Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks

# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java

@@ -1401,6 +1401,41 @@ public enum Pointcut {
 		"ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails"
 	),
 
+	/**
+	 * Invoked when the storage engine is about to reuse the results of
+	 * a previously cached search.
+	 * <p>
+	 * Hooks may accept the following parameters:
+	 * </p>
+	 * <ul>
+	 * <li>
+	 * ca.uhn.fhir.jpa.searchparam.SearchParameterMap - Contains the details of the search being checked
+	 * </li>
+	 * <li>
+	 * ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that is about to be processed, including details such as the
+	 * resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
+	 * pulled out of the servlet request. Note that the bean
+	 * properties are not all guaranteed to be populated, depending on how early during processing the
+	 * exception occurred. <b>Note that this parameter may be null in contexts where the request is not
+	 * known, such as while processing searches</b>
+	 * </li>
+	 * <li>
+	 * ca.uhn.fhir.rest.server.servlet.ServletRequestDetails - A bean containing details about the request that is about to be processed, including details such as the
+	 * resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
+	 * pulled out of the servlet request. This parameter is identical to the RequestDetails parameter above but will
+	 * only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
+	 * </li>
+	 * </ul>
+	 * <p>
+	 * Hooks should return <code>void</code>.
+	 * </p>
+	 */
+	JPA_PERFTRACE_SEARCH_REUSING_CACHED(boolean.class,
+		"ca.uhn.fhir.jpa.searchparam.SearchParameterMap",
+		"ca.uhn.fhir.rest.api.server.RequestDetails",
+		"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"
+	),
+
 	/**
 	 * Note that this is a performance tracing hook. Use with caution in production
 	 * systems, since calling it may (or may not) carry a cost.

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

@@ -34,6 +34,7 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.hl7.fhir.instance.model.api.*;
 
+import javax.annotation.Nullable;
 import java.io.*;
 import java.lang.reflect.Modifier;
 import java.util.*;
@@ -65,6 +66,7 @@ public abstract class BaseParser implements IParser {
 	private boolean mySummaryMode;
 	private boolean mySuppressNarratives;
 	private Set<String> myDontStripVersionsFromReferencesAtPaths;
+
 	/**
 	 * Constructor
 	 */
@@ -165,8 +167,6 @@ public abstract class BaseParser implements IParser {
 								myNext = null;
 							} else if (!myNext.shouldBeEncoded(theContainedResource)) {
 								myNext = null;
-							} else if (isSummaryMode() && !myNext.getDef().isSummary()) {
-								myNext = null;
 							} else if (myNext.getDef() instanceof RuntimeChildNarrativeDefinition) {
 								if (isSuppressNarratives() || isSummaryMode()) {
 									myNext = null;
@@ -1004,7 +1004,7 @@ public abstract class BaseParser implements IParser {
 		private final RuntimeResourceDefinition myResDef;
 		private final EncodeContext myEncodeContext;
 
-		public CompositeChildElement(CompositeChildElement theParent, BaseRuntimeChildDefinition theDef, EncodeContext theEncodeContext) {
+		public CompositeChildElement(CompositeChildElement theParent, @Nullable BaseRuntimeChildDefinition theDef, EncodeContext theEncodeContext) {
 			myDef = theDef;
 			myParent = theParent;
 			myResDef = null;
@@ -1015,7 +1015,9 @@ public abstract class BaseParser implements IParser {
 					StringBuilder path = theParent.buildPath();
 					if (path != null) {
 						path.append('.');
+						if (myDef != null) {
 							path.append(myDef.getElementName());
+						}
 						ourLog.trace(" * Next path: {}", path.toString());
 					}
 				}
@@ -1165,6 +1167,21 @@ public abstract class BaseParser implements IParser {
 			if (theContainedResource) {
 				retVal = !notEncodeForContainedResource.contains(myDef.getElementName());
 			}
+			if (retVal && isSummaryMode() && (getDef() == null || !getDef().isSummary())) {
+				String resourceName = myEncodeContext.getLeafResourceName();
+				// Technically the spec says we shouldn't include extensions in CapabilityStatement
+				// but we will do so because there are people who depend on this behaviour, at least
+				// as of 2019-07. See
+				// https://github.com/smart-on-fhir/Swift-FHIR/issues/26
+				// for example.
+				if (("Conformance".equals(resourceName) || "CapabilityStatement".equals(resourceName)) &&
+					("extension".equals(myDef.getElementName()) || "extension".equals(myEncodeContext.getLeafElementName())
+					)) {
+					// skip
+				} else {
+					retVal = false;
+				}
+			}
 
 			return retVal;
 		}
@@ -1251,6 +1268,14 @@ public abstract class BaseParser implements IParser {
 			return myResourcePath;
 		}
 
+		public String getLeafElementName() {
+			return getPath().get(getPath().size() - 1).getName();
+		}
+
+		public String getLeafResourceName() {
+			return myResourcePath.get(myResourcePath.size() - 1).getName();
+		}
+
 		public String getLeafResourcePathFirstField() {
 			String retVal = null;
 			for (int i = getPath().size() - 1; i >= 0; i--) {

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

@@ -80,7 +80,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				theListToAddTo.add(null);
 			}
 			if (theListToAddTo.get(valueIdx) == null) {
-				theListToAddTo.set(valueIdx, new ArrayList<String>());
+				theListToAddTo.set(valueIdx, new ArrayList<>());
 			}
 			theListToAddTo.get(valueIdx).addAll(theCommentsToAdd);
 			return true;
@@ -89,21 +89,34 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem,
-													CompositeChildElement theParent) {
+													CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theContainingElement) {
+		boolean retVal = false;
 		if (ext.size() > 0) {
+			Boolean encodeExtension = null;
+			for (IBaseExtension<?, ?> next : ext) {
+
+				// Make sure we respect _summary and _elements
+				if (encodeExtension == null) {
+					encodeExtension = isEncodeExtension(theParent, theEncodeContext, theContainedResource, theContainingElement);
+				}
+
+				if (encodeExtension) {
+					HeldExtension extension = new HeldExtension(next, theIsModifier, theChildElem, theParent);
 					list.ensureCapacity(valueIdx);
 					while (list.size() <= valueIdx) {
 						list.add(null);
 					}
-			if (list.get(valueIdx) == null) {
+					ArrayList<HeldExtension> extensionList = list.get(valueIdx);
-				list.set(valueIdx, new ArrayList<JsonParser.HeldExtension>());
+					if (extensionList == null) {
+						extensionList = new ArrayList<>();
+						list.set(valueIdx, extensionList);
 					}
-			for (IBaseExtension<?, ?> next : ext) {
+					extensionList.add(extension);
-				list.get(valueIdx).add(new HeldExtension(next, theIsModifier, theChildElem, theParent));
+					retVal = true;
 				}
-			return true;
 			}
-		return false;
+		}
+		return retVal;
 	}
 
 	private void addToHeldIds(int theValueIdx, ArrayList<String> theListToAddTo, String theId) {
@@ -342,7 +355,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			if (nextChildElem.getDef().getElementName().equals("extension") || nextChildElem.getDef().getElementName().equals("modifierExtension")
 				|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
 				if (!haveWrittenExtensions) {
-					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent, theEncodeContext);
+					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent, theEncodeContext, theContainedResource);
 					haveWrittenExtensions = true;
 				}
 				continue;
@@ -433,20 +446,20 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				if (primitive) {
 					if (nextValue instanceof ISupportsUndeclaredExtensions) {
 						List<ExtensionDt> ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredExtensions();
-						force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent);
+						force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
 
 						ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredModifierExtensions();
-						force |= addToHeldExtensions(valueIdx, ext, modifierExtensions, true, nextChildElem, theParent);
+						force |= addToHeldExtensions(valueIdx, ext, modifierExtensions, true, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
 					} else {
 						if (nextValue instanceof IBaseHasExtensions) {
 							IBaseHasExtensions element = (IBaseHasExtensions) nextValue;
 							List<? extends IBaseExtension<?, ?>> ext = element.getExtension();
-							force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent);
+							force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
 						}
 						if (nextValue instanceof IBaseHasModifierExtensions) {
 							IBaseHasModifierExtensions element = (IBaseHasModifierExtensions) nextValue;
 							List<? extends IBaseExtension<?, ?>> ext = element.getModifierExtension();
-							force |= addToHeldExtensions(valueIdx, ext, extensions, true, nextChildElem, theParent);
+							force |= addToHeldExtensions(valueIdx, ext, extensions, true, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
 						}
 					}
 					if (nextValue.hasFormatComment()) {
@@ -486,6 +499,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				theEventWriter.endArray();
 			}
 
+
 			if (!extensions.isEmpty() || !modifierExtensions.isEmpty() || !comments.isEmpty()) {
 				if (inArray) {
 					// If this is a repeatable field, the extensions go in an array too
@@ -541,7 +555,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 							}
 							theEventWriter.endArray();
 						}
-						writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, heldExts, heldModExts, theEncodeContext);
+						writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, heldExts, heldModExts, theEncodeContext, theContainedResource);
 						if (inArray) {
 							theEventWriter.endObject();
 						}
@@ -626,7 +640,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			final List<HeldExtension> extensions = new ArrayList<>(0);
 			final List<HeldExtension> modifierExtensions = new ArrayList<>(0);
 			// Undeclared extensions
-			extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
+			extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null, theEncodeContext, theContainedResource);
 			boolean haveExtension = false;
 			if (!extensions.isEmpty()) {
 				haveExtension = true;
@@ -638,7 +652,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					writeCommentsPreAndPost(theResourceId, theEventWriter);
 				}
 				if (haveExtension) {
-					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
+					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext, theContainedResource);
 				}
 				theEventWriter.endObject();
 			}
@@ -741,12 +755,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	 * called _name): resource extensions, and extension extensions
 	 */
 	private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef,
-																		 IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent, EncodeContext theEncodeContext) throws IOException {
+																		 IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
 		List<HeldExtension> extensions = new ArrayList<>(0);
 		List<HeldExtension> modifierExtensions = new ArrayList<>(0);
 
 		// Undeclared extensions
-		extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem, theParent);
+		extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem, theParent, theEncodeContext, theContainedResource);
 
 		// Declared extensions
 		if (theElementDef != null) {
@@ -754,7 +768,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 
 		// Write the extensions
-		writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
+		writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext, theContainedResource);
 	}
 
 	private void extractDeclaredExtensions(IBase theResource, BaseRuntimeElementDefinition<?> resDef, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions,
@@ -782,7 +796,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void extractUndeclaredExtensions(IBase theElement, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions, CompositeChildElement theChildElem,
-														  CompositeChildElement theParent) {
+														  CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource) {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
 			ISupportsUndeclaredExtensions element = (ISupportsUndeclaredExtensions) theElement;
 			List<ExtensionDt> ext = element.getUndeclaredExtensions();
@@ -804,11 +818,21 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			if (theElement instanceof IBaseHasExtensions) {
 				IBaseHasExtensions element = (IBaseHasExtensions) theElement;
 				List<? extends IBaseExtension<?, ?>> ext = element.getExtension();
+				Boolean encodeExtension = null;
 				for (IBaseExtension<?, ?> next : ext) {
 					if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
 						continue;
 					}
-					extensions.add(new HeldExtension(next, false, theChildElem, theParent));
+
+					// Make sure we respect _elements and _summary
+					if (encodeExtension == null) {
+						encodeExtension = isEncodeExtension(theParent, theEncodeContext, theContainedResource, element);
+					}
+					if (encodeExtension) {
+						HeldExtension extension = new HeldExtension(next, false, theChildElem, theParent);
+						extensions.add(extension);
+					}
+
 				}
 			}
 			if (theElement instanceof IBaseHasModifierExtensions) {
@@ -818,12 +842,28 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					if (next == null || next.isEmpty()) {
 						continue;
 					}
-					modifierExtensions.add(new HeldExtension(next, true, theChildElem, theParent));
+
+					HeldExtension extension = new HeldExtension(next, true, theChildElem, theParent);
+					modifierExtensions.add(extension);
 				}
 			}
 		}
 	}
 
+	private boolean isEncodeExtension(CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theElement) {
+//		theEncodeContext.pushPath("extension", false);
+		BaseRuntimeElementDefinition<?> runtimeElementDefinition = myContext.getElementDefinition(theElement.getClass());
+		boolean retVal = true;
+		if (runtimeElementDefinition instanceof BaseRuntimeElementCompositeDefinition) {
+			BaseRuntimeElementCompositeDefinition definition = (BaseRuntimeElementCompositeDefinition) runtimeElementDefinition;
+			BaseRuntimeChildDefinition childDef = definition.getChildByName("extension");
+			CompositeChildElement c = new CompositeChildElement(theParent, childDef, theEncodeContext);
+			retVal = c.shouldBeEncoded(theContainedResource);
+		}
+//		theEncodeContext.popPath();
+		return retVal;
+	}
+
 	@Override
 	public EncodingEnum getEncoding() {
 		return EncodingEnum.JSON;
@@ -1275,21 +1315,24 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void writeExtensionsAsDirectChild(IBaseResource theResource, JsonLikeWriter theEventWriter, RuntimeResourceDefinition resDef, List<HeldExtension> extensions,
-															List<HeldExtension> modifierExtensions, EncodeContext theEncodeContext) throws IOException {
+															List<HeldExtension> modifierExtensions, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
+		// Write Extensions
 		if (extensions.isEmpty() == false) {
 			theEncodeContext.pushPath("extension", false);
 			beginArray(theEventWriter, "extension");
 			for (HeldExtension next : extensions) {
-				next.write(resDef, theResource, theEventWriter, theEncodeContext);
+				next.write(resDef, theResource, theEventWriter, theEncodeContext, theContainedResource);
 			}
 			theEventWriter.endArray();
 			theEncodeContext.popPath();
 		}
+
+		// Write ModifierExtensions
 		if (modifierExtensions.isEmpty() == false) {
 			theEncodeContext.pushPath("modifierExtension", false);
 			beginArray(theEventWriter, "modifierExtension");
 			for (HeldExtension next : modifierExtensions) {
-				next.write(resDef, theResource, theEventWriter, theEncodeContext);
+				next.write(resDef, theResource, theEventWriter, theEncodeContext, theContainedResource);
 			}
 			theEventWriter.endArray();
 			theEncodeContext.popPath();
@@ -1353,12 +1396,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			return url1.compareTo(url2);
 		}
 
-		private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName, EncodeContext theEncodeContext) throws IOException {
+		private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
 			if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
 				final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
 				final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
 				// Undeclared extensions
-				extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
+				extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null, theEncodeContext, theContainedResource);
 				// Declared extensions
 				if (def != null) {
 					extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
@@ -1369,15 +1412,15 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				}
 				if (haveContent) {
 					beginObject(theEventWriter, '_' + childName);
-					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
+					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext, theContainedResource);
 					theEventWriter.endObject();
 				}
 			}
 		}
 
-		public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, EncodeContext theEncodeContext) throws IOException {
+		public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
 			if (myUndeclaredExtension != null) {
-				writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension, theEncodeContext);
+				writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension, theEncodeContext, theContainedResource);
 			} else {
 				theEventWriter.beginObject();
 
@@ -1410,18 +1453,18 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 				BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());
 				if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) {
-					extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null, theEncodeContext);
+					extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null, theEncodeContext, theContainedResource);
 				} else {
 					String childName = myDef.getChildNameByDatatype(myValue.getClass());
 					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false,  myParent, false, theEncodeContext);
-					managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName, theEncodeContext);
+					managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName, theEncodeContext, theContainedResource);
 				}
 
 				theEventWriter.endObject();
 			}
 		}
 
-		private void writeUndeclaredExtension(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBaseExtension<?, ?> ext, EncodeContext theEncodeContext) throws IOException {
+		private void writeUndeclaredExtension(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBaseExtension<?, ?> ext, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
 			IBase value = ext.getValue();
 			final String extensionUrl = getExtensionUrl(ext.getUrl());
 
@@ -1465,7 +1508,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					}
 
 					for (Object next : ext.getExtension()) {
-						writeUndeclaredExtension(theResDef, theResource, theEventWriter, (IBaseExtension<?, ?>) next, theEncodeContext);
+						writeUndeclaredExtension(theResDef, theResource, theEventWriter, (IBaseExtension<?, ?>) next, theEncodeContext, theContainedResource);
 					}
 					theEventWriter.endArray();
 
@@ -1473,6 +1516,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 				// Write value
 				if (!noValue) {
+					theEncodeContext.pushPath("value", false);
 
 					/*
 					 * Pre-process value - This is called in case the value is a reference
@@ -1490,8 +1534,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 						throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
 					}
 					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, false, myParent,false, theEncodeContext);
-					managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName, theEncodeContext);
+					managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName, theEncodeContext, theContainedResource);
 
+					theEncodeContext.popPath();
 				}
 			}
 

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

@@ -51,15 +51,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * This class is the FHIR XML parser/encoder. Users should not interact with this class directly, but should use
  * {@link FhirContext#newXmlParser()} to get an instance.
  */
-public class XmlParser extends BaseParser /* implements IParser */ {
+public class XmlParser extends BaseParser {
 
-	static final String ATOM_NS = "http://www.w3.org/2005/Atom";
 	static final String FHIR_NS = "http://hl7.org/fhir";
-	static final String OPENSEARCH_NS = "http://a9.com/-/spec/opensearch/1.1/";
-	static final String RESREF_DISPLAY = "display";
-	static final String RESREF_REFERENCE = "reference";
-	static final String TOMBSTONES_NS = "http://purl.org/atompub/tombstones/1.0";
-	static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
 
 	// private static final Set<String> RESOURCE_NAMESPACES;

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

@@ -23,7 +23,7 @@ package ca.uhn.fhir.util;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.*;
 
 public class ValidateUtil {
 
@@ -37,7 +37,7 @@ public class ValidateUtil {
 	}
 
 	/**
-	 * Throws {@link IllegalArgumentException} if theValue is <= theMinimum
+	 * Throws {@link IllegalArgumentException} if theValue is < theMinimum
 	 */
 	public static void isGreaterThanOrEqualTo(long theValue, long theMinimum, String theMessage) {
 		if (theValue < theMinimum) {
@@ -45,6 +45,12 @@ public class ValidateUtil {
 		}
 	}
 
