Merge branch 'master' into ng_validation_s13n_interceptors

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

@@ -30,7 +30,6 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
 import ca.uhn.fhir.context.RuntimeChildContainedResources;
-import ca.uhn.fhir.context.RuntimeChildDirectResource;
 import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.IIdentifiableElement;
@@ -39,16 +38,15 @@ import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.parser.path.EncodeContextPath;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
@@ -58,7 +56,6 @@ import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
 import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IDomainResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -77,7 +74,6 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -102,7 +98,7 @@ public abstract class BaseParser implements IParser {
 
 	private static final Set<String> notEncodeForContainedResource = new HashSet<>(Arrays.asList("security", "versionId", "lastUpdated"));
 
-	private ContainedResources myContainedResources;
+	private FhirTerser.ContainedResources myContainedResources;
 	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private FhirContext myContext;
 	private List<EncodeContextPath> myDontEncodeElements;
@@ -118,7 +114,6 @@ public abstract class BaseParser implements IParser {
 	private boolean mySummaryMode;
 	private boolean mySuppressNarratives;
 	private Set<String> myDontStripVersionsFromReferencesAtPaths;
-
 	/**
 	 * Constructor
 	 */
@@ -127,6 +122,10 @@ public abstract class BaseParser implements IParser {
 		myErrorHandler = theParserErrorHandler;
 	}
 
+	protected FhirContext getContext() {
+		return myContext;
+	}
+
 	List<EncodeContextPath> getDontEncodeElements() {
 		return myDontEncodeElements;
 	}
@@ -213,156 +212,6 @@ public abstract class BaseParser implements IParser {
 		});
 	}
 
-	private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, IBaseResource theTarget) {
-		List<IBaseReference> allReferences = getAllBaseReferences(theResource);
-		for (IBaseReference next : allReferences) {
-			IBaseResource resource = next.getResource();
-			if (resource == null && next.getReferenceElement().isLocal()) {
-				if (theContained.hasExistingIdToContainedResource()) {
-					IBaseResource potentialTarget = theContained.getExistingIdToContainedResource().remove(next.getReferenceElement().getValue());
-					if (potentialTarget != null) {
-						theContained.addContained(next.getReferenceElement(), potentialTarget);
-						containResourcesForEncoding(theContained, potentialTarget, theTarget);
-					}
-				}
-			}
-		}
-
-		for (IBaseReference next : allReferences) {
-			IBaseResource resource = next.getResource();
-			if (resource != null) {
-				if (resource.getIdElement().isEmpty() || resource.getIdElement().isLocal()) {
-					if (theContained.getResourceId(resource) != null) {
-						// Prevent infinite recursion if there are circular loops in the contained resources
-						continue;
-					}
-					theContained.addContained(resource);
-					if (resource.getIdElement().isLocal() && theContained.hasExistingIdToContainedResource()) {
-						theContained.getExistingIdToContainedResource().remove(resource.getIdElement().getValue());
-					}
-				} else {
-					continue;
-				}
-
-				containResourcesForEncoding(theContained, resource, theTarget);
-			}
-
-		}
-
-	}
-
-	protected void containResourcesForEncoding(IBaseResource theResource) {
-		ContainedResources contained = new ContainedResources();
-
-		if (theResource instanceof IResource) {
-			List<? extends IResource> containedResources = ((IResource) theResource).getContained().getContainedResources();
-			for (IResource next : containedResources) {
-				String nextId = next.getId().getValue();
-				if (StringUtils.isNotBlank(nextId)) {
-					if (!nextId.startsWith("#")) {
-						nextId = '#' + nextId;
-					}
-					contained.getExistingIdToContainedResource().put(nextId, next);
-				}
-			}
-		} else if (theResource instanceof IDomainResource) {
-			List<? extends IAnyResource> containedResources = ((IDomainResource) theResource).getContained();
-			for (IAnyResource next : containedResources) {
-				String nextId = next.getIdElement().getValue();
-				if (StringUtils.isNotBlank(nextId)) {
-					if (!nextId.startsWith("#")) {
-						nextId = '#' + nextId;
-					}
-					contained.getExistingIdToContainedResource().put(nextId, next);
-				}
-			}
-		}
-
-		containResourcesForEncoding(contained, theResource, theResource);
-		contained.assignIdsToContainedResources();
-		myContainedResources = contained;
-
-	}
-
-	protected List<IBaseReference> getAllBaseReferences(IBaseResource theResource) {
-		final ArrayList<IBaseReference> retVal = new ArrayList<IBaseReference>();
-		findBaseReferences(retVal, theResource, myContext.getResourceDefinition(theResource));
-		return retVal;
-	}
-
-	/**
-	 * A customised traversal of the tree to find the 'top level' base references. Nested references are found via the recursive traversal
-	 * of contained resources.
-	 */
-	protected void findBaseReferences(List<IBaseReference> allElements, IBase theElement, BaseRuntimeElementDefinition<?> theDefinition) {
-		if (theElement instanceof IBaseReference) {
-			allElements.add((IBaseReference) theElement);
-		}
-
-		BaseRuntimeElementDefinition<?> def = theDefinition;
-		if (def.getChildType() == ChildTypeEnum.CONTAINED_RESOURCE_LIST) {
-			def = myContext.getElementDefinition(theElement.getClass());
-		}
-
-		switch (def.getChildType()) {
-			case ID_DATATYPE:
-			case PRIMITIVE_XHTML_HL7ORG:
-			case PRIMITIVE_XHTML:
-			case PRIMITIVE_DATATYPE:
-				// These are primitive types
-				break;
-			case RESOURCE:
-			case RESOURCE_BLOCK:
-			case COMPOSITE_DATATYPE: {
-				BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) def;
-				for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
-
-					List<?> values = nextChild.getAccessor().getValues(theElement);
-					if (values != null) {
-						for (Object nextValueObject : values) {
-							IBase nextValue;
-							try {
-								nextValue = (IBase) nextValueObject;
-							} catch (ClassCastException e) {
-								String s = "Found instance of " + nextValueObject.getClass() + " - Did you set a field value to the incorrect type? Expected " + IBase.class.getName();
-								throw new ClassCastException(s);
-							}
-							if (nextValue == null) {
-								continue;
-							}
-							if (nextValue.isEmpty()) {
-								continue;
-							}
-							BaseRuntimeElementDefinition<?> childElementDef;
-							childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
-
-							if (childElementDef == null) {
-								childElementDef = myContext.getElementDefinition(nextValue.getClass());
-							}
-
-							if (nextChild instanceof RuntimeChildDirectResource) {
-								// Don't descend into embedded resources
-								if (nextValue instanceof IBaseReference) {
-									allElements.add((IBaseReference) nextValue);
-								}
-							} else {
-								findBaseReferences(allElements, nextValue, childElementDef);
-							}
-						}
-					}
-				}
-				break;
-			}
-			case CONTAINED_RESOURCES:
-				// skip contained resources when looking for resources to contain
-				break;
-			case CONTAINED_RESOURCE_LIST:
-			case EXTENSION_DECLARED:
-			case UNDECL_EXT: {
-				throw new IllegalStateException("state should not happen: " + def.getChildType());
-			}
-		}
-	}
 
