Syncing master into working branch.

hapi-fhir-base/pom.xml

@@ -69,6 +69,12 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.jena</groupId>
+			<artifactId>apache-jena-libs</artifactId>
+			<optional>true</optional>
+			<type>pom</type>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-text</artifactId>

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

@@ -20,6 +20,7 @@ import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.VersionUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import org.apache.commons.lang3.Validate;
+import org.apache.jena.riot.Lang;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -111,7 +112,7 @@ public class FhirContext {
 	 * of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
 	 */
 	@Deprecated
-	public FhirContext(Class<? extends IBaseResource> theResourceType) {
+	public FhirContext(final Class<? extends IBaseResource> theResourceType) {
 		this(toCollection(theResourceType));
 	}
 
@@ -120,7 +121,7 @@ public class FhirContext {
 	 * of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
 	 */
 	@Deprecated
-	public FhirContext(Class<?>... theResourceTypes) {
+	public FhirContext(final Class<?>... theResourceTypes) {
 		this(toCollection(theResourceTypes));
 	}
 
@@ -129,7 +130,7 @@ public class FhirContext {
 	 * of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
 	 */
 	@Deprecated
-	public FhirContext(Collection<Class<? extends IBaseResource>> theResourceTypes) {
+	public FhirContext(final Collection<Class<? extends IBaseResource>> theResourceTypes) {
 		this(null, theResourceTypes);
 	}
 
@@ -138,11 +139,11 @@ public class FhirContext {
 	 * of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}, but
 	 * this method can also be used if you wish to supply the version programmatically.
 	 */
-	public FhirContext(FhirVersionEnum theVersion) {
+	public FhirContext(final FhirVersionEnum theVersion) {
 		this(theVersion, null);
 	}
 
-	private FhirContext(FhirVersionEnum theVersion, Collection<Class<? extends IBaseResource>> theResourceTypes) {
+	private FhirContext(final FhirVersionEnum theVersion, final Collection<Class<? extends IBaseResource>> theResourceTypes) {
 		VersionUtil.getVersion();
 
 		if (theVersion != null) {
@@ -191,7 +192,7 @@ public class FhirContext {
 
 	}
 
-	private String createUnknownResourceNameError(String theResourceName, FhirVersionEnum theVersion) {
+	private String createUnknownResourceNameError(final String theResourceName, final FhirVersionEnum theVersion) {
 		return getLocalizer().getMessage(FhirContext.class, "unknownResourceName", theResourceName, theVersion);
 	}
 
@@ -232,7 +233,7 @@ public class FhirContext {
 	 *
 	 * @param theAddProfileTagWhenEncoding The add profile mode (must not be <code>null</code>)
 	 */
-	public void setAddProfileTagWhenEncoding(AddProfileTagEnum theAddProfileTagWhenEncoding) {
+	public void setAddProfileTagWhenEncoding(final AddProfileTagEnum theAddProfileTagWhenEncoding) {
 		Validate.notNull(theAddProfileTagWhenEncoding, "theAddProfileTagWhenEncoding must not be null");
 		myAddProfileTagWhenEncoding = theAddProfileTagWhenEncoding;
 	}
@@ -247,7 +248,7 @@ public class FhirContext {
 	 *
 	 * @see #setDefaultTypeForProfile(String, Class)
 	 */
-	public Class<? extends IBaseResource> getDefaultTypeForProfile(String theProfile) {
+	public Class<? extends IBaseResource> getDefaultTypeForProfile(final String theProfile) {
 		validateInitialized();
 		return myDefaultTypeForProfile.get(theProfile);
 	}
@@ -257,7 +258,7 @@ public class FhirContext {
 	 * for extending the core library.
 	 */
 	@SuppressWarnings("unchecked")
-	public BaseRuntimeElementDefinition<?> getElementDefinition(Class<? extends IBase> theElementType) {
+	public BaseRuntimeElementDefinition<?> getElementDefinition(final Class<? extends IBase> theElementType) {
 		validateInitialized();
 		BaseRuntimeElementDefinition<?> retVal = myClassToElementDefinition.get(theElementType);
 		if (retVal == null) {
@@ -273,7 +274,7 @@ public class FhirContext {
 	 * Note that this method is case insensitive!
 	 * </p>
 	 */
-	public BaseRuntimeElementDefinition<?> getElementDefinition(String theElementName) {
+	public BaseRuntimeElementDefinition<?> getElementDefinition(final String theElementName) {
 		validateInitialized();
 		return myNameToElementDefinition.get(theElementName.toLowerCase());
 	}
@@ -301,7 +302,7 @@ public class FhirContext {
 	 * This feature is not yet in its final state and should be considered an internal part of HAPI for now - use with
 	 * caution
 	 */
-	public void setLocalizer(HapiLocalizer theMessages) {
+	public void setLocalizer(final HapiLocalizer theMessages) {
 		myLocalizer = theMessages;
 	}
 
@@ -309,7 +310,7 @@ public class FhirContext {
 		return myNarrativeGenerator;
 	}
 
-	public void setNarrativeGenerator(INarrativeGenerator theNarrativeGenerator) {
+	public void setNarrativeGenerator(final INarrativeGenerator theNarrativeGenerator) {
 		myNarrativeGenerator = theNarrativeGenerator;
 	}
 
@@ -329,7 +330,7 @@ public class FhirContext {
 	 *
 	 * @param theParserOptions The parser options object - Must not be <code>null</code>
 	 */
-	public void setParserOptions(ParserOptions theParserOptions) {
+	public void setParserOptions(final ParserOptions theParserOptions) {
 		Validate.notNull(theParserOptions, "theParserOptions must not be null");
 		myParserOptions = theParserOptions;
 	}
@@ -360,7 +361,7 @@ public class FhirContext {
 	 *
 	 * @see PerformanceOptionsEnum for a list of available options
 	 */
-	public void setPerformanceOptions(Collection<PerformanceOptionsEnum> theOptions) {
+	public void setPerformanceOptions(final Collection<PerformanceOptionsEnum> theOptions) {
 		myPerformanceOptions.clear();
 		if (theOptions != null) {
 			myPerformanceOptions.addAll(theOptions);
@@ -371,7 +372,7 @@ public class FhirContext {
 	 * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
 	 * for extending the core library.
 	 */
-	public RuntimeResourceDefinition getResourceDefinition(Class<? extends IBaseResource> theResourceType) {
+	public RuntimeResourceDefinition getResourceDefinition(final Class<? extends IBaseResource> theResourceType) {
 		validateInitialized();
 		if (theResourceType == null) {
 			throw new NullPointerException("theResourceType can not be null");
@@ -387,7 +388,7 @@ public class FhirContext {
 		return retVal;
 	}
 
-	public RuntimeResourceDefinition getResourceDefinition(FhirVersionEnum theVersion, String theResourceName) {
+	public RuntimeResourceDefinition getResourceDefinition(final FhirVersionEnum theVersion, final String theResourceName) {
 		Validate.notNull(theVersion, "theVersion can not be null");
 		validateInitialized();
 
@@ -419,7 +420,7 @@ public class FhirContext {
 	 * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
 	 * for extending the core library.
 	 */
-	public RuntimeResourceDefinition getResourceDefinition(IBaseResource theResource) {
+	public RuntimeResourceDefinition getResourceDefinition(final IBaseResource theResource) {
 		validateInitialized();
 		Validate.notNull(theResource, "theResource must not be null");
 		return getResourceDefinition(theResource.getClass());
@@ -434,7 +435,7 @@ public class FhirContext {
 	 *
 	 * @throws DataFormatException If the resource name is not known
 	 */
-	public RuntimeResourceDefinition getResourceDefinition(String theResourceName) throws DataFormatException {
+	public RuntimeResourceDefinition getResourceDefinition(final String theResourceName) throws DataFormatException {
 		validateInitialized();
 		Validate.notBlank(theResourceName, "theResourceName must not be blank");
 
@@ -462,7 +463,7 @@ public class FhirContext {
 	 * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
 	 * for extending the core library.
 	 */
-	public RuntimeResourceDefinition getResourceDefinitionById(String theId) {
+	public RuntimeResourceDefinition getResourceDefinitionById(final String theId) {
 		validateInitialized();
 		return myIdToResourceDefinition.get(theId);
 	}
@@ -528,7 +529,7 @@ public class FhirContext {
 	 *
 	 * @param theRestfulClientFactory
 	 */
-	public void setRestfulClientFactory(IRestfulClientFactory theRestfulClientFactory) {
+	public void setRestfulClientFactory(final IRestfulClientFactory theRestfulClientFactory) {
 		Validate.notNull(theRestfulClientFactory, "theRestfulClientFactory must not be null");
 		this.myRestfulClientFactory = theRestfulClientFactory;
 	}
@@ -619,6 +620,23 @@ public class FhirContext {
 		return new JsonParser(this, myParserErrorHandler);
 	}
 
+	/**
+	 * Create and return a new RDF parser.
+	 *
+	 * <p>
+	 * Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread
+	 * or every message being parsed/encoded.
+	 * </p>
+	 * <p>
+	 * Performance Note: <b>This method is cheap</b> to call, and may be called once for every message being processed
+	 * without incurring any performance penalty
+	 * </p>
+	 */
+	public IParser newRDFParser() {
+		return new RDFParser(this, myParserErrorHandler, Lang.TURTLE);
+	}
+
+
 	/**
 	 * Instantiates a new client instance. This method requires an interface which is defined specifically for your use
 	 * cases to contain methods for each of the RESTful operations you wish to implement (e.g. "read ImagingStudy",
@@ -637,7 +655,7 @@ public class FhirContext {
 	 * @return A newly created client
 	 * @throws ConfigurationException If the interface type is not an interface
 	 */
-	public <T extends IRestfulClient> T newRestfulClient(Class<T> theClientType, String theServerBase) {
+	public <T extends IRestfulClient> T newRestfulClient(final Class<T> theClientType, final String theServerBase) {
 		return getRestfulClientFactory().newClient(theClientType, theServerBase);
 	}
 
@@ -653,7 +671,7 @@ public class FhirContext {
 	 *
 	 * @param theServerBase The URL of the base for the restful FHIR server to connect to
 	 */
-	public IGenericClient newRestfulGenericClient(String theServerBase) {
+	public IGenericClient newRestfulGenericClient(final String theServerBase) {
 		return getRestfulClientFactory().newGenericClient(theServerBase);
 	}
 
@@ -704,7 +722,7 @@ public class FhirContext {
 	 *
 	 * @param theType The custom type to add (must not be <code>null</code>)
 	 */
-	public void registerCustomType(Class<? extends IBase> theType) {
+	public void registerCustomType(final Class<? extends IBase> theType) {
 		Validate.notNull(theType, "theType must not be null");
 
 		ensureCustomTypeList();
@@ -723,7 +741,7 @@ public class FhirContext {
 	 *
 	 * @param theTypes The custom types to add (must not be <code>null</code> or contain null elements in the collection)
 	 */
-	public void registerCustomTypes(Collection<Class<? extends IBase>> theTypes) {
+	public void registerCustomTypes(final Collection<Class<? extends IBase>> theTypes) {
 		Validate.notNull(theTypes, "theTypes must not be null");
 		Validate.noNullElements(theTypes.toArray(), "theTypes must not contain any null elements");
 
@@ -732,22 +750,22 @@ public class FhirContext {
 		myCustomTypes.addAll(theTypes);
 	}
 
-	private BaseRuntimeElementDefinition<?> scanDatatype(Class<? extends IElement> theResourceType) {
+	private BaseRuntimeElementDefinition<?> scanDatatype(final Class<? extends IElement> theResourceType) {
-		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<>();
+		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<Class<? extends IElement>>();
 		resourceTypes.add(theResourceType);
 		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> defs = scanResourceTypes(resourceTypes);
 		return defs.get(theResourceType);
 	}
 
-	private RuntimeResourceDefinition scanResourceType(Class<? extends IBaseResource> theResourceType) {
+	private RuntimeResourceDefinition scanResourceType(final Class<? extends IBaseResource> theResourceType) {
-		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<>();
+		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<Class<? extends IElement>>();
 		resourceTypes.add(theResourceType);
 		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> defs = scanResourceTypes(resourceTypes);
 		return (RuntimeResourceDefinition) defs.get(theResourceType);
 	}
 
-	private synchronized Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> scanResourceTypes(Collection<Class<? extends IElement>> theResourceTypes) {
+	private synchronized Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> scanResourceTypes(final Collection<Class<? extends IElement>> theResourceTypes) {
-		List<Class<? extends IBase>> typesToScan = new ArrayList<>();
+		List<Class<? extends IBase>> typesToScan = new ArrayList<Class<? extends IBase>>();
 		if (theResourceTypes != null) {
 			typesToScan.addAll(theResourceTypes);
 		}
@@ -819,7 +837,7 @@ public class FhirContext {
 	 *                   <code>null</code> or empty.
 	 * @param theClass   The resource type, or <code>null</code> to clear any existing type
 	 */
-	public void setDefaultTypeForProfile(String theProfile, Class<? extends IBaseResource> theClass) {
+	public void setDefaultTypeForProfile(final String theProfile, final Class<? extends IBaseResource> theClass) {
 		Validate.notBlank(theProfile, "theProfile must not be null or empty");
 		if (theClass == null) {
 			myDefaultTypeForProfile.remove(theProfile);
@@ -833,7 +851,7 @@ public class FhirContext {
 	 *
 	 * @param theParserErrorHandler The error handler
 	 */
-	public void setParserErrorHandler(IParserErrorHandler theParserErrorHandler) {
+	public void setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
 		Validate.notNull(theParserErrorHandler, "theParserErrorHandler must not be null");
 		myParserErrorHandler = theParserErrorHandler;
 	}
@@ -843,7 +861,7 @@ public class FhirContext {
 	 *
 	 * @see PerformanceOptionsEnum for a list of available options
 	 */
-	public void setPerformanceOptions(PerformanceOptionsEnum... thePerformanceOptions) {
+	public void setPerformanceOptions(final PerformanceOptionsEnum... thePerformanceOptions) {
 		Collection<PerformanceOptionsEnum> asList = null;
 		if (thePerformanceOptions != null) {
 			asList = Arrays.asList(thePerformanceOptions);
@@ -852,7 +870,7 @@ public class FhirContext {
 	}
 
 	@SuppressWarnings({"cast"})
-	private List<Class<? extends IElement>> toElementList(Collection<Class<? extends IBaseResource>> theResourceTypes) {
+	private List<Class<? extends IElement>> toElementList(final Collection<Class<? extends IBaseResource>> theResourceTypes) {
 		if (theResourceTypes == null) {
 			return null;
 		}
@@ -922,8 +940,8 @@ public class FhirContext {
 	}
 