+	public static void isNotBlankOrThrowIllegalArgument(String theString, String theMessage) {
+		if (isBlank(theString)) {
+			throw new IllegalArgumentException(theMessage);
+		}
+	}
+
 	public static void isNotBlankOrThrowInvalidRequest(String theString, String theMessage) {
 		if (isBlank(theString)) {
 			throw new InvalidRequestException(theMessage);
@@ -57,6 +63,12 @@ public class ValidateUtil {
 		}
 	}
 
+	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) {
 		if (theSuccess == false) {
 			throw new InvalidRequestException(theMessage);

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseHasExtensions.java

@@ -22,7 +22,7 @@ package org.hl7.fhir.instance.model.api;
 
 import java.util.List;
 
-public interface IBaseHasExtensions {
+public interface IBaseHasExtensions extends IBase {
 
 	IBaseExtension<?, ?> addExtension();
 

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -115,8 +115,9 @@ ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor.noParam=Note that cascadi
 
 ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
 
+ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
 ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
 ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
 
 ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

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

@@ -145,6 +145,10 @@ public class DaoConfig {
 	private boolean myEnableInMemorySubscriptionMatching = true;
 	private boolean myEnforceReferenceTargetTypes = true;
 	private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
+	/**
+	 * EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
+	 */
+	private boolean myPreExpandValueSetsExperimental = false;
 
 	/**
 	 * Constructor
@@ -1600,6 +1604,34 @@ public class DaoConfig {
 		myModelConfig.setWebsocketContextPath(theWebsocketContextPath);
 	}
 
+	/**
+	 * EXPERIMENTAL - Do not use in production!
+	 * <p>
+	 * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
+	 * future optimization of the $expand operation on large ValueSets.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}.
+	 * </p>
+	 */
+	public boolean isPreExpandValueSetsExperimental() {
+		return myPreExpandValueSetsExperimental;
+	}
+
+	/**
+	 * EXPERIMENTAL - Do not use in production!
+	 * <p>
+	 * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
+	 * future optimization of the $expand operation on large ValueSets.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}.
+	 * </p>
+	 */
+	public void setPreExpandValueSetsExperimental(boolean thePreExpandValueSetsExperimental) {
+		myPreExpandValueSetsExperimental = thePreExpandValueSetsExperimental;
+	}
+
 	public enum IndexEnabledEnum {
 		ENABLED,
 		DISABLED

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

@@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.entity.ResourceSearchView;
 import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
 import ca.uhn.fhir.jpa.model.entity.*;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
+import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
 import ca.uhn.fhir.jpa.model.util.StringNormalizer;
 import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
@@ -60,7 +61,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.UrlUtil;
-import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
@@ -113,10 +113,6 @@ public class SearchBuilder implements ISearchBuilder {
 	 */
 	private static final int MAXIMUM_PAGE_SIZE = 800;
 	private static Long NO_MORE = -1L;
-	private static HandlerTypeEnum ourLastHandlerMechanismForUnitTest;
-	private static SearchParameterMap ourLastHandlerParamsForUnitTest;
-	private static String ourLastHandlerThreadForUnitTest;
-	private static boolean ourTrackHandlersForUnitTest;
 	private final boolean myDontUseHashesForSearch;
 	private final DaoConfig myDaoConfig;
 	@Autowired
@@ -1546,12 +1542,6 @@ public class SearchBuilder implements ISearchBuilder {
 		myBuilder = myEntityManager.getCriteriaBuilder();
 		mySearchUuid = theSearchRuntimeDetails.getSearchUuid();
 
-		if (ourTrackHandlersForUnitTest) {
-			ourLastHandlerParamsForUnitTest = theParams;
-			ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.STANDARD_QUERY;
-			ourLastHandlerThreadForUnitTest = Thread.currentThread().getName();
-		}
-
 		if (myPidSet == null) {
 			myPidSet = new HashSet<>();
 		}
@@ -2214,9 +2204,16 @@ public class SearchBuilder implements ISearchBuilder {
 				if (sb != null) {
 					String indexString = sb.toString();
 					ourLog.debug("Checking for unique index for query: {}", indexString);
-					if (ourTrackHandlersForUnitTest) {
+
-						ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.UNIQUE_INDEX;
+					// Interceptor broadcast: JPA_PERFTRACE_INFO
-					}
+					StorageProcessingMessage msg = new StorageProcessingMessage()
+						.setMessage("Using unique index for query for search: " + indexString);
+					HookParams params = new HookParams()
+						.add(RequestDetails.class, theRequest)
+						.addIfMatchesType(ServletRequestDetails.class, theRequest)
+						.add(StorageProcessingMessage.class, msg);
+					JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.JPA_PERFTRACE_INFO, params);
+
 					addPredicateCompositeStringUnique(theParams, indexString);
 				}
 			}
@@ -2788,24 +2785,6 @@ public class SearchBuilder implements ISearchBuilder {
 		return query.getResultList();
 	}
 
-	@VisibleForTesting
-	public static HandlerTypeEnum getLastHandlerMechanismForUnitTest() {
-		return ourLastHandlerMechanismForUnitTest;
-	}
-
-	@VisibleForTesting
-	public static String getLastHandlerParamsForUnitTest() {
-		return ourLastHandlerParamsForUnitTest.toString() + " on thread [" + ourLastHandlerThreadForUnitTest + "]";
-	}
-
-	@VisibleForTesting
-	public static void resetLastHandlerMechanismForUnitTest() {
-		ourLastHandlerMechanismForUnitTest = null;
-		ourLastHandlerParamsForUnitTest = null;
-		ourLastHandlerThreadForUnitTest = null;
-		ourTrackHandlersForUnitTest = true;
-	}
-
 	private static Predicate[] toArray(List<Predicate> thePredicates) {
 		return thePredicates.toArray(new Predicate[0]);
 	}

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

@@ -34,7 +34,7 @@ public interface ITermCodeSystemDao  extends JpaRepository<TermCodeSystem, Long>
 	TermCodeSystem findByCodeSystemUri(@Param("code_system_uri") String theCodeSystemUri);
 
 	@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myResourcePid = :resource_pid")
-	TermCodeSystem findByResourcePid(@Param("resource_pid") Long theReourcePid);
+	TermCodeSystem findByResourcePid(@Param("resource_pid") Long theResourcePid);
 
 	@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myCurrentVersion.myId = :csv_pid")
 	Optional<TermCodeSystem> findWithCodeSystemVersionAsCurrentVersion(@Param("csv_pid") Long theCodeSystemVersionPid);

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

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+/*
+ * #%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.TermValueSetCode;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+public interface ITermValueSetCodeDao extends JpaRepository<TermValueSetCode, Long> {
+
+	@Query("DELETE FROM TermValueSetCode vsc WHERE vsc.myValueSet.myId = :pid")
+	@Modifying
+	void deleteTermValueSetCodesByValueSetId(@Param("pid") Long theValueSetId);
+
+}

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

@@ -0,0 +1,43 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+/*
+ * #%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.TermValueSet;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+import java.util.Optional;
+
+public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
+
+	@Query("DELETE FROM TermValueSet vs WHERE vs.myId = :pid")
+	@Modifying
+	void deleteTermValueSetById(@Param("pid") Long theId);
+
+	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myResourcePid = :resource_pid")
+	Optional<TermValueSet> findByResourcePid(@Param("resource_pid") Long theResourcePid);
+
+	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url")
+	Optional<TermValueSet> findByUrl(@Param("url") String theUrl);
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java

@@ -23,11 +23,15 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 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.util.ElementUtil;
 import org.apache.commons.codec.binary.StringUtils;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.dstu3.model.*;
@@ -37,6 +41,8 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.slf4j.Logger;
@@ -45,14 +51,18 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 
 import java.util.Collections;
+import java.util.Date;
 import java.util.List;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
-
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
+
+	@Autowired
+	private IHapiTerminologySvc myHapiTerminologySvc;
+
 	@Autowired
 	@Qualifier("myJpaValidationSupportChainDstu3")
 	private IValidationSupport myValidationSupport;
@@ -295,4 +305,26 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 		// nothing
 	}
 
+	@Override
+	protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
+
+		if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+			if (retVal.getDeleted() == null) {
+				try {
+					ValueSet valueSet = (ValueSet) theResource;
+					org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
+					myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, converted);
+				} catch (FHIRException fe) {
+					throw new InternalErrorException(fe);
+				}
+			} else {
+				myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
+			}
+		}
+
+		return retVal;
+	}
+
 }

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

@@ -96,6 +96,8 @@ public class ExpungeEverythingService {
 		counter.addAndGet(expungeEverythingByType(ResourceLink.class));
 		counter.addAndGet(expungeEverythingByType(SearchResult.class));
 		counter.addAndGet(expungeEverythingByType(SearchInclude.class));
+		counter.addAndGet(expungeEverythingByType(TermValueSetCode.class));
+		counter.addAndGet(expungeEverythingByType(TermValueSet.class));
 		counter.addAndGet(expungeEverythingByType(TermConceptParentChildLink.class));
 		counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElementTarget.class));
 		counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElement.class));

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

@@ -57,6 +57,14 @@ public class IdHelperService {
 		myForcedIdDao.delete(forcedId);
 	}
 
+	/**
+	 * @throws ResourceNotFoundException If the ID can not be found
+	 */
+	@Nonnull
+	public Long translateForcedIdToPid(IIdType theId, RequestDetails theRequestDetails) {
+		return translateForcedIdToPid(theId.getResourceType(), theId.getIdPart(), theRequestDetails);
+	}
+
 	/**
 	 * @throws ResourceNotFoundException If the ID can not be found
 	 */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java

@@ -20,34 +20,43 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.util.Collections;
-import java.util.List;
-
-import org.apache.commons.codec.binary.StringUtils;
-import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
-import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
-import org.hl7.fhir.r4.model.ValueSet.*;
-import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.ElementUtil;
+import org.apache.commons.codec.binary.StringUtils;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
+import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
+import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
+import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
+import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 
+	@Autowired
+	private IHapiTerminologySvc myHapiTerminologySvc;
+
 	@Autowired
 	@Qualifier("myJpaValidationSupportChainR4")
 	private IValidationSupport myValidationSupport;
@@ -296,4 +305,21 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
 		// nothing
 	}
 
+	@Override
+	protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
+
+		if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+			if (retVal.getDeleted() == null) {
+				ValueSet valueSet = (ValueSet) theResource;
+				myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, valueSet);
+			} else {
+				myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
+			}
+		}
+
+		return retVal;
+	}
+
 }

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

@@ -21,13 +21,16 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 
 import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
 
 //@formatter:off
 @Table(name = "TRM_CODESYSTEM", uniqueConstraints = {
@@ -37,9 +40,11 @@ import static org.apache.commons.lang3.StringUtils.left;
 //@formatter:on
 public class TermCodeSystem implements Serializable {
 	private static final long serialVersionUID = 1L;
-	public static final int CS_NAME_LENGTH = 200;
 
-	@Column(name = "CODE_SYSTEM_URI", nullable = false)
+	private static final int MAX_NAME_LENGTH = 200;
+	public static final int MAX_URL_LENGTH = 200;
+
+	@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
 	private String myCodeSystemUri;
 
 	@OneToOne()
@@ -55,7 +60,7 @@ public class TermCodeSystem implements Serializable {
 	private ResourceTable myResource;
 	@Column(name = "RES_ID", insertable = false, updatable = false)
 	private Long myResourcePid;
-	@Column(name = "CS_NAME", nullable = true)
+	@Column(name = "CS_NAME", nullable = true, length = MAX_NAME_LENGTH)
 	private String myName;
 
 	public String getCodeSystemUri() {
@@ -66,16 +71,21 @@ public class TermCodeSystem implements Serializable {
 		return myName;
 	}
 
-	public void setCodeSystemUri(String theCodeSystemUri) {
+	public TermCodeSystem setCodeSystemUri(@Nonnull String theCodeSystemUri) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theCodeSystemUri, "theCodeSystemUri must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCodeSystemUri, MAX_URL_LENGTH,
+			"URI exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theCodeSystemUri));
 		myCodeSystemUri = theCodeSystemUri;
+		return this;
 	}
 
 	public TermCodeSystemVersion getCurrentVersion() {
 		return myCurrentVersion;
 	}
 
-	public void setCurrentVersion(TermCodeSystemVersion theCurrentVersion) {
+	public TermCodeSystem setCurrentVersion(TermCodeSystemVersion theCurrentVersion) {
 		myCurrentVersion = theCurrentVersion;
+		return this;
 	}
 
 	public Long getPid() {
@@ -86,12 +96,14 @@ public class TermCodeSystem implements Serializable {
 		return myResource;
 	}
 
-	public void setName(String theName) {
+	public TermCodeSystem setName(String theName) {
-		myName = left(theName, CS_NAME_LENGTH);
+		myName = left(theName, MAX_NAME_LENGTH);
+		return this;
 	}
 
-	public void setResource(ResourceTable theResource) {
+	public TermCodeSystem setResource(ResourceTable theResource) {
 		myResource = theResource;
+		return this;
 	}
 
 	@Override

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

@@ -22,12 +22,15 @@ package ca.uhn.fhir.jpa.entity;
 
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.util.CoverageIgnore;
+import ca.uhn.fhir.util.ValidateUtil;
 
 import javax.persistence.*;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 
+import static org.apache.commons.lang3.StringUtils.length;
+
 //@formatter:off
 @Table(name = "TRM_CODESYSTEM_VER"
 	// Note, we used to have a constraint named IDX_CSV_RESOURCEPID_AND_VER (don't reuse this)
@@ -37,6 +40,8 @@ import java.util.Collection;
 public class TermCodeSystemVersion implements Serializable {
 	private static final long serialVersionUID = 1L;
 
+	static final int MAX_VERSION_LENGTH = 200;
+
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")
 	private Collection<TermConcept> myConcepts;
 
@@ -50,7 +55,7 @@ public class TermCodeSystemVersion implements Serializable {
 	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
 	private ResourceTable myResource;
 
-	@Column(name = "CS_VERSION_ID", nullable = true, updatable = false)
+	@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
 	private String myCodeSystemVersionId;
 	/**
 	 * This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
@@ -104,16 +109,21 @@ public class TermCodeSystemVersion implements Serializable {
 		return myCodeSystem;
 	}
 
-	public void setCodeSystem(TermCodeSystem theCodeSystem) {
+	public TermCodeSystemVersion setCodeSystem(TermCodeSystem theCodeSystem) {
 		myCodeSystem = theCodeSystem;
+		return this;
 	}
 
 	public String getCodeSystemVersionId() {
 		return myCodeSystemVersionId;
 	}
 
-	public void setCodeSystemVersionId(String theCodeSystemVersionId) {
+	public TermCodeSystemVersion setCodeSystemVersionId(String theCodeSystemVersionId) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(
+			theCodeSystemVersionId, MAX_VERSION_LENGTH,
+			"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemVersionId));
 		myCodeSystemVersionId = theCodeSystemVersionId;
+		return this;
 	}
 
 	public Collection<TermConcept> getConcepts() {
@@ -131,8 +141,9 @@ public class TermCodeSystemVersion implements Serializable {
 		return myResource;
 	}
 
-	public void setResource(ResourceTable theResource) {
+	public TermCodeSystemVersion setResource(ResourceTable theResource) {
 		myResource = theResource;
+		return this;
 	}
 
 	@Override

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

@@ -1,25 +1,5 @@
 package ca.uhn.fhir.jpa.entity;
 
-import ca.uhn.fhir.context.support.IContextValidationSupport;
-import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
-import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
-import ca.uhn.fhir.util.ValidateUtil;
-import org.apache.commons.lang3.Validate;
-import org.apache.commons.lang3.builder.EqualsBuilder;
-import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.apache.commons.lang3.builder.ToStringBuilder;
-import org.apache.commons.lang3.builder.ToStringStyle;
-import org.hibernate.search.annotations.*;
-import org.hl7.fhir.r4.model.Coding;
-
-import javax.annotation.Nonnull;
-import javax.persistence.*;
-import javax.persistence.Index;
-import java.io.Serializable;
-import java.util.*;
-
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -40,6 +20,27 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
+import ca.uhn.fhir.util.ValidateUtil;
+import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hibernate.search.annotations.*;
+import org.hl7.fhir.r4.model.Coding;
+
+import javax.annotation.Nonnull;
+import javax.persistence.Index;
+import javax.persistence.*;
+import java.io.Serializable;
+import java.util.*;
+
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Indexed(interceptor = DeferConceptIndexingInterceptor.class)
 @Table(name = "TRM_CONCEPT", uniqueConstraints = {
@@ -49,16 +50,17 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 	@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
 })
 public class TermConcept implements Serializable {
-	public static final int CODE_LENGTH = 500;
-	protected 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;
 
+	public static final int MAX_CODE_LENGTH = 500;
+	public static final int MAX_DESC_LENGTH = 400;
+
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
 	private Collection<TermConceptParentChildLink> myChildren;
 
-	@Column(name = "CODE", length = CODE_LENGTH, nullable = false)
+	@Column(name = "CODE", 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")),})
 	private String myCode;
 	@Temporal(TemporalType.TIMESTAMP)
@@ -70,7 +72,7 @@ public class TermConcept implements Serializable {
 	@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
 	@Fields({@Field(name = "myCodeSystemVersionPid")})
 	private long myCodeSystemVersionPid;
-	@Column(name = "DISPLAY", length = MAX_DESC_LENGTH, nullable = true)
+	@Column(name = "DISPLAY", nullable = true, length = MAX_DESC_LENGTH)
 	@Fields({
 		@Field(name = "myDisplay", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
 		@Field(name = "myDisplayEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
@@ -187,20 +189,24 @@ public class TermConcept implements Serializable {
 		return myCode;
 	}
 
-	public void setCode(String theCode) {
+	public TermConcept setCode(@Nonnull String theCode) {
-		ValidateUtil.isNotBlankOrThrowInvalidRequest(theCode, "Code must not be null or empty");
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, MAX_CODE_LENGTH,
+			"Code exceeds maximum length (" + MAX_CODE_LENGTH + "): " + length(theCode));
 		myCode = theCode;
+		return this;
 	}
 
 	public TermCodeSystemVersion getCodeSystemVersion() {
 		return myCodeSystem;
 	}
 
