theSubResource, CompositeChildElement nextChildElem, BaseRuntimeChildDefinition nextChild, IBase nextValue, String childName, String extensionUrl, BaseRuntimeElementDefinition<?> childDef)
+	private void encodeExtension(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement nextChildElem, BaseRuntimeChildDefinition nextChild, IBase nextValue, String childName, String extensionUrl, BaseRuntimeElementDefinition<?> childDef, EncodeContext theEncodeContext)
 		throws XMLStreamException {
 		BaseRuntimeDeclaredChildDefinition extDef = (BaseRuntimeDeclaredChildDefinition) nextChild;
 		if (extDef.isModifier()) {
@@ -417,27 +429,27 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 		}
 
 		theEventWriter.writeAttribute("url", extensionUrl);
-		encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, null, theContainedResource, theSubResource, nextChildElem);
+		encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, null, theContainedResource, nextChildElem, theEncodeContext);
 		theEventWriter.writeEndElement();
 	}
 
-	private void encodeExtensionsIfPresent(IBaseResource theResource, XMLStreamWriter theWriter, IBase theElement, boolean theIncludedResource, boolean theSubResource) throws XMLStreamException, DataFormatException {
+	private void encodeExtensionsIfPresent(IBaseResource theResource, XMLStreamWriter theWriter, IBase theElement, boolean theIncludedResource, EncodeContext theEncodeContext) throws XMLStreamException, DataFormatException {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
 			ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theElement;
-			encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredExtensions()), "extension", theIncludedResource, theSubResource);
+			encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredExtensions()), "extension", theIncludedResource, theEncodeContext);
-			encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredModifierExtensions()), "modifierExtension", theIncludedResource,theSubResource);
+			encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredModifierExtensions()), "modifierExtension", theIncludedResource, theEncodeContext);
 		}
 		if (theElement instanceof IBaseHasExtensions) {
 			IBaseHasExtensions res = (IBaseHasExtensions) theElement;
-			encodeUndeclaredExtensions(theResource, theWriter, res.getExtension(), "extension", theIncludedResource,theSubResource);
+			encodeUndeclaredExtensions(theResource, theWriter, res.getExtension(), "extension", theIncludedResource, theEncodeContext);
 		}
 		if (theElement instanceof IBaseHasModifierExtensions) {
 			IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) theElement;
-			encodeUndeclaredExtensions(theResource, theWriter, res.getModifierExtension(), "modifierExtension", theIncludedResource,theSubResource);
+			encodeUndeclaredExtensions(theResource, theWriter, res.getModifierExtension(), "modifierExtension", theIncludedResource, theEncodeContext);
 		}
 	}
 
-	private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, boolean theSubResource) throws XMLStreamException, DataFormatException {
+	private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, EncodeContext theEncodeContext) throws XMLStreamException, DataFormatException {
 		IIdType resourceId = null;
 
 		if (StringUtils.isNotBlank(theResource.getIdElement().getIdPart())) {
@@ -448,17 +460,17 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 		}
 
 		if (!theIncludedResource) {
-			if (super.shouldEncodeResourceId(theResource, theSubResource) == false) {
+			if (super.shouldEncodeResourceId(theResource, theEncodeContext) == false) {
 				resourceId = null;
-			} else if (theSubResource == false && getEncodeForceResourceId() != null) {
+			} else if (theEncodeContext.getResourcePath().size() == 1 && getEncodeForceResourceId() != null) {
 				resourceId = getEncodeForceResourceId();
 			}
 		}
 
-		encodeResourceToXmlStreamWriter(theResource, theEventWriter, theIncludedResource, theSubResource, resourceId);
+		encodeResourceToXmlStreamWriter(theResource, theEventWriter, theIncludedResource, resourceId, theEncodeContext);
 	}
 
-	private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, boolean theSubResource,  IIdType theResourceId) throws XMLStreamException {
+	private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, IIdType theResourceId, EncodeContext theEncodeContext) throws XMLStreamException {
 		if (!theContainedResource) {
 			super.containResourcesForEncoding(theResource);
 		}
@@ -477,12 +489,12 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 				writeCommentsPre(theEventWriter, theResourceId);
 				theEventWriter.writeStartElement("id");
 				theEventWriter.writeAttribute("value", theResourceId.getIdPart());
-        encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false, false);
+				encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false, theEncodeContext);
 				theEventWriter.writeEndElement();
 				writeCommentsPost(theEventWriter, theResourceId);
 			}
 
-			encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
+			encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef, theEncodeContext), theEncodeContext);
 
 		} else {
 
@@ -495,7 +507,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 					    writeCommentsPost(theEventWriter, theResourceId);*/
 				theEventWriter.writeStartElement("id");
 				theEventWriter.writeAttribute("value", theResourceId.getIdPart());
-          encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false,false);
+				encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false, theEncodeContext);
 				theEventWriter.writeEndElement();
 				writeCommentsPost(theEventWriter, theResourceId);
 			}
@@ -510,7 +522,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 			List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
 			profiles = super.getProfileTagsForEncoding(resource, profiles);
 
-			TagList tags = getMetaTagsForEncoding((resource));
+			TagList tags = getMetaTagsForEncoding((resource), theEncodeContext);
 
 			if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
 				theEventWriter.writeStartElement("meta");
@@ -526,7 +538,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 				}
 				for (BaseCodingDt securityLabel : securityLabels) {
 					theEventWriter.writeStartElement("security");
-					encodeCompositeElementToStreamWriter(resource, securityLabel, theEventWriter, theContainedResource, theSubResource, null);
+					encodeCompositeElementToStreamWriter(resource, securityLabel, theEventWriter, theContainedResource, null, theEncodeContext);
 					theEventWriter.writeEndElement();
 				}
 				if (tags != null) {
@@ -549,7 +561,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 				writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
 				writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
 			} else {
-				encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
+				encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef, theEncodeContext), theEncodeContext);
 			}
 
 		}
@@ -557,7 +569,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 		theEventWriter.writeEndElement();
 	}
 
-	private void encodeUndeclaredExtensions(IBaseResource theResource, XMLStreamWriter theEventWriter, List<? extends IBaseExtension<?, ?>> theExtensions, String tagName, boolean theIncludedResource, boolean theSubResource)
+	private void encodeUndeclaredExtensions(IBaseResource theResource, XMLStreamWriter theEventWriter, List<? extends IBaseExtension<?, ?>> theExtensions, String tagName, boolean theIncludedResource, EncodeContext theEncodeContext)
 		throws XMLStreamException, DataFormatException {
 		for (IBaseExtension<?, ?> next : theExtensions) {
 			if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
@@ -593,11 +605,11 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 						throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
 					}
 				}
-				encodeChildElementToStreamWriter(theResource, theEventWriter, value, childName, childDef, null, theIncludedResource, theSubResource, null);
+				encodeChildElementToStreamWriter(theResource, theEventWriter, value, childName, childDef, null, theIncludedResource, null, theEncodeContext);
 			}
 
 			// child extensions
-			encodeExtensionsIfPresent(theResource, theEventWriter, next, theIncludedResource,theSubResource);
+			encodeExtensionsIfPresent(theResource, theEventWriter, next, theIncludedResource, theEncodeContext);
 
 			theEventWriter.writeEndElement();
 

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

@@ -137,6 +137,7 @@ public class Constants {
 	public static final String PARAM_COUNT = "_count";
 	public static final String PARAM_DELETE = "_delete";
 	public static final String PARAM_ELEMENTS = "_elements";
+	public static final String PARAM_ELEMENTS_EXCLUDE_MODIFIER = ":exclude";
 	public static final String PARAM_FORMAT = "_format";
 	public static final String PARAM_HAS = "_has";
 	public static final String PARAM_HISTORY = "_history";

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

@@ -106,6 +106,9 @@ public enum EncodingEnum {
 		myFormatContentType = theFormatContentType;
 	}
 
+	/**
+	 * Returns <code>xml</code> or <code>json</code> as used on the <code>_format</code> search parameter
+	 */
 	public String getFormatContentType() {
 		return myFormatContentType;
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/PortUtil.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -55,6 +56,24 @@ public class PortUtil {
 			server = new ServerSocket(0);
 			server.setReuseAddress(true);
 			int port = server.getLocalPort();
+
+			/*
+			 * Try to connect to the newly allocated port to make sure
+			 * it's free
+			 */
+			for (int i = 0; i < 10; i++) {
+				try {
+					Socket client = new Socket();
+					client.connect(new InetSocketAddress(port), 1000);
+					break;
+				} catch (Exception e) {
+					if (i == 9) {
+						throw new InternalErrorException("Can not connect to port: " + port);
+					}
+					Thread.sleep(250);
+				}
+			}
+
 			server.close();
 