 	private String determineReferenceText(IBaseReference theRef, CompositeChildElement theCompositeChildElement) {
 		IIdType ref = theRef.getReferenceElement();
@@ -529,10 +378,14 @@ public abstract class BaseParser implements IParser {
 		return elementId;
 	}
 
-	ContainedResources getContainedResources() {
+	FhirTerser.ContainedResources getContainedResources() {
 		return myContainedResources;
 	}
 
+	void setContainedResources(FhirTerser.ContainedResources theContainedResources) {
+		myContainedResources = theContainedResources;
+	}
+
 	@Override
 	public Set<String> getDontStripVersionsFromReferencesAtPaths() {
 		return myDontStripVersionsFromReferencesAtPaths;
@@ -1359,126 +1212,6 @@ public abstract class BaseParser implements IParser {
 	}
 
 
-	static class ContainedResources {
-		private long myNextContainedId = 1;
-
-		private List<IBaseResource> myResourceList;
-		private IdentityHashMap<IBaseResource, IIdType> myResourceToIdMap;
-		private Map<String, IBaseResource> myExistingIdToContainedResourceMap;
-
-		public Map<String, IBaseResource> getExistingIdToContainedResource() {
-			if (myExistingIdToContainedResourceMap == null) {
-				myExistingIdToContainedResourceMap = new HashMap<>();
-			}
-			return myExistingIdToContainedResourceMap;
-		}
-
-		public void addContained(IBaseResource theResource) {
-			if (getResourceToIdMap().containsKey(theResource)) {
-				return;
-			}
-
-			IIdType newId;
-			if (theResource.getIdElement().isLocal()) {
-				newId = theResource.getIdElement();
-			} else {
-				newId = null;
-			}
-
-			getResourceToIdMap().put(theResource, newId);
-			getResourceList().add(theResource);
-		}
-
-		public void addContained(IIdType theId, IBaseResource theResource) {
-			if (!getResourceToIdMap().containsKey(theResource)) {
-				getResourceToIdMap().put(theResource, theId);
-				getResourceList().add(theResource);
-			}
-		}
-
-		public List<IBaseResource> getContainedResources() {
-			if (getResourceToIdMap() == null) {
-				return Collections.emptyList();
-			}
-			return getResourceList();
-		}
-
-		public IIdType getResourceId(IBaseResource theNext) {
-			if (getResourceToIdMap() == null) {
-				return null;
-			}
-			return getResourceToIdMap().get(theNext);
-		}
-
-		private List<IBaseResource> getResourceList() {
-			if (myResourceList == null) {
-				myResourceList = new ArrayList<>();
-			}
-			return myResourceList;
-		}
-
-		private IdentityHashMap<IBaseResource, IIdType> getResourceToIdMap() {
-			if (myResourceToIdMap == null) {
-				myResourceToIdMap = new IdentityHashMap<>();
-			}
-			return myResourceToIdMap;
-		}
-
-		public boolean isEmpty() {
-			if (myResourceToIdMap == null) {
-				return true;
-			}
-			return myResourceToIdMap.isEmpty();
-		}
-
-		public boolean hasExistingIdToContainedResource() {
-			return myExistingIdToContainedResourceMap != null;
-		}
-
-		public void assignIdsToContainedResources() {
-
-			if (getResourceList() != null) {
-
-				/*
-				 * The idea with the code block below:
-				 *
-				 * We want to preserve any IDs that were user-assigned, so that if it's really
-				 * important to someone that their contained resource have the ID of #FOO
-				 * or #1 we will keep that.
-				 *
-				 * For any contained resources where no ID was assigned by the user, we
-				 * want to manually create an ID but make sure we don't reuse an existing ID.
-				 */
-
-				Set<String> ids = new HashSet<>();
-
-				// Gather any user assigned IDs
-				for (IBaseResource nextResource : getResourceList()) {
-					if (getResourceToIdMap().get(nextResource) != null) {
-						ids.add(getResourceToIdMap().get(nextResource).getValue());
-					}
-				}
-
-				// Automatically assign IDs to the rest
-				for (IBaseResource nextResource : getResourceList()) {
-
-					while (getResourceToIdMap().get(nextResource) == null) {
-						String nextCandidate = "#" + myNextContainedId;
-						myNextContainedId++;
-						if (!ids.add(nextCandidate)) {
-							continue;
-						}
-
-						getResourceToIdMap().put(nextResource, new IdDt(nextCandidate));
-					}
-
-				}
-
-			}
-
-		}
-	}
-
 	protected static <T> List<T> extractMetadataListNotNull(IResource resource, ResourceMetadataKeyEnum<List<T>> key) {
 		List<? extends T> securityLabels = key.get(resource);
 		if (securityLabels == null) {

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

@@ -45,6 +45,7 @@ import ca.uhn.fhir.parser.json.JsonLikeWriter;
 import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.util.ElementUtil;
+import ca.uhn.fhir.util.FhirTerser;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.text.WordUtils;
@@ -74,7 +75,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParser.HeldExtension.class);
 
-	private FhirContext myContext;
 	private boolean myPrettyPrint;
 