-	public void setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
+	public TermConcept setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
 		myCodeSystem = theCodeSystemVersion;
 		if (theCodeSystemVersion.getPid() != null) {
 			myCodeSystemVersionPid = theCodeSystemVersion.getPid();
 		}
+		return this;
 	}
 
 	public List<Coding> getCodingProperties(String thePropertyName) {
@@ -231,10 +237,7 @@ public class TermConcept implements Serializable {
 	}
 
 	public TermConcept setDisplay(String theDisplay) {
-		myDisplay = theDisplay;
+		myDisplay = left(theDisplay, MAX_DESC_LENGTH);
-		if (isNotBlank(theDisplay) && theDisplay.length() > MAX_DESC_LENGTH) {
-			myDisplay = myDisplay.substring(0, MAX_DESC_LENGTH);
-		}
 		return this;
 	}
 
@@ -246,8 +249,9 @@ public class TermConcept implements Serializable {
 		return myIndexStatus;
 	}
 
-	public void setIndexStatus(Long theIndexStatus) {
+	public TermConcept setIndexStatus(Long theIndexStatus) {
 		myIndexStatus = theIndexStatus;
+		return this;
 	}
 
 	public String getParentPidsAsString() {
@@ -272,8 +276,9 @@ public class TermConcept implements Serializable {
 		return mySequence;
 	}
 
-	public void setSequence(Integer theSequence) {
+	public TermConcept setSequence(Integer theSequence) {
 		mySequence = theSequence;
+		return this;
 	}
 
 	public List<String> getStringProperties(String thePropertyName) {
@@ -300,8 +305,9 @@ public class TermConcept implements Serializable {
 		return myUpdated;
 	}
 
-	public void setUpdated(Date theUpdated) {
+	public TermConcept setUpdated(Date theUpdated) {
 		myUpdated = theUpdated;
+		return this;
 	}
 
 	@Override
@@ -355,8 +361,9 @@ public class TermConcept implements Serializable {
 		myParentPids = b.toString();
 	}
 
-	public void setParentPids(String theParentPids) {
+	public TermConcept setParentPids(String theParentPids) {
 		myParentPids = theParentPids;
+		return this;
 	}
 
 	@Override

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

@@ -20,16 +20,24 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.util.ValidateUtil;
+
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Table(name = "TRM_CONCEPT_DESIG", uniqueConstraints = {
 }, indexes = {
 })
 public class TermConceptDesignation implements Serializable {
-
 	private static final long serialVersionUID = 1L;
+
+	private static final int MAX_LENGTH = 500;
+
 	@ManyToOne
 	@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CONCEPT"))
 	private TermConcept myConcept;
@@ -38,15 +46,15 @@ public class TermConceptDesignation implements Serializable {
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_DESIG_PID")
 	@Column(name = "PID")
 	private Long myId;
-	@Column(name = "LANG", length = 500, nullable = true)
+	@Column(name = "LANG", nullable = true, length = MAX_LENGTH)
 	private String myLanguage;
-	@Column(name = "USE_SYSTEM", length = 500, nullable = true)
+	@Column(name = "USE_SYSTEM", nullable = true, length = MAX_LENGTH)
 	private String myUseSystem;
-	@Column(name = "USE_CODE", length = 500, nullable = true)
+	@Column(name = "USE_CODE", nullable = true, length = MAX_LENGTH)
 	private String myUseCode;
-	@Column(name = "USE_DISPLAY", length = 500, nullable = true)
+	@Column(name = "USE_DISPLAY", nullable = true, length = MAX_LENGTH)
 	private String myUseDisplay;
-	@Column(name = "VAL", length = 500, nullable = false)
+	@Column(name = "VAL", nullable = false, length = MAX_LENGTH)
 	private String myValue;
 	/**
 	 * TODO: Make this non-null
@@ -62,6 +70,8 @@ public class TermConceptDesignation implements Serializable {
 	}
 
 	public TermConceptDesignation setLanguage(String theLanguage) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theLanguage, MAX_LENGTH,
+			"Language exceeds maximum length (" + MAX_LENGTH + "): " + length(theLanguage));
 		myLanguage = theLanguage;
 		return this;
 	}
@@ -71,6 +81,8 @@ public class TermConceptDesignation implements Serializable {
 	}
 
 	public TermConceptDesignation setUseCode(String theUseCode) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUseCode, MAX_LENGTH,
+			"Use code exceeds maximum length (" + MAX_LENGTH + "): " + length(theUseCode));
 		myUseCode = theUseCode;
 		return this;
 	}
@@ -80,7 +92,7 @@ public class TermConceptDesignation implements Serializable {
 	}
 
 	public TermConceptDesignation setUseDisplay(String theUseDisplay) {
-		myUseDisplay = theUseDisplay;
+		myUseDisplay = left(theUseDisplay, MAX_LENGTH);
 		return this;
 	}
 
@@ -89,6 +101,9 @@ public class TermConceptDesignation implements Serializable {
 	}
 
 	public TermConceptDesignation setUseSystem(String theUseSystem) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUseSystem, MAX_LENGTH,
+			"Use system exceeds maximum length (" + MAX_LENGTH + "): " + length(theUseSystem));
+
 		myUseSystem = theUseSystem;
 		return this;
 	}
@@ -97,7 +112,10 @@ public class TermConceptDesignation implements Serializable {
 		return myValue;
 	}
 
-	public TermConceptDesignation setValue(String theValue) {
+	public TermConceptDesignation setValue(@Nonnull String theValue) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theValue, "theValue must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theValue, MAX_LENGTH,
+			"Value exceeds maximum length (" + MAX_LENGTH + "): " + length(theValue));
 		myValue = theValue;
 		return this;
 	}

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

@@ -21,19 +21,27 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Table(name = "TRM_CONCEPT_MAP", uniqueConstraints = {
 	@UniqueConstraint(name = "IDX_CONCEPT_MAP_URL", columnNames = {"URL"})
 })
 public class TermConceptMap implements Serializable {
+	private static final long serialVersionUID = 1L;
+
+	static final int MAX_URL_LENGTH = 200;
+
 	@Id()
 	@SequenceGenerator(name = "SEQ_CONCEPT_MAP_PID", sequenceName = "SEQ_CONCEPT_MAP_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_PID")
@@ -47,13 +55,13 @@ public class TermConceptMap implements Serializable {
 	@Column(name = "RES_ID", insertable = false, updatable = false)
 	private Long myResourcePid;
 
-	@Column(name = "SOURCE_URL", nullable = true, length = 200)
+	@Column(name = "SOURCE_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
 	private String mySource;
 
-	@Column(name = "TARGET_URL", nullable = true, length = 200)
+	@Column(name = "TARGET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
 	private String myTarget;
 
-	@Column(name = "URL", length = 200, nullable = false)
+	@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
 	private String myUrl;
 
 	@OneToMany(mappedBy = "myConceptMap")
@@ -75,47 +83,58 @@ public class TermConceptMap implements Serializable {
 		return myResource;
 	}
 
-	public void setResource(ResourceTable resource) {
+	public TermConceptMap setResource(ResourceTable theResource) {
-		myResource = resource;
+		myResource = theResource;
+		return this;
 	}
 
 	public Long getResourcePid() {
 		return myResourcePid;
 	}
 
-	public void setResourcePid(Long resourcePid) {
+	public TermConceptMap setResourcePid(Long theResourcePid) {
-		myResourcePid = resourcePid;
+		myResourcePid = theResourcePid;
+		return this;
 	}
 
 	public String getSource() {
 		return mySource;
 	}
 
-	public void setSource(String source) {
+	public TermConceptMap setSource(String theSource) {
-		mySource = source;
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSource, TermValueSet.MAX_URL_LENGTH,
+			"Source exceeds maximum length (" + TermValueSet.MAX_URL_LENGTH + "): " + length(theSource));
+		mySource = theSource;
+		return this;
 	}
 
 	public String getTarget() {
 		return myTarget;
 	}
 
-	public void setTarget(String target) {
+	public TermConceptMap setTarget(String theTarget) {
-		myTarget = target;
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTarget, TermValueSet.MAX_URL_LENGTH,
+			"Target exceeds maximum length (" + TermValueSet.MAX_URL_LENGTH + "): " + length(theTarget));
+		myTarget = theTarget;
+		return this;
 	}
 
 	public String getUrl() {
 		return myUrl;
 	}
 
-	public void setUrl(String theUrl) {
+	public TermConceptMap setUrl(@Nonnull String theUrl) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theUrl, "theUrl must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUrl, MAX_URL_LENGTH,
+			"URL exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theUrl));
 		myUrl = theUrl;
+		return this;
 	}
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
 			.append("myId", myId)
-			.append("myResource", myResource.toString())
 			.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
 			.append("myResourcePid", myResourcePid)
 			.append("mySource", mySource)

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

@@ -20,17 +20,23 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Table(name = "TRM_CONCEPT_MAP_GROUP")
 public class TermConceptMapGroup implements Serializable {
+	private static final long serialVersionUID = 1L;
+
 	@Id()
 	@SequenceGenerator(name = "SEQ_CONCEPT_MAP_GROUP_PID", sequenceName = "SEQ_CONCEPT_MAP_GROUP_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_GROUP_PID")
@@ -41,36 +47,37 @@ public class TermConceptMapGroup implements Serializable {
 	@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGROUP_CONCEPTMAP"))
 	private TermConceptMap myConceptMap;
 
-	@Column(name = "SOURCE_URL", nullable = false, length = 200)
+	@Column(name = "SOURCE_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
 	private String mySource;
 
-	@Column(name = "SOURCE_VERSION", length = 100)
+	@Column(name = "SOURCE_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
 	private String mySourceVersion;
 
-	@Column(name = "TARGET_URL", nullable = false, length = 200)
+	@Column(name = "TARGET_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
 	private String myTarget;
 
-	@Column(name = "TARGET_VERSION", length = 100)
+	@Column(name = "TARGET_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
 	private String myTargetVersion;
 
 	@OneToMany(mappedBy = "myConceptMapGroup")
 	private List<TermConceptMapGroupElement> myConceptMapGroupElements;
 
-	@Column(name= "CONCEPT_MAP_URL", length = 200, nullable = true)
+	@Column(name= "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
 	private String myConceptMapUrl;
 
-	@Column(name= "SOURCE_VS", length = 200, nullable = true)
+	@Column(name= "SOURCE_VS", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
 	private String mySourceValueSet;
 
-	@Column(name= "TARGET_VS", length = 200, nullable = true)
+	@Column(name= "TARGET_VS", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
 	private String myTargetValueSet;
 
 	public TermConceptMap getConceptMap() {
 		return myConceptMap;
 	}
 
-	public void setConceptMap(TermConceptMap theTermConceptMap) {
+	public TermConceptMapGroup setConceptMap(TermConceptMap theTermConceptMap) {
 		myConceptMap = theTermConceptMap;
+		return this;
 	}
 
 	public List<TermConceptMapGroupElement> getConceptMapGroupElements() {
@@ -96,8 +103,12 @@ public class TermConceptMapGroup implements Serializable {
 		return mySource;
 	}
 
-	public void setSource(String theSource) {
+	public TermConceptMapGroup setSource(@Nonnull String theSource) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theSource, "theSource must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSource, TermCodeSystem.MAX_URL_LENGTH,
+			"Source exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theSource));
 		this.mySource = theSource;
+		return this;
 	}
 
 	public String getSourceValueSet() {
@@ -111,16 +122,23 @@ public class TermConceptMapGroup implements Serializable {
 		return mySourceVersion;
 	}
 
-	public void setSourceVersion(String theSourceVersion) {
+	public TermConceptMapGroup setSourceVersion(String theSourceVersion) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSourceVersion, TermCodeSystemVersion.MAX_VERSION_LENGTH,
+			"Source version ID exceeds maximum length (" + TermCodeSystemVersion.MAX_VERSION_LENGTH + "): " + length(theSourceVersion));
 		mySourceVersion = theSourceVersion;
+		return this;
 	}
 
 	public String getTarget() {
 		return myTarget;
 	}
 
-	public void setTarget(String theTarget) {
+	public TermConceptMapGroup setTarget(@Nonnull String theTarget) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theTarget, "theTarget must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTarget, TermCodeSystem.MAX_URL_LENGTH,
+			"Target exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theTarget));
 		this.myTarget = theTarget;
+		return this;
 	}
 
 	public String getTargetValueSet() {
@@ -134,13 +152,16 @@ public class TermConceptMapGroup implements Serializable {
 		return myTargetVersion;
 	}
 
-	public void setTargetVersion(String theTargetVersion) {
+	public TermConceptMapGroup setTargetVersion(String theTargetVersion) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTargetVersion, TermCodeSystemVersion.MAX_VERSION_LENGTH,
+			"Target version ID exceeds maximum length (" + TermCodeSystemVersion.MAX_VERSION_LENGTH + "): " + length(theTargetVersion));
 		myTargetVersion = theTargetVersion;
+		return this;
 	}
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
 			.append("myId", myId)
 			.append(myConceptMap != null ? ("myConceptMap - id=" + myConceptMap.getId()) : ("myConceptMap=(null)"))
 			.append("mySource", mySource)

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

@@ -20,22 +20,28 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
-import org.apache.commons.lang3.Validate;
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Table(name = "TRM_CONCEPT_MAP_GRP_ELEMENT", indexes = {
 	@Index(name = "IDX_CNCPT_MAP_GRP_CD", columnList = "SOURCE_CODE")
 })
 public class TermConceptMapGroupElement implements Serializable {
+	private static final long serialVersionUID = 1L;
+
 	@Id()
 	@SequenceGenerator(name = "SEQ_CONCEPT_MAP_GRP_ELM_PID", sequenceName = "SEQ_CONCEPT_MAP_GRP_ELM_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_GRP_ELM_PID")
@@ -46,7 +52,7 @@ public class TermConceptMapGroupElement implements Serializable {
 	@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGELEMENT_GROUP"))
 	private TermConceptMapGroup myConceptMapGroup;
 
-	@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
+	@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
 	private String myCode;
 
 	@Column(name = "SOURCE_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
@@ -55,33 +61,37 @@ public class TermConceptMapGroupElement implements Serializable {
 	@OneToMany(mappedBy = "myConceptMapGroupElement")
 	private List<TermConceptMapGroupElementTarget> myConceptMapGroupElementTargets;
 
-	@Column(name = "CONCEPT_MAP_URL", length = 200)
+	@Column(name = "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
 	private String myConceptMapUrl;
 
-	@Column(name = "SYSTEM_URL", length = 200)
+	@Column(name = "SYSTEM_URL", nullable = true, length = TermCodeSystem.MAX_URL_LENGTH)
 	private String mySystem;
 
-	@Column(name = "SYSTEM_VERSION", length = 200)
+	@Column(name = "SYSTEM_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
 	private String mySystemVersion;
 
-	@Column(name = "VALUESET_URL", length = 200)
+	@Column(name = "VALUESET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
 	private String myValueSet;
 
 	public String getCode() {
 		return myCode;
 	}
 
-	public void setCode(String theCode) {
+	public TermConceptMapGroupElement setCode(@Nonnull String theCode) {
-		Validate.notBlank(theCode, "theCode must not be blank");
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
+			"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
 		myCode = theCode;
+		return this;
 	}
 
 	public TermConceptMapGroup getConceptMapGroup() {
 		return myConceptMapGroup;
 	}
 
-	public void setConceptMapGroup(TermConceptMapGroup theTermConceptMapGroup) {
+	public TermConceptMapGroupElement setConceptMapGroup(TermConceptMapGroup theTermConceptMapGroup) {
 		myConceptMapGroup = theTermConceptMapGroup;
+		return this;
 	}
 
 	public List<TermConceptMapGroupElementTarget> getConceptMapGroupElementTargets() {
@@ -103,8 +113,9 @@ public class TermConceptMapGroupElement implements Serializable {
 		return myDisplay;
 	}
 
-	public void setDisplay(String theDisplay) {
+	public TermConceptMapGroupElement setDisplay(String theDisplay) {
-		myDisplay = theDisplay;
+		myDisplay = left(theDisplay, TermConcept.MAX_DESC_LENGTH);
+		return this;
 	}
 
 	public Long getId() {
@@ -158,7 +169,7 @@ public class TermConceptMapGroupElement implements Serializable {
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
 			.append("myId", myId)
 			.append(myConceptMapGroup != null ? ("myConceptMapGroup - id=" + myConceptMapGroup.getId()) : ("myConceptMapGroup=(null)"))
 			.append("myCode", myCode)

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

@@ -20,20 +20,28 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
 
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Table(name = "TRM_CONCEPT_MAP_GRP_ELM_TGT", indexes = {
 	@Index(name = "IDX_CNCPT_MP_GRP_ELM_TGT_CD", columnList = "TARGET_CODE")
 })
 public class TermConceptMapGroupElementTarget implements Serializable {
+	private static final long serialVersionUID = 1L;
+
+	static final int MAX_EQUIVALENCE_LENGTH = 50;
+
 	@Id()
 	@SequenceGenerator(name = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID", sequenceName = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID")
@@ -44,31 +52,38 @@ public class TermConceptMapGroupElementTarget implements Serializable {
 	@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGETARGET_ELEMENT"))
 	private TermConceptMapGroupElement myConceptMapGroupElement;
 
-	@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
+	@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
 	private String myCode;
 
-	@Column(name = "TARGET_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
+	@Column(name = "TARGET_DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
 	private String myDisplay;
 
 	@Enumerated(EnumType.STRING)
-	@Column(name = "TARGET_EQUIVALENCE", length = 50)
+	@Column(name = "TARGET_EQUIVALENCE", nullable = true, length = MAX_EQUIVALENCE_LENGTH)
 	private ConceptMapEquivalence myEquivalence;
 