 			/*

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/PortUtilTest.java

@@ -0,0 +1,31 @@
+package ca.uhn.fhir.util;
+
+import org.junit.Test;
+
+import java.io.IOException;
+import java.net.InetSocketAddress;
+import java.net.ServerSocket;
+
+import static org.junit.Assert.*;
+
+public class PortUtilTest {
+
+	@Test
+	public void testFindFreePort() throws IOException {
+		int port = PortUtil.findFreePort();
+
+		// First bind should succeed, second bind should fail
+		try (ServerSocket ss = new ServerSocket()) {
+			ss.bind(new InetSocketAddress("0.0.0.0", port));
+
+			try (ServerSocket ss2 = new ServerSocket()) {
+				ss2.bind(new InetSocketAddress("0.0.0.0", port));
+				fail();
+			} catch (IOException e) {
+				// good
+			}
+
+		}
+	}
+
+}

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsProvider.java

@@ -84,7 +84,7 @@ public abstract class AbstractJaxRsProvider implements IRestfulServerDefaults {
 
 	/**
 	 * This method returns the server base, including the resource path.
-	 * {@link javax.ws.rs.core.UriInfo#getBaseUri() UriInfo#getBaseUri()}
+	 * {@link UriInfo#getBaseUri() UriInfo#getBaseUri()}
 	 * 
 	 * @return the ascii string for the base resource provider path
 	 */
@@ -119,6 +119,14 @@ public abstract class AbstractJaxRsProvider implements IRestfulServerDefaults {
 		return ETagSupportEnum.DISABLED;
 	}
 
+	/**
+	 * DEFAULT = {@link ElementsSupportEnum#STANDARD}
+	 */
+	@Override
+	public ElementsSupportEnum getElementsSupport() {
+		return ElementsSupportEnum.STANDARD;
+	}
+
 	@Override
 	public FhirContext getFhirContext() {
 		return CTX;
@@ -243,14 +251,6 @@ public abstract class AbstractJaxRsProvider implements IRestfulServerDefaults {
 		return true;
 	}
 
-	/**
-	 * DEFAULT = false
-	 */
-	@Override
-	public boolean isUseBrowserFriendlyContentTypes() {
-		return true;
-	}
-
 	/**
 	 * Set the headers
 	 * 

hapi-fhir-jaxrsserver-example/src/main/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientRestProvider.java

@@ -150,11 +150,6 @@ public class JaxRsPatientRestProvider extends AbstractJaxRsResourceProvider<Pati
 		return true;
 	}
 
-	@Override
-	public boolean isUseBrowserFriendlyContentTypes() {
-		return true;
-	}
-
 	@GET
 	@Path("/{id}/$firstVersion")
 	public Response operationFirstVersionUsingGet(@PathParam("id") String id) throws IOException {

hapi-fhir-jaxrsserver-example/src/main/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientRestProviderDstu3.java

@@ -151,11 +151,6 @@ public class JaxRsPatientRestProviderDstu3 extends AbstractJaxRsResourceProvider
 		return true;
 	}
 
-	@Override
-	public boolean isUseBrowserFriendlyContentTypes() {
-		return true;
-	}
-
 	@GET
 	@Path("/{id}/$firstVersion")
 	public Response operationFirstVersionUsingGet(@PathParam("id") String id) throws IOException {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java

@@ -102,10 +102,10 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 
 			// Only delete if we don't have results left in this search
 			if (resultPids.getNumberOfElements() < max) {
-				ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), new InstantType(searchToDelete.getCreated()), new InstantType(searchToDelete.getSearchLastReturned()));
+				ourLog.debug("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), new InstantType(searchToDelete.getCreated()), new InstantType(searchToDelete.getSearchLastReturned()));
 				mySearchDao.deleteByPid(searchToDelete.getId());
 			} else {
-				ourLog.info("Purged {} search results for deleted search {}/{}", resultPids.getSize(), searchToDelete.getId(), searchToDelete.getUuid());
+				ourLog.debug("Purged {} search results for deleted search {}/{}", resultPids.getSize(), searchToDelete.getId(), searchToDelete.getUuid());
 			}
 		});
 	}
@@ -149,7 +149,7 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 		int count = toDelete.getContent().size();
 		if (count > 0) {
 			long total = tt.execute(t -> mySearchDao.count());
-			ourLog.info("Deleted {} searches, {} remaining", count, total);
+			ourLog.debug("Deleted {} searches, {} remaining", count, total);
 		}
 
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderTransactionSearchDstu2Test.java

@@ -46,7 +46,6 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 	@SuppressWarnings("deprecation")
 	@After
 	public void after() {
-		myRestServer.setUseBrowserFriendlyContentTypes(true);
 		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
 		myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java

@@ -47,7 +47,6 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	@SuppressWarnings("deprecation")
 	@After
 	public void after() {
-		myRestServer.setUseBrowserFriendlyContentTypes(true);
 		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
 		myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/EmptyIndexesR4Test.java

@@ -62,7 +62,6 @@ public class EmptyIndexesR4Test extends BaseJpaR4Test {
 	@SuppressWarnings("deprecation")
 	@After
 	public void after() {
-		myRestServer.setUseBrowserFriendlyContentTypes(true);
 		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
 		myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java

@@ -67,7 +67,6 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
 	@SuppressWarnings("deprecation")
 	@After
 	public void after() {
-		myRestServer.setUseBrowserFriendlyContentTypes(true);
 		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
 	}
 
@@ -250,7 +249,6 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
 	@SuppressWarnings("deprecation")
 	@Test
 	public void testResponseUsesCorrectContentType() throws Exception {
-		myRestServer.setUseBrowserFriendlyContentTypes(true);
 		myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
 
 		HttpGet get = new HttpGet(ourServerBase);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderTransactionSearchR4Test.java

@@ -51,7 +51,6 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 	@SuppressWarnings("deprecation")
 	@After
 	public void after() {
-		myRestServer.setUseBrowserFriendlyContentTypes(true);
 		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
 		myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
 	}

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

@@ -15,10 +15,7 @@ import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.rest.server.ETagSupportEnum;
+import ca.uhn.fhir.rest.server.*;
-import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
-import ca.uhn.fhir.rest.server.IResourceProvider;
-import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.BanUnsupportedHttpMethodsInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
@@ -204,6 +201,11 @@ public class TestRestfulServer extends RestfulServer {
 		setDefaultPrettyPrint(true);
 		setDefaultResponseEncoding(EncodingEnum.JSON);
 
+		/*
+		 * Use extended support for the _elements parameter
+		 */
+		setElementsSupport(ElementsSupportEnum.EXTENDED);
+
 		/*
 		 * The server's base URL (e.g. http://fhirtest.uhn.ca/baseDstu2) is
 		 * pulled from a system property, which is helpful if you want to try

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

@@ -0,0 +1,22 @@
+package ca.uhn.fhir.rest.server;
+
+/**
+ * @see <a href="http://hapifhir.io/doc_rest_server.html#extended_elements_support">Extended Elements Support</a>
+ */
+public enum ElementsSupportEnum {
+
+	/**
+	 * The server will support only the FHIR standard features for the <code>_elements</code>
+	 * parameter.
+	 *
+	 * @see <a href="http://hl7.org/fhir/search.html#elements">http://hl7.org/fhir/search.html#elements</a>
+	 */
+	STANDARD,
+
+	/**
+	 * The server will support both the standard features as well as support for elements
+	 * exclusion.
+	 */
+	EXTENDED
+
+}

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

@@ -49,6 +49,13 @@ public interface IRestfulServerDefaults {
 	 */
 	ETagSupportEnum getETagSupport();
 
+	/**
+	 * @return Returns the support option for the <code>_elements</code> parameter on search
+	 * and read operations.
+	 * @see <a href="http://hapifhir.io/doc_rest_server.html#extended_elements_support">Extended Elements Support</a>
+	 */
+	ElementsSupportEnum getElementsSupport();
+
 	/**
 	 * Gets the {@link FhirContext} associated with this server. For efficient processing, resource providers and plain
 	 * providers should generally use this context if one is needed, as opposed to
@@ -78,12 +85,6 @@ public interface IRestfulServerDefaults {
 	 */
 	boolean isDefaultPrettyPrint();
 
-	/**
-	 * @return If <code>true</code> the server will use browser friendly content-types (instead of standard FHIR ones)
-	 *         when it detects that the request is coming from a browser
-	 *         instead of a FHIR
-	 */
-	boolean isUseBrowserFriendlyContentTypes();
 
 
 }

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

@@ -40,7 +40,6 @@ import ca.uhn.fhir.rest.server.RestfulServerUtils.ResponseEncoding;
 import ca.uhn.fhir.rest.server.exceptions.*;
 import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
 import ca.uhn.fhir.rest.server.method.ConformanceMethodBinding;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@@ -126,10 +125,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	private String myServerVersion = createPoweredByHeaderProductVersion();
 	private boolean myStarted;
 	private boolean myUncompressIncomingContents = true;
-	private boolean myUseBrowserFriendlyContentTypes;
 	private ITenantIdentificationStrategy myTenantIdentificationStrategy;
 	private Date myConformanceDate;
 	private PreferReturnEnum myDefaultPreferReturn = DEFAULT_PREFER_RETURN;
+	private ElementsSupportEnum myElementsSupport = ElementsSupportEnum.EXTENDED;
 