 	@SuppressWarnings("unchecked")
-	private static List<Class<? extends IBaseResource>> toCollection(Class<?>[] theResourceTypes) {
+	private static List<Class<? extends IBaseResource>> toCollection(final Class<?>[] theResourceTypes) {
-		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<>(1);
+		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
 		for (Class<?> clazz : theResourceTypes) {
 			if (!IResource.class.isAssignableFrom(clazz)) {
 				throw new IllegalArgumentException(clazz.getCanonicalName() + " is not an instance of " + IResource.class.getSimpleName());

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

@@ -0,0 +1,542 @@
+package ca.uhn.fhir.parser;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
+import ca.uhn.fhir.narrative.INarrativeGenerator;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.util.ElementUtil;
+import ca.uhn.fhir.util.rdf.RDFUtil;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.system.StreamRDF;
+import org.hl7.fhir.instance.model.api.*;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+/**
+ * This class is the FHIR RDF parser/encoder. Users should not interact with this class directly, but should use
+ * {@link FhirContext#newRDFParser()} to get an instance.
+ */
+public class RDFParser extends BaseParser {
+
+	private static final String FHIR_NS = "http://hl7.org/fhir";
+	private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(RDFParser.class);
+
+	private FhirContext context;
+	private Lang lang;
+
+	/**
+	 * Do not use this constructor, the recommended way to obtain a new instance of the RDF parser is to invoke
+	 * {@link FhirContext#newRDFParser()}.
+	 *
+	 * @param parserErrorHandler the Parser Error Handler
+	 */
+	public RDFParser(final FhirContext context, final IParserErrorHandler parserErrorHandler, final Lang lang) {
+		super(context, parserErrorHandler);
+		this.context = context;
+		this.lang = lang;
+	}
+
+	@Override
+	protected void doEncodeResourceToWriter(final IBaseResource resource,
+														 final Writer writer,
+														 final EncodeContext encodeContext) {
+		StreamRDF eventWriter = RDFUtil.createRDFWriter(writer, this.lang);
+		eventWriter.base(FHIR_NS);
+		encodeResourceToRDFStreamWriter(resource, eventWriter, encodeContext);
+	}
+
+	@Override
+	protected <T extends IBaseResource> T doParseResource(final Class<T> resourceType,
+																			final Reader reader) throws DataFormatException {
+
+		StreamRDF streamReader = RDFUtil.createRDFReader(reader, this.lang);
+		streamReader.base(FHIR_NS);
+		return parseResource(resourceType, streamReader);
+	}
+
+	@Override
+	public EncodingEnum getEncoding() {
+		return EncodingEnum.RDF;
+	}
+
+	@Override
+	public IParser setPrettyPrint(final boolean prettyPrint) {
+		return this;
+	}
+
+	private void encodeResourceToRDFStreamWriter(final IBaseResource resource,
+																final StreamRDF streamWriter,
+																final boolean containedResource,
+																final IIdType resourceId,
+																final EncodeContext encodeContext) {
+		RuntimeResourceDefinition resDef = this.context.getResourceDefinition(resource);
+		if (resDef == null) {
+			throw new ConfigurationException("Unknown resource type: " + resource.getClass());
+		}
+
+		if (!containedResource) {
+			super.containResourcesForEncoding(resource);
+		}
+
+		if (resource instanceof IAnyResource) {
+			// HL7.org Structures
+			if (resourceId != null) {
+				writeCommentsPre(streamWriter, resourceId);
+				streamWriter.start();
+				streamWriter.triple(RDFUtil.triple("<value> " + resourceId.getIdPart() + " </value>"));
+				streamWriter.finish();
+				writeCommentsPost(streamWriter, resourceId);
+			}
+
+			encodeCompositeElementToStreamWriter(resource, resource, streamWriter, containedResource, new CompositeChildElement(resDef, encodeContext), encodeContext);
+
+		} else {
+
+			// DSTU2+
+			if (resourceId != null) {
+				streamWriter.start();
+				streamWriter.triple(RDFUtil.triple("<value> " + resourceId.getIdPart() + " </value>"));
+				encodeExtensionsIfPresent(resource, streamWriter, resourceId, false, encodeContext);
+				streamWriter.finish();
+				writeCommentsPost(streamWriter, resourceId);
+			}
+			/*
+			InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
+			IdDt idDt = resource.getId();
+			String versionIdPart = idDt.getVersionIdPart();
+			if (isBlank(versionIdPart)) {
+				versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
+			}
+			List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
+			List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+			profiles = super.getProfileTagsForEncoding(resource, profiles);
+
+			TagList tags = getMetaTagsForEncoding((resource), encodeContext);
+
+			if (!ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles)) {
+				streamWriter.start();
+
+				for (IIdType profile : profiles) {
+					streamWriter.start();
+					streamWriter.triple(RDFUtil.triple("<value> " + profile.getValue() + " </value>"));
+					streamWriter.finish();
+				}
+				for (BaseCodingDt securityLabel : securityLabels) {
+					streamWriter.start();
+					encodeCompositeElementToStreamWriter(resource, securityLabel, streamWriter, containedResource, null, encodeContext);
+					streamWriter.finish();
+				}
+				if (tags != null) {
+					for (Tag tag : tags) {
+						if (tag.isEmpty()) {
+							continue;
+						}
+						streamWriter.start();
+					   streamWriter.triple(RDFUtil.triple("<system> " + tag.getScheme() + " </system>"));
+						streamWriter.triple(RDFUtil.triple("<code> "  + tag.getTerm() + " </code>"));
+   					streamWriter.triple(RDFUtil.triple("<display> " + tag.getLabel() + " </display>"));
+						streamWriter.finish();
+					}
+				}
+				streamWriter.finish();
+			}
+			*/
+			if (resource instanceof IBaseBinary) {
+				IBaseBinary bin = (IBaseBinary) resource;
+				streamWriter.triple(RDFUtil.triple("<contentType> " + bin.getContentType() + " </contentType>"));
+				streamWriter.triple(RDFUtil.triple("<content> " + bin.getContentAsBase64() + " </content>"));
+			} else {
+				encodeCompositeElementToStreamWriter(resource, resource, streamWriter, containedResource, new CompositeChildElement(resDef, encodeContext), encodeContext);
+			}
+
+		}
+
+		streamWriter.finish();
+	}
+
+	private void writeCommentsPre(final StreamRDF eventWriter, final IBase element) {
+		if (element != null && element.hasFormatComment()) {
+			for (String next : element.getFormatCommentsPre()) {
+				if (isNotBlank(next)) {
+					eventWriter.base(next);
+				}
+			}
+		}
+	}
+
+	private void writeCommentsPost(final StreamRDF eventWriter, final IBase element) {
+		if (element != null && element.hasFormatComment()) {
+			for (String next : element.getFormatCommentsPost()) {
+				if (isNotBlank(next)) {
+					eventWriter.base(next);
+				}
+			}
+		}
+	}
+
+	private void encodeChildElementToStreamWriter(final IBaseResource resource,
+																 final StreamRDF eventWriter,
+																 final BaseRuntimeChildDefinition childDefinition,
+																 final IBase element,
+																 final String childName,
+																 final BaseRuntimeElementDefinition<?> childDef,
+																 final String extensionUrl,
+																 final boolean includedResource,
+																 final CompositeChildElement parent,
+																 final EncodeContext encodeContext) {
+
+		String childGenericName = childDefinition.getElementName();
+
+		encodeContext.pushPath(childGenericName, false);
+		try {
+
+			if (element == null || element.isEmpty()) {
+				if (!isChildContained(childDef, includedResource)) {
+					return;
+				}
+			}
+
+			writeCommentsPre(eventWriter, element);
+
+			switch (childDef.getChildType()) {
+				case ID_DATATYPE: {
+					IIdType value = (IIdType) element;
+					assert value != null;
+					String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue();
+					if (StringUtils.isNotBlank(encodedValue) || !hasNoExtensions(value)) {
+						eventWriter.start();
+						if (StringUtils.isNotBlank(encodedValue)) {
+							eventWriter.triple(RDFUtil.triple("<value> " + encodedValue + " </value>"));
+						}
+						encodeExtensionsIfPresent(resource, eventWriter, element, includedResource, encodeContext);
+						eventWriter.finish();
+					}
+					break;
+				}
+				case PRIMITIVE_DATATYPE: {
+					IPrimitiveType<?> pd = (IPrimitiveType) element;
+					assert pd != null;
+					String value = pd.getValueAsString();
+					if (value != null || !hasNoExtensions(pd)) {
+						eventWriter.start();
+						String elementId = getCompositeElementId(element);
+						if (isNotBlank(elementId)) {
+							eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
+						}
+						if (value != null) {
+							eventWriter.triple(RDFUtil.triple("<value> " + value + " </value>"));
+						}
+						encodeExtensionsIfPresent(resource, eventWriter, element, includedResource, encodeContext);
+						eventWriter.finish();
+					}
+					break;
+				}
+				case RESOURCE_BLOCK:
+				case COMPOSITE_DATATYPE: {
+					eventWriter.start();
+					String elementId = getCompositeElementId(element);
+					if (isNotBlank(elementId)) {
+						eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
+					}
+					if (isNotBlank(extensionUrl)) {
+						eventWriter.triple(RDFUtil.triple("<url> " + extensionUrl + " </url>"));
+					}
+					encodeCompositeElementToStreamWriter(resource, element, eventWriter, includedResource, parent, encodeContext);
+					eventWriter.finish();
+					break;
+				}
+				case CONTAINED_RESOURCE_LIST:
+				case CONTAINED_RESOURCES: {
+					/*
+					 * Disable per #103 for (IResource next : value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
+					 * theEventWriter.writeStartElement("contained"); encodeResourceToRDFStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue()));
+					 * theEventWriter.writeEndElement(); }
+					 */
+					for (IBaseResource next : getContainedResources().getContainedResources()) {
+						IIdType resourceId = getContainedResources().getResourceId(next);
+						eventWriter.start();
+						encodeResourceToRDFStreamWriter(next, eventWriter, true, fixContainedResourceId(resourceId.getValue()), encodeContext);
+						eventWriter.finish();
+					}
+					break;
+				}
+				case RESOURCE: {
+					IBaseResource baseResource = (IBaseResource) element;
+					String resourceName = this.context.getResourceDefinition(baseResource).getName();
+					if (!super.shouldEncodeResource(resourceName)) {
+						break;
+					}
+					eventWriter.start();
+					encodeContext.pushPath(resourceName, true);
+					encodeResourceToRDFStreamWriter(resource, eventWriter, encodeContext);
+					encodeContext.popPath();
+					eventWriter.finish();
+					break;
+				}
+				case EXTENSION_DECLARED:
+				case UNDECL_EXT: {
+					throw new IllegalStateException("state should not happen: " + childDef.getName());
+				}
+			}
+
+			writeCommentsPost(eventWriter, element);
+
+		} finally {
+			encodeContext.popPath();
+		}
+
+	}
+
+	private void encodeResourceToRDFStreamWriter(final IBaseResource resource,
+																final StreamRDF eventWriter,
+																final EncodeContext encodeContext) {
+		IIdType resourceId = null;
+
+		if (StringUtils.isNotBlank(resource.getIdElement().getIdPart())) {
+			resourceId = resource.getIdElement();
+			if (resource.getIdElement().getValue().startsWith("urn:")) {
+				resourceId = null;
+			}
+		}
+
+		if (!super.shouldEncodeResourceId(resource, encodeContext)) {
+			resourceId = null;
+		} else if (encodeContext.getResourcePath().size() == 1 && getEncodeForceResourceId() != null) {
+			resourceId = getEncodeForceResourceId();
+		}
+
+		encodeResourceToRDFStreamWriter(resource, eventWriter, false, resourceId, encodeContext);
+	}
+
+	private void encodeUndeclaredExtensions(final IBaseResource resource,
+														 final StreamRDF eventWriter,
+														 final List<? extends IBaseExtension<?, ?>> extensions,
+														 final boolean includedResource,
+														 final EncodeContext encodeContext) {
+		for (IBaseExtension<?, ?> next : extensions) {
+			if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
+				continue;
+			}
+
+			writeCommentsPre(eventWriter, next);
+
+			eventWriter.start();
+
+			String elementId = getCompositeElementId(next);
+			if (isNotBlank(elementId)) {
+				eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
+			}
+
+			String url = getExtensionUrl(next.getUrl());
+			eventWriter.triple(RDFUtil.triple("<url> " + url + " </url>"));
+
+			if (next.getValue() != null) {
+				IBaseDatatype value = next.getValue();
+				RuntimeChildUndeclaredExtensionDefinition extDef = this.context.getRuntimeChildUndeclaredExtensionDefinition();
+				String childName = extDef.getChildNameByDatatype(value.getClass());
+				BaseRuntimeElementDefinition<?> childDef;
+				if (childName == null) {
+					childDef = this.context.getElementDefinition(value.getClass());
+					if (childDef == null) {
+						throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
+					}
+					childName = RuntimeChildUndeclaredExtensionDefinition.createExtensionChildName(childDef);
+				} else {
+					childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
+					if (childDef == null) {
+						throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
+					}
+				}
+				encodeChildElementToStreamWriter(resource, eventWriter, extDef, value, childName,
+					childDef, null, includedResource, null, encodeContext);
+			}
+
+			// child extensions
+			encodeExtensionsIfPresent(resource, eventWriter, next, includedResource, encodeContext);
+
+			eventWriter.finish();
+
+			writeCommentsPost(eventWriter, next);
+
+		}
+	}
+
+	private void encodeExtensionsIfPresent(final IBaseResource resource,
+														final StreamRDF writer,
+														final IBase element,
+														final boolean includedResource,
+														final EncodeContext encodeContext) {
+		if (element instanceof ISupportsUndeclaredExtensions) {
+			ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) element;
+			encodeUndeclaredExtensions(resource, writer, toBaseExtensionList(res.getUndeclaredExtensions()), includedResource, encodeContext);
+			encodeUndeclaredExtensions(resource, writer, toBaseExtensionList(res.getUndeclaredModifierExtensions()), includedResource, encodeContext);
+		}
+		if (element instanceof IBaseHasExtensions) {
+			IBaseHasExtensions res = (IBaseHasExtensions) element;
+			encodeUndeclaredExtensions(resource, writer, res.getExtension(), includedResource, encodeContext);
+		}
+		if (element instanceof IBaseHasModifierExtensions) {
+			IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) element;
+			encodeUndeclaredExtensions(resource, writer, res.getModifierExtension(), includedResource, encodeContext);
+		}
+	}
+
+	private void encodeExtension(final IBaseResource resource,
+										  final StreamRDF eventWriter,
+										  final boolean containedResource,
+										  final CompositeChildElement nextChildElem,
+										  final BaseRuntimeChildDefinition nextChild,
+										  final IBase nextValue,
+										  final String childName,
+										  final String extensionUrl,
+										  final BaseRuntimeElementDefinition<?> childDef,
+										  final EncodeContext encodeContext) {
+		BaseRuntimeDeclaredChildDefinition extDef = (BaseRuntimeDeclaredChildDefinition) nextChild;
+		eventWriter.start();
+
+		String elementId = getCompositeElementId(nextValue);
+		if (isNotBlank(elementId)) {
+			eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
+		}
+		eventWriter.triple(RDFUtil.triple("<url> " + extensionUrl + " </url>"));
+		encodeChildElementToStreamWriter(resource, eventWriter, nextChild, nextValue, childName,
+			childDef, null, containedResource, nextChildElem, encodeContext);
+		eventWriter.finish();
+	}
+
+	private void encodeCompositeElementToStreamWriter(final IBaseResource resource,
+																	  final IBase element,
+																	  final StreamRDF streamRDF,
+																	  final boolean containedResource,
+																	  final CompositeChildElement parent,
+																	  final EncodeContext encodeContext) {
+
+		for (CompositeChildElement nextChildElem : super.compositeChildIterator(element, containedResource, parent, encodeContext)) {
+
+			BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
+
+			if (nextChild.getElementName().equals("url") && element instanceof IBaseExtension) {
+				/*
+				 * RDF encoding is a one-off for extensions. The URL element goes in an attribute
+				 * instead of being encoded as a normal element, only for RDF encoding
+				 */
+				continue;
+			}
+
+			if (nextChild instanceof RuntimeChildNarrativeDefinition) {
+				INarrativeGenerator gen = this.context.getNarrativeGenerator();
+				INarrative narr;
+				if (resource instanceof IResource) {
+					narr = ((IResource) resource).getText();
+				} else if (resource instanceof IDomainResource) {
+					narr = ((IDomainResource) resource).getText();
+				} else {
+					narr = null;
+				}
+				assert narr != null;
+				if (gen != null && narr.isEmpty()) {
+					gen.populateResourceNarrative(this.context, resource);
+				}
+				if (!narr.isEmpty()) {
+					RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
+					String childName = nextChild.getChildNameByDatatype(child.getDatatype());
+					BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
+					encodeChildElementToStreamWriter(resource,
+						streamRDF, nextChild, narr, childName, type, null,
+						containedResource, nextChildElem, encodeContext);
+					continue;
+				}
+			}
+
+			if (nextChild instanceof RuntimeChildContainedResources) {
+				encodeChildElementToStreamWriter(resource, streamRDF, nextChild, null,
+					nextChild.getChildNameByDatatype(null),
+					nextChild.getChildElementDefinitionByDatatype(null), null,
+					containedResource, nextChildElem, encodeContext);
+			} else {
+
+				List<? extends IBase> values = nextChild.getAccessor().getValues(element);
+				values = super.preProcessValues(nextChild, resource, values, nextChildElem, encodeContext);
+
+				if (values == null || values.isEmpty()) {
+					continue;
+				}
+				for (IBase nextValue : values) {
+					if ((nextValue == null || nextValue.isEmpty())) {
+						continue;
+					}
+
+					ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
+					if (childNameAndDef == null) {
+						continue;
+					}
+
+					String childName = childNameAndDef.getChildName();
+					BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
+					String extensionUrl = getExtensionUrl(nextChild.getExtensionUrl());
+
+					if (extensionUrl != null && !childName.equals("extension")) {
+						encodeExtension(resource, streamRDF, containedResource, nextChildElem, nextChild,
+							nextValue, childName, extensionUrl, childDef, encodeContext);
+					} else if (nextChild instanceof RuntimeChildExtension) {
+						IBaseExtension<?, ?> extension = (IBaseExtension<?, ?>) nextValue;
+						if ((extension.getValue() == null || extension.getValue().isEmpty())) {
+							if (extension.getExtension().isEmpty()) {
+								continue;
+							}
+						}
+						encodeChildElementToStreamWriter(resource, streamRDF, nextChild, nextValue,
+							childName, childDef, getExtensionUrl(extension.getUrl()),
+							containedResource, nextChildElem, encodeContext);
+					} else if (!(nextChild instanceof RuntimeChildNarrativeDefinition) || !containedResource) {
+						encodeChildElementToStreamWriter(resource, streamRDF, nextChild, nextValue,
+							childName, childDef, extensionUrl, containedResource, nextChildElem, encodeContext);
+					}
+				}
+			}
+		}
+	}
+
+	private <Q extends IBaseExtension<?, ?>> List<IBaseExtension<?, ?>> toBaseExtensionList(final List<Q> theList) {
+		List<IBaseExtension<?, ?>> retVal = new ArrayList<>(theList.size());
+		retVal.addAll(theList);
+		return retVal;
+	}
+
+	private <T extends IBaseResource> T parseResource(Class<T> resourceType, StreamRDF streamReader) {
+		ParserState<T> parserState = ParserState.getPreResourceInstance(this, resourceType, context, false, getErrorHandler());
+		return doRDFLoop(streamReader, parserState);
+	}
+
+
+	private <T> T doRDFLoop(StreamRDF streamReader, ParserState<T> parserState) {
+		logger.trace("Entering RDF parsing loop with state: {}", parserState);
+		return parserState.getObject();
+	}
+}