-	@Column(name = "CONCEPT_MAP_URL", length = 200)
+	@Column(name = "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
 	private String myConceptMapUrl;
-	@Column(name = "SYSTEM_URL", length = 200)
+
+	@Column(name = "SYSTEM_URL", nullable = true, length = TermCodeSystem.MAX_URL_LENGTH)
 	private String mySystem;
-	@Column(name = "SYSTEM_VERSION", length = 200)
+
+	@Column(name = "SYSTEM_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
 	private String mySystemVersion;
-	@Column(name = "VALUESET_URL", length = 200)
+
+	@Column(name = "VALUESET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
 	private String myValueSet;
 
 	public String getCode() {
 		return myCode;
 	}
 
-	public void setCode(String theCode) {
+	public TermConceptMapGroupElementTarget setCode(@Nonnull String theCode) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
+			"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
 		myCode = theCode;
+		return this;
 	}
 
 	public TermConceptMapGroupElement getConceptMapGroupElement() {
@@ -90,16 +105,18 @@ public class TermConceptMapGroupElementTarget implements Serializable {
 		return myDisplay;
 	}
 
-	public void setDisplay(String theDisplay) {
+	public TermConceptMapGroupElementTarget setDisplay(String theDisplay) {
 		myDisplay = theDisplay;
+		return this;
 	}
 
 	public ConceptMapEquivalence getEquivalence() {
 		return myEquivalence;
 	}
 
-	public void setEquivalence(ConceptMapEquivalence theEquivalence) {
+	public TermConceptMapGroupElementTarget setEquivalence(ConceptMapEquivalence theEquivalence) {
 		myEquivalence = theEquivalence;
+		return this;
 	}
 
 	public Long getId() {
@@ -155,7 +172,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
 			.append("myId", myId)
 			.append(myConceptMapGroupElement != null ? ("myConceptMapGroupElement - id=" + myConceptMapGroupElement.getId()) : ("myConceptMapGroupElement=(null)"))
 			.append("myCode", myCode)

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

@@ -20,21 +20,9 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import javax.persistence.*;
 import java.io.Serializable;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.ForeignKey;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-
 @Entity
 @Table(name = "TRM_CONCEPT_PC_LINK")
 public class TermConceptParentChildLink implements Serializable {
@@ -136,20 +124,24 @@ public class TermConceptParentChildLink implements Serializable {
 		return result;
 	}
 
-	public void setChild(TermConcept theChild) {
+	public TermConceptParentChildLink setChild(TermConcept theChild) {
 		myChild = theChild;
+		return this;
 	}
 
-	public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
+	public TermConceptParentChildLink setCodeSystem(TermCodeSystemVersion theCodeSystem) {
 		myCodeSystem = theCodeSystem;
+		return this;
 	}
 
-	public void setParent(TermConcept theParent) {
+	public TermConceptParentChildLink setParent(TermConcept theParent) {
 		myParent = theParent;
+		return this;
 	}
 
-	public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
+	public TermConceptParentChildLink setRelationshipType(RelationshipTypeEnum theRelationshipType) {
 		myRelationshipType = theRelationshipType;
+		return this;
 	}
 
 	public enum RelationshipTypeEnum {

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

@@ -20,21 +20,29 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.util.ValidateUtil;
+import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.validator.constraints.NotBlank;
 
+import javax.annotation.Nonnull;
 import javax.persistence.*;
 import java.io.Serializable;
 
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
+
 @Entity
 @Table(name = "TRM_CONCEPT_PROPERTY", uniqueConstraints = {
 }, indexes = {
 })
 public class TermConceptProperty implements Serializable {
-
-	static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
 	private static final long serialVersionUID = 1L;
+
+	private static final int MAX_LENGTH = 500;
+	static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
+
 	@ManyToOne
 	@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
 	private TermConcept myConcept;
@@ -51,22 +59,22 @@ public class TermConceptProperty implements Serializable {
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PROP_PID")
 	@Column(name = "PID")
 	private Long myId;
-	@Column(name = "PROP_KEY", length = 500, nullable = false)
+	@Column(name = "PROP_KEY", nullable = false, length = MAX_LENGTH)
 	@NotBlank
 	private String myKey;
-	@Column(name = "PROP_VAL", length = 500, nullable = true)
+	@Column(name = "PROP_VAL", nullable = true, length = MAX_LENGTH)
 	private String myValue;
-	@Column(name = "PROP_TYPE", length = MAX_PROPTYPE_ENUM_LENGTH, nullable = false)
+	@Column(name = "PROP_TYPE", nullable = false, length = MAX_PROPTYPE_ENUM_LENGTH)
 	private TermConceptPropertyTypeEnum myType;
 	/**
 	 * Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
 	 */
-	@Column(name = "PROP_CODESYSTEM", length = 500, nullable = true)
+	@Column(name = "PROP_CODESYSTEM", length = MAX_LENGTH, nullable = true)
 	private String myCodeSystem;
 	/**
 	 * Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
 	 */
-	@Column(name = "PROP_DISPLAY", length = 500, nullable = true)
+	@Column(name = "PROP_DISPLAY", length = MAX_LENGTH, nullable = true)
 	private String myDisplay;
 
 	/**
@@ -80,6 +88,8 @@ public class TermConceptProperty implements Serializable {
 	 * Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
 	 */
 	public TermConceptProperty setCodeSystem(String theCodeSystem) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCodeSystem, MAX_LENGTH,
+			"Property code system exceeds maximum length (" + MAX_LENGTH + "): " + length(theCodeSystem));
 		myCodeSystem = theCodeSystem;
 		return this;
 	}
@@ -95,7 +105,7 @@ public class TermConceptProperty implements Serializable {
 	 * Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
 	 */
 	public TermConceptProperty setDisplay(String theDisplay) {
-		myDisplay = theDisplay;
+		myDisplay = left(theDisplay, MAX_LENGTH);
 		return this;
 	}
 
@@ -103,15 +113,20 @@ public class TermConceptProperty implements Serializable {
 		return myKey;
 	}
 
-	public void setKey(String theKey) {
+	public TermConceptProperty setKey(@Nonnull String theKey) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theKey, "theKey must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theKey, MAX_LENGTH,
+			"Code exceeds maximum length (" + MAX_LENGTH + "): " + length(theKey));
 		myKey = theKey;
+		return this;
 	}
 
 	public TermConceptPropertyTypeEnum getType() {
 		return myType;
 	}
 
-	public TermConceptProperty setType(TermConceptPropertyTypeEnum theType) {
+	public TermConceptProperty setType(@Nonnull TermConceptPropertyTypeEnum theType) {
+		Validate.notNull(theType);
 		myType = theType;
 		return this;
 	}
@@ -128,8 +143,9 @@ public class TermConceptProperty implements Serializable {
 	 * This will contain the value for a {@link TermConceptPropertyTypeEnum#STRING string}
 	 * property, and the code for a {@link TermConceptPropertyTypeEnum#CODING coding} property.
 	 */
-	public void setValue(String theValue) {
+	public TermConceptProperty setValue(String theValue) {
-		myValue = theValue;
+		myValue = left(theValue, MAX_LENGTH);
+		return this;
 	}
 
 	public TermConceptProperty setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
@@ -137,8 +153,9 @@ public class TermConceptProperty implements Serializable {
 		return this;
 	}
 
-	public void setConcept(TermConcept theConcept) {
+	public TermConceptProperty setConcept(TermConcept theConcept) {
 		myConcept = theConcept;
+		return this;
 	}
 
 	@Override

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

@@ -0,0 +1,144 @@
+package ca.uhn.fhir.jpa.entity;
+
+/*
+ * #%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.model.entity.ResourceTable;
+import ca.uhn.fhir.util.ValidateUtil;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
+
+import javax.annotation.Nonnull;
+import javax.persistence.*;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
+
+@Table(name = "TRM_VALUESET", uniqueConstraints = {
+	@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL"})
+})
+@Entity()
+public class TermValueSet implements Serializable {
+	private static final long serialVersionUID = 1L;
+
+	public static final int MAX_NAME_LENGTH = 200;
+	public static final int MAX_URL_LENGTH = 200;
+
+	@Id()
+	@SequenceGenerator(name = "SEQ_VALUESET_PID", sequenceName = "SEQ_VALUESET_PID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_VALUESET_PID")
+	@Column(name = "PID")
+	private Long myId;
+
+	@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
+	private String myUrl;
+
+	@OneToOne()
+	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMVALUESET_RES"))
+	private ResourceTable myResource;
+
+	@Column(name = "RES_ID", insertable = false, updatable = false)
+	private Long myResourcePid;
+
+	@Column(name = "NAME", nullable = true, length = MAX_NAME_LENGTH)
+	private String myName;
+
+	@OneToMany(mappedBy = "myValueSet")
+	private List<TermValueSetCode> myCodes;
+
+	public Long getId() {
+		return myId;
+	}
+
+	public String getUrl() {
+		return myUrl;
+	}
+
+	public TermValueSet setUrl(@Nonnull String theUrl) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theUrl, "theUrl must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUrl, MAX_URL_LENGTH,
+			"URL exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theUrl));
+		myUrl = theUrl;
+		return this;
+	}
+
+	public ResourceTable getResource() {
+		return myResource;
+	}
+
+	public TermValueSet setResource(ResourceTable theResource) {
+		myResource = theResource;
+		return this;
+	}
+
+	public String getName() {
+		return myName;
+	}
+
+	public TermValueSet setName(String theName) {
+		myName = left(theName, MAX_NAME_LENGTH);
+		return this;
+	}
+
+	public List<TermValueSetCode> getCodes() {
+		if (myCodes == null) {
+			myCodes = new ArrayList<>();
+		}
+
+		return myCodes;
+	}
+
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) return true;
+
+		if (!(theO instanceof TermValueSet)) return false;
+
+		TermValueSet that = (TermValueSet) theO;
+
+		return new EqualsBuilder()
+			.append(getUrl(), that.getUrl())
+			.isEquals();
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(17, 37)
+			.append(getUrl())
+			.toHashCode();
+	}
+
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
+			.append("myId", myId)
+			.append("myUrl", myUrl)
+			.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
+			.append("myResourcePid", myResourcePid)
+			.append("myName", myName)
+			.append(myCodes != null ? ("myCodes - size=" + myCodes.size()) : ("myCodes=(null)"))
+			.toString();
+	}
+}

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

@@ -0,0 +1,166 @@
+package ca.uhn.fhir.jpa.entity;
+
+/*
+ * #%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.util.ValidateUtil;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
+
+import javax.annotation.Nonnull;
+import javax.persistence.*;
+import java.io.Serializable;
+
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.length;
+
+@Table(name = "TRM_VALUESET_CODE", indexes = {
+	@Index(name = "IDX_VALUESET_CODE_CS_CD", columnList = "SYSTEM, CODE")
+})
+@Entity()
+public class TermValueSetCode implements Serializable {
+	private static final long serialVersionUID = 1L;
+
+	@Id()
+	@SequenceGenerator(name = "SEQ_VALUESET_CODE_PID", sequenceName = "SEQ_VALUESET_CODE_PID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_VALUESET_CODE_PID")
+	@Column(name = "PID")
+	private Long myId;
+
+	@ManyToOne()
+	@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_PID"))
+	private TermValueSet myValueSet;
+
+	@Transient
+	private String myValueSetUrl;
+
+	@Transient
+	private String myValueSetName;
+
+	@Column(name = "SYSTEM", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
+	private String mySystem;
+
+	@Column(name = "CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
+	private String myCode;
+
+	@Column(name = "DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
+	private String myDisplay;
+
+	public Long getId() {
+		return myId;
+	}
+
+	public TermValueSet getValueSet() {
+		return myValueSet;
+	}
+
+	public TermValueSetCode setValueSet(TermValueSet theValueSet) {
+		myValueSet = theValueSet;
+		return this;
+	}
+
+	public String getValueSetUrl() {
+		if (myValueSetUrl == null) {
+			myValueSetUrl = getValueSet().getUrl();
+		}
+
+		return myValueSetUrl;
+	}
+
+	public String getValueSetName() {
+		if (myValueSetName == null) {
+			myValueSetName = getValueSet().getName();
+		}
+
+		return myValueSetName;
+	}
+
+	public String getSystem() {
+		return mySystem;
+	}
+
+	public TermValueSetCode setSystem(@Nonnull String theSystem) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theSystem, "theSystem must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSystem, TermCodeSystem.MAX_URL_LENGTH,
+			"System exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theSystem));
+		mySystem = theSystem;
+		return this;
+	}
+
+	public String getCode() {
+		return myCode;
+	}
+
+	public TermValueSetCode setCode(@Nonnull String theCode) {
+		ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
+			"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
+		myCode = theCode;
+		return this;
+	}
+
+	public String getDisplay() {
+		return myDisplay;
+	}
+
+	public TermValueSetCode setDisplay(String theDisplay) {
+		myDisplay = left(theDisplay, TermConcept.MAX_DESC_LENGTH);
+		return this;
+	}
+
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) return true;
+
+		if (!(theO instanceof TermValueSetCode)) return false;
+
+		TermValueSetCode that = (TermValueSetCode) theO;
+
+		return new EqualsBuilder()
+			.append(getValueSetUrl(), that.getValueSetUrl())
+			.append(getSystem(), that.getSystem())
+			.append(getCode(), that.getCode())
+			.isEquals();
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(17, 37)
+			.append(getValueSetUrl())
+			.append(getSystem())
+			.append(getCode())
+			.toHashCode();
+	}
+
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
+			.append("myId", myId)
+			.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
+			.append("myValueSetUrl", this.getValueSetUrl())
+			.append("myValueSetName", this.getValueSetName())
+			.append("mySystem", mySystem)
+			.append("myCode", myCode)
+			.append("myDisplay", myDisplay)
+			.toString();
+	}
+}

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

@@ -410,6 +410,14 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 					PersistedJpaBundleProvider retVal = null;
 					if (searchToUse != null) {
 						ourLog.debug("Reusing search {} from cache", searchToUse.getUuid());
+
+						// Interceptor call: JPA_PERFTRACE_SEARCH_REUSING_CACHED
+						params = new HookParams()
+							.add(SearchParameterMap.class, theParams)
+							.add(RequestDetails.class, theRequestDetails)
+							.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
+						JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_SEARCH_REUSING_CACHED, params);
+
 						searchToUse.setSearchLastReturned(new Date());
 						mySearchDao.updateSearchLastReturned(searchToUse.getId(), new Date());
 

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

@@ -119,6 +119,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	@Autowired
 	protected ITermConceptDesignationDao myConceptDesignationDao;
 	@Autowired
+	protected ITermValueSetDao myValueSetDao;
+	@Autowired
+	protected ITermValueSetCodeDao myValueSetCodeDao;
+	@Autowired
 	protected FhirContext myContext;
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
@@ -388,6 +392,31 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		deleteConceptMap(theResourceTable);
 	}
 
+	public void deleteValueSet(ResourceTable theResourceTable) {
+		// Get existing entity so it can be deleted.
+		Optional<TermValueSet> optionalExistingTermValueSetById = myValueSetDao.findByResourcePid(theResourceTable.getId());
+
+		if (optionalExistingTermValueSetById.isPresent()) {
+			TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
+
+			ourLog.info("Deleting existing TermValueSet {} and its children...", existingTermValueSet.getId());
+			myValueSetCodeDao.deleteTermValueSetCodesByValueSetId(existingTermValueSet.getId());
+			myValueSetDao.deleteTermValueSetById(existingTermValueSet.getId());
+			ourLog.info("Done deleting existing TermValueSet {} and its children.", existingTermValueSet.getId());
+
+			ourLog.info("Flushing...");
+			myValueSetCodeDao.flush();
+			myValueSetDao.flush();
+			ourLog.info("Done flushing.");
+		}
+	}
+
+	@Override
+	@Transactional
+	public void deleteValueSetAndChildren(ResourceTable theResourceTable) {
+		deleteValueSet(theResourceTable);
+	}
+
 	private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
 		int count;
 		ourLog.info(" * Deleting {}", theDescriptor);
@@ -690,7 +719,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	private void expandWithoutHibernateSearch(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
 		ourLog.trace("Hibernate search is not enabled");
-		Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not exapnd ValueSet with parameters - Hibernate Search is not enabled on this server.");
+		Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
 		Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
 		Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
 
@@ -1144,7 +1173,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 			myCodeSystemDao.save(codeSystem);
 		} else {
 			if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
-				String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
+				String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
 					codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
 				throw new UnprocessableEntityException(msg);
 			}
@@ -1310,7 +1339,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 									myConceptMapGroupElementTargetDao.save(termConceptMapGroupElementTarget);
 
 									if (codesSaved++ % 250 == 0) {
-										ourLog.info("Have saved {} codes in conceptmap", codesSaved);
+										ourLog.info("Have saved {} codes in ConceptMap", codesSaved);
 										myConceptMapGroupElementTargetDao.flush();
 									}
 								}
@@ -1334,6 +1363,69 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		ourLog.info("Done storing TermConceptMap.");
 	}
 
+	@Override
+	@Transactional
+	public void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet) {
+		ourLog.info("Storing TermValueSet {}", theValueSet.getIdElement().getValue());
+
+		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
+		ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
+
+		TermValueSet termValueSet = new TermValueSet();
+		termValueSet.setResource(theResourceTable);
+		termValueSet.setUrl(theValueSet.getUrl());
+		termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
+
+		// We delete old versions; we don't support versioned ValueSets.
+		deleteValueSet(theResourceTable);
+
+		/*
+		 * Do the upload.
+		 */
+		String url = termValueSet.getUrl();
+		Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
+		if (!optionalExistingTermValueSetByUrl.isPresent()) {
+			myValueSetDao.save(termValueSet);
+			int codesSaved = 0;
+
+			ValueSet expandedValueSet = expandValueSet(theValueSet);
+			if (expandedValueSet.hasExpansion()) {
+				if (expandedValueSet.getExpansion().hasTotal() && expandedValueSet.getExpansion().getTotal() > 0) {
+					TermValueSetCode code;
+					for (ValueSet.ValueSetExpansionContainsComponent contains : expandedValueSet.getExpansion().getContains()) {
+						ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getSystem(), "ValueSet contains a code with no system value");
+						ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getCode(), "ValueSet contains a code with no code value");
+
+						code = new TermValueSetCode();
+						code.setValueSet(termValueSet);
+						code.setSystem(contains.getSystem());
+						code.setCode(contains.getCode());
+						code.setDisplay(contains.hasDisplay() ? contains.getDisplay() : null);
+						myValueSetCodeDao.save(code);
+
+						if (codesSaved++ % 250 == 0) {
+							ourLog.info("Have pre-expanded {} codes in ValueSet", codesSaved);
+							myValueSetCodeDao.flush();
+						}
+					}
+				}
+			}
+
+		} else {
+			TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
+
+			String msg = myContext.getLocalizer().getMessage(
+				BaseHapiTerminologySvcImpl.class,
+				"cannotCreateDuplicateValueSetUrl",
+				url,
+				existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+
+			throw new UnprocessableEntityException(msg);
+		}
+
+		ourLog.info("Done storing TermValueSet.");
+	}
+
 	@Override
 	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
 		VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
@@ -1581,9 +1673,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
 													  IdentityHashMap<TermConcept, Object> theAllConcepts) {
-		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodesystemValue is null");
+		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodeSystemVersion is null");
 		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() == theCodeSystem, "CodeSystems are not equal");
-		ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code with no code value");
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "CodeSystem contains a code with no code value");
 
 		if (theConceptsStack.contains(theConcept.getCode())) {
 			throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());