 	/**
 	 * Constructor. Note that if no {@link FhirContext} is passed in to the server (either through the constructor, or
@@ -500,6 +499,21 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		return myETagSupport;
 	}
 
+	@Override
+	public ElementsSupportEnum getElementsSupport() {
+		return myElementsSupport;
+	}
+
+	/**
+	 * Sets the elements support mode.
+	 *
+	 * @see <a href="http://hapifhir.io/doc_rest_server.html#extended_elements_support">Extended Elements Support</a>
+	 */
+	public void setElementsSupport(ElementsSupportEnum theElementsSupport) {
+		Validate.notNull(theElementsSupport, "theElementsSupport must not be null");
+		myElementsSupport = theElementsSupport;
+	}
+
 	/**
 	 * Sets (enables/disables) the server support for ETags. Must not be <code>null</code>. Default is
 	 * {@link #DEFAULT_ETAG_SUPPORT}
@@ -1025,6 +1039,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 			 */
 			requestDetails.removeParameter(Constants.PARAM_SUMMARY);
 			requestDetails.removeParameter(Constants.PARAM_ELEMENTS);
+			requestDetails.removeParameter(Constants.PARAM_ELEMENTS + Constants.PARAM_ELEMENTS_EXCLUDE_MODIFIER);
 
 			/*
 			 * If nobody handles it, default behaviour is to stream back the OperationOutcome to the client.
@@ -1251,26 +1266,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		myUncompressIncomingContents = theUncompressIncomingContents;
 	}
 
-	/**
-	 * @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor}
-	 * instead as an interceptor on your server and it will provide more useful syntax
-	 * highlighting. Deprocated in 1.4
-	 */
-	@Deprecated
-	@Override
-	public boolean isUseBrowserFriendlyContentTypes() {
-		return myUseBrowserFriendlyContentTypes;
-	}
-
-	/**
-	 * @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor}
-	 * instead as an interceptor on your server and it will provide more useful syntax
-	 * highlighting. Deprocated in 1.4
-	 */
-	@Deprecated
-	public void setUseBrowserFriendlyContentTypes(boolean theUseBrowserFriendlyContentTypes) {
-		myUseBrowserFriendlyContentTypes = theUseBrowserFriendlyContentTypes;
-	}
 
 	public void populateRequestDetailsFromRequestPath(RequestDetails theRequestDetails, String theRequestPath) {
 		UrlPathTokenizer tok = new UrlPathTokenizer(theRequestPath);

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

@@ -46,6 +46,7 @@ import java.io.Writer;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.*;
 
@@ -54,7 +55,7 @@ public class RestfulServerUtils {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestfulServerUtils.class);
 
-	private static final HashSet<String> TEXT_ENCODE_ELEMENTS = new HashSet<String>(Arrays.asList("Bundle", "*.text", "*.(mandatory)"));
+	private static final HashSet<String> TEXT_ENCODE_ELEMENTS = new HashSet<>(Arrays.asList("*.text", "*.id", "*.meta", "*.(mandatory)"));
 	private static Map<FhirVersionEnum, FhirContext> myFhirContextMap = Collections.synchronizedMap(new HashMap<FhirVersionEnum, FhirContext>());
 
 	private enum NarrativeModeEnum {
@@ -125,13 +126,15 @@ public class RestfulServerUtils {
 		Set<SummaryEnum> summaryMode = RestfulServerUtils.determineSummaryMode(theRequestDetails);
 
 		// _elements
-		Set<String> elements = ElementsParameter.getElementsValueOrNull(theRequestDetails);
+		Set<String> elements = ElementsParameter.getElementsValueOrNull(theRequestDetails, false);
 		if (elements != null && summaryMode != null && !summaryMode.equals(Collections.singleton(SummaryEnum.FALSE))) {
 			throw new InvalidRequestException("Cannot combine the " + Constants.PARAM_SUMMARY + " and " + Constants.PARAM_ELEMENTS + " parameters");
 		}
-		Set<String> elementsAppliesTo = null;
+
-		if (elements != null && isNotBlank(theRequestDetails.getResourceName())) {
+		// _elements:exclude
-			elementsAppliesTo = Collections.singleton(theRequestDetails.getResourceName());
+		Set<String> elementsExclude = ElementsParameter.getElementsValueOrNull(theRequestDetails, true);
+		if (elementsExclude != null) {
+			parser.setDontEncodeElements(elementsExclude);
 		}
 
 		if (summaryMode != null) {
@@ -139,15 +142,27 @@ public class RestfulServerUtils {
 				parser.setEncodeElements(Collections.singleton("Bundle.total"));
 			} else if (summaryMode.contains(SummaryEnum.TEXT) && summaryMode.size() == 1) {
 				parser.setEncodeElements(TEXT_ENCODE_ELEMENTS);
+				parser.setEncodeElementsAppliesToChildResourcesOnly(true);
 			} else {
 				parser.setSuppressNarratives(summaryMode.contains(SummaryEnum.DATA));
 				parser.setSummaryMode(summaryMode.contains(SummaryEnum.TRUE));
 			}
 		}
 		if (elements != null && elements.size() > 0) {
+			String elementsAppliesTo = "*";
+			if (isNotBlank(theRequestDetails.getResourceName())) {
+				elementsAppliesTo = theRequestDetails.getResourceName();
+			}
+
 			Set<String> newElements = new HashSet<>();
 			for (String next : elements) {
-				newElements.add("*." + next);
+				if (isNotBlank(next)) {
+					if (Character.isUpperCase(next.charAt(0))) {
+						newElements.add(next);
+					} else {
+						newElements.add(elementsAppliesTo + "." + next);
+					}
+				}
 			}
 
 			/*
@@ -158,13 +173,6 @@ public class RestfulServerUtils {
 			 * the client has explicitly scoped the Bundle
 			 * (i.e. with Bundle.total or something like that)
 			 */
-			switch (theRequestDetails.getRestOperationType()) {
-				case SEARCH_SYSTEM:
-				case SEARCH_TYPE:
-				case HISTORY_SYSTEM:
-				case HISTORY_TYPE:
-				case HISTORY_INSTANCE:
-				case GET_PAGE:
 			boolean haveExplicitBundleElement = false;
 			for (String next : newElements) {
 				if (next.startsWith("Bundle.")) {
@@ -172,6 +180,13 @@ public class RestfulServerUtils {
 					break;
 				}
 			}
+			switch (theRequestDetails.getRestOperationType()) {
+				case SEARCH_SYSTEM:
+				case SEARCH_TYPE:
+				case HISTORY_SYSTEM:
+				case HISTORY_TYPE:
+				case HISTORY_INSTANCE:
+				case GET_PAGE:
 					if (!haveExplicitBundleElement) {
 						parser.setEncodeElementsAppliesToChildResourcesOnly(true);
 					}
@@ -181,26 +196,28 @@ public class RestfulServerUtils {
 			}
 
 			parser.setEncodeElements(newElements);
-			parser.setEncodeElementsAppliesToResourceTypes(elementsAppliesTo);
 		}
 	}
 
-	public static String createPagingLink(Set<Include> theIncludes, String theServerBase, String theSearchId, int theOffset, int theCount, Map<String, String[]> theRequestParameters, boolean thePrettyPrint,
+	public static String createPagingLink(Set<Include> theIncludes, RequestDetails theRequestDetails, String theSearchId, int theOffset, int theCount, Map<String, String[]> theRequestParameters, boolean thePrettyPrint,
 													  BundleTypeEnum theBundleType) {
-		return createPagingLink(theIncludes, theServerBase, theSearchId, theOffset, theCount, theRequestParameters, thePrettyPrint,
+		return createPagingLink(theIncludes, theRequestDetails, theSearchId, theOffset, theCount, theRequestParameters, thePrettyPrint,
 			theBundleType, null);
 	}
 
-	public static String createPagingLink(Set<Include> theIncludes, String theServerBase, String theSearchId, String thePageId, Map<String, String[]> theRequestParameters, boolean thePrettyPrint,
+	public static String createPagingLink(Set<Include> theIncludes, RequestDetails theRequestDetails, String theSearchId, String thePageId, Map<String, String[]> theRequestParameters, boolean thePrettyPrint,
 													  BundleTypeEnum theBundleType) {
-		return createPagingLink(theIncludes, theServerBase, theSearchId, null, null, theRequestParameters, thePrettyPrint,
+		return createPagingLink(theIncludes, theRequestDetails, theSearchId, null, null, theRequestParameters, thePrettyPrint,
 			theBundleType, thePageId);
 	}
 
-	private static String createPagingLink(Set<Include> theIncludes, String theServerBase, String theSearchId, Integer theOffset, Integer theCount, Map<String, String[]> theRequestParameters, boolean thePrettyPrint,
+	private static String createPagingLink(Set<Include> theIncludes, RequestDetails theRequestDetails, String theSearchId, Integer theOffset, Integer theCount, Map<String, String[]> theRequestParameters, boolean thePrettyPrint,
 														BundleTypeEnum theBundleType, String thePageId) {
+
+		String serverBase = theRequestDetails.getFhirServerBase();
+
 		StringBuilder b = new StringBuilder();
-		b.append(theServerBase);
+		b.append(serverBase);
 		b.append('?');
 		b.append(Constants.PARAM_PAGINGACTION);
 		b.append('=');
@@ -258,16 +275,33 @@ public class RestfulServerUtils {
 			b.append(theBundleType.getCode());
 		}
 