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

@@ -43,6 +43,7 @@ public class Constants {
 	 */
 	public static final Set<String> CORS_ALLWED_METHODS;
 	public static final String CT_FHIR_JSON = "application/json+fhir";
+	public static final String CT_RDF_TURTLE = "application/x-turtle";
 	/**
 	 * The FHIR MimeType for JSON encoding in FHIR DSTU3+
 	 */
@@ -71,6 +72,9 @@ public class Constants {
 	public static final String FORMAT_HTML = "html";
 	public static final String FORMAT_JSON = "json";
 	public static final String FORMAT_XML = "xml";
+	public static final String FORMAT_TURTLE = "text/turtle";
+
+
 	/**
 	 * "text/html" and "html"
 	 */

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

@@ -42,16 +42,25 @@ public enum EncodingEnum {
 		public IParser newParser(FhirContext theContext) {
 			return theContext.newXmlParser();
 		}
+	},
+
+	RDF(Constants.CT_RDF_TURTLE, Constants.CT_RDF_TURTLE, Constants.FORMAT_TURTLE) {
+		@Override
+		public IParser newParser(FhirContext theContext) {
+			return theContext.newRDFParser();
+		}
 	};
 
 	/**
 	 * "json"
 	 */
 	public static final String JSON_PLAIN_STRING = "json";
+
 	/**
 	 * "xml"
 	 */
 	public static final String XML_PLAIN_STRING = "xml";
+
 	private static Map<String, EncodingEnum> ourContentTypeToEncoding;
 	private static Map<String, EncodingEnum> ourContentTypeToEncodingLegacy;
 	private static Map<String, EncodingEnum> ourContentTypeToEncodingStrict;
@@ -127,9 +136,9 @@ public enum EncodingEnum {
 		return myResourceContentTypeNonLegacy;
 	}
 
-	public abstract IParser newParser(FhirContext theContext);
+	public abstract IParser newParser(final FhirContext theContext);
 
-	public static EncodingEnum detectEncoding(String theBody) {
+	public static EncodingEnum detectEncoding(final String theBody) {
 		EncodingEnum retVal = detectEncodingNoDefault(theBody);
 		retVal = ObjectUtils.defaultIfNull(retVal, EncodingEnum.XML);
 		return retVal;
@@ -158,7 +167,7 @@ public enum EncodingEnum {
 	 * even if the "+fhir" part is missing from the expected content type.
 	 * </p>
 	 */
-	public static EncodingEnum forContentType(String theContentType) {
+	public static EncodingEnum forContentType(final String theContentType) {
 		String contentTypeSplitted = getTypeWithoutCharset(theContentType);
 		if (contentTypeSplitted == null) {
 			return null;
@@ -177,7 +186,7 @@ public enum EncodingEnum {
 	 *
 	 * @see #forContentType(String)
 	 */
-	public static EncodingEnum forContentTypeStrict(String theContentType) {
+	public static EncodingEnum forContentTypeStrict(final String theContentType) {
 		String contentTypeSplitted = getTypeWithoutCharset(theContentType);
 		if (contentTypeSplitted == null) {
 			return null;
@@ -186,7 +195,7 @@ public enum EncodingEnum {
 		}
 	}
 
-	private static String getTypeWithoutCharset(String theContentType) {
+	private static String getTypeWithoutCharset(final String theContentType) {
 		if (theContentType == null) {
 			return null;
 		} else {
@@ -198,7 +207,7 @@ public enum EncodingEnum {
 	/**
 	 * Is the given type a FHIR legacy (pre-DSTU3) content type?
 	 */
-	public static boolean isLegacy(String theContentType) {
+	public static boolean isLegacy(final String theContentType) {
 		String contentTypeSplitted = getTypeWithoutCharset(theContentType);
 		if (contentTypeSplitted == null) {
 			return false;

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

@@ -165,6 +165,13 @@ public class ParametersUtil {
 
 	}
 
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersCode(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("code").newInstance();
+		value.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, value);
+	}
+
 	@SuppressWarnings("unchecked")
 	public static void addParameterToParametersInteger(FhirContext theCtx, IBaseParameters theParameters, String theName, int theValue) {
 		IPrimitiveType<Integer> count = (IPrimitiveType<Integer>) theCtx.getElementDefinition("integer").newInstance();
@@ -184,6 +191,13 @@ public class ParametersUtil {
 		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("string").newInstance();
 		value.setValue(theValue);
 		addParameterToParameters(theCtx, theParameters, theName, value);
+	}
+
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersUri(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("uri").newInstance();
+		value.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, value);
 
 	}
 

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

@@ -221,7 +221,7 @@ public class StopWatch {
 	 *
 	 * @see #formatThroughput(int, TimeUnit)
 	 */
-	public double getThroughput(int theNumOperations, TimeUnit theUnit) {
+	public double getThroughput(long theNumOperations, TimeUnit theUnit) {
 		if (theNumOperations <= 0) {
 			return 0.0f;
 		}
@@ -229,10 +229,9 @@ public class StopWatch {
 		long millisElapsed = Math.max(1, getMillis());
 		long periodMillis = theUnit.toMillis(1);
 
-		double numerator = theNumOperations;
 		double denominator = ((double) millisElapsed) / ((double) periodMillis);
 
-		return numerator / denominator;
+		return (double) theNumOperations / denominator;
 	}
 
 	public void restart() {

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

@@ -63,15 +63,21 @@ public class ValidateUtil {
 		}
 	}
 
+	public static void isNotNullOrThrowUnprocessableEntity(Object theObject, String theMessage, Object... theValues) {
+		if (theObject == null) {
+			throw new UnprocessableEntityException(String.format(theMessage, theValues));
+		}
+	}
+
 	public static void isNotTooLongOrThrowIllegalArgument(String theString, int theMaxLength, String theMessage) {
 		if (length(theString) > theMaxLength) {
 			throw new IllegalArgumentException(theMessage);
 		}
 	}
 
-	public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
+	public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage, Object... theValues) {
 		if (theSuccess == false) {
-			throw new InvalidRequestException(theMessage);
+			throw new InvalidRequestException(String.format(theMessage, theValues));
 		}
 	}
 

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

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.util.rdf;
+
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.apache.commons.io.input.ReaderInputStream;
+import org.apache.commons.io.output.WriterOutputStream;
+import org.apache.jena.graph.Triple;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.system.StreamRDF;
+import org.apache.jena.riot.system.StreamRDFWriter;
+
+import java.io.*;
+import java.nio.charset.Charset;
+import java.util.*;
+
+public class RDFUtil {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RDFUtil.class);
+	private static final Map<String, Integer> VALID_ENTITY_NAMES;
+
+	static {
+		HashMap<String, Integer> validEntityNames = new HashMap<>(1448);
+		VALID_ENTITY_NAMES = Collections.unmodifiableMap(validEntityNames);
+	}
+
+	public static StreamRDF createRDFWriter(final Writer writer, final Lang lang) {
+		WriterOutputStream wos = new WriterOutputStream(writer, Charset.defaultCharset());
+		return StreamRDFWriter.getWriterStream(wos, lang);
+	}
+
+	public static StreamRDF createRDFReader(final Reader reader, final Lang lang) {
+		ReaderInputStream ris = new ReaderInputStream(reader, Charset.defaultCharset());
+		return StreamRDFWriter.getWriterStream(null, lang);
+	}
+
+	public static Triple triple(String tripleAsTurtle) {
+		Model m = ModelFactory.createDefaultModel();
+		m.read(new StringReader(tripleAsTurtle), "urn:x-base:", "TURTLE");
+		return m.listStatements().next().asTriple();
+	}
+
+}

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

@@ -0,0 +1,82 @@
+package ca.uhn.fhir.util.rdf;
+
+import java.util.HashSet;
+import java.util.LinkedList;
+
+import org.apache.jena.graph.Triple;
+import org.apache.jena.riot.system.StreamRDF;
+import org.apache.jena.sparql.core.Quad;
+
+/**
+ * Wraps another {@link StreamRDF} and attempts to remove duplicate
+ * triples and quads. To maintain streaming, duplicates are only
+ * removed within a sliding window of configurable size. Default
+ * size is 10000 triples and quads.
+ */
+public class StreamRDFDedup implements StreamRDF {
+	private final StreamRDF wrapped;
+	private final int windowSize;
+	private final HashSet<Object> tripleAndQuadCache;
+	private final LinkedList<Object> tripleAndQuadList = new LinkedList<Object>();
+
+	public StreamRDFDedup(StreamRDF wrapped) {
+		this(wrapped, 10000);
+	}
+
+	public StreamRDFDedup(StreamRDF wrapped, int windowSize) {
+		this.wrapped = wrapped;
+		this.windowSize = windowSize;
+		// Initial capacity big enough to avoid rehashing
+		this.tripleAndQuadCache = new HashSet<Object>(windowSize * 3 / 2);
+	}
+
+	@Override
+	public void start() {
+		wrapped.start();
+	}
+
+	@Override
+	public void triple(Triple triple) {
+		if (!seen(triple)) {
+			wrapped.triple(triple);
+		}
+	}
+
+	@Override
+	public void quad(Quad quad) {
+		if (!seen(quad)) {
+			wrapped.quad(quad);
+		}
+	}
+
+	@Override
+	public void base(String base) {
+		wrapped.base(base);
+	}
+
+	@Override
+	public void prefix(String prefix, String iri) {
+		wrapped.prefix(prefix, iri);
+	}
+
+	@Override
+	public void finish() {
+		wrapped.finish();
+	}
+
+	private boolean seen(Object tuple) {
+		if (tripleAndQuadCache.contains(tuple)) {
+			return true;
+		}
+		tripleAndQuadCache.add(tuple);
+		tripleAndQuadList.add(tuple);
+		if (tripleAndQuadList.size() > windowSize) {
+			forgetOldest();
+		}
+		return false;
+	}
+
+	private void forgetOldest() {
+		tripleAndQuadCache.remove(tripleAndQuadList.removeFirst());
+	}
+}