 	/**
@@ -85,7 +85,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	 */
 	public JsonParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
 		super(theContext, theParserErrorHandler);
-		myContext = theContext;
 	}
 
 	private boolean addToHeldComments(int valueIdx, List<String> theCommentsToAdd, ArrayList<ArrayList<String>> theListToAddTo) {
@@ -177,7 +176,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 		theEventWriter.init();
 
-		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
+		RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);
 		encodeResourceToJsonStreamWriter(resDef, theResource, theEventWriter, null, false, theEncodeContext);
 		theEventWriter.flush();
 	}
@@ -209,7 +208,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 		String resourceType = resourceTypeObj.getAsString();
 
-		ParserState<? extends IBaseResource> state = ParserState.getPreResourceInstance(this, theResourceType, myContext, true, getErrorHandler());
+		ParserState<? extends IBaseResource> state = ParserState.getPreResourceInstance(this, theResourceType, getContext(), true, getErrorHandler());
 		state.enteringNewElement(null, resourceType);
 
 		parseChildren(object, state);
@@ -355,7 +354,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			}
 			case RESOURCE:
 				IBaseResource resource = (IBaseResource) theNextValue;
-				RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
+				RuntimeResourceDefinition def = getContext().getResourceDefinition(resource);
 
 				theEncodeContext.pushPath(def.getName(), true);
 				encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, theContainedResource, theEncodeContext);
@@ -387,14 +386,14 @@ 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, theContainedResource);
+					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, getContext().getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent, theEncodeContext, theContainedResource);
 					haveWrittenExtensions = true;
 				}
 				continue;
 			}
 
 			if (nextChild instanceof RuntimeChildNarrativeDefinition) {
-				INarrativeGenerator gen = myContext.getNarrativeGenerator();
+				INarrativeGenerator gen = getContext().getNarrativeGenerator();
 				if (gen != null) {
 					INarrative narr;
 					if (theResource instanceof IResource) {
@@ -405,7 +404,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 						narr = null;
 					}
 					if (narr != null && narr.isEmpty()) {
-						gen.populateResourceNarrative(myContext, theResource);
+						gen.populateResourceNarrative(getContext(), theResource);
 						if (!narr.isEmpty()) {
 							RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
 							String childName = nextChild.getChildNameByDatatype(child.getDatatype());
@@ -619,13 +618,13 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		Validate.notNull(theResource, "theResource can not be null");
 		Validate.notNull(theJsonLikeWriter, "theJsonLikeWriter can not be null");
 
-		if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
+		if (theResource.getStructureFhirVersionEnum() != getContext().getVersion().getVersion()) {
 			throw new IllegalArgumentException(
-				"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
+				"This parser is for FHIR version " + getContext().getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
 		}
 
 		EncodeContext encodeContext = new EncodeContext();
-		String resourceName = myContext.getResourceType(theResource);
+		String resourceName = getContext().getResourceType(theResource);
 		encodeContext.pushPath(resourceName, true);
 		doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter, encodeContext);
 	}
@@ -660,10 +659,10 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 
 		if (!theContainedResource) {
-			super.containResourcesForEncoding(theResource);
+			setContainedResources(getContext().newTerser().containResources(theResource));
 		}
 
-		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
+		RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);
 
 		if (theObjectNameOrNull == null) {
 			theEventWriter.beginObject();
@@ -888,8 +887,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private boolean isEncodeExtension(CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theElement) {
-//		theEncodeContext.pushPath("extension", false);
+		BaseRuntimeElementDefinition<?> runtimeElementDefinition = getContext().getElementDefinition(theElement.getClass());
-		BaseRuntimeElementDefinition<?> runtimeElementDefinition = myContext.getElementDefinition(theElement.getClass());
 		boolean retVal = true;
 		if (runtimeElementDefinition instanceof BaseRuntimeElementCompositeDefinition) {
 			BaseRuntimeElementCompositeDefinition definition = (BaseRuntimeElementCompositeDefinition) runtimeElementDefinition;
@@ -897,7 +895,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			CompositeChildElement c = new CompositeChildElement(theParent, childDef, theEncodeContext);
 			retVal = c.shouldBeEncoded(theContainedResource);
 		}
-//		theEncodeContext.popPath();
 		return retVal;
 	}
 
@@ -917,37 +914,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		return object.getAsArray();
 	}
 
-	// private JsonObject parse(Reader theReader) {
-	//
-	// PushbackReader pbr = new PushbackReader(theReader);
-	// JsonObject object;
-	// try {
-	// while(true) {
-	// int nextInt;
-	// nextInt = pbr.read();
-	// if (nextInt == -1) {
-	// throw new DataFormatException("Did not find any content to parse");
-	// }
-	// if (nextInt == '{') {
-	// pbr.unread('{');
-	// break;
-	// }
-	// if (Character.isWhitespace(nextInt)) {
-	// continue;
-	// }
-	// throw new DataFormatException("Content does not appear to be FHIR JSON, first non-whitespace character was: '" + (char)nextInt + "' (must be '{')");
-	// }
-	//
-	// Gson gson = newGson();
-	//
-	// object = gson.fromJson(pbr, JsonObject.class);
-	// } catch (Exception e) {
-	// throw new DataFormatException("Failed to parse JSON content, error was: " + e.getMessage(), e);
-	// }
-	//
-	// return object;
-	// }
-
 	private void parseAlternates(JsonLikeValue theAlternateVal, ParserState<?> theState, String theElementName, String theAlternateName) {
 		if (theAlternateVal == null || theAlternateVal.isNull()) {
 			return;
@@ -1234,13 +1200,13 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		 * the correct FHIR version
 		 */
 		if (theResourceType != null) {
-			myContext.getResourceDefinition(theResourceType);
+			getContext().getResourceDefinition(theResourceType);
 		}
 
 		// Actually do the parse
 		T retVal = doParseResource(theResourceType, theJsonLikeStructure);
 
-		RuntimeResourceDefinition def = myContext.getResourceDefinition(retVal);
+		RuntimeResourceDefinition def = getContext().getResourceDefinition(retVal);
 		if ("Bundle".equals(def.getName())) {
 