-		String paramName = Constants.PARAM_ELEMENTS;
+		// _elements
-		String[] params = theRequestParameters.get(paramName);
+		Set<String> elements = ElementsParameter.getElementsValueOrNull(theRequestDetails, false);
-		if (params != null) {
+		if (elements != null) {
-			for (String nextValue : params) {
-				if (isNotBlank(nextValue)) {
 			b.append('&');
-					b.append(paramName);
+			b.append(Constants.PARAM_ELEMENTS);
 			b.append('=');
-					b.append(UrlUtil.escapeUrlParam(nextValue));
+			String nextValue = elements
+				.stream()
+				.sorted()
+				.map(UrlUtil::escapeUrlParam)
+				.collect(Collectors.joining(","));
+			b.append(nextValue);
 		}
+
+		// _elements:exclude
+		if (theRequestDetails.getServer().getElementsSupport() == ElementsSupportEnum.EXTENDED) {
+			Set<String> elementsExclude = ElementsParameter.getElementsValueOrNull(theRequestDetails, true);
+			if (elementsExclude != null) {
+				b.append('&');
+				b.append(Constants.PARAM_ELEMENTS + Constants.PARAM_ELEMENTS_EXCLUDE_MODIFIER);
+				b.append('=');
+				String nextValue = elementsExclude
+					.stream()
+					.sorted()
+					.map(UrlUtil::escapeUrlParam)
+					.collect(Collectors.joining(","));
+				b.append(nextValue);
 			}
 		}
 

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

@@ -192,19 +192,19 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
 			// We're doing named pages
 			searchId = theResult.getUuid();
 			if (isNotBlank(theResult.getNextPageId())) {
-				linkNext = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, theResult.getNextPageId(), theRequest.getParameters(), prettyPrint, theBundleType);
+				linkNext = RestfulServerUtils.createPagingLink(theIncludes, theRequest, searchId, theResult.getNextPageId(), theRequest.getParameters(), prettyPrint, theBundleType);
 			}
 			if (isNotBlank(theResult.getPreviousPageId())) {
-				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, theResult.getPreviousPageId(), theRequest.getParameters(), prettyPrint, theBundleType);
+				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, theRequest, searchId, theResult.getPreviousPageId(), theRequest.getParameters(), prettyPrint, theBundleType);
 			}
 		} else if (searchId != null) {
 			// We're doing offset pages
 			if (numTotalResults == null || theOffset + numToReturn < numTotalResults) {
-				linkNext = (RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, theOffset + numToReturn, numToReturn, theRequest.getParameters(), prettyPrint, theBundleType));
+				linkNext = (RestfulServerUtils.createPagingLink(theIncludes, theRequest, searchId, theOffset + numToReturn, numToReturn, theRequest.getParameters(), prettyPrint, theBundleType));
 			}
 			if (theOffset > 0) {
 				int start = Math.max(0, theOffset - theLimit);
-				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, start, theLimit, theRequest.getParameters(), prettyPrint, theBundleType);
+				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, theRequest, searchId, start, theLimit, theRequest.getParameters(), prettyPrint, theBundleType);
 			}
 		}
 

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

@@ -19,20 +19,24 @@ package ca.uhn.fhir.rest.server.method;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.lang.reflect.Method;
-import java.util.*;
-
-import org.apache.commons.lang3.StringUtils;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.binder.CollectionBinder;
+import ca.uhn.fhir.rest.server.ElementsSupportEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import org.apache.commons.lang3.StringUtils;
+
+import java.lang.reflect.Method;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.StringTokenizer;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class ElementsParameter implements IParameter {
 
@@ -42,7 +46,7 @@ public class ElementsParameter implements IParameter {
 	@Override
 	@SuppressWarnings({"rawtypes", "unchecked"})
 	public Object translateQueryParametersIntoServerArgument(RequestDetails theRequest, BaseMethodBinding<?> theMethodBinding) throws InternalErrorException, InvalidRequestException {
-		Set<String> value = getElementsValueOrNull(theRequest);
+		Set<String> value = getElementsValueOrNull(theRequest, false);
 		if (value == null || value.isEmpty()) {
 			return null;
 		}
@@ -62,32 +66,6 @@ public class ElementsParameter implements IParameter {
 		}
 	}
 
-	public static Set<String> getElementsValueOrNull(RequestDetails theRequest) {
-		String[] summary = theRequest.getParameters().get(Constants.PARAM_ELEMENTS);
-
-		if (summary != null && summary.length > 0) {
-			Set<String> retVal = new HashSet<String>();
-			for (String next : summary) {
-				StringTokenizer tok = new StringTokenizer(next, ",");
-				while (tok.hasMoreTokens()) {
-					String token = tok.nextToken();
-					if (isNotBlank(token)) {
-						retVal.add(token);
-					}
-				}
-			}
-			if (retVal.isEmpty()) {
-				return null;
-			}
-
-			// Always include the meta element even for subsetted values
-			retVal.add("meta");
-
-			return retVal;
-		}
-		return null;
-	}
-
 	@Override
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
 		if (theOuterCollectionType != null) {
@@ -99,4 +77,44 @@ public class ElementsParameter implements IParameter {
 		}
 	}
 
+	public static Set<String> getElementsValueOrNull(RequestDetails theRequest, boolean theExclude) {
+		boolean standardMode = theRequest.getServer().getElementsSupport() != ElementsSupportEnum.EXTENDED;
+		if (theExclude && standardMode) {
+			return null;
+		}
+
+		String paramName = Constants.PARAM_ELEMENTS;
+		if (theExclude) {
+			paramName = Constants.PARAM_ELEMENTS + Constants.PARAM_ELEMENTS_EXCLUDE_MODIFIER;
+		}
+		String[] summary = theRequest.getParameters().get(paramName);
+
+		if (summary != null && summary.length > 0) {
+			Set<String> retVal = new HashSet<String>();
+			for (String next : summary) {
+				StringTokenizer tok = new StringTokenizer(next, ",");
+				while (tok.hasMoreTokens()) {
+					String token = tok.nextToken();
+					if (isNotBlank(token)) {
+						if (token.contains(".") && standardMode) {
+							continue;
+						}
+						retVal.add(token);
+					}
+				}
+			}
+			if (retVal.isEmpty()) {
+				return null;
+			}
+
+			// Always include the meta element even for subsetted values
+			if (!theExclude) {
+				retVal.add("meta");
+			}
+
+			return retVal;
+		}
+		return null;
+	}
+
 }

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java

@@ -1011,6 +1011,7 @@ public class JsonParserDstu2_1Test {
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
 			assertThat(out, not(containsString("meta")));
+			assertThat(out, not(containsString("SUBSETTED")));
 		}
 	}
 

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2_1Test.java

@@ -1630,7 +1630,7 @@ public class XmlParserDstu2_1Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(patient);
 			ourLog.info(out);
@@ -1639,6 +1639,7 @@ public class XmlParserDstu2_1Test {
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
 			assertThat(out, not(containsString("meta")));
+			assertThat(out, not(containsString("SUBSETTED")));
 		}
 	}
 
@@ -1667,7 +1668,6 @@ public class XmlParserDstu2_1Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1679,7 +1679,6 @@ public class XmlParserDstu2_1Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -2701,12 +2700,6 @@ public class XmlParserDstu2_1Test {
 		assertTrue(d.toString(), !d.hasDifferences());
 	}
 
-	public static void main(String[] args) {
-		IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
-		// c.registerInterceptor(new LoggingInterceptor(true));
-		c.read().resource("Patient").withId("324").execute();
-	}
-
 	@ResourceDef(name = "Patient")
 	public static class TestPatientFor327 extends Patient {
 

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

@@ -1769,7 +1769,7 @@ public class XmlParserDstu2Test {
 
 		{
 			IParser p = ourCtx.newXmlParser();
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name", "Bundle.entry")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1780,8 +1780,7 @@ public class XmlParserDstu2Test {
 		}
 		{
 			IParser p = ourCtx.newXmlParser();
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1792,8 +1791,7 @@ public class XmlParserDstu2Test {
 		}
 		{
 			IParser p = ourCtx.newXmlParser();
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Patient")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1818,7 +1816,7 @@ public class XmlParserDstu2Test {
 
 		{
 			IParser p = ourCtx.newXmlParser();
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Bundle.entry", "*.text", "*.(mandatory)")));
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Bundle.entry", "*.text", "*.(mandatory)")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ElementsParamTest.java