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

@@ -81,8 +81,12 @@ public interface IHapiTerminologySvc {
 
 	void deleteConceptMapAndChildren(ResourceTable theResourceTable);
 
+	void deleteValueSetAndChildren(ResourceTable theResourceTable);
+
 	void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap);
 
+	void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet);
+
 	boolean supportsSystem(String theCodeSystem);
 
 	List<TermConceptMapGroupElementTarget> translate(TranslationRequest theTranslationRequest);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -5,7 +5,6 @@ import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import net.ttddyy.dsproxy.listener.SingleQueryCountHolder;
-import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.springframework.context.annotation.Bean;
@@ -104,7 +103,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 
 		DataSource dataSource = ProxyDataSourceBuilder
 			.create(retVal)
-			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
+//			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
 //			.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
 //			.countQuery(new ThreadQueryCountHolder())
 			.beforeQuery(new BlockLargeNumbersOfParamsListener())

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -1,31 +1,13 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.hamcrest.Matchers.containsStringIgnoringCase;
-import static org.hamcrest.Matchers.empty;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
-
-import java.util.*;
-
-import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
-import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
-import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
-import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
-import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.*;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.*;
-import org.springframework.beans.factory.annotation.Autowired;
-
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
-import ca.uhn.fhir.jpa.model.entity.*;
+import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -35,6 +17,25 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
+import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
+import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
+import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
+import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.*;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
 
 public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
@@ -226,7 +227,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 			myCodeSystemDao.create(codeSystem, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
+			assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java

@@ -1,345 +0,0 @@
-package ca.uhn.fhir.jpa.dao.dstu3;
-
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
-import ca.uhn.fhir.jpa.model.entity.ModelConfig;
-import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
-import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
-import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.DateParam;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
-import ca.uhn.fhir.util.TestUtil;
-import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.context.TestPropertySource;
-
-import java.util.List;
-
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.hamcrest.Matchers.empty;
-import static org.junit.Assert.*;
-
-@SuppressWarnings({"unchecked", "deprecation"})
-@TestPropertySource(properties = {
-	// Since scheduled tasks can cause searches, which messes up the
-	// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
-	"scheduling_disabled=true"
-})
-public class FhirResourceDaoDstu3UniqueSearchParamTest extends BaseJpaDstu3Test {
-
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3UniqueSearchParamTest.class);
-
-	@After
-	public void after() {
-		myModelConfig.setDefaultSearchParamsCanBeOverridden(new ModelConfig().isDefaultSearchParamsCanBeOverridden());
-	}
-
-	@Before
-	public void before() {
-		myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
-	}
-
-	private void createUniqueBirthdateAndGenderSps() {
-		SearchParameter sp = new SearchParameter();
-		sp.setId("SearchParameter/patient-gender");
-		sp.setType(Enumerations.SearchParamType.TOKEN);
-		sp.setCode("gender");
-		sp.setExpression("Patient.gender");
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Patient");
-		mySearchParameterDao.update(sp);
-
-		sp = new SearchParameter();
-		sp.setId("SearchParameter/patient-birthdate");
-		sp.setType(Enumerations.SearchParamType.DATE);
-		sp.setCode("birthdate");
-		sp.setExpression("Patient.birthDate");
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Patient");
-		mySearchParameterDao.update(sp);
-
-		sp = new SearchParameter();
-		sp.setId("SearchParameter/patient-gender-birthdate");
-		sp.setType(Enumerations.SearchParamType.COMPOSITE);
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Patient");
-		sp.addComponent()
-			.setExpression("Patient")
-			.setDefinition(new Reference("SearchParameter/patient-gender"));
-		sp.addComponent()
-			.setExpression("Patient")
-			.setDefinition(new Reference("SearchParameter/patient-birthdate"));
-		sp.addExtension()
-			.setUrl(SearchParamConstants.EXT_SP_UNIQUE)
-			.setValue(new BooleanType(true));
-		mySearchParameterDao.update(sp);
-
-		mySearchParamRegistry.forceRefresh();
-	}
-
-	private void createUniqueIndexCoverageBeneficiary() {
-		SearchParameter sp = new SearchParameter();
-		sp.setId("SearchParameter/coverage-beneficiary");
-		sp.setCode("beneficiary");
-		sp.setExpression("Coverage.beneficiary");
-		sp.setType(Enumerations.SearchParamType.REFERENCE);
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Coverage");
-		mySearchParameterDao.update(sp);
-
-		sp = new SearchParameter();
-		sp.setId("SearchParameter/coverage-identifier");
-		sp.setCode("identifier");
-		sp.setExpression("Coverage.identifier");
-		sp.setType(Enumerations.SearchParamType.TOKEN);
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Coverage");
-		mySearchParameterDao.update(sp);
-
-		sp = new SearchParameter();
-		sp.setId("SearchParameter/coverage-beneficiary-identifier");
-		sp.setCode("coverage-beneficiary-identifier");
-		sp.setExpression("Coverage.beneficiary");
-		sp.setType(Enumerations.SearchParamType.COMPOSITE);
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Coverage");
-		sp.addComponent()
-			.setExpression("Coverage")
-			.setDefinition(new Reference("/SearchParameter/coverage-beneficiary"));
-		sp.addComponent()
-			.setExpression("Coverage")
-			.setDefinition(new Reference("/SearchParameter/coverage-identifier"));
-		sp.addExtension()
-			.setUrl(SearchParamConstants.EXT_SP_UNIQUE)
-			.setValue(new BooleanType(true));
-		mySearchParameterDao.update(sp);
-		mySearchParamRegistry.forceRefresh();
-	}
-
-	private void createUniqueNameAndManagingOrganizationSps() {
-		SearchParameter sp = new SearchParameter();
-		sp.setId("SearchParameter/patient-name");
-		sp.setType(Enumerations.SearchParamType.STRING);
-		sp.setCode("name");
-		sp.setExpression("Patient.name");
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Patient");
-		mySearchParameterDao.update(sp);
-
-		sp = new SearchParameter();
-		sp.setId("SearchParameter/patient-organization");
-		sp.setType(Enumerations.SearchParamType.REFERENCE);
-		sp.setCode("organization");
-		sp.setExpression("Patient.managingOrganization");
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Patient");
-		mySearchParameterDao.update(sp);
-
-		sp = new SearchParameter();
-		sp.setId("SearchParameter/patient-name-organization");
-		sp.setType(Enumerations.SearchParamType.COMPOSITE);
-		sp.setStatus(PublicationStatus.ACTIVE);
-		sp.addBase("Patient");
-		sp.addComponent()
-			.setExpression("Patient")
-			.setDefinition(new Reference("SearchParameter/patient-name"));
-		sp.addComponent()
-			.setExpression("Patient")
-			.setDefinition(new Reference("SearchParameter/patient-organization"));
-		sp.addExtension()
-			.setUrl(SearchParamConstants.EXT_SP_UNIQUE)
-			.setValue(new BooleanType(true));
-		mySearchParameterDao.update(sp);
-
-		mySearchParamRegistry.forceRefresh();
-	}
-
-	@Test
-	public void testDetectUniqueSearchParams() {
-		createUniqueBirthdateAndGenderSps();
-		List<JpaRuntimeSearchParam> params = mySearchParamRegistry.getActiveUniqueSearchParams("Patient");
-
-		assertEquals(1, params.size());
-		assertEquals(params.get(0).isUnique(), true);
-		assertEquals(2, params.get(0).getCompositeOf().size());
-		// Should be alphabetical order
-		assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
-		assertEquals("gender", params.get(0).getCompositeOf().get(1).getName());
-	}
-
-	@Test
-	public void testDuplicateUniqueValuesAreRejected() {
-		createUniqueBirthdateAndGenderSps();
-
-		Patient pt1 = new Patient();
-		pt1.setGender(Enumerations.AdministrativeGender.MALE);
-		pt1.setBirthDateElement(new DateType("2011-01-01"));
-		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
-
-		try {
-			myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
-			fail();
-		} catch (PreconditionFailedException e) {
-			// good
-		}
-
-		Patient pt2 = new Patient();
-		pt2.setGender(Enumerations.AdministrativeGender.MALE);
-		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
-
-		pt2 = new Patient();
-		pt2.setId(id2);
-		pt2.setGender(Enumerations.AdministrativeGender.MALE);
-		pt2.setBirthDateElement(new DateType("2011-01-01"));
-		try {
-			myPatientDao.update(pt2);
-			fail();
-		} catch (PreconditionFailedException e) {
-			// good
-		}
-
-	}
-
-	@Test
-	public void testReplaceOneWithAnother() {
-		createUniqueBirthdateAndGenderSps();
-
-		Patient pt1 = new Patient();
-		pt1.setGender(Enumerations.AdministrativeGender.MALE);
-		pt1.setBirthDateElement(new DateType("2011-01-01"));
-		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualified();
-		assertNotNull(id1);
-
-		ourLog.info("** Replacing");
-
-		pt1 = new Patient();
-		pt1.setId(id1);
-		pt1.setGender(Enumerations.AdministrativeGender.FEMALE);
-		pt1.setBirthDateElement(new DateType("2011-01-01"));
-		id1 = myPatientDao.update(pt1).getId().toUnqualified();
-		assertNotNull(id1);
-		assertEquals("2", id1.getVersionIdPart());
-
-		Patient pt2 = new Patient();
-		pt2.setGender(Enumerations.AdministrativeGender.MALE);
-		pt2.setBirthDateElement(new DateType("2011-01-01"));
-		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
-
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
-		SearchParameterMap params = new SearchParameterMap();
-		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
-		params.add("birthdate", new DateParam("2011-01-01"));
-		IBundleProvider results = myPatientDao.search(params);
-		String searchId = results.getUuid();
-		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id2.getValue()));
-		assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
-
-	}
-
-	@Test
-	public void testSearchSynchronousUsingUniqueComposite() {
-		createUniqueBirthdateAndGenderSps();
-
-		Patient pt1 = new Patient();
-		pt1.setGender(Enumerations.AdministrativeGender.MALE);
-		pt1.setBirthDateElement(new DateType("2011-01-01"));
-		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
-
-		Patient pt2 = new Patient();
-		pt2.setGender(Enumerations.AdministrativeGender.MALE);
-		pt2.setBirthDateElement(new DateType("2011-01-02"));
-		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
-
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
-		SearchParameterMap params = new SearchParameterMap();
-		params.setLoadSynchronousUpTo(100);
-		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
-		params.add("birthdate", new DateParam("2011-01-01"));
-		IBundleProvider results = myPatientDao.search(params);
-		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
-		assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
-	}
-
-	@Test
-	public void testSearchUsingUniqueComposite() {
-		createUniqueBirthdateAndGenderSps();
-
-		Patient pt1 = new Patient();
-		pt1.setGender(Enumerations.AdministrativeGender.MALE);
-		pt1.setBirthDateElement(new DateType("2011-01-01"));
-		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
-		assertNotNull(id1);
-
-		Patient pt2 = new Patient();
-		pt2.setGender(Enumerations.AdministrativeGender.MALE);
-		pt2.setBirthDateElement(new DateType("2011-01-02"));
-		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
-
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
-		SearchParameterMap params = new SearchParameterMap();
-		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
-		params.add("birthdate", new DateParam("2011-01-01"));
-		IBundleProvider results = myPatientDao.search(params);
-		String searchId = results.getUuid();
-		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
-		assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
-
-		// Other order
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
-		params = new SearchParameterMap();
-		params.add("birthdate", new DateParam("2011-01-01"));
-		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
-		results = myPatientDao.search(params);
-		assertEquals(searchId, results.getUuid());
-		String id1Value = id1.getValue();
-		List<String> actualValues = toUnqualifiedVersionlessIdValues(results);
-		assertThat(actualValues, containsInAnyOrder(id1Value));
-		// Null because we just reuse the last search
-		assertEquals(null, SearchBuilder.getLastHandlerMechanismForUnitTest());
-
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
-		params = new SearchParameterMap();
-		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
-		params.add("birthdate", new DateParam("2011-01-03"));
-		results = myPatientDao.search(params);
-		assertThat(toUnqualifiedVersionlessIdValues(results), empty());
-		assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
-
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
-		params = new SearchParameterMap();
-		params.add("birthdate", new DateParam("2011-01-03"));
-		results = myPatientDao.search(params);
-		assertThat(toUnqualifiedVersionlessIdValues(results), empty());
-		assertEquals(SearchBuilder.HandlerTypeEnum.STANDARD_QUERY, SearchBuilder.getLastHandlerMechanismForUnitTest());
-
-	}
-
-	@Test
-	public void testUniqueValuesAreIndexed_DateAndToken() {
-		createUniqueBirthdateAndGenderSps();
-
-		Patient pt1 = new Patient();
-		pt1.setGender(Enumerations.AdministrativeGender.MALE);
-		pt1.setBirthDateElement(new DateType("2011-01-01"));
-		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
-
-		List<ResourceIndexedCompositeStringUnique> uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
-		assertEquals(1, uniques.size());
-		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
-		assertEquals("Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale", uniques.get(0).getIndexString());
-	}
-
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -118,6 +118,10 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myCodeSystemDaoR4")
 	protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
 	@Autowired
+	protected ITermCodeSystemDao myTermCodeSystemDao;
+	@Autowired
+	protected ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
+	@Autowired
 	@Qualifier("myCompartmentDefinitionDaoR4")
 	protected IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;
 	@Autowired
@@ -287,6 +291,10 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myValueSetDaoR4")
 	protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
 	@Autowired
+	protected ITermValueSetDao myTermValueSetDao;
+	@Autowired
+	protected ITermValueSetCodeDao myTermValueSetCodeDao;
+	@Autowired
 	protected ITermConceptMapDao myTermConceptMapDao;
 	@Autowired
 	protected ITermConceptMapGroupElementTargetDao myTermConceptMapGroupElementTargetDao;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java

@@ -222,7 +222,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 			myCodeSystemDao.create(codeSystem, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
+			assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java

@@ -1,15 +1,18 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.interceptor.api.HookParams;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
@@ -17,6 +20,7 @@ import ca.uhn.fhir.rest.param.TokenAndListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
+import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
@@ -25,6 +29,7 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
+import org.mockito.ArgumentMatchers;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.transaction.TransactionStatus;
@@ -32,6 +37,7 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
@@ -40,8 +46,10 @@ import java.util.stream.Collectors;
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.INDEX_STATUS_INDEXED;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
-@SuppressWarnings({"unchecked", "deprecation"})
 @TestPropertySource(properties = {
 	// Since scheduled tasks can cause searches, which messes up the
 	// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
@@ -52,6 +60,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4UniqueSearchParamTest.class);
 	@Autowired
 	private ISearchParamRegistry mySearchParamRegistry;
+	private IInterceptorBroadcaster myInterceptorBroadcaster;
+	private List<String> myMessages = new ArrayList<>();
 
 	@After
 	public void after() {
@@ -66,9 +76,31 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
 		myDaoConfig.setSchedulingDisabled(true);
 		myDaoConfig.setUniqueIndexesEnabled(true);
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+
+		myInterceptorBroadcaster = mock(IInterceptorBroadcaster.class);
+		when(mySrd.getInterceptorBroadcaster()).thenReturn(myInterceptorBroadcaster);
+		when(mySrd.getServer().getPagingProvider()).thenReturn(new DatabaseBackedPagingProvider());
+
+		when(myInterceptorBroadcaster.hasHooks(eq(Pointcut.JPA_PERFTRACE_WARNING))).thenReturn(true);
+		when(myInterceptorBroadcaster.hasHooks(eq(Pointcut.JPA_PERFTRACE_INFO))).thenReturn(true);
+		when(myInterceptorBroadcaster.callHooks(eq(Pointcut.JPA_PERFTRACE_INFO), ArgumentMatchers.any(HookParams.class))).thenAnswer(t -> {
+			HookParams params = t.getArgument(1, HookParams.class);
+			myMessages.add("INFO " + params.get(StorageProcessingMessage.class).getMessage());
+			return null;
+		});
+		when(myInterceptorBroadcaster.callHooks(eq(Pointcut.JPA_PERFTRACE_WARNING), ArgumentMatchers.any(HookParams.class))).thenAnswer(t -> {
+			HookParams params = t.getArgument(1, HookParams.class);
+			myMessages.add("WARN " + params.get(StorageProcessingMessage.class).getMessage());
+			return null;
+		});
+		when(myInterceptorBroadcaster.callHooks(eq(Pointcut.JPA_PERFTRACE_SEARCH_REUSING_CACHED), ArgumentMatchers.any(HookParams.class))).thenAnswer(t -> {
+			HookParams params = t.getArgument(1, HookParams.class);
+			myMessages.add("REUSING CACHED SEARCH");
+			return null;
+		});
 	}
 
+
 	private void createUniqueBirthdateAndGenderSps() {
 		SearchParameter sp = new SearchParameter();
 		sp.setId("SearchParameter/patient-gender");
@@ -106,7 +138,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 
 		mySearchParamRegistry.forceRefresh();
 