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

@@ -0,0 +1,90 @@
+package ca.uhn.fhir.util.rdf;
+
+import java.io.OutputStream;
+import java.util.Iterator;
+import java.util.Map.Entry;
+
+import org.apache.jena.atlas.io.IndentedWriter;
+import org.apache.jena.graph.Triple;
+import org.apache.jena.riot.system.RiotLib;
+import org.apache.jena.riot.system.StreamOps;
+import org.apache.jena.riot.system.StreamRDF;
+import org.apache.jena.riot.writer.WriterStreamRDFBlocks;
+import org.apache.jena.riot.writer.WriterStreamRDFPlain;
+import org.apache.jena.shared.PrefixMapping;
+import org.apache.jena.shared.impl.PrefixMappingImpl;
+import org.apache.jena.vocabulary.RDF;
+
+
+/**
+ * Writes an iterator over triples to N-Triples or Turtle
+ * in a streaming fashion, that is, without needing to hold
+ * the entire thing in memory.
+ * <p>
+ * Instances are single-use.
+ * <p>
+ * There doesn't seem to be a pre-packaged version of this
+ * functionality in Jena/ARQ that doesn't require a Graph or Model.
+ */
+public class StreamingRDFWriter {
+	private final OutputStream out;
+	private final Iterator<Triple> triples;
+	private int dedupWindowSize = 10000;
+
+	public StreamingRDFWriter(OutputStream out, Iterator<Triple> triples) {
+		this.out = out;
+		this.triples = triples;
+	}
+
+	public void setDedupWindowSize(int newSize) {
+		this.dedupWindowSize = newSize;
+	}
+
+	public void writeNTriples() {
+		StreamRDF writer = new WriterStreamRDFPlain(new IndentedWriter(out));
+		if (dedupWindowSize > 0) {
+			writer = new StreamRDFDedup(writer, dedupWindowSize);
+		}
+		writer.start();
+		StreamOps.sendTriplesToStream(triples, writer);
+		writer.finish();
+	}
+
+	public void writeTurtle(String baseIRI, PrefixMapping prefixes, boolean writeBase) {
+		// Auto-register RDF prefix so that rdf:type is displayed well
+		// All other prefixes come from the query and should be as author intended
+		prefixes = ensureRDFPrefix(prefixes);
+
+		if (writeBase) {
+			// Jena's streaming Turtle writers don't output base even if it is provided,
+			// so we write it directly.
+			IndentedWriter w = new IndentedWriter(out);
+			RiotLib.writeBase(w, baseIRI);
+			w.flush();
+		}
+
+		StreamRDF writer = new WriterStreamRDFBlocks(out);
+		if (dedupWindowSize > 0) {
+			writer = new StreamRDFDedup(writer, dedupWindowSize);
+		}
+		writer.start();
+		writer.base(baseIRI);
+		for (Entry<String, String> e : prefixes.getNsPrefixMap().entrySet()) {
+			writer.prefix(e.getKey(), e.getValue());
+		}
+		StreamOps.sendTriplesToStream(triples, writer);
+		writer.finish();
+	}
+
+	private PrefixMapping ensureRDFPrefix(PrefixMapping prefixes) {
+		// Some prefix already registered for the RDF namespace -- good enough
+		if (prefixes.getNsURIPrefix(RDF.getURI()) != null) return prefixes;
+		// rdf: is registered to something else -- give up
+		if (prefixes.getNsPrefixURI("rdf") != null) return prefixes;
+		// Register rdf:
+		PrefixMapping newPrefixes = new PrefixMappingImpl();
+		newPrefixes.setNsPrefixes(prefixes);
+		newPrefixes.setNsPrefix("rdf", RDF.getURI());
+		return newPrefixes;
+	}
+}

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.util;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;
 
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.junit.Test;
 
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -69,4 +70,18 @@ public class ValidateUtilTest {
 		}
 	}
 
+
+	@Test
+	public void testIsNotNull() {
+		ValidateUtil.isNotNullOrThrowUnprocessableEntity("aa", "");
+
+		try {
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(null, "The message %s", "123");
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("The message 123", e.getMessage());
+		}
+
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.util.ParametersUtil;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
@@ -56,6 +57,7 @@ public class UploadTerminologyCommand extends BaseCommand {
 		addBaseUrlOption(options);
 		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
 		addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
+		addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
 		addBasicAuthOption(options);
 		addVerboseLoggingOption(options);
 
@@ -78,23 +80,13 @@ public class UploadTerminologyCommand extends BaseCommand {
 		}
 
 		IGenericClient client = super.newClient(theCommandLine);
-		IBaseParameters inputParameters;
+		IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
-		if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
+		ParametersUtil.addParameterToParametersUri(myFhirCtx, inputParameters, "url", termUrl);
-			org.hl7.fhir.dstu3.model.Parameters p = new org.hl7.fhir.dstu3.model.Parameters();
-			p.addParameter().setName("url").setValue(new org.hl7.fhir.dstu3.model.UriType(termUrl));
 		for (String next : datafile) {
-				p.addParameter().setName("localfile").setValue(new org.hl7.fhir.dstu3.model.StringType(next));
+			ParametersUtil.addParameterToParametersString(myFhirCtx, inputParameters, "localfile", next);
 		}
-			inputParameters = p;
+		if (theCommandLine.hasOption("custom")) {
-		} else if (ctx.getVersion().getVersion() == FhirVersionEnum.R4) {
+			ParametersUtil.addParameterToParametersCode(myFhirCtx, inputParameters, "contentMode", "custom");
-			org.hl7.fhir.r4.model.Parameters p = new org.hl7.fhir.r4.model.Parameters();
-			p.addParameter().setName("url").setValue(new org.hl7.fhir.r4.model.UriType(termUrl));
-			for (String next : datafile) {
-				p.addParameter().setName("localfile").setValue(new org.hl7.fhir.r4.model.StringType(next));
-			}
-			inputParameters = p;
-		} else {
-			throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
 		}
 
 		if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {

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

@@ -220,7 +220,7 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
      * @see <a href="https://www.hl7.org/fhir/http.html#read">https://www.hl7.org/fhir/http.html#read</a>
      */
     @GET
-    @Path("/{id}")
+    @Path("/{id : ((?!_history).)*}")
     public Response find(@PathParam("id") final String id)
             throws IOException {
         return execute(getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.READ).id(id));
@@ -245,7 +245,7 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
     }
 
     /**
-     * Retrieve the update history for a particular resource
+     * Retrieve a version of a resource
      * 
      * @param id the id of the resource
      * @param version the version of the resource
@@ -254,12 +254,41 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
      */
     @GET
     @Path("/{id}/_history/{version}")
-    public Response findHistory(@PathParam("id") final String id, @PathParam("version") final String version)
+    public Response findVersion(@PathParam("id") final String id, @PathParam("version") final String version)
             throws IOException {
         final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.VREAD).id(id).version(version);
         return execute(theRequest);
     }
 
+	/**
+	 * Retrieve the update history for a particular resource
+	 *
+	 * @param id the id of the resource
+	 * @return the response
+	 * @see <a href="https://www.hl7.org/fhir/http.html#history">https://www.hl7.org/fhir/http.html#history</a>
+	 */
+	@GET
+	@Path("/{id}/_history")
+	public Response historyForInstance(@PathParam("id") final String id)
+		throws IOException {
+		final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.HISTORY_INSTANCE).id(id);
+		return execute(theRequest);
+	}
+
+	/**
+	 * Retrieve the update history for a particular type
+	 *
+	 * @return the response
+	 * @see <a href="https://www.hl7.org/fhir/http.html#history">https://www.hl7.org/fhir/http.html#history</a>
+	 */
+	@GET
+	@Path("/_history")
+	public Response historyForType()
+		throws IOException {
+		final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.HISTORY_TYPE);
+		return execute(theRequest);
+	}
+
 	/**
      * Compartment Based Access
      * 
@@ -270,7 +299,7 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
      * @see <a href="https://www.hl7.org/fhir/compartments.html#compartment">https://www.hl7.org/fhir/compartments.html#compartment</a>
      */
     @GET
-    @Path("/{id}/{compartment}")
+    @Path("/{id}/{compartment : ((?!_history).)*}")
 	 public Response findCompartment(@PathParam("id") final String id, @PathParam("compartment") final String compartment)
             throws IOException {
         final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.SEARCH_TYPE).id(id).compartment(

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProviderTest.java

@@ -22,6 +22,7 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.lang3.StringUtils;
@@ -36,6 +37,7 @@ import org.mockito.Matchers;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import static org.junit.Assert.*;
@@ -83,6 +85,12 @@ public class AbstractJaxRsResourceProviderTest {
 		return theResource;
 	}
 
+	private Patient createPatient(long id, String version) {
+		Patient theResource = new Patient();
+		theResource.setId(new IdDt(id).withVersion(version));
+		return theResource;
+	}
+
 	private List<Patient> createPatients(int firstId, int lastId) {
 		List<Patient> result = new ArrayList<Patient>(lastId - firstId);
 		for (long i = firstId; i <= lastId; i++) {
@@ -341,7 +349,7 @@ public class AbstractJaxRsResourceProviderTest {
 
 	@Test
 	public void testVRead() {
-		when(mock.findHistory(idCaptor.capture())).thenReturn(createPatient(1));
+		when(mock.findVersion(idCaptor.capture())).thenReturn(createPatient(1));
 		final Patient patient = client.vread(Patient.class, "1", "2");
 		compareResultId(1, patient);
 		compareResultUrl("/Patient/1", patient);
@@ -349,6 +357,26 @@ public class AbstractJaxRsResourceProviderTest {
 		assertEquals("2", idCaptor.getValue().getVersionIdPart());
 	}
 
+	@Test
+	public void testInstanceHistory() {
+		when(mock.getHistoryForInstance(idCaptor.capture())).thenReturn(new SimpleBundleProvider(Collections.singletonList(createPatient(1, "1"))));
+		final Bundle bundle = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
+		Patient patient = (Patient) bundle.getEntryFirstRep().getResource();
+		compareResultId(1, patient);
+		compareResultUrl("/Patient/1/_history/1", patient);
+		assertEquals("1", idCaptor.getValue().getIdPart());
+		assertNull(idCaptor.getValue().getVersionIdPart());
+	}
+
+	@Test
+	public void testTypeHistory() {
+		when(mock.getHistoryForType()).thenReturn(new SimpleBundleProvider(Collections.singletonList(createPatient(1, "1"))));
+		final Bundle bundle = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
+		Patient patient = (Patient) bundle.getEntryFirstRep().getResource();
+		compareResultId(1, patient);
+		compareResultUrl("/Patient/1/_history/1", patient);
+	}
+
 	@Test
 	public void testXFindUnknownPatient() {
 		try {

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/test/TestJaxRsMockPatientRestProvider.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jaxrs.server.test;
 
+import java.util.Collections;
+import java.util.Date;
 import java.util.List;
 
 import javax.ejb.Stateless;
@@ -8,6 +10,11 @@ import javax.ws.rs.*;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.mockito.Mockito;
 
 import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
@@ -68,8 +75,18 @@ public class TestJaxRsMockPatientRestProvider extends AbstractJaxRsResourceProvi
 	}
 
 	@Read(version = true)
-	public Patient findHistory(@IdParam final IdDt theId) {
+	public Patient findVersion(@IdParam final IdDt theId) {
-		return mock.findHistory(theId);
+		return mock.findVersion(theId);
+	}
+
+	@History
+	public IBundleProvider getHistoryForInstance(@IdParam IIdType theId) {
+		return mock.getHistoryForInstance(theId);
+	}
+
+	@History
+	public IBundleProvider getHistoryForType() {
+		return mock.getHistoryForType();
 	}
 
 	@Create

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

@@ -19,6 +19,9 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.annotation.*;
 import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.*;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -89,7 +92,7 @@ public class JaxRsPatientRestProvider extends AbstractJaxRsResourceProvider<Pati
 	}
 
 	@Read(version = true)
-	public Patient findHistory(@IdParam final IdDt theId) {
+	public Patient findVersion(@IdParam final IdDt theId) {
 		if (patients.containsKey(theId.getIdPart())) {
 			final List<Patient> list = patients.get(theId.getIdPart());
 			for (final Patient patient : list) {
@@ -101,6 +104,17 @@ public class JaxRsPatientRestProvider extends AbstractJaxRsResourceProvider<Pati
 		throw new ResourceNotFoundException(theId);
 	}
 
+	// from BaseJpaResourceProvider
+	@History
+	public IBundleProvider getHistoryForInstance(@IdParam IdDt theId, @Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
+		return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
+	}
+
+	@History
+	public IBundleProvider getHistoryForType(@Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
+		return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
+	}
+
 	@Operation(name = "firstVersion", idempotent = true, returnParameters = { @OperationParam(name = "return", type = StringDt.class) })
 	public Parameters firstVersion(@IdParam final IdDt theId, @OperationParam(name = "dummy") StringDt dummyInput) {
 		Parameters parameters = new Parameters();

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

@@ -10,6 +10,9 @@ import javax.ws.rs.*;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
@@ -90,7 +93,7 @@ public class JaxRsPatientRestProviderDstu3 extends AbstractJaxRsResourceProvider
 	}
 
 	@Read(version = true)
-	public Patient findHistory(@IdParam final IdType theId) {
+	public Patient findVersion(@IdParam final IdType theId) {
 		if (patients.containsKey(theId.getIdPart())) {
 			final List<Patient> list = patients.get(theId.getIdPart());
 			for (final Patient patient : list) {
@@ -102,6 +105,16 @@ public class JaxRsPatientRestProviderDstu3 extends AbstractJaxRsResourceProvider
 		throw new ResourceNotFoundException(theId);
 	}
 
+	@History
+	public IBundleProvider getHistoryForInstance(@IdParam IdType theId, @Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
+		return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
+	}
+
+	@History
+	public IBundleProvider getHistoryForType(@Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
+		return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
+	}
+
 	@Operation(name = "firstVersion", idempotent = true, returnParameters = { @OperationParam(name = "return", type = StringType.class) })
 	public Parameters firstVersion(@IdParam final IdType theId, @OperationParam(name = "dummy") StringType dummyInput) {
 		Parameters parameters = new Parameters();

hapi-fhir-jaxrsserver-example/src/main/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientRestProviderR4.java