@@ -1,178 +0,0 @@
-package ca.uhn.fhir.rest.server;
-
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
-
-import java.util.Set;
-import java.util.concurrent.TimeUnit;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.http.HttpResponse;
-import org.apache.http.client.methods.HttpGet;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
-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.*;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.dstu2.valueset.MaritalStatusCodesEnum;
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.annotation.*;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.util.PortUtil;
-import ca.uhn.fhir.util.TestUtil;
-
-public class ElementsParamTest {
-
-	private static CloseableHttpClient ourClient;
-	private static FhirContext ourCtx = FhirContext.forDstu2();
-	private static Set<String> ourLastElements;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElementsParamTest.class);
-	private static int ourPort;
-	private static Server ourServer;
-
-	@Before
-	public void before() {
-		ourLastElements = null;
-	}
-
-
-	@Test
-	public void testReadSummaryData() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_elements=name,maritalStatus");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-		ourLog.info(responseContent);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertEquals(Constants.CT_FHIR_XML + Constants.CHARSET_UTF8_CTSUFFIX.replace(" ", "").toLowerCase(), status.getEntity().getContentType().getValue().replace(" ", "").replace("UTF", "utf"));
-		assertThat(responseContent, not(containsString("<Bundle")));
-		assertThat(responseContent, (containsString("<Patien")));
-		assertThat(responseContent, not(containsString("<div>THE DIV</div>")));
-		assertThat(responseContent, (containsString("family")));
-		assertThat(responseContent, (containsString("maritalStatus")));
-		assertThat(ourLastElements, containsInAnyOrder("meta", "name", "maritalStatus"));
-	}
-
-	@Test
-	public void testReadSummaryTrue() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_elements=name");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-		ourLog.info(responseContent);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertEquals(Constants.CT_FHIR_XML + Constants.CHARSET_UTF8_CTSUFFIX.replace(" ", "").toLowerCase(), status.getEntity().getContentType().getValue().replace(" ", "").replace("UTF", "utf"));
-		assertThat(responseContent, not(containsString("<Bundle")));
-		assertThat(responseContent, (containsString("<Patien")));
-		assertThat(responseContent, not(containsString("<div>THE DIV</div>")));
-		assertThat(responseContent, (containsString("family")));
-		assertThat(responseContent, not(containsString("maritalStatus")));
-		assertThat(ourLastElements, containsInAnyOrder("meta", "name"));
-	}
-
-	@Test
-	public void testSearchSummaryData() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_elements=name,maritalStatus");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-		ourLog.info(responseContent);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertThat(responseContent, containsString("<Patient"));
-		assertThat(responseContent, not(containsString("THE DIV")));
-		assertThat(responseContent, containsString("family"));
-		assertThat(responseContent, containsString("maritalStatus"));
-		assertThat(ourLastElements, containsInAnyOrder("meta", "name", "maritalStatus"));
-	}
-
-	@Test
-	public void testSearchSummaryText() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_elements=text");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-		ourLog.info(responseContent);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertThat(responseContent, (containsString("<total value=\"1\"/>")));
-		assertThat(responseContent, (containsString("entry")));
-		assertThat(responseContent, (containsString("THE DIV")));
-		assertThat(responseContent, not(containsString("family")));
-		assertThat(responseContent, not(containsString("maritalStatus")));
-		assertThat(ourLastElements, containsInAnyOrder("meta", "text"));
-	}
-
-
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		ourServer.stop();
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-	@BeforeClass
-	public static void beforeClass() throws Exception {
-		ourPort = PortUtil.findFreePort();
-		ourServer = new Server(ourPort);
-
-		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
-
-		ServletHandler proxyHandler = new ServletHandler();
-		RestfulServer servlet = new RestfulServer(ourCtx);
-
-		servlet.setResourceProviders(patientProvider);
-		ServletHolder servletHolder = new ServletHolder(servlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		ourServer.setHandler(proxyHandler);
-		ourServer.start();
-
-		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
-		HttpClientBuilder builder = HttpClientBuilder.create();
-		builder.setConnectionManager(connectionManager);
-		ourClient = builder.build();
-
-	}
-
-	public static class DummyPatientResourceProvider implements IResourceProvider {
-
-		@Override
-		public Class<? extends IResource> getResourceType() {
-			return Patient.class;
-		}
-
-		@Read
-		public Patient read(@IdParam IdDt theId, @Elements Set<String> theElements) {
-			ourLastElements = theElements;
-			Patient patient = new Patient();
-			patient.setId("Patient/1/_history/1");
-			patient.getText().setDiv("<div>THE DIV</div>");
-			patient.addName().addFamily("FAMILY");
-			patient.setMaritalStatus(MaritalStatusCodesEnum.D);
-			return patient;
-		}
-
-		@Search()
-		public Patient search(@Elements Set<String> theElements) {
-			ourLastElements = theElements;
-			Patient patient = new Patient();
-			patient.setId("Patient/1/_history/1");
-			patient.getText().setDiv("<div>THE DIV</div>");
-			patient.addName().addFamily("FAMILY");
-			patient.setMaritalStatus(MaritalStatusCodesEnum.D);
-			return patient;
-		}
-
-	}
-
-}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -1232,6 +1232,7 @@ public class JsonParserDstu3Test {
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
 			assertThat(out, not(containsString("meta")));
+			assertThat(out, not(containsString("SUBSETTED")));
 		}
 	}
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -1862,6 +1862,7 @@ public class XmlParserDstu3Test {
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
 			assertThat(out, not(containsString("meta")));
+			assertThat(out, not(containsString("SUBSETTED")));
 		}
 	}
 
@@ -1890,7 +1891,6 @@ public class XmlParserDstu3Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1902,7 +1902,6 @@ public class XmlParserDstu3Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

@@ -8,6 +8,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.hl7.fhir.r4.model.*;
 import org.junit.AfterClass;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -252,6 +253,7 @@ public class JsonParserR4Test {
 	}
 
 	@Test
+	@Ignore
 	public void testExcludeRootStuff() {
 		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
 		Set<String> excludes = new HashSet<>();