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		myMessages.clear();
 	}
 
 	private void createUniqueIndexCoverageBeneficiary() {
@@ -322,19 +354,6 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		mySearchParamRegistry.forceRefresh();
 	}
 
-	@Test
-	public void testDetectUniqueSearchParams() {
-		createUniqueBirthdateAndGenderSps();
-		List<JpaRuntimeSearchParam> params = mySearchParamRegistry.getActiveUniqueSearchParams("Patient");
-
-		assertEquals(1, params.size());
-		assertTrue(params.get(0).isUnique());
-		assertEquals(2, params.get(0).getCompositeOf().size());
-		// Should be alphabetical order
-		assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
-		assertEquals("gender", params.get(0).getCompositeOf().get(1).getName());
-	}
-
 	@Test
 	public void testDoubleMatchingOnAnd_Search() {
 		createUniqueIndexPatientIdentifier();
@@ -981,15 +1000,19 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
 
 		myCaptureQueriesListener.clear();
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		myMessages.clear();
 		SearchParameterMap params = new SearchParameterMap();
 		params.setLoadSynchronousUpTo(100);
 		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
 		params.add("birthdate", new DateParam("2011-01-01"));
-		IBundleProvider results = myPatientDao.search(params);
+		IBundleProvider results = myPatientDao.search(params, mySrd);
 		myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
 		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
-		assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
+
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
+		myMessages.clear();
+
 	}
 
 
@@ -1007,40 +1030,50 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		pt2.setBirthDateElement(new DateType("2011-01-02"));
 		myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
 
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		myMessages.clear();
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
 		params.add("birthdate", new DateParam("2011-01-01"));
-		IBundleProvider results = myPatientDao.search(params);
+		IBundleProvider results = myPatientDao.search(params, mySrd);
 		String searchId = results.getUuid();
 		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
-		assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
+		myMessages.clear();
 
 		// Other order
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		myMessages.clear();
 		params = new SearchParameterMap();
 		params.add("birthdate", new DateParam("2011-01-01"));
 		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
-		results = myPatientDao.search(params);
+		results = myPatientDao.search(params, mySrd);
 		assertEquals(searchId, results.getUuid());
 		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
-		// Null because we just reuse the last search
+		// Because we just reuse the last search
-		assertNull(SearchBuilder.getLastHandlerMechanismForUnitTest());
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("REUSING"));
+		assertThat(myMessages.toString(), not(containsString("Using unique index")));
+		myMessages.clear();
 
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		myMessages.clear();
 		params = new SearchParameterMap();
 		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
 		params.add("birthdate", new DateParam("2011-01-03"));
-		results = myPatientDao.search(params);
+		results = myPatientDao.search(params, mySrd);
 		assertThat(toUnqualifiedVersionlessIdValues(results), empty());
-		assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-03&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
+		myMessages.clear();
 
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		myMessages.clear();
 		params = new SearchParameterMap();
 		params.add("birthdate", new DateParam("2011-01-03"));
-		results = myPatientDao.search(params);
+		results = myPatientDao.search(params, mySrd);
 		assertThat(toUnqualifiedVersionlessIdValues(results), empty());
-		assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.STANDARD_QUERY, SearchBuilder.getLastHandlerMechanismForUnitTest());
+		// STANDARD QUERY
+		logCapturedMessages();
+		assertThat(myMessages.toString(), not(containsString("unique index")));
+		myMessages.clear();
 
 	}
 
@@ -1104,9 +1137,12 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		pt1.addName().setFamily("FAMILY1");
 		pt1.setManagingOrganization(new Reference("Organization/ORG"));
 
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		IIdType id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG", mySrd).getId().toUnqualifiedVersionless();
-		IIdType id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG").getId().toUnqualifiedVersionless();
+
-		assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?name=FAMILY1&organization=Organization%2FORG"));
+		myMessages.clear();
+
 		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
 		assertEquals(1, uniques.size());
 		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
@@ -1118,9 +1154,12 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		pt1.addName().setFamily("FAMILY1");
 		pt1.setManagingOrganization(new Reference("Organization/ORG"));
 
-		SearchBuilder.resetLastHandlerMechanismForUnitTest();
+		id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG", mySrd).getId().toUnqualifiedVersionless();
-		id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG").getId().toUnqualifiedVersionless();
+
-		assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?name=FAMILY1&organization=Organization%2FORG"));
+		myMessages.clear();
+
 		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
 		assertEquals(1, uniques.size());
 		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
@@ -1128,6 +1167,10 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 
 	}
 
+	private void logCapturedMessages() {
+		ourLog.info("Messages:\n  {}", String.join("\n  ", myMessages));
+	}
+
 	@Test
 	public void testUniqueValuesAreIndexed_StringAndReference() {
 		createUniqueNameAndManagingOrganizationSps();
@@ -1375,6 +1418,93 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 
 	}
 
+
+	@Test
+	public void testDetectUniqueSearchParams() {
+		createUniqueBirthdateAndGenderSps();
+		List<JpaRuntimeSearchParam> params = mySearchParamRegistry.getActiveUniqueSearchParams("Patient");
+
+		assertEquals(1, params.size());
+		assertEquals(params.get(0).isUnique(), true);
+		assertEquals(2, params.get(0).getCompositeOf().size());
+		// Should be alphabetical order
+		assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
+		assertEquals("gender", params.get(0).getCompositeOf().get(1).getName());
+	}
+
+	@Test
+	public void testDuplicateUniqueValuesAreRejected() {
+		createUniqueBirthdateAndGenderSps();
+
+		Patient pt1 = new Patient();
+		pt1.setGender(Enumerations.AdministrativeGender.MALE);
+		pt1.setBirthDateElement(new DateType("2011-01-01"));
+		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
+
+		try {
+			myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
+			fail();
+		} catch (PreconditionFailedException e) {
+			// good
+		}
+
+		Patient pt2 = new Patient();
+		pt2.setGender(Enumerations.AdministrativeGender.MALE);
+		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
+
+		pt2 = new Patient();
+		pt2.setId(id2);
+		pt2.setGender(Enumerations.AdministrativeGender.MALE);
+		pt2.setBirthDateElement(new DateType("2011-01-01"));
+		try {
+			myPatientDao.update(pt2);
+			fail();
+		} catch (PreconditionFailedException e) {
+			// good
+		}
+
+	}
+
+	@Test
+	public void testReplaceOneWithAnother() {
+		createUniqueBirthdateAndGenderSps();
+
+		Patient pt1 = new Patient();
+		pt1.setGender(Enumerations.AdministrativeGender.MALE);
+		pt1.setBirthDateElement(new DateType("2011-01-01"));
+		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualified();
+		assertNotNull(id1);
+
+		ourLog.info("** Replacing");
+
+		pt1 = new Patient();
+		pt1.setId(id1);
+		pt1.setGender(Enumerations.AdministrativeGender.FEMALE);
+		pt1.setBirthDateElement(new DateType("2011-01-01"));
+		id1 = myPatientDao.update(pt1).getId().toUnqualified();
+		assertNotNull(id1);
+		assertEquals("2", id1.getVersionIdPart());
+
+		Patient pt2 = new Patient();
+		pt2.setGender(Enumerations.AdministrativeGender.MALE);
+		pt2.setBirthDateElement(new DateType("2011-01-01"));
+		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
+
+		myMessages.clear();
+		SearchParameterMap params = new SearchParameterMap();
+		params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
+		params.add("birthdate", new DateParam("2011-01-01"));
+		IBundleProvider results = myPatientDao.search(params, mySrd);
+		String searchId = results.getUuid();
+		assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id2.getValue()));
+
+		logCapturedMessages();
+		assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
+		myMessages.clear();
+
+	}
+
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java

@@ -1,34 +1,20 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.hamcrest.Matchers.containsString;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
-import static org.hamcrest.Matchers.not;
+import ca.uhn.fhir.util.TestUtil;
-import static org.hamcrest.Matchers.stringContainsInOrder;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.CodeType;
-import org.hl7.fhir.r4.model.CodeableConcept;
-import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.StringType;
-import org.hl7.fhir.r4.model.UriType;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.*;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
+import java.io.IOException;
-import ca.uhn.fhir.util.TestUtil;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
 
 public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
 
@@ -224,7 +210,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
 
 	
 	@Test
-	public void testValiedateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
+	public void testValidateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
 		IPrimitiveType<String> display = null;
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu3Test.java

@@ -36,6 +36,7 @@ import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.TimeUnit;
 import java.util.stream.Collectors;
 
+import static org.awaitility.Awaitility.await;
 import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.*;
 
@@ -471,6 +472,9 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
 		assertEquals(SubscriptionMatchingStrategy.IN_MEMORY.toString(), tag.getCode());
 		assertEquals("In-memory", tag.getDisplay());
 
+		// Wait for subscription to be moved to active
+		await().until(()-> Subscription.SubscriptionStatus.ACTIVE.equals(ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute().getStatus()));
+
 		Subscription subscriptionActivated = ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute();
 		assertEquals(Subscription.SubscriptionStatus.ACTIVE, subscriptionActivated.getStatus());
 		tags = subscriptionActivated.getMeta().getTag();
@@ -495,6 +499,9 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
 		assertEquals(SubscriptionMatchingStrategy.DATABASE.toString(), tag.getCode());
 		assertEquals("Database", tag.getDisplay());
 
+		// Wait for subscription to be moved to active
+		await().until(()-> Subscription.SubscriptionStatus.ACTIVE.equals(ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute().getStatus()));
+
 		Subscription subscription = ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute();
 		assertEquals(Subscription.SubscriptionStatus.ACTIVE, subscription.getStatus());
 		tags = subscription.getMeta().getTag();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java

@@ -177,7 +177,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 			myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertThat(e.getMessage(), containsString("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
+			assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
 		}
 
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java

@@ -2,17 +2,12 @@ package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
-import ca.uhn.fhir.jpa.entity.TermConceptMap;
+import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
-import org.hl7.fhir.r4.model.UriType;
 import org.junit.*;
 import org.junit.rules.ExpectedException;
 import org.slf4j.Logger;
@@ -21,6 +16,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import java.io.IOException;
 import java.util.List;
 import java.util.Optional;
 
@@ -31,6 +27,8 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 	@Rule
 	public final ExpectedException expectedException = ExpectedException.none();
 	private IIdType myConceptMapId;
+	private IIdType myExtensionalCsId;
+	private IIdType myExtensionalVsId;
 
 	@Before
 	public void before() {
@@ -40,6 +38,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 	@After
 	public void after() {
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
 	}
 	
 	private void createAndPersistConceptMap() {
@@ -56,6 +55,39 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		});
 	}
 
+	private void loadAndPersistCodeSystemAndValueSet() throws IOException {
+		loadAndPersistCodeSystem();
+		loadAndPersistValueSet();
+	}
+
+	private void loadAndPersistCodeSystem() throws IOException {
+		CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
+		persistCodeSystem(codeSystem);
+	}
+
+	private void persistCodeSystem(CodeSystem theCodeSystem) {
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+				myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
+			}
+		});
+	}
+
+	private void loadAndPersistValueSet() throws IOException {
+		ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
+		persistValueSet(valueSet);
+	}
+
+	private void persistValueSet(ValueSet theValueSet) {
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+				myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
+			}
+		});
+	}
+
 	@Test
 	public void testCreateConceptMapWithMissingSourceSystem() {
 		ConceptMap conceptMap = new ConceptMap();
@@ -137,6 +169,16 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testDuplicateCodeSystemUrls() throws Exception {
+		loadAndPersistCodeSystem();
+
+		expectedException.expect(UnprocessableEntityException.class);
+		expectedException.expectMessage("Can not create multiple CodeSystem resources with CodeSystem.url \"http://acme.org\", already have one with resource ID: CodeSystem/" + myExtensionalCsId.getIdPart());
+
+		loadAndPersistCodeSystem();
+	}
+
 	@Test
 	public void testDuplicateConceptMapUrls() {
 		createAndPersistConceptMap();
@@ -147,6 +189,19 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		createAndPersistConceptMap();
 	}
 
+	@Test
+	public void testDuplicateValueSetUrls() throws Exception {
+		myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+		// DM 2019-03-05 - We pre-load our custom CodeSystem otherwise pre-expansion of the ValueSet will fail.
+		loadAndPersistCodeSystemAndValueSet();
+
+		expectedException.expect(UnprocessableEntityException.class);
+		expectedException.expectMessage("Can not create multiple ValueSet resources with ValueSet.url \"http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2\", already have one with resource ID: ValueSet/" + myExtensionalVsId.getIdPart());
+
+		loadAndPersistValueSet();
+	}
+
 	@Test
 	public void testStoreTermConceptMapAndChildren() {
 		createAndPersistConceptMap();
@@ -325,6 +380,63 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		});
 	}
 
+	@Test
+	public void testStoreTermValueSetAndChildren() throws Exception {
+		myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+		loadAndPersistCodeSystemAndValueSet();
+
+		CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+		ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+		ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+		ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+				Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
+				assertTrue(optionalValueSetByResourcePid.isPresent());
+
+				Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
+				assertTrue(optionalValueSetByUrl.isPresent());
+
+				TermValueSet valueSet = optionalValueSetByUrl.get();
+				assertSame(optionalValueSetByResourcePid.get(), valueSet);
+				ourLog.info("ValueSet:\n" + valueSet.toString());
+				assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", valueSet.getUrl());
+				assertEquals("Terminology Services Connectation #1 Extensional case #2", valueSet.getName());
+				assertEquals(codeSystem.getConcept().size(), valueSet.getCodes().size());
+
+				TermValueSetCode code = valueSet.getCodes().get(0);
+				ourLog.info("Code:\n" + code.toString());
+				assertEquals("http://acme.org", code.getSystem());
+				assertEquals("8450-9", code.getCode());
+				assertEquals("Systolic blood pressure--expiration", code.getDisplay());
+
+				code = valueSet.getCodes().get(1);
+				ourLog.info("Code:\n" + code.toString());
+				assertEquals("http://acme.org", code.getSystem());
+				assertEquals("11378-7", code.getCode());
+				assertEquals("Systolic blood pressure at First encounter", code.getDisplay());
+
+				// ...
+
+				code = valueSet.getCodes().get(22);
+				ourLog.info("Code:\n" + code.toString());
+				assertEquals("http://acme.org", code.getSystem());
+				assertEquals("8491-3", code.getCode());
+				assertEquals("Systolic blood pressure 1 hour minimum", code.getDisplay());
+
+				code = valueSet.getCodes().get(23);
+				ourLog.info("Code:\n" + code.toString());
+				assertEquals("http://acme.org", code.getSystem());
+				assertEquals("8492-1", code.getCode());
+				assertEquals("Systolic blood pressure 8 hour minimum", code.getDisplay());
+			}
+		});
+	}
+
 	@Test
 	public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
 		createAndPersistConceptMap();

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java

@@ -102,7 +102,7 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
 		Validate.notNull(myNullable);
 
 		if (myColumnType == ColumnTypeEnum.STRING) {
-			Validate.notNull(myColumnLength);
+			Validate.notNull(myColumnLength, "No length specified for " + ColumnTypeEnum.STRING + " column {}.", getColumnName());
 		} else {
 			Validate.isTrue(myColumnLength == null);
 		}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -20,6 +20,9 @@ package ca.uhn.fhir.jpa.migrate.tasks;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import ca.uhn.fhir.jpa.migrate.taskdef.AddColumnTask;
 import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
@@ -56,7 +59,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		init400();
 	}
 
-	private void init400() {
+	protected void init400() {
 		Builder version = forVersion(VersionEnum.V4_0_0);
 
 		version.onTable("TRM_CONCEPT_MAP_GROUP")
@@ -75,6 +78,41 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			.renameColumn("mySystem", "SYSTEM_URL")
 			.renameColumn("mySystemVersion", "SYSTEM_VERSION")
 			.renameColumn("myValueSet", "VALUESET_URL");
+
+		// TermValueSet
+		version.startSectionWithMessage("Processing table: TRM_VALUESET");
+		version.addIdGenerator("SEQ_VALUESET_PID");
+		Builder.BuilderAddTableByColumns termValueSetTable = version.addTableByColumns("TRM_VALUESET", "PID");
+		termValueSetTable.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
+		termValueSetTable.addColumn("URL").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermValueSet.MAX_URL_LENGTH);
+		termValueSetTable
+			.addIndex("IDX_VALUESET_URL")
+			.unique(true)
+			.withColumns("URL");
+		termValueSetTable.addColumn("RES_ID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
+		termValueSetTable
+			.addForeignKey("FK_TRMVALUESET_RES")
+			.toColumn("RES_ID")
+			.references("HFJ_RESOURCE", "RES_ID");
+		termValueSetTable.addColumn("NAME").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermValueSet.MAX_NAME_LENGTH);
+
+		// TermValueSetCode
+		version.startSectionWithMessage("Processing table: TRM_VALUESET_CODE");
+		version.addIdGenerator("SEQ_VALUESET_CODE_PID");
+		Builder.BuilderAddTableByColumns termValueSetCodeTable = version.addTableByColumns("TRM_VALUESET_CODE", "PID");
+		termValueSetCodeTable.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
+		termValueSetCodeTable.addColumn("VALUESET_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
+		termValueSetCodeTable
+			.addForeignKey("FK_TRM_VALUESET_PID")
+			.toColumn("VALUESET_PID")
+			.references("TRM_VALUESET", "PID");
+		termValueSetCodeTable.addColumn("SYSTEM").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermCodeSystem.MAX_URL_LENGTH);
+		termValueSetCodeTable.addColumn("CODE").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermConcept.MAX_CODE_LENGTH);
+		termValueSetCodeTable
+			.addIndex("IDX_VALUESET_CODE_CS_CD")
+			.unique(false)
+			.withColumns("SYSTEM", "CODE");
+		termValueSetCodeTable.addColumn("DISPLAY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermConcept.MAX_DESC_LENGTH);
 	}
 