@@ -0,0 +1,241 @@
+package ca.uhn.fhir.jaxrs.server.example;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.api.AddProfileTagEnum;
+import ca.uhn.fhir.context.api.BundleInclusionRule;
+import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.ETagSupportEnum;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.IPagingProvider;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.*;
+
+import javax.ejb.Local;
+import javax.ejb.Stateless;
+import javax.ws.rs.*;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+import java.io.IOException;
+import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
+
+/**
+ * A demo JaxRs Patient Rest Provider
+ */
+@Local
+@Path(JaxRsPatientRestProviderR4.PATH)
+@Stateless
+@Produces({ MediaType.APPLICATION_JSON, Constants.CT_FHIR_JSON, Constants.CT_FHIR_XML })
+public class JaxRsPatientRestProviderR4 extends AbstractJaxRsResourceProvider<Patient> {
+
+	private static Long counter = 1L;
+
+	/**
+	 * The HAPI paging provider for this server
+	 */
+	public static final IPagingProvider PAGE_PROVIDER;
+
+	static final String PATH = "/Patient";
+	private static final ConcurrentHashMap<String, List<Patient>> patients = new ConcurrentHashMap<String, List<Patient>>();
+
+	static {
+		PAGE_PROVIDER = new FifoMemoryPagingProvider(10);
+	}
+
+	static {
+		patients.put(String.valueOf(counter), createPatient("Van Houte"));
+		patients.put(String.valueOf(counter), createPatient("Agnew"));
+		for (int i = 0; i < 20; i++) {
+			patients.put(String.valueOf(counter), createPatient("Random Patient " + counter));
+		}
+	}
+
+	public JaxRsPatientRestProviderR4() {
+		super(FhirContext.forDstu3(), JaxRsPatientRestProviderR4.class);
+	}
+
+	@Create
+	public MethodOutcome create(@ResourceParam final Patient patient, @ConditionalUrlParam String theConditional) throws Exception {
+		patients.put("" + counter, createPatient(patient));
+		final MethodOutcome result = new MethodOutcome().setCreated(true);
+		result.setResource(patient);
+		result.setId(new IdType(patient.getId()));
+		return result;
+	}
+
+	@Delete
+	public MethodOutcome delete(@IdParam final IdType theId) {
+		final Patient deletedPatient = find(theId);
+		patients.remove(deletedPatient.getIdElement().getIdPart());
+		final MethodOutcome result = new MethodOutcome().setCreated(true);
+		result.setResource(deletedPatient);
+		return result;
+	}
+
+	@Read
+	public Patient find(@IdParam final IdType theId) {
+		if (patients.containsKey(theId.getIdPart())) {
+			return getLast(patients.get(theId.getIdPart()));
+		} else {
+			throw new ResourceNotFoundException(theId);
+		}
+	}
+
+	@Read(version = true)
+	public Patient findVersion(@IdParam final IdType theId) {
+		if (patients.containsKey(theId.getIdPart())) {
+			final List<Patient> list = patients.get(theId.getIdPart());
+			for (final Patient patient : list) {
+				if (patient.getIdElement().getVersionIdPartAsLong().equals(theId.getVersionIdPartAsLong())) {
+					return patient;
+				}
+			}
+		}
+		throw new ResourceNotFoundException(theId);
+	}
+
+	@History
+	public IBundleProvider getHistoryForInstance(@IdParam IdType theId, @Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
+		return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
+	}
+
+	@History
+	public IBundleProvider getHistoryForType(@Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
+		return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
+	}
+
+	@Operation(name = "firstVersion", idempotent = true, returnParameters = { @OperationParam(name = "return", type = StringType.class) })
+	public Parameters firstVersion(@IdParam final IdType theId, @OperationParam(name = "dummy") StringType dummyInput) {
+		Parameters parameters = new Parameters();
+		Patient patient = find(new IdType(theId.getResourceType(), theId.getIdPart(), "0"));
+		parameters.addParameter().setName("return").setResource(patient).setValue(new StringType((counter - 1) + "" + "inputVariable [ " + dummyInput.getValue() + "]"));
+		return parameters;
+	}
+
+	@Override
+	public AddProfileTagEnum getAddProfileTag() {
+		return AddProfileTagEnum.NEVER;
+	}
+
+	@Override
+	public BundleInclusionRule getBundleInclusionRule() {
+		return BundleInclusionRule.BASED_ON_INCLUDES;
+	}
+
+	@Override
+	public ETagSupportEnum getETagSupport() {
+		return ETagSupportEnum.DISABLED;
+	}
+
+	/** THE DEFAULTS */
+
+	@Override
+	public List<IServerInterceptor> getInterceptors_() {
+		return Collections.emptyList();
+	}
+
+	private Patient getLast(final List<Patient> list) {
+		return list.get(list.size() - 1);
+	}
+
+	@Override
+	public IPagingProvider getPagingProvider() {
+		return PAGE_PROVIDER;
+	}
+
+	@Override
+	public Class<Patient> getResourceType() {
+		return Patient.class;
+	}
+
+	@Override
+	public boolean isDefaultPrettyPrint() {
+		return true;
+	}
+
+	@GET
+	@Path("/{id}/$firstVersion")
+	public Response operationFirstVersionUsingGet(@PathParam("id") String id) throws IOException {
+		return customOperation(null, RequestTypeEnum.GET, id, "$firstVersion", RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE);
+	}
+
+	@POST
+	@Path("/{id}/$firstVersion")
+	public Response operationFirstVersionUsingGet(@PathParam("id") String id, final String resource) throws Exception {
+		return customOperation(resource, RequestTypeEnum.POST, id, "$firstVersion", RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE);
+	}
+
+	@Search
+	public List<Patient> search(@RequiredParam(name = Patient.SP_NAME) final StringParam name) {
+		final List<Patient> result = new LinkedList<Patient>();
+		for (final List<Patient> patientIterator : patients.values()) {
+			Patient single = null;
+			for (Patient patient : patientIterator) {
+				if (name == null || patient.getName().get(0).getFamilyElement().getValueNotNull().equals(name.getValueNotNull())) {
+					single = patient;
+				}
+			}
+			if (single != null) {
+				result.add(single);
+			}
+		}
+		return result;
+	}
+
+	@Search(compartmentName = "Condition")
+	public List<IBaseResource> searchCompartment(@IdParam IdType thePatientId) {
+		List<IBaseResource> retVal = new ArrayList<IBaseResource>();
+		Condition condition = new Condition();
+		condition.setId(new IdType("665577"));
+		retVal.add(condition);
+		return retVal;
+	}
+
+	@Update
+	public MethodOutcome update(@IdParam final IdType theId, @ResourceParam final Patient patient) {
+		final String idPart = theId.getIdPart();
+		if (patients.containsKey(idPart)) {
+			final List<Patient> patientList = patients.get(idPart);
+			final Patient lastPatient = getLast(patientList);
+			patient.setId(createId(theId.getIdPartAsLong(), lastPatient.getIdElement().getVersionIdPartAsLong() + 1));
+			patientList.add(patient);
+			final MethodOutcome result = new MethodOutcome().setCreated(false);
+			result.setResource(patient);
+			result.setId(new IdType(patient.getId()));
+			return result;
+		} else {
+			throw new ResourceNotFoundException(theId);
+		}
+	}
+
+	private static IdType createId(final Long id, final Long theVersionId) {
+		return new IdType("Patient", "" + id, "" + theVersionId);
+	}
+
+	private static List<Patient> createPatient(final Patient patient) {
+		patient.setId(createId(counter, 1L));
+		final LinkedList<Patient> list = new LinkedList<Patient>();
+		list.add(patient);
+		counter++;
+		return list;
+	}
+
+	private static List<Patient> createPatient(final String name) {
+		final Patient patient = new Patient();
+		patient.getName().add(new HumanName().setFamily(name));
+		return createPatient(patient);
+	}
+
+}

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderDstu3Test.java

@@ -5,6 +5,7 @@ import static org.junit.Assert.*;
 import java.util.Arrays;
 import java.util.List;
 
+import ca.uhn.fhir.model.primitive.IdDt;
 import org.apache.commons.lang3.StringUtils;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
@@ -285,4 +286,16 @@ public class JaxRsPatientProviderDstu3Test {
         System.out.println(patient);
     }
 
+	@Test
+	public void testInstanceHistory() {
+		final Bundle history = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
+		assertEquals("myTestId", history.getIdElement().getIdPart());
+	}
+
+	@Test
+	public void testTypeHistory() {
+		final Bundle history = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
+		assertEquals("myTestId", history.getIdElement().getIdPart());
+	}
+
 }

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderR4Test.java

@@ -0,0 +1,308 @@
+package ca.uhn.fhir.jaxrs.server.example;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.client.JaxRsRestfulClientFactory;
+import ca.uhn.fhir.model.primitive.BoundCodeDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.SearchStyleEnum;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.util.TestUtil;
+import org.apache.commons.lang3.StringUtils;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.r4.model.*;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
+public class JaxRsPatientProviderR4Test {
+
+	private static IGenericClient client;
+	private static FhirContext ourCtx = FhirContext.forR4();
+	private static final String PATIENT_NAME = "Van Houte";
+	private static int ourPort;
+	private static Server jettyServer;
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		JettyUtil.closeServer(jettyServer);
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void setUpClass()
+			throws Exception {
+		ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
+		context.setContextPath("/");
+		jettyServer = new Server(0);
+		jettyServer.setHandler(context);
+		ServletHolder jerseyServlet = context.addServlet(org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.class, "/*");
+		jerseyServlet.setInitOrder(0);
+		//@formatter:off
+		jerseyServlet.setInitParameter("resteasy.resources",
+				StringUtils.join(Arrays.asList(
+						JaxRsConformanceProvider.class.getCanonicalName(),
+						JaxRsPatientRestProvider.class.getCanonicalName(),
+						JaxRsPageProvider.class.getCanonicalName()
+					), ","));
+		//@formatter:on
+		JettyUtil.startServer(jettyServer);
+        ourPort = JettyUtil.getPortForStartedServer(jettyServer);
+
+		ourCtx.setRestfulClientFactory(new JaxRsRestfulClientFactory(ourCtx));
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+		client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/");
+		client.setEncoding(EncodingEnum.JSON);
+		client.registerInterceptor(new LoggingInterceptor(true));
+	}
+
+	/** Search/Query - Type */
+	@Test
+	public void findUsingGenericClientBySearch() {
+		// Perform a search
+		final Bundle results = client
+				.search()
+				.forResource(Patient.class)
+				.where(Patient.NAME.matchesExactly().value(PATIENT_NAME))
+				.returnBundle(Bundle.class)
+				.execute();
+		System.out.println(results.getEntry().get(0));
+		assertEquals(results.getEntry().size(), 1);
+	}
+
+	/** Search - Multi-valued Parameters (ANY/OR) */
+	@Test
+	public void findUsingGenericClientBySearchWithMultiValues() {
+		final Bundle response = client
+				.search()
+				.forResource(Patient.class)
+				.where(Patient.ADDRESS.matches().values("Toronto")).and(Patient.ADDRESS.matches().values("Ontario"))
+				.and(Patient.ADDRESS.matches().values("Canada"))
+				.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("SHORTNAME", "TOYS"))
+				.returnBundle(Bundle.class)
+				.execute();
+		System.out.println(response.getEntry().get(0));
+	}
+
+	/** Search - Paging */
+	@Test
+	public void findWithPaging() {
+		// Perform a search
+		final Bundle results = client.search().forResource(Patient.class).limitTo(8).returnBundle(Bundle.class).execute();
+		System.out.println(results.getEntry().size());
+
+		if (results.getLink(Bundle.LINK_NEXT) != null) {
+
+			// load next page
+			final Bundle nextPage = client.loadPage().next(results).execute();
+			System.out.println(nextPage.getEntry().size());
+		}
+	}
+
+	/** */
+	@Test
+	public void testSearchPost() {
+		Bundle response = client.search()
+				.forResource("Patient")
+				.usingStyle(SearchStyleEnum.POST)
+				.returnBundle(Bundle.class)
+				.execute();
+		assertTrue(response.getEntry().size() > 0);
+	}
+
+	/** Search - Compartments */
+	@Test
+	public void testSearchCompartements() {
+		Bundle response = client.search()
+				.forResource(Patient.class)
+				.withIdAndCompartment("1", "Condition")
+				.returnBundle(Bundle.class)
+				.execute();
+		assertTrue(response.getEntry().size() > 0);
+	}
+
+	/** Search - Subsetting (_summary and _elements) */
+	@Test
+	@Ignore
+	public void testSummary() {
+		client.search()
+				.forResource(Patient.class)
+				.returnBundle(Bundle.class)
+				.execute();
+	}
+
+	@Test
+	public void testCreatePatient() {
+		final Patient existing = new Patient();
+		existing.setId((IdDt) null);
+		existing.getNameFirstRep().setFamily("Created Patient 54");
+		client.setEncoding(EncodingEnum.JSON);
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		System.out.println(results.getId());
+		final Patient patient = (Patient) results.getResource();
+		System.out.println(patient);
+		assertNotNull(client.read().resource(Patient.class).withId(patient.getId()));
+		client.setEncoding(EncodingEnum.JSON);
+	}
+
+	/** Conditional Creates */
+	@Test
+	public void testConditionalCreate() {
+		final Patient existing = new Patient();
+		existing.setId((IdDt) null);
+		existing.getNameFirstRep().setFamily("Created Patient 54");
+		client.setEncoding(EncodingEnum.XML);
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		System.out.println(results.getId());
+		final Patient patient = (Patient) results.getResource();
+
+		client.create()
+				.resource(patient)
+				.conditional()
+				.where(Patient.IDENTIFIER.exactly().identifier(patient.getIdentifierFirstRep().toString()))
+				.execute();
+	}
+
+	/** Find By Id */
+	@Test
+	public void findUsingGenericClientById() {
+		final Patient results = client.read().resource(Patient.class).withId("1").execute();
+		assertEquals(results.getIdElement().getIdPartAsLong().longValue(), 1L);
+	}
+
+	@Test
+	public void testUpdateById() {
+		final Patient existing = client.read().resource(Patient.class).withId("1").execute();
+		final List<HumanName> name = existing.getName();
+		name.get(0).addSuffix("The Second");
+		existing.setName(name);
+		client.setEncoding(EncodingEnum.XML);
+		final MethodOutcome results = client.update().resource(existing).withId("1").execute();
+	}
+
+	@Test
+	public void testDeletePatient() {
+		final Patient existing = new Patient();
+		existing.getNameFirstRep().setFamily("Created Patient XYZ");
+		final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		System.out.println(results.getId());
+		final Patient patient = (Patient) results.getResource();
+		client.delete().resource(patient).execute();
+		try {
+			client.read().resource(Patient.class).withId(patient.getId()).execute();
+			fail();
+		} catch (final Exception e) {
+			// assertEquals(e.getStatusCode(), Constants.STATUS_HTTP_404_NOT_FOUND);
+		}
+	}
+
+	/** Transaction - Server */
+	@Ignore
+	@Test
+	public void testTransaction() {
+		Bundle bundle = new Bundle();
+		Bundle.BundleEntryComponent entry = bundle.addEntry();
+		final Patient existing = new Patient();
+		existing.getNameFirstRep().setFamily("Created with bundle");
+		entry.setResource(existing);
+
+		BoundCodeDt<BundleEntryTransactionMethodEnum> theTransactionOperation = new BoundCodeDt(
+				BundleEntryTransactionMethodEnum.VALUESET_BINDER,
+				BundleEntryTransactionMethodEnum.POST);
+		Bundle response = client.transaction().withBundle(bundle).execute();
+	}
+
+	/** Conformance - Server */
+	@Test
+	@Ignore
+	public void testConformance() {
+		final CapabilityStatement caps = client.capabilities().ofType(CapabilityStatement.class).execute();
+		System.out.println(caps.getRest().get(0).getResource().get(0).getType());
+		assertEquals(caps.getRest().get(0).getResource().get(0).getType().toString(), "Patient");
+	}
+
+	/** Extended Operations */
+	// Create a client to talk to the HeathIntersections server
+	@Test
+	public void testExtendedOperations() {
+		client.registerInterceptor(new LoggingInterceptor(true));
+
+		// Create the input parameters to pass to the server
+		Parameters inParams = new Parameters();
+		inParams.addParameter().setName("start").setValue(new DateTimeType("2001-01-01"));
+		inParams.addParameter().setName("end").setValue(new DateTimeType("2015-03-01"));
+		inParams.addParameter().setName("dummy").setValue(new StringType("myAwesomeDummyValue"));
+
+		// Invoke $everything on "Patient/1"
+		Parameters outParams = client
+				.operation()
+				.onInstance(new IdDt("Patient", "1"))
+				.named("$firstVersion")
+				.withParameters(inParams)
+				// .useHttpGet() // Use HTTP GET instead of POST
+				.execute();
+		String resultValue = outParams.getParameter().get(0).getValue().toString();
+		System.out.println(resultValue);
+		assertEquals("expected but found : " + resultValue, resultValue.contains("myAwesomeDummyValue"), true);
+	}
+
+	@Test
+	public void testExtendedOperationsUsingGet() {
+		// Create the input parameters to pass to the server
+		Parameters inParams = new Parameters();
+		inParams.addParameter().setName("start").setValue(new DateTimeType("2001-01-01"));
+		inParams.addParameter().setName("end").setValue(new DateTimeType("2015-03-01"));
+		inParams.addParameter().setName("dummy").setValue(new StringType("myAwesomeDummyValue"));
+
+		// Invoke $everything on "Patient/1"
+		Parameters outParams = client
+				.operation()
+				.onInstance(new IdDt("Patient", "1"))
+				.named("$firstVersion")
+				.withParameters(inParams)
+				.useHttpGet() // Use HTTP GET instead of POST
+				.execute();
+		String resultValue = outParams.getParameter().get(0).getValue().toString();
+		System.out.println(resultValue);
+		assertEquals("expected but found : " + resultValue, resultValue.contains("myAwesomeDummyValue"), true);
+	}
+
+	@Test
+	public void testVRead() {
+		final Patient patient = client.read().resource(Patient.class).withIdAndVersion("1", "1").execute();
+		System.out.println(patient);
+	}
+
+	@Test
+	public void testRead() {
+		final Patient patient = client.read().resource(Patient.class).withId("1").execute();
+		System.out.println(patient);
+	}
+
+	@Test
+	public void testInstanceHistory() {
+		final Bundle history = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
+		assertEquals("myTestId", history.getIdElement().getIdPart());
+	}
+
+	@Test
+	public void testTypeHistory() {
+		final Bundle history = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
+		assertEquals("myTestId", history.getIdElement().getIdPart());
+	}
+}