 			BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
@@ -1553,10 +1519,10 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					 */
 					value = preProcessValues(myDef, theResource, Collections.singletonList(value), myChildElem, theEncodeContext).get(0);
 
-					RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
+					RuntimeChildUndeclaredExtensionDefinition extDef = getContext().getRuntimeChildUndeclaredExtensionDefinition();
 					String childName = extDef.getChildNameByDatatype(value.getClass());
 					if (childName == null) {
-						childName = "value" + WordUtils.capitalize(myContext.getElementDefinition(value.getClass()).getName());
+						childName = "value" + WordUtils.capitalize(getContext().getElementDefinition(value.getClass()).getName());
 					}
 					BaseRuntimeElementDefinition<?> childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
 					if (childDef == null) {

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

@@ -1149,7 +1149,7 @@ class ParserState<T> {
 			for (IBaseReference nextRef : myLocalReferences) {
 				String ref = nextRef.getReferenceElement().getValue();
 				if (isNotBlank(ref)) {
-					if (ref.startsWith("#")) {
+					if (ref.startsWith("#") && ref.length() > 1) {
 						IBaseResource target = myContainedResources.get(ref);
 						if (target != null) {
 							ourLog.debug("Resource contains local ref {}", ref);
@@ -1187,12 +1187,6 @@ class ParserState<T> {
 			assert theResourceType == null || IResource.class.isAssignableFrom(theResourceType);
 		}
 
-		// @Override
-		// public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
-		// super.enteringNewElement(theNamespaceUri, theLocalPart);
-		// populateTarget();
-		// }
-
 		@Override
 		protected void populateTarget() {
 			weaveContainedResources();

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

@@ -73,7 +73,6 @@ public class RDFParser extends BaseParser {
 	public static final String MODIFIER_EXTENSION = "modifierExtension";
 	private final Map<Class, String> classToFhirTypeMap = new HashMap<>();
 
-	private final FhirContext context;
 	private final Lang lang;
 
 	/**
@@ -84,7 +83,6 @@ public class RDFParser extends BaseParser {
 	 */
 	public RDFParser(final FhirContext context, final IParserErrorHandler parserErrorHandler, final Lang lang) {
 		super(context, parserErrorHandler);
-		this.context = context;
 		this.lang = lang;
 	}
 
@@ -148,13 +146,13 @@ public class RDFParser extends BaseParser {
 																	 final EncodeContext encodeContext,
 																	 final boolean rootResource, Resource parentResource) {
 
-		RuntimeResourceDefinition resDef = this.context.getResourceDefinition(resource);
+		RuntimeResourceDefinition resDef = getContext().getResourceDefinition(resource);
 		if (resDef == null) {
 			throw new ConfigurationException("Unknown resource type: " + resource.getClass());
 		}
 
 		if (!containedResource) {
-			super.containResourcesForEncoding(resource);
+			setContainedResources(getContext().newTerser().containResources(resource));
 		}
 
 		if (!(resource instanceof IAnyResource)) {
@@ -323,7 +321,7 @@ public class RDFParser extends BaseParser {
 								if (hasExtension.getExtension() != null && hasExtension.getExtension().size() > 0) {
 									int i = 0;
 									for (IBaseExtension extension : hasExtension.getExtension()) {
-										RuntimeResourceDefinition resDef = this.context.getResourceDefinition(resource);
+										RuntimeResourceDefinition resDef = getContext().getResourceDefinition(resource);
 										Resource extensionResource = rdfModel.createResource();
 										extensionResource.addProperty(rdfModel.createProperty(FHIR_NS+FHIR_INDEX), rdfModel.createTypedLiteral(i, XSDDatatype.XSDinteger));
 										valueResource.addProperty(rdfModel.createProperty(FHIR_NS + ELEMENT_EXTENSION), extensionResource);
@@ -375,7 +373,7 @@ public class RDFParser extends BaseParser {
 				}
 				case RESOURCE: {
 					IBaseResource baseResource = (IBaseResource) element;
-					String resourceName = this.context.getResourceType(baseResource);
+					String resourceName = getContext().getResourceType(baseResource);
 					if (!super.shouldEncodeResource(resourceName)) {
 						break;
 					}
@@ -486,7 +484,7 @@ public class RDFParser extends BaseParser {
 			BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
 
 			if (nextChild instanceof RuntimeChildNarrativeDefinition) {
-				INarrativeGenerator gen = this.context.getNarrativeGenerator();
+				INarrativeGenerator gen = getContext().getNarrativeGenerator();
 				if (gen != null) {
 					INarrative narrative;
 					if (resource instanceof IResource) {
@@ -498,7 +496,7 @@ public class RDFParser extends BaseParser {
 					}
 					assert narrative != null;
 					if (narrative.isEmpty()) {
-						gen.populateResourceNarrative(this.context, resource);
+						gen.populateResourceNarrative(getContext(), resource);
 					}
 					else {
 						RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
@@ -619,7 +617,7 @@ public class RDFParser extends BaseParser {
 	private <T extends IBaseResource> T parseResource(Class<T> resourceType, Model rdfModel) {
 		// jsonMode of true is passed in so that the xhtml parser state behaves as expected
 		// Push PreResourceState
-		ParserState<T> parserState = ParserState.getPreResourceInstance(this, resourceType, context, true, getErrorHandler());
+		ParserState<T> parserState = ParserState.getPreResourceInstance(this, resourceType, getContext(), true, getErrorHandler());
 		return parseRootResource(rdfModel, parserState, resourceType);
 	}
 
@@ -646,7 +644,7 @@ public class RDFParser extends BaseParser {
 				fhirTypeString = resourceType.getSimpleName();
 			}
 