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java

@@ -446,7 +446,7 @@ public class SearchParameterMap implements Serializable {
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		if (isEmpty() == false) {
-			b.append("params", super.toString());
+			b.append("params", mySearchParameterMap);
 		}
 		if (getIncludes().isEmpty() == false) {
 			b.append("includes", getIncludes());

hapi-fhir-structures-dstu2/pom.xml

@@ -210,6 +210,12 @@
 			<artifactId>spring-web</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-test-utilities</artifactId>
+			<version>${project.version}</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<build>

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

@@ -1,14 +1,18 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.hamcrest.Matchers.containsString;
+import ca.uhn.fhir.context.FhirContext;
-import static org.hamcrest.Matchers.emptyOrNullString;
+import ca.uhn.fhir.model.api.IResource;
-import static org.hamcrest.Matchers.is;
+import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
-import static org.junit.Assert.assertEquals;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
-import static org.junit.Assert.assertNull;
+import ca.uhn.fhir.model.primitive.IdDt;
-import static org.junit.Assert.assertThat;
+import ca.uhn.fhir.rest.annotation.Create;
-
+import ca.uhn.fhir.rest.annotation.IdParam;
-import java.util.concurrent.TimeUnit;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
-
+import ca.uhn.fhir.rest.annotation.Update;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpPost;
@@ -26,19 +30,12 @@ import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.context.FhirContext;
+import java.util.concurrent.TimeUnit;
-import ca.uhn.fhir.model.api.IResource;
+
-import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
+import static org.hamcrest.CoreMatchers.is;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
+import static org.hamcrest.Matchers.containsString;
-import ca.uhn.fhir.model.primitive.IdDt;
+import static org.hamcrest.Matchers.emptyOrNullString;
-import ca.uhn.fhir.rest.annotation.Create;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.ResourceParam;
-import ca.uhn.fhir.rest.annotation.Update;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.util.TestUtil;
 
 public class PreferTest {
 	private static CloseableHttpClient ourClient;

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/InterceptorUserDataMapDstu2Test.java

@@ -1,19 +1,27 @@
 package ca.uhn.fhir.rest.server.interceptor;
 
-import static org.hamcrest.Matchers.contains;
+import ca.uhn.fhir.context.FhirContext;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertThat;
-import static org.mockito.Mockito.mock;
-
-import java.util.*;
-import java.util.concurrent.TimeUnit;
-
 import ca.uhn.fhir.interceptor.api.Hook;
 import ca.uhn.fhir.interceptor.api.Interceptor;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
+import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
+import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.primitive.DateDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -24,37 +32,30 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.junit.*;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
 
-import ca.uhn.fhir.context.FhirContext;
+import java.util.*;
-import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
+import java.util.concurrent.TimeUnit;
-import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
+
-import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import static org.awaitility.Awaitility.await;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
+import static org.hamcrest.Matchers.contains;
-import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
-import ca.uhn.fhir.model.primitive.*;
-import ca.uhn.fhir.rest.annotation.*;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.IResourceProvider;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
-import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.util.TestUtil;
 
 public class InterceptorUserDataMapDstu2Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(InterceptorUserDataMapDstu2Test.class);
 	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx = FhirContext.forDstu2();
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(InterceptorUserDataMapDstu2Test.class);
 	private static int ourPort;
 	private static Server ourServer;
 	private static RestfulServer servlet;
 	private final Object myKey = "KEY";
+	private final Object myValue = "VALUE";
 	private Map<Object, Object> myMap;
 	private Set<String> myMapCheckMethods;
-	private final Object myValue = "VALUE";
 
 	@Before
 	public void before() {
@@ -78,7 +79,7 @@ public class InterceptorUserDataMapDstu2Test {
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info(myMapCheckMethods.toString());
-		assertThat(myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "preProcessOutgoingException", "handleException", "processingCompleted"));
+		await().until(() -> myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "preProcessOutgoingException", "handleException", "processingCompleted"));
 	}
 
 	@Test
@@ -95,8 +96,7 @@ public class InterceptorUserDataMapDstu2Test {
 
 		}
 
-		ourLog.info(myMapCheckMethods.toString());
+		await().until(() -> myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "outgoingResponse", "processingCompletedNormally", "processingCompleted"));
-		assertThat(myMapCheckMethods.toString(), myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "outgoingResponse", "processingCompletedNormally", "processingCompleted"));
 	}
 
 	private void updateMapUsing(Map<Object, Object> theUserData, String theMethod) {
@@ -111,125 +111,6 @@ public class InterceptorUserDataMapDstu2Test {
 		myMapCheckMethods.add(theMethod);
 	}
 
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		JettyUtil.closeServer(ourServer);
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-	@BeforeClass
-	public static void beforeClass() throws Exception {
-		ourServer = new Server(0);
-
-		ServletHandler proxyHandler = new ServletHandler();
-		servlet = new RestfulServer(ourCtx);
-		
-		servlet.setResourceProviders(new DummyPatientResourceProvider());
-		servlet.setPlainProviders(new PlainProvider());
-		
-		ServletHolder servletHolder = new ServletHolder(servlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		ourServer.setHandler(proxyHandler);
-		JettyUtil.startServer(ourServer);
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
-
-		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
-		HttpClientBuilder builder = HttpClientBuilder.create();
-		builder.setConnectionManager(connectionManager);
-		ourClient = builder.build();
-
-	}
-
-	public static class DummyPatientResourceProvider implements IResourceProvider {
-
-		private Patient createPatient1() {
-			Patient patient = new Patient();
-			patient.addIdentifier();
-			patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
-			patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
-			patient.getIdentifier().get(0).setValue("00001");
-			patient.addName();
-			patient.getName().get(0).addFamily("Test");
-			patient.getName().get(0).addGiven("PatientOne");
-			patient.setGender(AdministrativeGenderEnum.MALE);
-			patient.getId().setValue("1");
-			return patient;
-		}
-
-		public Map<String, Patient> getIdToPatient() {
-			Map<String, Patient> idToPatient = new HashMap<String, Patient>();
-			{
-				Patient patient = createPatient1();
-				idToPatient.put("1", patient);
-			}
-			{
-				Patient patient = new Patient();
-				patient.getIdentifier().add(new IdentifierDt());
-				patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
-				patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
-				patient.getIdentifier().get(0).setValue("00002");
-				patient.getName().add(new HumanNameDt());
-				patient.getName().get(0).addFamily("Test");
-				patient.getName().get(0).addGiven("PatientTwo");
-				patient.setGender(AdministrativeGenderEnum.FEMALE);
-				patient.getId().setValue("2");
-				idToPatient.put("2", patient);
-			}
-			return idToPatient;
-		}
-
-		/**
-		 * Retrieve the resource by its identifier
-		 * 
-		 * @param theId
-		 *            The resource identity
-		 * @return The resource
-		 */
-		@Read()
-		public Patient getResourceById(@IdParam IdDt theId) {
-			if (theId.getIdPart().equals("EX")) {
-				throw new InvalidRequestException("FOO");
-			}
-			String key = theId.getIdPart();
-			Patient retVal = getIdToPatient().get(key);
-			return retVal;
-		}
-
-		/**
-		 * Retrieve the resource by its identifier
-		 * 
-		 * @param theId
-		 *            The resource identity
-		 * @return The resource
-		 */
-		@Search()
-		public List<Patient> getResourceById(@RequiredParam(name = "_id") String theId) {
-			throw new InvalidRequestException("FOO");
-		}
-
-		@Override
-		public Class<Patient> getResourceType() {
-			return Patient.class;
-		}
-
-		@Operation(name = "$everything", idempotent = true)
-		public Bundle patientTypeOperation(@OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
-
-			Bundle retVal = new Bundle();
-			// Populate bundle with matching resources
-			return retVal;
-		}
-
-		@Operation(name = "$everything", idempotent = true)
-		public Bundle patientTypeOperation(@IdParam IdDt theId, @OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
-
-			Bundle retVal = new Bundle();
-			// Populate bundle with matching resources
-			return retVal;
-		}
-
-	}
-
 	@Interceptor
 	public class MyInterceptor {
 
@@ -276,6 +157,94 @@ public class InterceptorUserDataMapDstu2Test {
 
 	}
 
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		private Patient createPatient1() {
+			Patient patient = new Patient();
+			patient.addIdentifier();
+			patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
+			patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+			patient.getIdentifier().get(0).setValue("00001");
+			patient.addName();
+			patient.getName().get(0).addFamily("Test");
+			patient.getName().get(0).addGiven("PatientOne");
+			patient.setGender(AdministrativeGenderEnum.MALE);
+			patient.getId().setValue("1");
+			return patient;
+		}
+
+		public Map<String, Patient> getIdToPatient() {
+			Map<String, Patient> idToPatient = new HashMap<String, Patient>();
+			{
+				Patient patient = createPatient1();
+				idToPatient.put("1", patient);
+			}
+			{
+				Patient patient = new Patient();
+				patient.getIdentifier().add(new IdentifierDt());
+				patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
+				patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+				patient.getIdentifier().get(0).setValue("00002");
+				patient.getName().add(new HumanNameDt());
+				patient.getName().get(0).addFamily("Test");
+				patient.getName().get(0).addGiven("PatientTwo");
+				patient.setGender(AdministrativeGenderEnum.FEMALE);
+				patient.getId().setValue("2");
+				idToPatient.put("2", patient);
+			}
+			return idToPatient;
+		}
+
+		/**
+		 * Retrieve the resource by its identifier
+		 *
+		 * @param theId The resource identity
+		 * @return The resource
+		 */
+		@Read()
+		public Patient getResourceById(@IdParam IdDt theId) {
+			if (theId.getIdPart().equals("EX")) {
+				throw new InvalidRequestException("FOO");
+			}
+			String key = theId.getIdPart();
+			Patient retVal = getIdToPatient().get(key);
+			return retVal;
+		}
+
+		/**
+		 * Retrieve the resource by its identifier
+		 *
+		 * @param theId The resource identity
+		 * @return The resource
+		 */
+		@Search()
+		public List<Patient> getResourceById(@RequiredParam(name = "_id") String theId) {
+			throw new InvalidRequestException("FOO");
+		}
+
+		@Override
+		public Class<Patient> getResourceType() {
+			return Patient.class;
+		}
+
+		@Operation(name = "$everything", idempotent = true)
+		public Bundle patientTypeOperation(@OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
+
+			Bundle retVal = new Bundle();
+			// Populate bundle with matching resources
+			return retVal;
+		}
+
+		@Operation(name = "$everything", idempotent = true)
+		public Bundle patientTypeOperation(@IdParam IdDt theId, @OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
+
+			Bundle retVal = new Bundle();
+			// Populate bundle with matching resources
+			return retVal;
+		}
+
+	}
+
 	public static class PlainProvider {
 
 		@Operation(name = "$everything", idempotent = true)
@@ -288,4 +257,33 @@ public class InterceptorUserDataMapDstu2Test {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		JettyUtil.closeServer(ourServer);
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourServer = new Server(0);
+
+		ServletHandler proxyHandler = new ServletHandler();
+		servlet = new RestfulServer(ourCtx);
+
+		servlet.setResourceProviders(new DummyPatientResourceProvider());
+		servlet.setPlainProviders(new PlainProvider());
+
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		JettyUtil.startServer(ourServer);
+		ourPort = JettyUtil.getPortForStartedServer(ourServer);
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
 }

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

@@ -18,9 +18,9 @@ import net.sf.json.JsonConfig;
 import org.apache.commons.io.IOUtils;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Address.AddressUse;
 import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
-import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Bundle.BundleType;
 import org.hl7.fhir.dstu3.model.CapabilityStatement.UnknownContentCode;
@@ -33,7 +33,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
-import org.mockito.Mockito;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -45,9 +44,8 @@ import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
-import static org.mockito.Matchers.any;
+import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Matchers.eq;
+import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Matchers.isNull;
 import static org.mockito.Mockito.nullable;
 import static org.mockito.Mockito.*;
 
@@ -110,16 +108,16 @@ public class JsonParserDstu3Test {
 		// Deserialize then check that valueReference value is still correct
 		fhirPat = parser.parseResource(Patient.class, output);
 
-		List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
+		List<Extension> extensions = fhirPat.getExtensionsByUrl("x1");
-		Assert.assertEquals(1, extlst.size());
+		Assert.assertEquals(1, extensions.size());
-		Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
+		Assert.assertEquals(refVal, ((Reference) extensions.get(0).getValue()).getReference());
 	}
 
 	/**
 	 * See #544
 	 */
 	@Test
-	public void testBundleStitchReferencesByUuid() throws Exception {
+	public void testBundleStitchReferencesByUuid() {
 		Bundle bundle = new Bundle();
 
 		DocumentManifest dm = new DocumentManifest();
@@ -175,7 +173,7 @@ public class JsonParserDstu3Test {
 	}
 
 	@Test
-	public void testCustomUrlExtensioninBundle() {
+	public void testCustomUrlExtensionInBundle() {
 		final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
 
 		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
@@ -213,7 +211,7 @@ public class JsonParserDstu3Test {
 	 * See #276
 	 */
 	@Test
-	public void testDoubleEncodingContainedResources() throws Exception {
+	public void testDoubleEncodingContainedResources() {
 		Patient patient = new Patient();
 		patient.setId("#patient-1");
 		patient.setActive(true);
@@ -236,7 +234,7 @@ public class JsonParserDstu3Test {
 	}
 
 	@Test
-	public void testEncodeAndParseExtensions() throws Exception {
+	public void testEncodeAndParseExtensions() {
 
 		Patient patient = new Patient();
 		patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
@@ -402,6 +400,7 @@ public class JsonParserDstu3Test {
 	/**
 	 * See #336
 	 */
+	@SuppressWarnings("SpellCheckingInspection")
 	@Test
 	public void testEncodeAndParseNullPrimitiveWithExtensions() {
 
@@ -458,7 +457,7 @@ public class JsonParserDstu3Test {
 		Patient p = new Patient();
 		p.addName().setFamily("FAMILY");
 
-		List<Coding> labels = new ArrayList<Coding>();
+		List<Coding> labels = new ArrayList<>();
 		labels.add(new Coding().setSystem("SYSTEM1").setCode("CODE1").setDisplay("DISPLAY1").setVersion("VERSION1"));
 		labels.add(new Coding().setSystem("SYSTEM2").setCode("CODE2").setDisplay("DISPLAY2").setVersion("VERSION2"));
 		p.getMeta().getSecurity().addAll(labels);
@@ -602,7 +601,7 @@ public class JsonParserDstu3Test {
 	 */
 	@Test
 	public void testEncodeEmptyTag() {
-		ArrayList<Coding> tagList = new ArrayList<Coding>();
+		ArrayList<Coding> tagList = new ArrayList<>();
 		tagList.add(new Coding());
 		tagList.add(new Coding().setDisplay("Label"));
 
@@ -618,7 +617,7 @@ public class JsonParserDstu3Test {
 	 */
 	@Test
 	public void testEncodeEmptyTag2() {
-		ArrayList<Coding> tagList = new ArrayList<Coding>();
+		ArrayList<Coding> tagList = new ArrayList<>();
 		tagList.add(new Coding().setSystem("scheme").setCode("code"));
 		tagList.add(new Coding().setDisplay("Label"));
 
@@ -715,13 +714,26 @@ public class JsonParserDstu3Test {
 			.setValue(new Reference("Practitioner/A"));
 
 		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
-		parser.setDontEncodeElements(new HashSet<String>(Arrays.asList("*.id", "*.meta")));
+		parser.setDontEncodeElements(new HashSet<>(Arrays.asList("*.id", "*.meta")));
 
 		String encoded = parser.encodeResourceToString(p);
 		ourLog.info(encoded);
 
 		assertThat(encoded, containsString("http://foo"));
 		assertThat(encoded, containsString("Practitioner/A"));
+
+		// Now with exclude
+
+		parser = ourCtx.newJsonParser().setPrettyPrint(true);
+		parser.setDontEncodeElements(new HashSet<>(Arrays.asList("*.id", "*.meta", "*.extension")));
+
+		encoded = parser.encodeResourceToString(p);
+		ourLog.info(encoded);
+
+		assertThat(encoded, not(containsString("http://foo")));
+		assertThat(encoded, not(containsString("Practitioner/A")));
+
+
 	}
 
 	@Test
@@ -818,7 +830,7 @@ public class JsonParserDstu3Test {
 		TestPatientFor327 patient = new TestPatientFor327();
 		patient.setBirthDateElement(new DateType("2016-04-14"));
 
-		List<Reference> conditions = new ArrayList<Reference>();
+		List<Reference> conditions = new ArrayList<>();
 		Condition condition = new Condition();
 		condition.addBodySite().setText("BODY SITE");
 		conditions.add(new Reference(condition));
@@ -896,7 +908,7 @@ public class JsonParserDstu3Test {
 		ourLog.info(enc);
 		assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
 
-		parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
+		parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<>());
 		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
 		ourLog.info(enc);
 		assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
@@ -930,12 +942,12 @@ public class JsonParserDstu3Test {
 		ourLog.info(enc);
 		assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
 
-		ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(Arrays.asList("Patient.managingOrganization"));
+		ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(Collections.singletonList("Patient.managingOrganization"));
 		enc = parser.setPrettyPrint(true).encodeResourceToString(p);
 		ourLog.info(enc);
 		assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
 
-		ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(new HashSet<String>(Arrays.asList("Patient.managingOrganization")));
+		ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(new HashSet<>(Collections.singletonList("Patient.managingOrganization")));
 		enc = parser.setPrettyPrint(true).encodeResourceToString(p);
 		ourLog.info(enc);
 		assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
@@ -1013,7 +1025,7 @@ public class JsonParserDstu3Test {
 	}
 
 	@Test
-	public void testEncodeNarrativeSuppressed() throws Exception {
+	public void testEncodeNarrativeSuppressed() {
 		Patient patient = new Patient();
 		patient.setId("Patient/1/_history/1");
 		patient.getText().setDivAsString("<div>THE DIV</div>");
@@ -1064,6 +1076,57 @@ public class JsonParserDstu3Test {
 		assertThat(encoded, not(containsString("maritalStatus")));
 	}
 