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderTest.java

@@ -291,4 +291,15 @@ public class JaxRsPatientProviderTest {
 		System.out.println(patient);
 	}
 
+	@Test
+	public void testInstanceHistory() {
+		final Bundle history = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
+		assertEquals("myTestId", history.getId().getIdPart());
+	}
+
+	@Test
+	public void testTypeHistory() {
+		final Bundle history = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
+		assertEquals("myTestId", history.getId().getIdPart());
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -50,15 +50,12 @@ import static org.apache.commons.lang3.StringUtils.length;
 	@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
 })
 public class TermConcept implements Serializable {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
-
-	private static final long serialVersionUID = 1L;
-
 	public static final int MAX_CODE_LENGTH = 500;
 	public static final int MAX_DESC_LENGTH = 400;
-
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
+	private static final long serialVersionUID = 1L;
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
-	private Collection<TermConceptParentChildLink> myChildren;
+	private List<TermConceptParentChildLink> myChildren;
 
 	@Column(name = "CODEVAL", nullable = false, length = MAX_CODE_LENGTH)
 	@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
@@ -178,7 +175,7 @@ public class TermConcept implements Serializable {
 		return b.isEquals();
 	}
 
-	public Collection<TermConceptParentChildLink> getChildren() {
+	public List<TermConceptParentChildLink> getChildren() {
 		if (myChildren == null) {
 			myChildren = new ArrayList<>();
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java

@@ -177,6 +177,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 	public IBaseParameters uploadExternalCodeSystem(
 		HttpServletRequest theServletRequest,
 		@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
+		@OperationParam(name = "contentMode", min = 0, typeName = "code") IPrimitiveType<String> theContentMode,
 		@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
 		@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
 		RequestDetails theRequestDetails
@@ -245,11 +246,15 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 				}
 			}
 
-			String url = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
+			String codeSystemUrl = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
-			url = defaultString(url);
+			codeSystemUrl = defaultString(codeSystemUrl);
 
+			String contentMode = theContentMode != null ? theContentMode.getValue() : null;
 			UploadStatistics stats;
-			switch (url) {
+			if ("custom".equals(contentMode)) {
+				stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
+			} else {
+				switch (codeSystemUrl) {
 					case IHapiTerminologyLoaderSvc.SCT_URI:
 						stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
 						break;
@@ -260,7 +265,8 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 						stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
 						break;
 					default:
-					throw new InvalidRequestException("Unknown URL: " + url);
+						throw new InvalidRequestException("Unknown URL: " + codeSystemUrl);
+				}
 			}
 
 			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java

@@ -39,6 +39,9 @@ public interface IHapiTerminologyLoaderSvc {
 
 	UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
 
+	// FIXME: remove the default implementation before 4.0.0
+	default UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
+
 	interface FileDescriptor {
 
 		String getFilename();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java

@@ -4,15 +4,19 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.term.custom.ConceptHandler;
+import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
 import ca.uhn.fhir.jpa.term.loinc.*;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
 import ca.uhn.fhir.jpa.util.Counter;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.ValidateUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
 import org.apache.commons.csv.CSVFormat;
@@ -83,15 +87,19 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	public static final String LOINC_GROUP_FILE = "Group.csv";
 	public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
 	public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
+	public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
+	public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
+	public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
+	public static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
+
 	private static final int LOG_INCREMENT = 1000;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
 
 	@Autowired
 	private IHapiTerminologySvc myTermSvc;
-	@Autowired(required = false)
+
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
+	// FYI: Hardcoded to R4 because that's what the term svc uses internally
-	@Autowired(required = false)
+	private final FhirContext myCtx = FhirContext.forR4();
-	private IHapiTerminologySvcR4 myTermSvcR4;
 
 	private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
 
@@ -203,8 +211,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 			ourLog.info("Beginning IMGTHLA processing");
 
 			return processImgthlaFiles(descriptors, theRequestDetails);
-		}
+		} finally {
-		finally {
 			IOUtils.closeQuietly(descriptors);
 		}
 	}
@@ -257,6 +264,67 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		}
 	}
 
+	@Override
+	public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
+		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
+			final Map<String, TermConcept> code2concept = new HashMap<>();
+			IRecordHandler handler;
+
+			Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
+			CodeSystem codeSystem;
+			if (codeSystemContent.isPresent()) {
+				codeSystem = EncodingEnum
+					.detectEncoding(codeSystemContent.get())
+					.newParser(myCtx)
+					.parseResource(CodeSystem.class, codeSystemContent.get());
+				ValidateUtil.isTrueOrThrowInvalidRequest(theSystem.equalsIgnoreCase(codeSystem.getUrl()), "CodeSystem.url does not match the supplied system: %s", theSystem);
+				ValidateUtil.isTrueOrThrowInvalidRequest(CodeSystem.CodeSystemContentMode.NOTPRESENT.equals(codeSystem.getContent()), "CodeSystem.content does not match the expected value: %s", CodeSystem.CodeSystemContentMode.NOTPRESENT.toCode());
+			} else {
+				codeSystem = new CodeSystem();
+				codeSystem.setUrl(theSystem);
+				codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+			}
+
+			TermCodeSystemVersion csv = new TermCodeSystemVersion();
+
+			// Concept File
+			handler = new ConceptHandler(code2concept, csv);
+			iterateOverZipFile(descriptors, CUSTOM_CONCEPTS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+
+			// Hierarchy
+			if (descriptors.hasFile(CUSTOM_HIERARCHY_FILE)) {
+				handler = new HierarchyHandler(code2concept);
+				iterateOverZipFile(descriptors, CUSTOM_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+			}
+
+			// Add root concepts to CodeSystemVersion
+			for (TermConcept nextConcept : code2concept.values()) {
+				if (nextConcept.getParents().isEmpty()) {
+					csv.getConcepts().add(nextConcept);
+				}
+			}
+
+			IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
+			return new UploadStatistics(code2concept.size(), target);
+		}
+	}
+
+	private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String... theFilenames) {
+		for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
+			for (String nextFilename : theFilenames) {
+				if (next.getFilename().endsWith(nextFilename)) {
+					try {
+						String contents = IOUtils.toString(next.getInputStream(), Charsets.UTF_8);
+						return Optional.of(contents);
+					} catch (IOException e) {
+						throw new InternalErrorException(e);
+					}
+				}
+			}
+		}
+		return Optional.empty();
+	}
+
 	UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
 		final Map<String, TermConcept> code2concept = new HashMap<>();
@@ -309,13 +377,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 					}
 
 					LineNumberReader lnr = new LineNumberReader(reader);
-					while(lnr.readLine() != null) {}
+					while (lnr.readLine() != null) {
+					}
 					ourLog.warn("Lines read from {}:  {}", nextFilename, lnr.getLineNumber());
 
 				} catch (IOException e) {
 					throw new InternalErrorException(e);
-				}
+				} finally {
-				finally {
 					IOUtils.closeQuietly(reader);
 				}
 
@@ -340,13 +408,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 					}
 
 					LineNumberReader lnr = new LineNumberReader(reader);
-					while(lnr.readLine() != null) {}
+					while (lnr.readLine() != null) {
+					}
 					ourLog.warn("Lines read from {}:  {}", nextFilename, lnr.getLineNumber());
 
 				} catch (IOException e) {
 					throw new InternalErrorException(e);
-				}
+				} finally {
-				finally {
 					IOUtils.closeQuietly(reader);
 				}
 
@@ -553,11 +621,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		return new UploadStatistics(code2concept.size(), target);
 	}
 
-	@VisibleForTesting
-	void setTermSvcDstu3ForUnitTest(IHapiTerminologySvcDstu3 theTermSvcDstu3) {
-		myTermSvcDstu3 = theTermSvcDstu3;
-	}
-
 	@VisibleForTesting
 	void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
 		myTermSvc = theTermSvc;
@@ -571,38 +634,12 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 		IIdType retVal;
 		myTermSvc.setProcessDeferred(false);
-		if (myTermSvcDstu3 != null) {
+		retVal = myTermSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-			retVal = myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-		} else {
-			retVal = myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-		}
 		myTermSvc.setProcessDeferred(true);
 
 		return retVal;
 	}
 
-
-	public static String firstNonBlank(String... theStrings) {
-		String retVal = "";
-		for (String nextString : theStrings) {
-			if (isNotBlank(nextString)) {
-				retVal = nextString;
-				break;
-			}
-		}
-		return retVal;
-	}
-
-	public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
-		TermConcept concept = id2concept.get(id);
-		if (concept == null) {
-			concept = new TermConcept();
-			id2concept.put(id, concept);
-			concept.setCodeSystemVersion(codeSystemVersion);
-		}
-		return concept;
-	}
-
 	static class LoadedFileDescriptors implements Closeable {
 
 		private List<File> myTemporaryFiles = new ArrayList<>();
@@ -651,6 +688,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 			}
 		}
 
+		boolean hasFile(String theFilename) {
+			return myUncompressedFileDescriptors
+				.stream()
+				.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
+				.anyMatch(t -> t.equals(theFilename));
+		}
+
 		@Override
 		public void close() {
 			for (File next : myTemporaryFiles) {
@@ -694,4 +738,25 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 
 	}
+
+	public static String firstNonBlank(String... theStrings) {
+		String retVal = "";
+		for (String nextString : theStrings) {
+			if (isNotBlank(nextString)) {
+				retVal = nextString;
+				break;
+			}
+		}
+		return retVal;
+	}
+
+	public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
+		TermConcept concept = id2concept.get(id);
+		if (concept == null) {
+			concept = new TermConcept();
+			id2concept.put(id, concept);
+			concept.setCodeSystemVersion(codeSystemVersion);
+		}
+		return concept;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/ConceptHandler.java

@@ -0,0 +1,63 @@
+package ca.uhn.fhir.jpa.term.custom;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import org.apache.commons.csv.CSVRecord;
+import org.apache.commons.lang3.Validate;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class ConceptHandler implements IRecordHandler {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ConceptHandler.class);
+	private final Map<String, TermConcept> myCode2Concept;
+	private final TermCodeSystemVersion myCodeSystemVersion;
+
+	public ConceptHandler(Map<String, TermConcept> theCode2concept, TermCodeSystemVersion theCodeSystemVersion) {
+		myCode2Concept = theCode2concept;
+		myCodeSystemVersion = theCodeSystemVersion;
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		String code = trim(theRecord.get("CODE"));
+		if (isNotBlank(code)) {
+			String display = trim(theRecord.get("DISPLAY"));
+
+			Validate.isTrue(!myCode2Concept.containsKey(code), "The code %s has appeared more than once", code);
+
+			TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myCode2Concept, code);
+			concept.setCode(code);
+			concept.setDisplay(display);
+
+			myCode2Concept.put(code, concept);
+		}
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/HierarchyHandler.java