-			RuntimeResourceDefinition definition = this.context.getResourceDefinition(fhirTypeString);
+			RuntimeResourceDefinition definition = getContext().getResourceDefinition(fhirTypeString);
 			fhirResourceType = definition.getName();
 
 			parseResource(parserState, fhirResourceType, rootResource);
@@ -777,7 +775,7 @@ public class RDFParser extends BaseParser {
 			String propertyUri = statement.getPredicate().getURI();
 			if (propertyUri.contains("Extension.value")) {
 				extensionValueType = propertyUri.replace(FHIR_NS + "Extension.", "");
-				BaseRuntimeElementDefinition<?> target = context.getRuntimeChildUndeclaredExtensionDefinition().getChildByName(extensionValueType);
+				BaseRuntimeElementDefinition<?> target = getContext().getRuntimeChildUndeclaredExtensionDefinition().getChildByName(extensionValueType);
 				if (target.getChildType().equals(ID_DATATYPE) || target.getChildType().equals(PRIMITIVE_DATATYPE)) {
 					extensionValueResource = statement.getObject().asResource().getProperty(resource.getModel().createProperty(FHIR_NS+VALUE)).getObject().asLiteral();
 				} else {

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

@@ -56,9 +56,6 @@ public class XmlParser extends BaseParser {
 
 	static final String FHIR_NS = "http://hl7.org/fhir";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
-
-	// private static final Set<String> RESOURCE_NAMESPACES;
-	private FhirContext myContext;
 	private boolean myPrettyPrint;
 
 	/**
@@ -69,7 +66,6 @@ public class XmlParser extends BaseParser {
 	 */
 	public XmlParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
 		super(theContext, theParserErrorHandler);
-		myContext = theContext;
 	}
 
 	private XMLEventReader createStreamReader(Reader theReader) {
@@ -295,7 +291,7 @@ public class XmlParser extends BaseParser {
 				}
 				case RESOURCE: {
 					IBaseResource resource = (IBaseResource) theElement;
-					String resourceName = myContext.getResourceType(resource);
+					String resourceName = getContext().getResourceType(resource);
 					if (!super.shouldEncodeResource(resourceName)) {
 						break;
 					}
@@ -354,9 +350,9 @@ public class XmlParser extends BaseParser {
 
 			if (nextChild instanceof RuntimeChildNarrativeDefinition) {
 				Optional<IBase> narr = nextChild.getAccessor().getFirstValueOrNull(theElement);
-				INarrativeGenerator gen = myContext.getNarrativeGenerator();
+				INarrativeGenerator gen = getContext().getNarrativeGenerator();
 				if (gen != null && narr.isPresent() == false) {
-					gen.populateResourceNarrative(myContext, theResource);
+					gen.populateResourceNarrative(getContext(), theResource);
 				}
 
 				narr = nextChild.getAccessor().getFirstValueOrNull(theElement);
@@ -490,13 +486,13 @@ public class XmlParser extends BaseParser {
 	}
 
 	private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, IIdType theResourceId, EncodeContext theEncodeContext) throws XMLStreamException {
-		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
+		RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);
 		if (resDef == null) {
 			throw new ConfigurationException("Unknown resource type: " + theResource.getClass());
 		}
 
 		if (!theContainedResource) {
-			super.containResourcesForEncoding(theResource);
+			setContainedResources(getContext().newTerser().containResources(theResource));
 		}
 
 		theEventWriter.writeStartElement(resDef.getName());
@@ -615,11 +611,11 @@ public class XmlParser extends BaseParser {
 
 			if (next.getValue() != null) {
 				IBaseDatatype value = next.getValue();
-				RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
+				RuntimeChildUndeclaredExtensionDefinition extDef = getContext().getRuntimeChildUndeclaredExtensionDefinition();
 				String childName = extDef.getChildNameByDatatype(value.getClass());
 				BaseRuntimeElementDefinition<?> childDef;
 				if (childName == null) {
-					childDef = myContext.getElementDefinition(value.getClass());
+					childDef = getContext().getElementDefinition(value.getClass());
 					if (childDef == null) {
 						throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
 					}
@@ -749,7 +745,7 @@ public class XmlParser extends BaseParser {
 	}
 
 	private <T extends IBaseResource> T parseResource(Class<T> theResourceType, XMLEventReader theStreamReader) {
-		ParserState<T> parserState = ParserState.getPreResourceInstance(this, theResourceType, myContext, false, getErrorHandler());
+		ParserState<T> parserState = ParserState.getPreResourceInstance(this, theResourceType, getContext(), false, getErrorHandler());
 		return doXmlLoop(theStreamReader, parserState);
 	}
 

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

@@ -13,14 +13,15 @@ import ca.uhn.fhir.context.RuntimeExtensionDtDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.model.api.ExtensionDt;
-import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IIdentifiableElement;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseElement;
@@ -29,6 +30,7 @@ import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IDomainResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -36,10 +38,14 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -47,6 +53,7 @@ import java.util.stream.Collectors;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.substring;
 
 /*
  * #%L
@@ -71,7 +78,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class FhirTerser {
 
 	private static final Pattern COMPARTMENT_MATCHER_PATH = Pattern.compile("([a-zA-Z.]+)\\.where\\(resolve\\(\\) is ([a-zA-Z]+)\\)");
-	private FhirContext myContext;
+	private static final EnumSet<OptionsEnum> EMPTY_OPTION_SET = EnumSet.noneOf(OptionsEnum.class);
+	private static final String USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED = FhirTerser.class.getName() + "_CONTAIN_RESOURCES_COMPLETED";
+	private final FhirContext myContext;
 
 	public FhirTerser(FhirContext theContext) {
 		super();
@@ -312,7 +321,6 @@ public class FhirTerser {
 		return Optional.ofNullable(getSingleValueOrNull(theTarget, thePath, theWantedType));
 	}
 
-
 	private <T extends IBase> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, IBase theCurrentObj, List<String> theSubList, Class<T> theWantedClass) {
 		return getValues(theCurrentDef, theCurrentObj, theSubList, theWantedClass, false, false);
 	}
@@ -1058,4 +1066,251 @@ public class FhirTerser {
 		});
 	}
 