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ElementsParamR4Test.java

@@ -0,0 +1,320 @@
+package ca.uhn.fhir.rest.server;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.util.PortUtil;
+import ca.uhn.fhir.util.TestUtil;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+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.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.*;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.IOException;
+import java.util.Collection;
+import java.util.Set;
+import java.util.concurrent.TimeUnit;
+import java.util.function.Consumer;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+public class ElementsParamR4Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElementsParamR4Test.class);
+	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx = FhirContext.forR4();
+	private static Set<String> ourLastElements;
+	private static int ourPort;
+	private static Server ourServer;
+	private static Procedure ourNextProcedure;
+	private static RestfulServer ourServlet;
+
+	@Before
+	public void before() {
+		ourLastElements = null;
+		ourNextProcedure = null;
+		ourServlet.setElementsSupport(new RestfulServer().getElementsSupport());
+	}
+
+	@Test
+	public void testReadSummaryData() throws Exception {
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Patient/1?_elements=name,maritalStatus",
+			Patient.class,
+			patient -> {
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(patient);
+				assertThat(responseContent, not(containsString("<Bundle")));
+				assertThat(responseContent, (containsString("<Patient")));
+				assertThat(responseContent, not(containsString("<div>THE DIV</div>")));
+				assertThat(responseContent, (containsString("family")));
+				assertThat(responseContent, (containsString("maritalStatus")));
+				assertThat(ourLastElements, containsInAnyOrder("meta", "name", "maritalStatus"));
+			}
+		);
+	}
+
+	@Test
+	public void testReadSummaryTrue() throws Exception {
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Patient/1?_elements=name",
+			Patient.class,
+			patient -> {
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(patient);
+				assertThat(responseContent, not(containsString("<div>THE DIV</div>")));
+				assertThat(responseContent, (containsString("family")));
+				assertThat(responseContent, not(containsString("maritalStatus")));
+				assertThat(ourLastElements, containsInAnyOrder("meta", "name"));
+			}
+		);
+	}
+
+	@Test
+	public void testSearchSummaryData() throws Exception {
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Patient?_elements=name,maritalStatus",
+			bundle -> {
+				assertEquals("1", bundle.getTotalElement().getValueAsString());
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle.getEntry().get(0).getResource());
+				assertThat(responseContent, containsString("<Patient"));
+				assertThat(responseContent, not(containsString("THE DIV")));
+				assertThat(responseContent, containsString("family"));
+				assertThat(responseContent, containsString("maritalStatus"));
+				assertThat(ourLastElements, containsInAnyOrder("meta", "name", "maritalStatus"));
+			}
+		);
+	}
+
+	@Test
+	public void testSearchSummaryText() throws Exception {
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Patient?_elements=text&_pretty=true",
+			bundle -> {
+				assertEquals("1", bundle.getTotalElement().getValueAsString());
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle.getEntry().get(0).getResource());
+				assertThat(responseContent, containsString("THE DIV"));
+				assertThat(responseContent, not(containsString("family")));
+				assertThat(responseContent, not(containsString("maritalStatus")));
+				assertThat(ourLastElements, containsInAnyOrder("meta", "text"));
+			}
+		);
+	}
+
+	/**
+	 * By default the elements apply only to the focal resource in a search
+	 * and not any included resources
+	 */
+	@Test
+	public void testStandardElementsFilter() throws IOException {
+		createProcedureWithLongChain();
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Procedure?_include=*&_elements=reasonCode,status",
+			bundle -> {
+				Procedure procedure = (Procedure) bundle.getEntry().get(0).getResource();
+				assertEquals("SUBSETTED", procedure.getMeta().getTag().get(0).getCode());
+				assertEquals("REASON_CODE", procedure.getReasonCode().get(0).getCoding().get(0).getCode());
+				assertEquals(0, procedure.getUsedCode().size());
+
+				DiagnosticReport dr = (DiagnosticReport) bundle.getEntry().get(1).getResource();
+				assertEquals(0, dr.getMeta().getTag().size());
+				assertEquals("Observation/OBSA", dr.getResult().get(0).getReference());
+
+				Observation obs = (Observation ) bundle.getEntry().get(2).getResource();
+				assertEquals(0, obs.getMeta().getTag().size());
+				assertEquals(Observation.ObservationStatus.FINAL, obs.getStatus());
+				assertEquals("1234-5", obs.getCode().getCoding().get(0).getCode());
+			});
+	}
+
+	@Test
+	public void testMultiResourceElementsFilter() throws IOException {
+		createProcedureWithLongChain();
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Procedure?_include=*&_elements=Procedure.reasonCode,Observation.status,Observation.subject,Observation.value",
+			bundle -> {
+				Procedure procedure = (Procedure) bundle.getEntry().get(0).getResource();
+				assertEquals("SUBSETTED", procedure.getMeta().getTag().get(0).getCode());
+				assertEquals("REASON_CODE", procedure.getReasonCode().get(0).getCoding().get(0).getCode());
+				assertEquals(0, procedure.getUsedCode().size());
+
+				DiagnosticReport dr = (DiagnosticReport) bundle.getEntry().get(1).getResource();
+				assertEquals(0, dr.getMeta().getTag().size());
+
+				Observation obs = (Observation ) bundle.getEntry().get(2).getResource();
+				assertEquals("SUBSETTED", obs.getMeta().getTag().get(0).getCode());
+				assertEquals(Observation.ObservationStatus.FINAL, obs.getStatus());
+				assertEquals(0, obs.getCode().getCoding().size());
+				assertEquals("STRING VALUE", obs.getValueStringType().getValue());
+			});
+	}
+
+	@Test
+	public void testMultiResourceElementsFilterWithMetadataExcluded() throws IOException {
+		createProcedureWithLongChain();
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Procedure?_include=*&_elements=Procedure.reasonCode,Observation.status,Observation.subject,Observation.value&_elements:exclude=*.meta",
+			bundle -> {
+				Procedure procedure = (Procedure) bundle.getEntry().get(0).getResource();
+				assertEquals(true, procedure.getMeta().isEmpty());
+				assertEquals("REASON_CODE", procedure.getReasonCode().get(0).getCoding().get(0).getCode());
+				assertEquals(0, procedure.getUsedCode().size());
+
+				DiagnosticReport dr = (DiagnosticReport) bundle.getEntry().get(1).getResource();
+				assertEquals(true, dr.getMeta().isEmpty());
+
+				Observation obs = (Observation ) bundle.getEntry().get(2).getResource();
+				assertEquals(true, obs.getMeta().isEmpty());
+				assertEquals(Observation.ObservationStatus.FINAL, obs.getStatus());
+				assertEquals(0, obs.getCode().getCoding().size());
+				assertEquals("STRING VALUE", obs.getValueStringType().getValue());
+			});
+	}
+
+	@Test
+	public void testElementsFilterWithComplexPath() throws IOException {
+		createProcedureWithLongChain();
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Procedure?_elements=Procedure.reasonCode.coding.code",
+			bundle -> {
+				Procedure procedure = (Procedure) bundle.getEntry().get(0).getResource();
+				assertEquals("SUBSETTED", procedure.getMeta().getTag().get(0).getCode());
+				assertEquals("REASON_CODE", procedure.getReasonCode().get(0).getCoding().get(0).getCode());
+				assertEquals(null, procedure.getReasonCode().get(0).getCoding().get(0).getSystem());
+				assertEquals(null, procedure.getReasonCode().get(0).getCoding().get(0).getDisplay());
+				assertEquals(0, procedure.getUsedCode().size());
+			});
+	}
+
+	private void createProcedureWithLongChain() {
+		ourNextProcedure = new Procedure();
+		ourNextProcedure.setId("Procedure/PROC");
+		ourNextProcedure.addReasonCode().addCoding().setCode("REASON_CODE").setSystem("REASON_SYSTEM").setDisplay("REASON_DISPLAY");
+		ourNextProcedure.addUsedCode().addCoding().setCode("USED_CODE");
+
+		DiagnosticReport dr = new DiagnosticReport();
+		dr.setId("DiagnosticReport/DRA");
+		ourNextProcedure.addReport().setResource(dr);
+
+		Observation obs = new Observation();
+		obs.setId("Observation/OBSA");
+		obs.setStatus(Observation.ObservationStatus.FINAL);
+		obs.setSubject(new Reference("Patient/123"));
+		obs.getCode().addCoding().setSystem("http://loinc.org").setCode("1234-5");
+		obs.setValue(new StringType("STRING VALUE"));
+		dr.addResult().setResource(obs);
+	}
+
+	private void verifyXmlAndJson(String theUri, Consumer<Bundle> theVerifier) throws IOException {
+		verifyXmlAndJson(theUri, Bundle.class, theVerifier);
+	}
+
+	private <T extends IBaseResource> void verifyXmlAndJson(String theUri, Class<T> theType, Consumer<T> theVerifier) throws IOException {
+		EncodingEnum encodingEnum;
+		HttpGet httpGet;
+
+		encodingEnum = EncodingEnum.JSON;
+		httpGet = new HttpGet(theUri + "&_pretty=true&_format=" + encodingEnum.getFormatContentType());
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info(responseContent);
+			T response = encodingEnum.newParser(ourCtx).parseResource(theType, responseContent);
+			theVerifier.accept(response);
+		}
+
+		encodingEnum = EncodingEnum.XML;
+		httpGet = new HttpGet(theUri + "&_pretty=true&_format=" + encodingEnum.getFormatContentType());
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info(responseContent);
+			T response = encodingEnum.newParser(ourCtx).parseResource(theType, responseContent);
+			theVerifier.accept(response);
+		}
+	}
+
+	public static class DummyProcedureResourceProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IBaseResource> getResourceType() {
+			return Procedure.class;
+		}
+
+		@Search
+		public Procedure search(@IncludeParam(allow = {"*"}) Collection<Include> theIncludes) {
+			return ourNextProcedure;
+		}
+
+	}
+
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IBaseResource> getResourceType() {
+			return Patient.class;
+		}
+
+		@Read
+		public Patient read(@IdParam IdType theId, @Elements Set<String> theElements) {
+			ourLastElements = theElements;
+			Patient patient = new Patient();
+			patient.setId("Patient/1/_history/1");
+			patient.getText().getDiv().setValueAsString("<div>THE DIV</div>");
+			patient.addName().setFamily("FAMILY");
+			patient.getMaritalStatus().addCoding().setCode("D");
+			return patient;
+		}
+
+		@Search()
+		public Patient search(@Elements Set<String> theElements) {
+			ourLastElements = theElements;
+			Patient patient = new Patient();
+			patient.setId("Patient/1/_history/1");
+			patient.getText().getDiv().setValueAsString("<div>THE DIV</div>");
+			patient.addName().setFamily("FAMILY");
+			patient.getMaritalStatus().addCoding().setCode("D");
+			return patient;
+		}
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		ServletHandler proxyHandler = new ServletHandler();
+		ourServlet = new RestfulServer(ourCtx);
+
+		ourServlet.registerProvider(new DummyPatientResourceProvider());
+		ourServlet.registerProvider(new DummyProcedureResourceProvider());
+		ServletHolder servletHolder = new ServletHolder(ourServlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+}

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SearchR4Test.java

@@ -89,36 +89,39 @@ public class SearchR4Test {
 		String linkSelf;
 
 		// Initial search
-		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_elements=name");
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_elements=name&_elements:exclude=birthDate,active");
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
-		assertThat(toJson(bundle), not(containsString("active")));
+		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkSelf = bundle.getLink(Constants.LINK_SELF).getUrl();
 		assertThat(linkSelf, containsString("_elements=name"));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=meta,name"));
 
 		ourLog.info(toJson(bundle));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
-		assertThat(toJson(bundle), not(containsString("active")));
+		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=meta,name"));
+		assertThat(linkNext, containsString("_elements:exclude=active,birthDate"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
-		assertThat(toJson(bundle), not(containsString("active")));
+		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=meta,name"));
+		assertThat(linkNext, containsString("_elements:exclude=active,birthDate"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
-		assertThat(toJson(bundle), not(containsString("active")));
+		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=meta,name"));
+		assertThat(linkNext, containsString("_elements:exclude=active,birthDate"));
 