@@ -0,0 +1,58 @@
+package ca.uhn.fhir.jpa.term.custom;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import ca.uhn.fhir.util.ValidateUtil;
+import org.apache.commons.csv.CSVRecord;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class HierarchyHandler implements IRecordHandler {
+
+	private final Map<String, TermConcept> myCode2Concept;
+
+	public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
+		myCode2Concept = theCode2concept;
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		String parent = trim(theRecord.get("PARENT"));
+		String child = trim(theRecord.get("CHILD"));
+		if (isNotBlank(parent) && isNotBlank(child)) {
+
+			TermConcept parentConcept = myCode2Concept.get(parent);
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found", parent);
+			TermConcept childConcept = myCode2Concept.get(child);
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
+
+			parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+		}
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/BaseLoaderTest.java

@@ -0,0 +1,58 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.runner.RunWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@RunWith(MockitoJUnitRunner.class)
+abstract class BaseLoaderTest {
+
+	@Mock
+	protected RequestDetails mySrd;
+	@Captor
+	protected ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
+	@Captor
+	protected ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
+	@Captor
+	protected ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
+	@Captor
+	protected ArgumentCaptor<CodeSystem> mySystemCaptor;
+
+	Map<String, ConceptMap> extractConceptMaps() {
+		Map<String, ConceptMap> conceptMaps = new HashMap<>();
+		for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
+			conceptMaps.put(next.getId(), next);
+		}
+		return conceptMaps;
+	}
+
+	Map<String, TermConcept> extractConcepts() {
+		Map<String, TermConcept> concepts = new HashMap<>();
+		for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
+			concepts.put(next.getCode(), next);
+		}
+		return concepts;
+	}
+
+	Map<String, ValueSet> extractValueSets() {
+		Map<String, ValueSet> valueSets = new HashMap<>();
+		for (ValueSet next : myValueSetsCaptor.getValue()) {
+			valueSets.put(next.getId(), next);
+		}
+		return valueSets;
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcCustomTest.java

@@ -0,0 +1,115 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
+	private TerminologyLoaderSvcImpl mySvc;
+
+	@Mock
+	private IHapiTerminologySvc myTermSvc;
+
+	private ZipCollectionBuilder myFiles;
+
+
+	@Before
+	public void before() {
+		mySvc = new TerminologyLoaderSvcImpl();
+		mySvc.setTermSvcForUnitTests(myTermSvc);
+
+		myFiles = new ZipCollectionBuilder();
+	}
+
+	@Test
+	public void testLoadComplete() throws Exception {
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CODESYSTEM_JSON);
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_HIERARCHY_FILE);
+
+		// Actually do the load
+		mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
+
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		Map<String, TermConcept> concepts = extractConcepts();
+
+		// Verify codesystem
+		assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
+		assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
+		assertEquals("Example Lab Codes", mySystemCaptor.getValue().getName());
+
+		// Root code
+		TermConcept code;
+		assertEquals(2, concepts.size());
+		code = concepts.get("CHEM");
+		assertEquals("CHEM", code.getCode());
+		assertEquals("Chemistry", code.getDisplay());
+
+		assertEquals(2, code.getChildren().size());
+		assertEquals("HB", code.getChildren().get(0).getChild().getCode());
+		assertEquals("Hemoglobin", code.getChildren().get(0).getChild().getDisplay());
+		assertEquals("NEUT", code.getChildren().get(1).getChild().getCode());
+		assertEquals("Neutrophils", code.getChildren().get(1).getChild().getDisplay());
+
+	}
+
+	@Test
+	public void testLoadWithNoCodeSystem() throws Exception {
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
+
+		// Actually do the load
+		mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
+
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		Map<String, TermConcept> concepts = extractConcepts();
+
+		// Verify codesystem
+		assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
+		assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
+
+	}
+
+	/**
+	 * No hierarchy file supplied
+	 */
+	@Test
+	public void testLoadCodesOnly() throws Exception {
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
+
+		// Actually do the load
+		mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
+
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		Map<String, TermConcept> concepts = extractConcepts();
+
+		TermConcept code;
+
+		// Root code
+		assertEquals(5, concepts.size());
+		code = concepts.get("CHEM");
+		assertEquals("CHEM", code.getCode());
+		assertEquals("Chemistry", code.getDisplay());
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImgthlaTest.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.term;
 
-import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
@@ -8,9 +7,7 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.runner.RunWith;
 import org.mockito.Mock;
-import org.mockito.junit.MockitoJUnitRunner;
 
 import java.io.IOException;
 
@@ -18,19 +15,12 @@ import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
-@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcImgthlaTest extends BaseLoaderTest {
-public class TerminologyLoaderSvcImgthlaTest {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImgthlaTest.class);
 	private TerminologyLoaderSvcImpl mySvc;
 
 	@Mock
 	private IHapiTerminologySvc myTermSvc;
 
-	@Mock
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
-
-	@Mock
-	private RequestDetails details;
 	private ZipCollectionBuilder myFiles;
 
 
@@ -38,7 +28,6 @@ public class TerminologyLoaderSvcImgthlaTest {
 	public void before() {
 		mySvc = new TerminologyLoaderSvcImpl();
 		mySvc.setTermSvcForUnitTests(myTermSvc);
-		mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
 
 		myFiles = new ZipCollectionBuilder();
 	}
@@ -49,7 +38,7 @@ public class TerminologyLoaderSvcImgthlaTest {
 
 		// Actually do the load
 		try {
-			mySvc.loadImgthla(myFiles.getFiles(), details);
+			mySvc.loadImgthla(myFiles.getFiles(), mySrd);
 			fail("Expected \"not yet fully implemented\" InternalErrorException");
 		} catch(InternalErrorException e) {
 			// for now, expect "not yet fully implemented" exception
@@ -65,7 +54,7 @@ public class TerminologyLoaderSvcImgthlaTest {
 		addImgthlaMandatoryFilesToZip(myFiles);
 
 		// Actually do the load
-		mySvc.loadImgthla(myFiles.getFiles(), details);
+		mySvc.loadImgthla(myFiles.getFiles(), mySrd);
 
 		// TODO:  verify the code system was loaded correctly (similarly to TerminologyLoaderSvcLoincTest.testLoadLoincMandatoryFilesOnly)
 	}
@@ -76,7 +65,7 @@ public class TerminologyLoaderSvcImgthlaTest {
 
 		// Actually do the load
 		try {
-			mySvc.loadImgthla(myFiles.getFiles(), details);
+			mySvc.loadImgthla(myFiles.getFiles(), mySrd);
 			fail("Expected UnprocessableEntityException");
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.loinc.*;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -15,46 +14,28 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
-import org.mockito.junit.MockitoJUnitRunner;
 
 import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 
-import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.*;
-import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.empty;
 import static org.junit.Assert.*;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
-@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
-public class TerminologyLoaderSvcLoincTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcLoincTest.class);
 	private TerminologyLoaderSvcImpl mySvc;
 
 	@Mock
 	private IHapiTerminologySvc myTermSvc;
-
-	@Mock
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
-
-	@Captor
-	private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
 	@Captor
 	private ArgumentCaptor<CodeSystem> mySystemCaptor;
-	@Mock
+
-	private RequestDetails details;
-	@Captor
-	private ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
-	@Captor
-	private ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
 	private ZipCollectionBuilder myFiles;
 
 
@@ -62,43 +43,18 @@ public class TerminologyLoaderSvcLoincTest {
 	public void before() {
 		mySvc = new TerminologyLoaderSvcImpl();
 		mySvc.setTermSvcForUnitTests(myTermSvc);
-		mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
 
 		myFiles = new ZipCollectionBuilder();
 	}
 
-	private Map<String, ConceptMap> extractConceptMaps() {
-		Map<String, ConceptMap> conceptMaps = new HashMap<>();
-		for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
-			conceptMaps.put(next.getId(), next);
-		}
-		return conceptMaps;
-	}
-
-	private Map<String, TermConcept> extractConcepts() {
-		Map<String, TermConcept> concepts = new HashMap<>();
-		for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
-			concepts.put(next.getCode(), next);
-		}
-		return concepts;
-	}
-
-	private Map<String, ValueSet> extractValueSets() {
-		Map<String, ValueSet> valueSets = new HashMap<>();
-		for (ValueSet next : myValueSetsCaptor.getValue()) {
-			valueSets.put(next.getId(), next);
-		}
-		return valueSets;
-	}
-
 	@Test
 	public void testLoadLoinc() throws Exception {
 		addLoincMandatoryFilesToZip(myFiles);
 
 		// Actually do the load
-		mySvc.loadLoinc(myFiles.getFiles(), details);
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 
-		verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		Map<String, TermConcept> concepts = extractConcepts();
 		Map<String, ValueSet> valueSets = extractValueSets();
 		Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@@ -347,9 +303,9 @@ public class TerminologyLoaderSvcLoincTest {
 		addLoincMandatoryFilesToZip(myFiles);
 
 		// Actually do the load
-		mySvc.loadLoinc(myFiles.getFiles(), details);
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 
-		verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		Map<String, TermConcept> concepts = extractConcepts();
 		Map<String, ValueSet> valueSets = extractValueSets();
 		Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@@ -371,7 +327,7 @@ public class TerminologyLoaderSvcLoincTest {
 
 		// Actually do the load
 		try {
-			mySvc.loadLoinc(myFiles.getFiles(), details);
+			mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcSnomedCtTest.java

@@ -4,39 +4,36 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
-import org.mockito.runners.MockitoJUnitRunner;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.FileInputStream;
 import java.io.InputStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.TreeSet;
 import java.util.zip.ZipOutputStream;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.CoreMatchers.containsString;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.hasItem;
-import static org.mockito.Matchers.any;
+import static org.hamcrest.Matchers.not;
-import static org.mockito.Matchers.anyListOf;
+import static org.junit.Assert.assertThat;
-import static org.mockito.Mockito.mock;
+import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.*;
 import static org.mockito.Mockito.verify;
 
-@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcSnomedCtTest extends BaseLoaderTest {
-public class TerminologyLoaderSvcSnomedCtTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcSnomedCtTest.class);
 	private TerminologyLoaderSvcImpl mySvc;
 
@@ -44,15 +41,12 @@ public class TerminologyLoaderSvcSnomedCtTest {
 	private IHapiTerminologySvc myTermSvc;
 	@Captor
 	private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
-	@Mock
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
 	private ZipCollectionBuilder myFiles;
 
 	@Before
 	public void before() {
 		mySvc = new TerminologyLoaderSvcImpl();
 		mySvc.setTermSvcForUnitTests(myTermSvc);
-		mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
 
 		myFiles = new ZipCollectionBuilder();
 	}
@@ -84,17 +78,16 @@ public class TerminologyLoaderSvcSnomedCtTest {
 		myFiles.addFileZip("/sct/", "sct2_StatedRelationship_Full_INT_20160131.txt");
 		myFiles.addFileZip("/sct/", "sct2_TextDefinition_Full-en_INT_20160131.txt");
 
-		RequestDetails details = mock(RequestDetails.class);
+		mySvc.loadSnomedCt(myFiles.getFiles(), mySrd);
-		mySvc.loadSnomedCt(myFiles.getFiles(), details);
 
-		verify(myTermSvcDstu3).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyListOf(ValueSet.class), anyListOf(ConceptMap.class));
+		verify(myTermSvc).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyList(), anyListOf(ConceptMap.class));
 
 		TermCodeSystemVersion csv = myCsvCaptor.getValue();
 		TreeSet<String> allCodes = toCodes(csv, true);
 		ourLog.info(allCodes.toString());
 
-		assertThat(allCodes, containsInRelativeOrder("116680003"));
+		assertThat(allCodes, hasItem("116680003"));
-		assertThat(allCodes, not(containsInRelativeOrder("207527008")));
+		assertThat(allCodes, not(hasItem("207527008")));
 
 		allCodes = toCodes(csv, false);
 		ourLog.info(allCodes.toString());
@@ -110,8 +103,7 @@ public class TerminologyLoaderSvcSnomedCtTest {
 	public void testLoadSnomedCtAgainstRealFile() throws Exception {
 		byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
 
-		RequestDetails details = mock(RequestDetails.class);
+		mySvc.loadSnomedCt(list(bytes), mySrd);
-		mySvc.loadSnomedCt(list(bytes), details);
 	}
 
 	@Test
@@ -123,9 +115,8 @@ public class TerminologyLoaderSvcSnomedCtTest {
 
 		ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
 
-		RequestDetails details = mock(RequestDetails.class);
 		try {
-			mySvc.loadSnomedCt(list(bos.toByteArray()), details);
+			mySvc.loadSnomedCt(list(bos.toByteArray()), mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input: "));

hapi-fhir-jpaserver-base/src/test/resources/custom_term/codesystem.json

@@ -0,0 +1,10 @@
+{
+	"resourceType": "CodeSystem",
+	"url": "http://example.com/labCodes",
+	"name": "Example Lab Codes",
+	"description": "A set of lab codes",
+	"status": "active",
+	"publisher": "Example Organization Corporation Worldwide",
+	"date": "2019-07-30",
+	"content": "not-present"
+}

hapi-fhir-jpaserver-base/src/test/resources/custom_term/concepts.csv

@@ -0,0 +1,8 @@
+CODE,DISPLAY
+
+CHEM,Chemistry
+HB,Hemoglobin
+NEUT,Neutrophils
+
+MICRO,Microbiology
+C&S,Culture and Sensitivity

hapi-fhir-jpaserver-base/src/test/resources/custom_term/hierarchy.csv

@@ -0,0 +1,6 @@
+PARENT,CHILD
+
+CHEM,HB
+CHEM,NEUT
+
+MICRO,C&S

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/any/AnyListResource.java

@@ -94,6 +94,10 @@ public class AnyListResource {
 		return (org.hl7.fhir.r4.model.ListResource) get();
 	}
 
+	public FhirVersionEnum getFhirVersion() {
+		return myFhirVersion;
+	}
+
 	public void addCode(String theSystem, String theCode) {
 		switch (myFhirVersion) {
 			case DSTU3:

hapi-fhir-structures-r4/pom.xml

@@ -186,6 +186,12 @@
 		</dependency>
 
 		<!-- UNIT TEST DEPENDENCIES -->
+		<dependency>
+			<groupId>org.apache.jena</groupId>
+			<artifactId>apache-jena-libs</artifactId>
+			<type>pom</type>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>net.sf.json-lib</groupId>
 			<artifactId>json-lib</artifactId>