+	private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, EnumSet<OptionsEnum> theOptions) {
+		List<IBaseReference> allReferences = getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
+		for (IBaseReference next : allReferences) {
+			IBaseResource resource = next.getResource();
+			if (resource == null && next.getReferenceElement().isLocal()) {
+				if (theContained.hasExistingIdToContainedResource()) {
+					IBaseResource potentialTarget = theContained.getExistingIdToContainedResource().remove(next.getReferenceElement().getValue());
+					if (potentialTarget != null) {
+						theContained.addContained(next.getReferenceElement(), potentialTarget);
+						containResourcesForEncoding(theContained, potentialTarget, theOptions);
+					}
+				}
+			}
+		}
+
+		for (IBaseReference next : allReferences) {
+			IBaseResource resource = next.getResource();
+			if (resource != null) {
+				if (resource.getIdElement().isEmpty() || resource.getIdElement().isLocal()) {
+					if (theContained.getResourceId(resource) != null) {
+						// Prevent infinite recursion if there are circular loops in the contained resources
+						continue;
+					}
+					IIdType id = theContained.addContained(resource);
+					if (theOptions.contains(OptionsEnum.MODIFY_RESOURCE)) {
+						getContainedResourceList(theResource).add(resource);
+						next.setReference(id.getValue());
+					}
+					if (resource.getIdElement().isLocal() && theContained.hasExistingIdToContainedResource()) {
+						theContained.getExistingIdToContainedResource().remove(resource.getIdElement().getValue());
+					}
+				} else {
+					continue;
+				}
+
+			}
+
+		}
+
+	}
+
+	/**
+	 * Iterate through the whole resource and identify any contained resources. Optionally this method
+	 * can also assign IDs and modify references where the resource link has been specified but not the
+	 * reference text.
+	 *
+	 * @since 5.4.0
+	 */
+	public ContainedResources containResources(IBaseResource theResource, OptionsEnum... theOptions) {
+		EnumSet<OptionsEnum> options = toOptionSet(theOptions);
+
+		if (options.contains(OptionsEnum.STORE_AND_REUSE_RESULTS)) {
+			Object cachedValue = theResource.getUserData(USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED);
+			if (cachedValue != null) {
+				return (ContainedResources) cachedValue;
+			}
+		}
+
+		ContainedResources contained = new ContainedResources();
+
+		List<? extends IBaseResource> containedResources = getContainedResourceList(theResource);
+		for (IBaseResource next : containedResources) {
+			String nextId = next.getIdElement().getValue();
+			if (StringUtils.isNotBlank(nextId)) {
+				if (!nextId.startsWith("#")) {
+					nextId = '#' + nextId;
+				}
+				next.getIdElement().setValue(nextId);
+			}
+			contained.addContained(next);
+		}
+
+		containResourcesForEncoding(contained, theResource, options);
+
+		if (options.contains(OptionsEnum.STORE_AND_REUSE_RESULTS)) {
+			theResource.setUserData(USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED, contained);
+		}
+
+		return contained;
+	}
+
+	private EnumSet<OptionsEnum> toOptionSet(OptionsEnum[] theOptions) {
+		EnumSet<OptionsEnum> options;
+		if (theOptions == null || theOptions.length == 0) {
+			options = EMPTY_OPTION_SET;
+		} else {
+			options = EnumSet.of(theOptions[0], theOptions);
+		}
+		return options;
+	}
+
+	@SuppressWarnings("unchecked")
+	private <T extends IBaseResource> List<T> getContainedResourceList(T theResource) {
+		List<T> containedResources = Collections.emptyList();
+		if (theResource instanceof IResource) {
+			containedResources = (List<T>) ((IResource) theResource).getContained().getContainedResources();
+		} else if (theResource instanceof IDomainResource) {
+			containedResources = (List<T>) ((IDomainResource) theResource).getContained();
+		}
+		return containedResources;
+	}
+
+
+	public enum OptionsEnum {
+
+		/**
+		 * Should we modify the resource in the case that contained resource IDs are assigned
+		 * during a {@link #containResources(IBaseResource, OptionsEnum...)} pass.
+		 */
+		MODIFY_RESOURCE,
+
+		/**
+		 * Store the results of the operation in the resource metadata and reuse them if
+		 * subsequent calls are made.
+		 */
+		STORE_AND_REUSE_RESULTS
+	}
+
+	public static class ContainedResources {
+		private long myNextContainedId = 1;
+
+		private List<IBaseResource> myResourceList;
+		private IdentityHashMap<IBaseResource, IIdType> myResourceToIdMap;
+		private Map<String, IBaseResource> myExistingIdToContainedResourceMap;
+
+		public Map<String, IBaseResource> getExistingIdToContainedResource() {
+			if (myExistingIdToContainedResourceMap == null) {
+				myExistingIdToContainedResourceMap = new HashMap<>();
+			}
+			return myExistingIdToContainedResourceMap;
+		}
+
+		public IIdType addContained(IBaseResource theResource) {
+			IIdType existing = getResourceToIdMap().get(theResource);
+			if (existing != null) {
+				return existing;
+			}
+
+			IIdType newId = theResource.getIdElement();
+			if (isBlank(newId.getValue())) {
+				newId.setValue("#" + myNextContainedId++);
+			} else {
+				// Avoid auto-assigned contained IDs colliding with pre-existing ones
+				String idPart = newId.getValue();
+				if (substring(idPart, 0, 1).equals("#")) {
+					idPart = idPart.substring(1);
+					if (StringUtils.isNumeric(idPart)) {
+						myNextContainedId = Long.parseLong(idPart) + 1;
+					}
+				}
+			}
+
+			getResourceToIdMap().put(theResource, newId);
+			getOrCreateResourceList().add(theResource);
+			return newId;
+		}
+
+		public void addContained(IIdType theId, IBaseResource theResource) {
+			if (!getResourceToIdMap().containsKey(theResource)) {
+				getResourceToIdMap().put(theResource, theId);
+				getOrCreateResourceList().add(theResource);
+			}
+		}
+
+		public List<IBaseResource> getContainedResources() {
+			if (getResourceToIdMap() == null) {
+				return Collections.emptyList();
+			}
+			return getOrCreateResourceList();
+		}
+
+		public IIdType getResourceId(IBaseResource theNext) {
+			if (getResourceToIdMap() == null) {
+				return null;
+			}
+			return getResourceToIdMap().get(theNext);
+		}
+
+		private List<IBaseResource> getOrCreateResourceList() {
+			if (myResourceList == null) {
+				myResourceList = new ArrayList<>();
+			}
+			return myResourceList;
+		}
+
+		private IdentityHashMap<IBaseResource, IIdType> getResourceToIdMap() {
+			if (myResourceToIdMap == null) {
+				myResourceToIdMap = new IdentityHashMap<>();
+			}
+			return myResourceToIdMap;
+		}
+
+		public boolean isEmpty() {
+			if (myResourceToIdMap == null) {
+				return true;
+			}
+			return myResourceToIdMap.isEmpty();
+		}
+
+		public boolean hasExistingIdToContainedResource() {
+			return myExistingIdToContainedResourceMap != null;
+		}
+
+		public void assignIdsToContainedResources() {
+
+			if (!getContainedResources().isEmpty()) {
+
+				/*
+				 * The idea with the code block below:
+				 *
+				 * We want to preserve any IDs that were user-assigned, so that if it's really
+				 * important to someone that their contained resource have the ID of #FOO
+				 * or #1 we will keep that.
+				 *
+				 * For any contained resources where no ID was assigned by the user, we
+				 * want to manually create an ID but make sure we don't reuse an existing ID.
+				 */
+
+				Set<String> ids = new HashSet<>();
+
+				// Gather any user assigned IDs
+				for (IBaseResource nextResource : getContainedResources()) {
+					if (getResourceToIdMap().get(nextResource) != null) {
+						ids.add(getResourceToIdMap().get(nextResource).getValue());
+					}
+				}
+
+				// Automatically assign IDs to the rest
+				for (IBaseResource nextResource : getContainedResources()) {
+
+					while (getResourceToIdMap().get(nextResource) == null) {
+						String nextCandidate = "#" + myNextContainedId;
+						myNextContainedId++;
+						if (!ids.add(nextCandidate)) {
+							continue;
+						}
+
+						getResourceToIdMap().put(nextResource, new IdDt(nextCandidate));
+					}
+
+				}
+
+			}
+
+		}
+	}
+
 }