 	}
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SummaryParamR4Test.java

@@ -5,11 +5,13 @@ import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Read;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.util.PortUtil;
 import ca.uhn.fhir.util.TestUtil;
+import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
-import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
@@ -18,18 +20,17 @@ import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.MedicationRequest;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Reference;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import java.util.Arrays;
+import java.io.IOException;
+import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.TimeUnit;
+import java.util.function.Consumer;
 
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.assertEquals;
@@ -37,11 +38,11 @@ import static org.junit.Assert.assertThat;
 
 public class SummaryParamR4Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SummaryParamR4Test.class);
 	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static SummaryEnum ourLastSummary;
 	private static List<SummaryEnum> ourLastSummaryList;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SummaryParamR4Test.class);
 	private static int ourPort;
 
 	private static Server ourServer;
@@ -51,16 +52,14 @@ public class SummaryParamR4Test {
 		ourLastSummary = null;
 		ourLastSummaryList = null;
 	}
+
 	@Test
 	public void testReadSummaryData() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_summary=" + SummaryEnum.DATA.getCode());
+		verifyXmlAndJson(
-		HttpResponse status = ourClient.execute(httpGet);
+			"http://localhost:" + ourPort + "/Patient/1?_summary=" + SummaryEnum.DATA.getCode(),
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			Patient.class,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			patient -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(patient);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertEquals(Constants.CT_FHIR_XML_NEW + Constants.CHARSET_UTF8_CTSUFFIX.replace(" ", "").toLowerCase(), status.getEntity().getContentType().getValue().replace(" ", "").replace("UTF", "utf"));
 				assertThat(responseContent, not(containsString("<Bundle")));
 				assertThat(responseContent, (containsString("<Patien")));
 				assertThat(responseContent, not(containsString("<div>THE DIV</div>")));
@@ -68,15 +67,15 @@ public class SummaryParamR4Test {
 				assertThat(responseContent, (containsString("maritalStatus")));
 				assertEquals(SummaryEnum.DATA, ourLastSummary);
 			}
-
+		);
+	}
 
 
 	@Test
 	public void testReadSummaryText() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_summary=" + SummaryEnum.TEXT.getCode());
-		HttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
-		IOUtils.closeQuietly(status.getEntity().getContent());
 			ourLog.info(responseContent);
 
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -87,13 +86,13 @@ public class SummaryParamR4Test {
 			assertThat(responseContent, not(containsString("efer")));
 			assertEquals(SummaryEnum.TEXT, ourLastSummary);
 		}
+	}
 
 	@Test
 	public void testReadSummaryTextWithMandatory() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/MedicationRequest/1?_summary=" + SummaryEnum.TEXT.getCode());
-		HttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
-		IOUtils.closeQuietly(status.getEntity().getContent());
 			ourLog.info(responseContent);
 
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -104,17 +103,16 @@ public class SummaryParamR4Test {
 			assertThat(responseContent, not(containsString("family")));
 			assertThat(responseContent, not(containsString("maritalStatus")));
 		}
+	}
 
 	@Test
 	public void testReadSummaryTrue() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_summary=" + SummaryEnum.TRUE.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient/1?_summary=" + SummaryEnum.TRUE.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			Patient.class,
-		ourLog.info(responseContent);
+			patient -> {
-
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertEquals(Constants.CT_FHIR_XML_NEW + Constants.CHARSET_UTF8_CTSUFFIX.replace(" ", "").toLowerCase(), status.getEntity().getContentType().getValue().replace(" ", "").replace("UTF", "utf"));
 				assertThat(responseContent, not(containsString("<Bundle")));
 				assertThat(responseContent, (containsString("<Patien")));
 				assertThat(responseContent, not(containsString("<div>THE DIV</div>")));
@@ -122,16 +120,17 @@ public class SummaryParamR4Test {
 				assertThat(responseContent, not(containsString("maritalStatus")));
 				assertEquals(SummaryEnum.TRUE, ourLastSummary);
 			}
+		);
+
+	}
 
 	@Test
 	public void testSearchSummaryCount() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_pretty=true&_summary=" + SummaryEnum.COUNT.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient?_pretty=true&_summary=" + SummaryEnum.COUNT.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, (containsString("<total value=\"1\"/>")));
 				assertThat(responseContent, not(containsString("entry")));
 				assertThat(responseContent, not(containsString("THE DIV")));
@@ -139,64 +138,65 @@ public class SummaryParamR4Test {
 				assertThat(responseContent, not(containsString("maritalStatus")));
 				assertEquals(SummaryEnum.COUNT, ourLastSummary);
 			}
+		);
+	}
 
 	@Test
 	public void testSearchSummaryCountAndData() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_pretty=true&_summary=" + SummaryEnum.COUNT.getCode() + "," + SummaryEnum.DATA.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient?_pretty=true&_summary=" + SummaryEnum.COUNT.getCode() + "," + SummaryEnum.DATA.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, (containsString("<total value=\"1\"/>")));
 				assertThat(responseContent, (containsString("entry")));
 				assertThat(responseContent, not(containsString("THE DIV")));
 				assertThat(responseContent, (containsString("family")));
 				assertThat(responseContent, (containsString("maritalStatus")));
 			}
+		);
+	}
 
 	@Test
 	public void testSearchSummaryData() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_summary=" + SummaryEnum.DATA.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient?_summary=" + SummaryEnum.DATA.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, containsString("<Patient"));
 				assertThat(responseContent, not(containsString("THE DIV")));
 				assertThat(responseContent, containsString("family"));
 				assertThat(responseContent, containsString("maritalStatus"));
 				assertEquals(SummaryEnum.DATA, ourLastSummary);
 			}
+		);
+
+	}
 
 	@Test
 	public void testSearchSummaryFalse() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_summary=false");
+		String url = "http://localhost:" + ourPort + "/Patient?_summary=false";
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, containsString("<Patient"));
 				assertThat(responseContent, containsString("THE DIV"));
 				assertThat(responseContent, containsString("family"));
 				assertThat(responseContent, containsString("maritalStatus"));
 				assertEquals(SummaryEnum.FALSE, ourLastSummary);
 			}
+		);
+	}
 
 	@Test
 	public void testSearchSummaryText() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_summary=" + SummaryEnum.TEXT.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient?_summary=" + SummaryEnum.TEXT.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, (containsString("<total value=\"1\"/>")));
 				assertThat(responseContent, (containsString("entry")));
 				assertThat(responseContent, (containsString("THE DIV")));
@@ -204,32 +204,34 @@ public class SummaryParamR4Test {
 				assertThat(responseContent, not(containsString("maritalStatus")));
 				assertEquals(SummaryEnum.TEXT, ourLastSummary);
 			}
+		);
+	}
 
 	@Test
 	public void testSearchSummaryTextWithMandatory() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/MedicationRequest?_summary=" + SummaryEnum.TEXT.getCode() + "&_pretty=true");
+		String url = "http://localhost:" + ourPort + "/MedicationRequest?_summary=" + SummaryEnum.TEXT.getCode() + "&_pretty=true";
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				assertEquals(0, bundle.getMeta().getTag().size());
-
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, (containsString("<total value=\"1\"/>")));
 				assertThat(responseContent, (containsString("entry")));
 				assertThat(responseContent, (containsString(">TEXT<")));
 				assertThat(responseContent, (containsString("Medication/123")));
 				assertThat(responseContent, not(containsStringIgnoringCase("note")));
 			}
+		);
+
+	}
 
 	@Test
 	public void testSearchSummaryTextMulti() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=multi&_summary=" + SummaryEnum.TEXT.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient?_query=multi&_summary=" + SummaryEnum.TEXT.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, (containsString("<total value=\"1\"/>")));
 				assertThat(responseContent, (containsString("entry")));
 				assertThat(responseContent, (containsString("THE DIV")));
@@ -237,60 +239,63 @@ public class SummaryParamR4Test {
 				assertThat(responseContent, not(containsString("maritalStatus")));
 				assertThat(ourLastSummaryList, contains(SummaryEnum.TEXT));
 			}
+		);
+	}
 
 	@Test
 	public void testSearchSummaryTrue() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_summary=" + SummaryEnum.TRUE.getCode());
+		String url = "http://localhost:" + ourPort + "/Patient?_summary=" + SummaryEnum.TRUE.getCode();
-		HttpResponse status = ourClient.execute(httpGet);
+		verifyXmlAndJson(
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			url,
-		IOUtils.closeQuietly(status.getEntity().getContent());
+			bundle -> {
-		ourLog.info(responseContent);
+				String responseContent = ourCtx.newXmlParser().encodeResourceToString(bundle);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
 				assertThat(responseContent, containsString("<Patient"));
 				assertThat(responseContent, not(containsString("THE DIV")));
 				assertThat(responseContent, containsString("family"));
 				assertThat(responseContent, not(containsString("maritalStatus")));
 				assertEquals(SummaryEnum.TRUE, ourLastSummary);
 			}
+		);
+
+	}
 