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserR4Test.java

@@ -0,0 +1,281 @@
+package ca.uhn.fhir.parser;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.TestUtil;
+import com.google.common.collect.Sets;
+import org.apache.commons.lang3.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;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.*;
+
+@Ignore
+public class RDFParserR4Test {
+	private static final Logger ourLog = LoggerFactory.getLogger(RDFParserR4Test.class);
+	private static FhirContext ourCtx = FhirContext.forR4();
+
+	/*
+	private Bundle createBundleWithPatient() {
+		Bundle b = new Bundle();
+		b.setId("BUNDLEID");
+		b.getMeta().addProfile("http://FOO");
+
+		Patient p = new Patient();
+		p.setId("PATIENTID");
+		p.getMeta().addProfile("http://BAR");
+		p.addName().addGiven("GIVEN");
+		b.addEntry().setResource(p);
+		return b;
+	}
+	*/
+
+	@Test
+	public void testDontStripVersions() {
+		FhirContext ctx = FhirContext.forR4();
+		ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("QuestionnaireResponse.questionnaire");
+
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.getQuestionnaireElement().setValueAsString("Questionnaire/123/_history/456");
+
+		String output = ctx.newRDFParser().setPrettyPrint(true).encodeResourceToString(qr);
+		ourLog.info(output);
+
+		assertThat(output, containsString("\"Questionnaire/123/_history/456\""));
+	}
+
+	@Test
+	public void testDuplicateContainedResourcesNotOutputtedTwice() {
+		MedicationDispense md = new MedicationDispense();
+
+		MedicationRequest mr = new MedicationRequest();
+		md.addAuthorizingPrescription().setResource(mr);
+
+		Medication med = new Medication();
+		md.setMedication(new Reference(med));
+		mr.setMedication(new Reference(med));
+
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(md);
+		ourLog.info(encoded);
+
+		int idx = encoded.indexOf("\"Medication\"");
+		assertNotEquals(-1, idx);
+
+		idx = encoded.indexOf("\"Medication\"", idx + 1);
+		assertEquals(-1, idx);
+	}
+
+	/**
+	 * See #814
+	 */
+	@Test
+	public void testDuplicateContainedResourcesNotOutputtedTwiceWithManualIds() {
+		MedicationDispense md = new MedicationDispense();
+
+		MedicationRequest mr = new MedicationRequest();
+		mr.setId("#MR");
+		md.addAuthorizingPrescription().setResource(mr);
+
+		Medication med = new Medication();
+		med.setId("#MED");
+		md.setMedication(new Reference(med));
+		mr.setMedication(new Reference(med));
+
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(md);
+		ourLog.info(encoded);
+
+		int idx = encoded.indexOf("\"Medication\"");
+		assertNotEquals(-1, idx);
+
+		idx = encoded.indexOf("\"Medication\"", idx + 1);
+		assertEquals(-1, idx);
+	}
+
+	/*
+	 * See #814
+	 */
+	@Test
+	public void testDuplicateContainedResourcesNotOutputtedTwiceWithManualIdsAndManualAddition() {
+		MedicationDispense md = new MedicationDispense();
+
+		MedicationRequest mr = new MedicationRequest();
+		mr.setId("#MR");
+		md.addAuthorizingPrescription().setResource(mr);
+
+		Medication med = new Medication();
+		med.setId("#MED");
+
+		Reference medRef = new Reference();
+		medRef.setReference("#MED");
+		md.setMedication(medRef);
+		mr.setMedication(medRef);
+
+		md.getContained().add(mr);
+		md.getContained().add(med);
+
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(md);
+		ourLog.info(encoded);
+
+		int idx = encoded.indexOf("\"Medication\"");
+		assertNotEquals(-1, idx);
+
+		idx = encoded.indexOf("\"Medication\"", idx + 1);
+		assertEquals(-1, idx);
+	}
+
+	@Test
+	public void testEncodeAndParseUnicodeCharacterInNarrative() {
+		Patient p = new Patient();
+		p.getText().getDiv().setValueAsString("<div>Copy © 1999</div>");
+		String encoded = ourCtx.newRDFParser().encodeResourceToString(p);
+		ourLog.info(encoded);
+
+		p = (Patient) ourCtx.newRDFParser().parseResource(encoded);
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">Copy &copy; 1999</div>", p.getText().getDivAsString());
+	}
+
+
+	@Test
+	public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalFirst() {
+		Observation obs = new Observation();
+
+		Patient pt = new Patient();
+		pt.setId("#1");
+		pt.addName().setFamily("FAM");
+		obs.getSubject().setReference("#1");
+		obs.getContained().add(pt);
+
+		Encounter enc = new Encounter();
+		enc.setStatus(Encounter.EncounterStatus.ARRIVED);
+		obs.getEncounter().setResource(enc);
+
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(obs);
+		ourLog.info(encoded);
+
+		obs = ourCtx.newRDFParser().parseResource(Observation.class, encoded);
+		assertEquals("#1", obs.getContained().get(0).getId());
+		assertEquals("#2", obs.getContained().get(1).getId());
+
+		pt = (Patient) obs.getSubject().getResource();
+		assertEquals("FAM", pt.getNameFirstRep().getFamily());
+
+		enc = (Encounter) obs.getEncounter().getResource();
+		assertEquals(Encounter.EncounterStatus.ARRIVED, enc.getStatus());
+	}
+
+
+	@Test
+	public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalLast() {
+		Observation obs = new Observation();
+
+		Patient pt = new Patient();
+		pt.addName().setFamily("FAM");
+		obs.getSubject().setResource(pt);
+
+		Encounter enc = new Encounter();
+		enc.setId("#1");
+		enc.setStatus(Encounter.EncounterStatus.ARRIVED);
+		obs.getEncounter().setReference("#1");
+		obs.getContained().add(enc);
+
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(obs);
+		ourLog.info(encoded);
+
+		obs = ourCtx.newRDFParser().parseResource(Observation.class, encoded);
+		assertEquals("#1", obs.getContained().get(0).getId());
+		assertEquals("#2", obs.getContained().get(1).getId());
+
+		pt = (Patient) obs.getSubject().getResource();
+		assertEquals("FAM", pt.getNameFirstRep().getFamily());
+
+		enc = (Encounter) obs.getEncounter().getResource();
+		assertEquals(Encounter.EncounterStatus.ARRIVED, enc.getStatus());
+	}
+
+	@Test
+	public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalLast2() {
+		MedicationRequest mr = new MedicationRequest();
+		Practitioner pract = new Practitioner().setActive(true);
+		mr.getRequester().setResource(pract);
+
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(mr);
+		ourLog.info(encoded);
+		mr = ourCtx.newRDFParser().parseResource(MedicationRequest.class, encoded);
+
+		mr.setMedication(new Reference(new Medication().setStatus(Medication.MedicationStatus.ACTIVE)));
+		encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(mr);
+		ourLog.info(encoded);
+		mr = ourCtx.newRDFParser().parseResource(MedicationRequest.class, encoded);
+
+		assertEquals("#2", mr.getContained().get(0).getId());
+		assertEquals("#1", mr.getContained().get(1).getId());
+	}
+
+
+	/**
+	 * Test that long JSON strings don't get broken up
+	 */
+	@Test
+	public void testNoBreakInLongString() {
+		String longString = StringUtils.leftPad("", 100000, 'A');
+
+		Patient p = new Patient();
+		p.addName().setFamily(longString);
+		String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(p);
+
+		assertThat(encoded, containsString(longString));
+	}
+
+
+	@Test
+	public void testParseAndEncodeExtensionWithValueWithExtension() {
+		String input = "{\n" +
+			"  \"resourceType\": \"Patient\",\n" +
+			"  \"extension\": [\n" +
+			"    {\n" +
+			"      \"url\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\",\n" +
+			"      \"_valueDecimal\": {\n" +
+			"        \"extension\": [\n" +
+			"          {\n" +
+			"            \"url\": \"http://www.hl7.org/fhir/extension-data-absent-reason.html\",\n" +
+			"            \"valueCoding\": {\n" +
+			"              \"system\": \"http://hl7.org/fhir/ValueSet/birthweight\",\n" +
+			"              \"code\": \"Underweight\",\n" +
+			"              \"userSelected\": false\n" +
+			"            }\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"identifier\": [\n" +
+			"    {\n" +
+			"      \"system\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\",\n" +
+			"      \"value\": \"1\"\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"gender\": \"female\"\n" +
+			"}";
+
+		IParser jsonParser = ourCtx.newRDFParser();
+		IParser xmlParser = ourCtx.newXmlParser();
+		jsonParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+		xmlParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+
+		Patient parsed = jsonParser.parseResource(Patient.class, input);
+
+		ourLog.info(jsonParser.setPrettyPrint(true).encodeResourceToString(parsed));
+		assertThat(xmlParser.encodeResourceToString(parsed), containsString("Underweight"));
+		assertThat(jsonParser.encodeResourceToString(parsed), containsString("Underweight"));
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

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

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.parser;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.json.*;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.hl7.fhir.r4.model.*;
+
+import java.io.StringReader;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+@Ignore
+public class RDFParserTest {
+
+	private static FhirContext ourCtx = FhirContext.forR4();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RDFParserTest.class);
+
+   private static final String TEST_STRUCTURELOADING_DATA =
+		"{" +
+			"    \"resourceType\":\"Organization\"," +
+			"    \"id\":\"11111\"," +
+			"    \"meta\":{" +
+			"        \"lastUpdated\":\"3900-09-20T10:10:10.000-07:00\"" +
+			"    }," +
+			"    \"identifier\":[" +
+			"        {" +
+			"            \"value\":\"15250\"" +
+			"        }" +
+			"    ]," +
+			"    \"type\":{" +
+			"        \"coding\":[" +
+			"            {" +
+			"                \"system\":\"http://test\"," +
+			"                \"code\":\"ins\"," +
+			"                \"display\":\"General Ledger System\"," +
+			"                \"userSelected\":false" +
+			"            }" +
+			"        ]" +
+			"    }," +
+			"    \"name\":\"Acme Investments\"" +
+			"}";
+
+	@Test
+	public void testDontStripVersions() {
+		FhirContext ctx = FhirContext.forR4();
+		ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("QuestionnaireResponse.questionnaire");
+
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.getQuestionnaireElement().setValueAsString("Questionnaire/123/_history/456");
+
+		String output = ctx.newRDFParser().setPrettyPrint(true).encodeResourceToString(qr);
+		ourLog.info(output);
+
+		assertThat(output, containsString("\"Questionnaire/123/_history/456\""));
+	}
+
+}

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/CachingValidationSupport.java

@@ -3,15 +3,17 @@ package org.hl7.fhir.r4.hapi.validation;
 import ca.uhn.fhir.context.FhirContext;
 import com.github.benmanes.caffeine.cache.Cache;
 import com.github.benmanes.caffeine.cache.Caffeine;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 
 import java.util.List;
 import java.util.concurrent.TimeUnit;
+import java.util.function.Function;
 
 @SuppressWarnings("unchecked")
 public class CachingValidationSupport implements IValidationSupport {
@@ -21,7 +23,11 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	public CachingValidationSupport(IValidationSupport theWrap) {
 		myWrap = theWrap;
-		myCache = Caffeine.newBuilder().expireAfterWrite(60, TimeUnit.SECONDS).build();
+		myCache = Caffeine
+			.newBuilder()
+			.expireAfterWrite(60, TimeUnit.SECONDS)
+			.maximumSize(5000)
+			.build();
 	}
 
 	@Override
@@ -31,14 +37,14 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	@Override
 	public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
-		return (List<IBaseResource>) myCache.get("fetchAllConformanceResources",
+		String key = "fetchAllConformanceResources";
-			t -> myWrap.fetchAllConformanceResources(theContext));
+		return loadFromCache(key, t -> myWrap.fetchAllConformanceResources(theContext));
 	}
 
 	@Override
 	public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
-		return (List<StructureDefinition>) myCache.get("fetchAllStructureDefinitions",
+		String key = "fetchAllStructureDefinitions";
-			t -> myWrap.fetchAllStructureDefinitions(theContext));
+		return loadFromCache(key, t -> myWrap.fetchAllStructureDefinitions(theContext));
 	}
 
 	@Override
@@ -63,7 +69,8 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	@Override
 	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
-		return myWrap.isCodeSystemSupported(theContext, theSystem);
+		String key = "isCodeSystemSupported " + theSystem;
+		return loadFromCache(key, t -> myWrap.isCodeSystemSupported(theContext, theSystem));
 	}
 
 	@Override
@@ -73,11 +80,18 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	@Override
 	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
-		return myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay);
+		String key = "validateCode " + theCodeSystem + " " + theCode;
+		return loadFromCache(key, t -> myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay));
 	}
 
 	@Override
 	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
-		return myWrap.lookupCode(theContext, theSystem, theCode);
+		String key = "lookupCode " + theSystem + " " + theCode;
+		return loadFromCache(key, t -> myWrap.lookupCode(theContext, theSystem, theCode));
+	}
+
+	@Nullable
+	private <T> T loadFromCache(String theKey, Function<String, T> theLoader) {
+		return (T) myCache.get(theKey, theLoader);
 	}
 }

pom.xml

@@ -530,6 +530,15 @@
 			<id>gteichrow</id>
 			<name>Gary Teichrow</name>
 		</developer>
+		<developer>
+			<id>sethrylan</id>
+			<name>Seth Rylan Gainey</name>
+			<url>http://sethrylan.org/</url>
+		</developer>
+		<developer>
+			<id>uurl</id>
+			<name>Raul Estrada</name>
+		</developer>
 	</developers>
 
 	<licenses>
@@ -971,6 +980,12 @@
 				<artifactId>httpcore</artifactId>
 				<version>${httpcore_version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.apache.jena</groupId>
+				<artifactId>apache-jena-libs</artifactId>
+				<version>3.12.0</version>
+				<type>pom</type>
+			</dependency>
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
 				<artifactId>lucene-highlighter</artifactId>

src/changes/changes.xml

@@ -79,6 +79,11 @@
 				</li>The rule list is now cached on a per-request basis, which should improve performance</ul>
 				]]>
 			</action>
+			<action type="add" issue="1321">
+				Support has been added for RDF encoding and parsing in the
+				<![CDATA[<a href="https://www.hl7.org/fhir/rdf.html#instance">Turtle</a>]]>
+				format. Thanks to Raul Estrada for the pull request!
+			</action>
 			<action type="add">
 				The $expunge global everything operation has been refactored to do deletes
 				in small batches. This change will likely reduce performance, but does allow
@@ -354,6 +359,16 @@
 				type for an operation declared on a plain provider without needing to use 
 				a specific version of the FHIR structures.
 			</action>
+			<action type="add">
+				The $upload-external-code-system operation and the corresponding HAPI FHIR CLI command
+				can now be used to upload custom vocabulary that has been converted into a standard file format
+				defined by HAPI FHIR. This is useful for uploading large organizational code systems.
+			</action>
+			<action type="fix" issue="1404">
+				In the JAX-RS server, the resource type history and instance vread
+				operations had ambiguous paths that could lead to the wrong method
+				being called. Thanks to Seth Rylan Gainey for the pull request!
+			</action>
 		</release>
 		<release version="3.8.0" date="2019-05-30" description="Hippo">
 			<action type="fix">