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2462-allow-references-to-containing.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2462
+title: "References from a contained resource to the containing resource are now possible in the JPA server."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2462-improve-large-transaction-performance.yaml

@@ -0,0 +1,6 @@
+---
+type: perf
+issue: 2462
+title: "Several optimizations have been made to the JPA server transaction processor that should result in
+   improved performance, particularly when processing large transaction Bundles, such as transactions
+   containing many entries, or transactions containing very large entries."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2462-preserve-contained-order.yaml

@@ -0,0 +1,4 @@
+---
+type: perf
+issue: 2462
+title: "The HAPI FHIR parser will now preserve the order of contained resources across round-trip parse/serialize passes."

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java

@@ -608,6 +608,11 @@ public class DaoConfig {
 	 * <code>_sort</code> parameter on searches): If the server is configured
 	 * to not index missing field.
 	 * </p>
+	 * <p>
+	 * The following index may need to be added into the indexed tables such as <code>HFJ_SPIDX_TOKEN</code> 
+	 * to improve the search performance while <code>:missing</code> is enabled.
+	 * <code>RES_TYPE, SP_NAME, SP_MISSING</code>
+	 * </p>
 	 */
 	public void setIndexMissingFields(IndexEnabledEnum theIndexMissingFields) {
 		Validate.notNull(theIndexMissingFields, "theIndexMissingFields must not be null");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -151,6 +151,7 @@ import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
 import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
 
 import javax.annotation.Nullable;
+import javax.annotation.PostConstruct;
 import java.util.Date;
 
 /*
@@ -200,6 +201,29 @@ public abstract class BaseConfig {
 	@Autowired
 	private DaoRegistry myDaoRegistry;
 
+	/**
+	 * Subclasses may override this method to provide settings such as search coordinator pool sizes.
+	 */
+	@PostConstruct
+	public void initSettings() {}
+
+	private Integer searchCoordCorePoolSize = 20;
+	private Integer searchCoordMaxPoolSize = 100;
+	private Integer searchCoordQueueCapacity = 200;
+
+	public void setSearchCoordCorePoolSize(Integer searchCoordCorePoolSize) {
+		this.searchCoordCorePoolSize = searchCoordCorePoolSize;
+	}
+
+	public void setSearchCoordMaxPoolSize(Integer searchCoordMaxPoolSize) {
+		this.searchCoordMaxPoolSize = searchCoordMaxPoolSize;
+	}
+
+	public void setSearchCoordQueueCapacity(Integer searchCoordQueueCapacity) {
+		this.searchCoordQueueCapacity = searchCoordQueueCapacity;
+	}
+
+
 	@Bean
 	public BatchConfigurer batchConfigurer() {
 		return new NonPersistedBatchConfigurer();
@@ -316,6 +340,9 @@ public abstract class BaseConfig {
 	public ThreadPoolTaskExecutor searchCoordinatorThreadFactory() {
 		final ThreadPoolTaskExecutor threadPoolTaskExecutor = new ThreadPoolTaskExecutor();
 		threadPoolTaskExecutor.setThreadNamePrefix("search_coord_");
+		threadPoolTaskExecutor.setCorePoolSize(searchCoordCorePoolSize);
+		threadPoolTaskExecutor.setMaxPoolSize(searchCoordMaxPoolSize);
+		threadPoolTaskExecutor.setQueueCapacity(searchCoordQueueCapacity);
 		threadPoolTaskExecutor.initialize();
 		return threadPoolTaskExecutor;
 	}

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

@@ -11,7 +11,6 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
 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.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IDao;
@@ -65,7 +64,6 @@ import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
@@ -237,6 +235,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	private IPartitionLookupSvc myPartitionLookupSvc;
 	@Autowired
 	private MemoryCacheService myMemoryCacheService;
+	@Autowired(required = false)
+	private IFulltextSearchSvc myFulltextSearchSvc;
+
+	@VisibleForTesting
+	public void setSearchParamPresenceSvc(ISearchParamPresenceSvc theSearchParamPresenceSvc) {
+		mySearchParamPresenceSvc = theSearchParamPresenceSvc;
+	}
 