+	/**
+	 * We specifically include extensions on CapabilityStatment even in
+	 * summary mode, since this is behaviour that people depend on
+	 */
+	@Test
+	public void testEncodeSummaryCapabilityStatementExtensions() {
+
+		CapabilityStatement cs = new CapabilityStatement();
+		CapabilityStatement.CapabilityStatementRestComponent rest = cs.addRest();
+		rest.setMode(CapabilityStatement.RestfulCapabilityMode.CLIENT);
+		rest.getSecurity()
+			.addExtension()
+			.setUrl("http://foo")
+			.setValue(new StringType("bar"));
+
+		cs.getVersionElement().addExtension()
+			.setUrl("http://goo")
+			.setValue(new StringType("ber"));
+
+		String encoded = ourCtx.newJsonParser().setSummaryMode(true).setPrettyPrint(true).setPrettyPrint(true).encodeResourceToString(cs);
+		ourLog.info(encoded);
+
+		assertThat(encoded, (containsString("http://foo")));
+		assertThat(encoded, (containsString("bar")));
+		assertThat(encoded, (containsString("http://goo")));
+		assertThat(encoded, (containsString("ber")));
+	}
+
+	@Test
+	public void testEncodeSummaryPatientExtensions() {
+
+		Patient cs = new Patient();
+		Address address = cs.addAddress();
+		address.setCity("CITY");
+		address
+			.addExtension()
+			.setUrl("http://foo")
+			.setValue(new StringType("bar"));
+		address.getCityElement().addExtension()
+			.setUrl("http://goo")
+			.setValue(new StringType("ber"));
+
+		String encoded = ourCtx.newJsonParser().setSummaryMode(true).setPrettyPrint(true).setPrettyPrint(true).encodeResourceToString(cs);
+		ourLog.info(encoded);
+
+		assertThat(encoded, not(containsString("http://foo")));
+		assertThat(encoded, not(containsString("bar")));
+		assertThat(encoded, not(containsString("http://goo")));
+		assertThat(encoded, not(containsString("ber")));
+	}
+
 	@Test
 	public void testEncodeSummary2() {
 		Patient patient = new Patient();
@@ -1107,7 +1170,7 @@ public class JsonParserDstu3Test {
 	 * See #241
 	 */
 	@Test
-	public void testEncodeThenParseShouldNotAddSpuriousId() throws Exception {
+	public void testEncodeThenParseShouldNotAddSpuriousId() {
 		Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatus.CONFIRMED);
 		Bundle bundle = new Bundle();
 		BundleEntryComponent entry = new Bundle.BundleEntryComponent();
@@ -1126,7 +1189,7 @@ public class JsonParserDstu3Test {
 	}
 
 	@Test
-	public void testEncodeUndeclaredBlock() throws Exception {
+	public void testEncodeUndeclaredBlock() {
 		FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
 		source.getMessageHeaderApplicationId().setValue("APPID");
 		source.setName("NAME");
@@ -1153,7 +1216,7 @@ public class JsonParserDstu3Test {
 		Patient patient = new Patient();
 		patient.addAddress().setUse(AddressUse.HOME);
 		EnumFactory<AddressUse> fact = new AddressUseEnumFactory();
-		PrimitiveType<AddressUse> enumeration = new Enumeration<AddressUse>(fact).setValue(AddressUse.HOME);
+		PrimitiveType<AddressUse> enumeration = new Enumeration<>(fact).setValue(AddressUse.HOME);
 		patient.addExtension().setUrl("urn:foo").setValue(enumeration);
 
 		String val = parser.encodeResourceToString(patient);
@@ -1168,7 +1231,7 @@ public class JsonParserDstu3Test {
 	}
 
 	@Test
-	public void testEncodeWithDontEncodeElements() throws Exception {
+	public void testEncodeWithDontEncodeElements() {
 		Patient patient = new Patient();
 		patient.setId("123");
 
@@ -1224,7 +1287,7 @@ public class JsonParserDstu3Test {
 		{
 			IParser p = ourCtx.newJsonParser();
 			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setEncodeElements(new HashSet<>(Collections.singletonList("Patient.name")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(patient);
 			ourLog.info(out);
@@ -1438,7 +1501,7 @@ public class JsonParserDstu3Test {
 		String res = "{ \"resourceType\": \"ValueSet\", \"url\": \"http://sample/ValueSet/education-levels\", \"version\": \"1\", \"name\": \"Education Levels\", \"status\": \"draft\", \"compose\": { \"include\": [ { \"filter\": [ { \"property\": \"n\", \"op\": \"n\", \"value\": \"365460000\" } ], \"system\": \"http://snomed.info/sct\" } ], \"exclude\": [ { \"concept\": [ { \"code\": \"224298008\" }, { \"code\": \"365460000\" }, { \"code\": \"473462005\" }, { \"code\": \"424587006\" } ], \"system\": \"http://snomed.info/sct\" } ] }, \"description\": \"A selection of Education Levels\", \"text\": { \"status\": \"generated\", \"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"><h2>Education Levels</h2><tt>http://csiro.au/ValueSet/education-levels</tt><p>A selection of Education Levels</p></div>\" }, \"experimental\": true, \"date\": \"2016-07-26\" }";
 		IParser parser = ourCtx.newJsonParser();
 		parser.setParserErrorHandler(new StrictErrorHandler());
-		ValueSet parsed = parser.parseResource(ValueSet.class, res);
+		parser.parseResource(ValueSet.class, res);
 		fail("DataFormat Invalid attribute exception should be thrown");
 	}
 
@@ -1671,53 +1734,6 @@ public class JsonParserDstu3Test {
 		assertThat(reencoded, containsString("contained"));
 	}
 
-	@Test
-	@Ignore
-	public void testParseAndEncodeBundleNewStyle() throws Exception {
-		String content = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/bundle-example.json"), StandardCharsets.UTF_8);
-
-		Bundle parsed = ourCtx.newJsonParser().parseResource(Bundle.class, content);
-		assertEquals("Bundle/example/_history/1", parsed.getIdElement().getValue());
-		assertEquals("1", parsed.getIdElement().getVersionIdPart());
-		assertEquals("2014-08-18T01:43:30Z", parsed.getMeta().getLastUpdatedElement().getValueAsString());
-		assertEquals("searchset", parsed.getType());
-		assertEquals(3, parsed.getTotal());
-		assertEquals("https://example.com/base/MedicationRequest?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink().get(0).getUrlElement().getValueAsString());
-		assertEquals("https://example.com/base/MedicationRequest?patient=347&_include=MedicationRequest.medication", parsed.getLink().get(1).getUrlElement().getValueAsString());
-
-		assertEquals(2, parsed.getEntry().size());
-		assertEquals("alternate", parsed.getEntry().get(0).getLink().get(0).getRelation());
-		assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", parsed.getEntry().get(0).getLink().get(0).getUrl());
-		assertEquals("http://foo?search", parsed.getEntry().get(0).getRequest().getUrlElement().getValueAsString());
-
-		MedicationRequest p = (MedicationRequest) parsed.getEntry().get(0).getResource();
-		assertEquals("Patient/347", p.getSubject().getReference());
-		assertEquals("2014-08-16T05:31:17Z", p.getMeta().getLastUpdatedElement().getValueAsString());
-		assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", p.getId());
-		// assertEquals("3123", p.getId());
-
-		Medication m = (Medication) parsed.getEntry().get(1).getResource();
-		assertEquals("http://example.com/base/Medication/example", m.getId());
-		assertSame(((Reference) p.getMedication()).getResource(), m);
-
-		String reencoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed);
-		ourLog.info(reencoded);
-
-		JsonConfig cfg = new JsonConfig();
-
-		JSON expected = JSONSerializer.toJSON(content.trim(), cfg);
-		JSON actual = JSONSerializer.toJSON(reencoded.trim(), cfg);
-
-		String exp = expected.toString().replace("\\r\\n", "\\n"); // .replace("&sect;", "§");
-		String act = actual.toString().replace("\\r\\n", "\\n");
-
-		ourLog.info("Expected: {}", exp);
-		ourLog.info("Actual  : {}", act);
-
-		assertEquals(exp, act);
-
-	}
-
 	@Test
 	public void testParseAndEncodeBundleWithUuidBase() {
 		//@formatter:off
@@ -2221,20 +2237,18 @@ public class JsonParserDstu3Test {
 
 	@Test(expected = DataFormatException.class)
 	public void testParseWithTrailingContent() {
-		//@formatter:off
 		String bundle = "{\n" +
 			"  \"resourceType\" : \"Bundle\",\n" +
 			"  \"total\" : 1\n" +
 			"}}";
-		//@formatter:on
 
-		Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
+		ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
 	}
 
 	@Test
 	@Ignore
 	public void testParseWithWrongTypeObjectShouldBeArray() throws Exception {
-		String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"));
+		String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"), Charsets.UTF_8);
 		try {
 			ourCtx.newJsonParser().parseResource(CapabilityStatement.class, input);
 			fail();
@@ -2346,14 +2360,14 @@ public class JsonParserDstu3Test {
 		ArgumentCaptor<ValueType> actual = ArgumentCaptor.forClass(ValueType.class);
 		ArgumentCaptor<ScalarType> expectedScalar = ArgumentCaptor.forClass(ScalarType.class);
 		ArgumentCaptor<ScalarType> actualScalar = ArgumentCaptor.forClass(ScalarType.class);
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(),
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(),
 			actualScalar.capture());
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR),
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), eq("_id"), eq(ValueType.OBJECT), expectedScalar.capture(), eq(ValueType.SCALAR),
 			actualScalar.capture());
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR),
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), eq("__v"), eq(ValueType.OBJECT), expectedScalar.capture(), eq(ValueType.SCALAR),
 			actualScalar.capture());
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(),
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), eq("_status"), eq(ValueType.OBJECT), expectedScalar.capture(),
-			Mockito.eq(ValueType.SCALAR), actualScalar.capture());
+			eq(ValueType.SCALAR), actualScalar.capture());
 
 		assertEquals("_id", elementName.getAllValues().get(0));
 		assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
@@ -2363,7 +2377,7 @@ public class JsonParserDstu3Test {
 	}
 
 	@Test
-	public void testValidateCustomStructure() throws Exception {
+	public void testValidateCustomStructure() {
 
 		FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
 		source.getMessageHeaderApplicationId().setValue("APPID");
@@ -2392,13 +2406,13 @@ public class JsonParserDstu3Test {
 		containedOrganization.getMeta().addProfile(UUID.randomUUID().toString());
 		containedOrganization.getMeta().setLastUpdated(new Date());
 		containedOrganization.getMeta().setVersionId(UUID.randomUUID().toString());
-		containedOrganization.getMeta().setSecurity(Arrays.asList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
+		containedOrganization.getMeta().setSecurity(Collections.singletonList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
-		containedOrganization.getMeta().setTag(Arrays.asList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
+		containedOrganization.getMeta().setTag(Collections.singletonList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
 
 		Patient patient = new Patient();
 		patient.setId(UUID.randomUUID().toString());
 		patient.getMeta().addProfile(UUID.randomUUID().toString());
-		patient.setGeneralPractitioner(Arrays.asList(new Reference(containedOrganization)));
+		patient.setGeneralPractitioner(Collections.singletonList(new Reference(containedOrganization)));
 
 		HashSet<String> excludeElementsInEncoded = new HashSet<>(); // ResourceMetaParams.EXCLUDE_ELEMENTS_IN_ENCODED
 		excludeElementsInEncoded.add("id");

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

@@ -12,6 +12,7 @@ import com.google.common.collect.Sets;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
+import org.hamcrest.Matchers;
 import org.hamcrest.collection.IsEmptyCollection;
 import org.hamcrest.core.StringContains;
 import org.hamcrest.text.StringContainsInOrder;
@@ -69,6 +70,35 @@ public class XmlParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
+	/**
+	 * We specifically include extensions on CapabilityStatment even in
+	 * summary mode, since this is behaviour that people depend on
+	 */
+	@Test
+	public void testEncodeSummaryCapabilityStatementExtensions() {
+
+		CapabilityStatement cs = new CapabilityStatement();
+		CapabilityStatement.CapabilityStatementRestComponent rest = cs.addRest();
+		rest.setMode(CapabilityStatement.RestfulCapabilityMode.CLIENT);
+		rest.getSecurity()
+			.addExtension()
+			.setUrl("http://foo")
+			.setValue(new StringType("bar"));
+
+		cs.getVersionElement().addExtension()
+			.setUrl("http://goo")
+			.setValue(new StringType("ber"));
+
+		String encoded = ourCtx.newXmlParser().setSummaryMode(true).setPrettyPrint(true).setPrettyPrint(true).encodeResourceToString(cs);
+		ourLog.info(encoded);
+
+		assertThat(encoded, Matchers.containsString("http://foo"));
+		assertThat(encoded, Matchers.containsString("bar"));
+		assertThat(encoded, Matchers.containsString("http://goo"));
+		assertThat(encoded, Matchers.containsString("ber"));
+	}
+
+
 	@Test
 	public void testEncodeInvalidMetaTime() {
 

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

@@ -264,6 +264,16 @@ public class ElementsParamR4Test {
 				assertEquals("mg", ((Quantity) procedure.getExtension().get(0).getValue()).getCode());
 			});
 
+		verifyXmlAndJson(
+			"http://localhost:" + ourPort + "/Procedure?_elements=Procedure.extension.value",
+			bundle -> {
+				Procedure procedure = (Procedure) bundle.getEntry().get(0).getResource();
+				assertEquals("SUBSETTED", procedure.getMeta().getTag().get(0).getCode());
+				assertEquals(0, procedure.getReasonCode().size());
+				assertEquals("1.1", ((Quantity) procedure.getExtension().get(0).getValue()).getValueElement().getValueAsString());
+				assertEquals("mg", ((Quantity) procedure.getExtension().get(0).getValue()).getCode());
+			});
+
 		verifyXmlAndJson(
 			"http://localhost:" + ourPort + "/Procedure?_elements=Procedure.extension.value.value",
 			bundle -> {

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

@@ -18,6 +18,7 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.hamcrest.CoreMatchers;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.*;
 import org.junit.AfterClass;
@@ -31,6 +32,8 @@ import java.util.List;
 import java.util.concurrent.TimeUnit;
 import java.util.function.Consumer;
 
+import static org.hamcrest.CoreMatchers.containsStringIgnoringCase;
+import static org.hamcrest.CoreMatchers.containsStringIgnoringCase;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
@@ -220,7 +223,7 @@ public class SummaryParamR4Test {
 				assertThat(responseContent, (containsString("entry")));
 				assertThat(responseContent, (containsString(">TEXT<")));
 				assertThat(responseContent, (containsString("Medication/123")));
-				assertThat(responseContent, not(containsStringIgnoringCase("note")));
+				assertThat(responseContent, not(CoreMatchers.containsStringIgnoringCase("note")));
 			}
 		);
 

hapi-fhir-test-utilities/pom.xml

@@ -46,6 +46,11 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+
+		<dependency>
+			<groupId>org.awaitility</groupId>
+			<artifactId>awaitility</artifactId>
+		</dependency>
 	</dependencies>
 
 	<build>

pom.xml

@@ -1022,6 +1022,25 @@
 				<artifactId>velocity-tools</artifactId>
 				<version>2.0</version>
 			</dependency>
+			<dependency>
+				<groupId>org.awaitility</groupId>
+				<artifactId>awaitility</artifactId>
+				<version>3.1.6</version>
+				<exclusions>
+					<exclusion>
+						<groupId>org.hamcrest</groupId>
+						<artifactId>java-hamcrest</artifactId>
+					</exclusion>
+					<exclusion>
+						<groupId>org.hamcrest</groupId>
+						<artifactId>hamcrest-core</artifactId>
+					</exclusion>
+					<exclusion>
+						<groupId>org.hamcrest</groupId>
+						<artifactId>hamcrest-library</artifactId>
+					</exclusion>
+				</exclusions>
+			</dependency>
 			<dependency>
 				<groupId>org.codehaus.plexus</groupId>
 				<artifactId>plexus-compiler-api</artifactId>
@@ -1792,23 +1811,6 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>license-maven-plugin</artifactId>
-				<inherited>false</inherited>
-				<executions>
-					<execution>
-						<id>update-project-license</id>
-						<phase>package</phase>
-						<goals>
-							<goal>update-project-license</goal>
-						</goals>
-						<configuration>
-							<licenseName>apache_v2</licenseName>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
 			<plugin>
 				<artifactId>maven-antrun-plugin</artifactId>
 				<inherited>false</inherited>
@@ -2196,9 +2198,27 @@
 	<profiles>
 		<profile>
 			<id>DIST</id>
-			<modules>
+			<build>
-				<!--<module>hapi-fhir-osgi-core</module>-->
+				<plugins>
-			</modules>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>license-maven-plugin</artifactId>
+						<inherited>false</inherited>
+						<executions>
+							<execution>
+								<id>update-project-license</id>
+								<phase>package</phase>
+								<goals>
+									<goal>update-project-license</goal>
+								</goals>
+								<configuration>
+									<licenseName>apache_v2</licenseName>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
 		</profile>
 		<profile>
 			<id>ROOT</id>

src/changes/changes.xml

@@ -266,6 +266,10 @@
 				A new server interceptor hook called PROCESSING_COMPLETED has been added. This
 				hook is called by the server at the end of processing every request (success and failure).
 			</action>
+			<action type="fix">
+				The <![CDATA[<code>_summary</code>]]> element was not always respected when encoding
+				JSON resources.
+			</action>
 		</release>
 		<release version="3.8.0" date="2019-05-30" description="Hippo">
 			<action type="fix">

src/site/xdoc/doc_jpa.xml

@@ -276,7 +276,7 @@ public DaoConfig daoConfig() {
 					If the client knows that they will only want a small number of results
 					(for example, a UI containing 20 results is being shown and the client
 					knows that they will never load the next page of results) the client
-					may also use the <code>nostore</code> directive along with a HAPI FHIR
+					may also use the <code>no-store</code> directive along with a HAPI FHIR
 					extension called <code>max-results</code> in order to specify that
 					only the given number of results should be fetched. This directive
 					disabled paging entirely for the request and causes the request to
@@ -285,7 +285,7 @@ public DaoConfig daoConfig() {
 				</p>
 				<div class="source">
 					<pre>
-						Cache-Control: nostore, max-results=20
+						Cache-Control: no-store, max-results=20
 					</pre>
 				</div>