 	@Test
 	public void testSearchSummaryWithTextAndOthers() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_summary=text&_summary=data");
+		String url = "http://localhost:" + ourPort + "/Patient?_summary=text&_summary=data";
-		HttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(new HttpGet(url))) {
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
-		IOUtils.closeQuietly(status.getEntity().getContent());
 			ourLog.info(responseContent);
 
 			assertEquals(400, status.getStatusLine().getStatusCode());
 			assertThat(responseContent, containsString("Can not combine _summary=text with other values for _summary"));
 		}
-
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		ourServer.stop();
-		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
-	@BeforeClass
+	private void verifyXmlAndJson(String theUri, Consumer<Bundle> theVerifier) throws IOException {
-	public static void beforeClass() throws Exception {
+		verifyXmlAndJson(theUri, Bundle.class, theVerifier);
-		ourPort = PortUtil.findFreePort();
+	}
-		ourServer = new Server(ourPort);
 
-		ServletHandler proxyHandler = new ServletHandler();
+	private <T extends IBaseResource> void verifyXmlAndJson(String theUri, Class<T> theType, Consumer<T> theVerifier) throws IOException {
-		RestfulServer servlet = new RestfulServer(ourCtx);
+		EncodingEnum encodingEnum;
+		HttpGet httpGet;
 
-		servlet.setResourceProviders(new DummyPatientResourceProvider(), new DummyMedicationRequestProvider());
+		encodingEnum = EncodingEnum.JSON;
-		ServletHolder servletHolder = new ServletHolder(servlet);
+		httpGet = new HttpGet(theUri + "&_pretty=true&_format=" + encodingEnum.getFormatContentType());
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		ourServer.setHandler(proxyHandler);
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
-		ourServer.start();
+			ourLog.info(responseContent);
-
+			T response = encodingEnum.newParser(ourCtx).parseResource(theType, responseContent);
-		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+			theVerifier.accept(response);
-		HttpClientBuilder builder = HttpClientBuilder.create();
+		}
-		builder.setConnectionManager(connectionManager);
-		ourClient = builder.build();
 
+		encodingEnum = EncodingEnum.XML;
+		httpGet = new HttpGet(theUri + "&_pretty=true&_format=" + encodingEnum.getFormatContentType());
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info(responseContent);
+			T response = encodingEnum.newParser(ourCtx).parseResource(theType, responseContent);
+			theVerifier.accept(response);
+		}
 	}
 
 	public static class DummyMedicationRequestProvider implements IResourceProvider {
@@ -312,7 +317,7 @@ public class SummaryParamR4Test {
 
 		@Search
 		public List<MedicationRequest> read() {
-			return Arrays.asList(read(new IdType("999")));
+			return Collections.singletonList(read(new IdType("999")));
 		}
 
 	}
@@ -359,4 +364,31 @@ public class SummaryParamR4Test {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+
+		servlet.setResourceProviders(new DummyPatientResourceProvider(), new DummyMedicationRequestProvider());
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
 }

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu21/JsonParserDstu2_1Test.java

@@ -940,7 +940,6 @@ public class JsonParserDstu2_1Test {
 			assertThat(out, containsString("name"));
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
-			assertThat(out, not(containsString("meta")));
 		}
 	}
 

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu21/XmlParserDstu2_1Test.java

@@ -1568,7 +1568,6 @@ public class XmlParserDstu2_1Test {
 			assertThat(out, containsString("name"));
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
-			assertThat(out, not(containsString("meta")));
 		}
 	}
 
@@ -1597,7 +1596,6 @@ public class XmlParserDstu2_1Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1609,7 +1607,6 @@ public class XmlParserDstu2_1Test {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/Dstu3JsonParserTest.java

@@ -1143,7 +1143,6 @@ public class Dstu3JsonParserTest {
 			assertThat(out, containsString("name"));
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
-			assertThat(out, not(containsString("meta")));
 		}
 	}
 

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/Dstu3XmlParserTest.java

@@ -1938,7 +1938,6 @@ public class Dstu3XmlParserTest {
 			assertThat(out, containsString("name"));
 			assertThat(out, containsString("id"));
 			assertThat(out, not(containsString("address")));
-			assertThat(out, not(containsString("meta")));
 		}
 	}
 
@@ -1967,7 +1966,6 @@ public class Dstu3XmlParserTest {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1979,7 +1977,6 @@ public class Dstu3XmlParserTest {
 		{
 			IParser p = ourCtx.newXmlParser();
 			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
-			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/r4/R4JsonParserTest.java

@@ -151,57 +151,6 @@ public class R4JsonParserTest {
 		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
 	}
 
-	@Test
-	public void testExcludeRootStuff() {
-		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
-		Set<String> excludes = new HashSet<>();
-		excludes.add("id");
-		excludes.add("meta");
-		parser.setDontEncodeElements(excludes);
-
-		Bundle b = createBundleWithPatient();
-
-		String encoded = parser.encodeResourceToString(b);
-		ourLog.info(encoded);
-
-		assertThat(encoded, not(containsString("BUNDLEID")));
-		assertThat(encoded, not(containsString("http://FOO")));
-		assertThat(encoded, (containsString("PATIENTID")));
-		assertThat(encoded, (containsString("http://BAR")));
-		assertThat(encoded, containsString("GIVEN"));
-
-		b = parser.parseResource(Bundle.class, encoded);
-
-		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
-		assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
-		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
-	}
-
-	@Test
-	public void testExcludeStarDotStuff() {
-		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
-		Set<String> excludes = new HashSet<>();
-		excludes.add("*.id");
-		excludes.add("*.meta");
-		parser.setDontEncodeElements(excludes);
-
-		Bundle b = createBundleWithPatient();
-
-		String encoded = parser.encodeResourceToString(b);
-		ourLog.info(encoded);
-
-		assertThat(encoded, not(containsString("BUNDLEID")));
-		assertThat(encoded, not(containsString("http://FOO")));
-		assertThat(encoded, not(containsString("PATIENTID")));
-		assertThat(encoded, not(containsString("http://BAR")));
-		assertThat(encoded, containsString("GIVEN"));
-
-		b = parser.parseResource(Bundle.class, encoded);
-
-		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
-		assertNotEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
-		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
-	}
 
 	/**
 	 * Test that long JSON strings don't get broken up

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/r4/R4XmlParserTest.java

@@ -106,32 +106,6 @@ public class R4XmlParserTest {
 		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
 	}
 
-	@Test
-	public void testExcludeRootStuff() {
-		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
-		Set<String> excludes = new HashSet<>();
-		excludes.add("id");
-		excludes.add("meta");
-		parser.setDontEncodeElements(excludes);
-
-		Bundle b = createBundleWithPatient();
-
-		String encoded = parser.encodeResourceToString(b);
-		ourLog.info(encoded);
-
-		assertThat(encoded, IsNot.not(containsString("BUNDLEID")));
-		assertThat(encoded, IsNot.not(containsString("http://FOO")));
-		assertThat(encoded, (containsString("PATIENTID")));
-		assertThat(encoded, (containsString("http://BAR")));
-		assertThat(encoded, containsString("GIVEN"));
-
-		b = parser.parseResource(Bundle.class, encoded);
-
-		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
-		assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
-		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
-	}
-
 	@Test
 	public void testExcludeStarDotStuff() {
 		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);

src/site/xdoc/doc_rest_server.xml

@@ -689,6 +689,55 @@
 
 		</section>
 
+		<section name="Extended Elements Support" id="extended_elements_support">
+
+			<p>
+				The HAPI FHIR server may be configured using the
+				<code>RestfulServer#setElementsSupport</code> to enable extended
+				support for the <code>_elements</code> filter.
+			</p>
+			<p>
+				In standard mode, elements are supported exactly as described in the
+				<a href="http://hl7.org/fhir/search.html#elements">Elements Documentation</a>
+				in the FHIR specification.
+			</p>
+			<p>
+				In extended mode, HAPI FHIR provides the same behaviour as described in the
+				FHIR specification, but also enabled the following additional options:
+			</p>
+			<ul>
+				<li>
+					Values may be prepended using Resource names in order to apply the
+					elements filter to multiple resources. For example, the following
+					parameter could be used to apply elements filtering to both the
+					DiagnosticReport and Observation resource in a search result:<br/>
+					<code>_elements=DiagnosticReport.subject,DiagnosticReport.result,Observation.value</code>
+				</li>
+				<li>
+					Values may be prepended with a wildcard star in order to apply them
+					to all resource types. For example, the following parameter could
+					be used to include the <code>subject</code> field in all resource
+					types:<br/>
+					<code>_elements=*.subject</code>
+				</li>
+				<li>
+					Values may include complex paths. For example, the following parameter could
+					be used to include only the code on a coded element:<br/>
+					<code>_elements=Procedure.reasonCode.coding.code</code>
+				</li>
+				<li>
+					Elements may be excluded using the <code>:exclude</code> modifier
+					on the elements parameter. For example, the following parameter
+					could be used to remove the resource metadata (meta) element from
+					all resources in the response:<br/>
+					<code>_elements:exclude=*.meta</code><br/>
+					Note that this can be used to suppress the <code>SUBSETTED</code> tag
+					which is automatically added to resources when an <code>_elements</code>
+					parameter is applied.
+				</li>
+			</ul>
+		</section>
+		
 	</body>
 
 </document>