 	@Override
 	protected IInterceptorBroadcaster getInterceptorBroadcaster() {
@@ -492,41 +497,37 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	/**
 	 * Returns true if the resource has changed (either the contents or the tags)
 	 */
-	protected EncodedResource populateResourceIntoEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, boolean theUpdateHash) {
+	protected EncodedResource populateResourceIntoEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, boolean thePerformIndexing) {
 		if (theEntity.getResourceType() == null) {
 			theEntity.setResourceType(toResourceName(theResource));
 		}
 
-		if (theResource != null) {
-			List<BaseResourceReferenceDt> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, BaseResourceReferenceDt.class);
-			for (BaseResourceReferenceDt nextRef : refs) {
-				if (nextRef.getReference().isEmpty() == false) {
-					if (nextRef.getReference().hasVersionIdPart()) {
-						nextRef.setReference(nextRef.getReference().toUnqualifiedVersionless());
-					}
-				}
-			}
-		}
-
 		byte[] bytes;
 		ResourceEncodingEnum encoding;
 		boolean changed = false;
 
 		if (theEntity.getDeleted() == null) {
 
+			if (thePerformIndexing) {
+
 				encoding = myConfig.getResourceEncoding();
 				Set<String> excludeElements = ResourceMetaParams.EXCLUDE_ELEMENTS_IN_ENCODED;
 				theEntity.setFhirVersion(myContext.getVersion().getVersion());
 
 				bytes = encodeResource(theResource, encoding, excludeElements, myContext);
 
-			if (theUpdateHash) {
 				HashFunction sha256 = Hashing.sha256();
 				String hashSha256 = sha256.hashBytes(bytes).toString();
 				if (hashSha256.equals(theEntity.getHashSha256()) == false) {
 					changed = true;
 				}
 				theEntity.setHashSha256(hashSha256);
+
+			} else {
+
+				encoding = null;
+				bytes = null;
+
 			}
 
 			Set<ResourceTag> allDefs = new HashSet<>();
@@ -543,13 +544,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				String profile = def.getResourceProfile("");
 				if (isNotBlank(profile)) {
 					TagDefinition profileDef = getTagOrNull(TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
-					if (def != null) {
+
 					ResourceTag tag = theEntity.addTag(profileDef);
 					allDefs.add(tag);
 					theEntity.setHasTags(true);
 				}
 			}
-			}
 
 			Set<ResourceTag> allTagsNew = getAllTagDefinitions(theEntity);
 			Set<TagDefinition> allDefsPresent = new HashSet<>();
@@ -580,7 +580,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			encoding = ResourceEncodingEnum.DEL;
 		}
 
-		if (changed == false) {
+		if (thePerformIndexing && changed == false) {
 			if (theEntity.getId() == null) {
 				changed = true;
 			} else {
@@ -988,6 +988,26 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		return updateEntity(theRequest, null, entity, updateTime, true, true, theTransactionDetails, false, true);
 	}
 
+	@VisibleForTesting
+	public void setEntityManager(EntityManager theEntityManager) {
+		myEntityManager = theEntityManager;
+	}
+
+	@VisibleForTesting
+	public void setSearchParamWithInlineReferencesExtractor(SearchParamWithInlineReferencesExtractor theSearchParamWithInlineReferencesExtractor) {
+		mySearchParamWithInlineReferencesExtractor = theSearchParamWithInlineReferencesExtractor;
+	}
+
+	@VisibleForTesting
+	public void setResourceHistoryTableDao(IResourceHistoryTableDao theResourceHistoryTableDao) {
+		myResourceHistoryTableDao = theResourceHistoryTableDao;
+	}
+
+	@VisibleForTesting
+	public void setDaoSearchParamSynchronizer(DaoSearchParamSynchronizer theDaoSearchParamSynchronizer) {
+		myDaoSearchParamSynchronizer = theDaoSearchParamSynchronizer;
+	}
+
 	@SuppressWarnings("unchecked")
 	@Override
 	public ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, IBasePersistedResource
@@ -1059,7 +1079,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 					newParams.populateResourceTableSearchParamsPresentFlags(entity);
 					entity.setIndexStatus(INDEX_STATUS_INDEXED);
 				}
+
+				if (myFulltextSearchSvc != null && !myFulltextSearchSvc.isDisabled()) {
 					populateFullTextFields(myContext, theResource, entity);
+				}
+
 			} else {
 
 				changed = populateResourceIntoEntity(theRequest, theResource, entity, false);
@@ -1071,7 +1095,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 		}
 
-		if (!changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
+		if (thePerformIndexing && changed != null && !changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
 			ourLog.debug("Resource {} has not changed", entity.getIdDt().toUnqualified().getValue());
 			if (theResource != null) {
 				updateResourceMetadata(entity, theResource);
@@ -1323,7 +1347,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		}
 	}
 
-	private void validateChildReferences(IBase theElement, String thePath) {
+	private void validateChildReferenceTargetTypes(IBase theElement, String thePath) {
 		if (theElement == null) {
 			return;
 		}
@@ -1343,7 +1367,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			String newPath = thePath + "." + nextChildDef.getElementName();
 
 			for (IBase nextChild : values) {
-				validateChildReferences(nextChild, newPath);
+				validateChildReferenceTargetTypes(nextChild, newPath);
 			}
 
 			if (nextChildDef instanceof RuntimeChildResourceDefinition) {
@@ -1426,8 +1450,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			throw new UnprocessableEntityException("Resource contains the 'subsetted' tag, and must not be stored as it may contain a subset of available data");
 		}
 
+		if (getConfig().isEnforceReferenceTargetTypes()) {
 			String resName = getContext().getResourceType(theResource);
-		validateChildReferences(theResource, resName);
+			validateChildReferenceTargetTypes(theResource, resName);
+		}
 
 		validateMetaCount(totalMetaCount);
 

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

@@ -97,6 +97,7 @@ import ca.uhn.fhir.validation.IValidationContext;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ValidationOptions;
 import ca.uhn.fhir.validation.ValidationResult;
+import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.text.WordUtils;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
@@ -222,11 +223,21 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return create(theResource, theIfNoneExist, true, new TransactionDetails(), theRequestDetails);
 	}
 
+	@VisibleForTesting
+	public void setTransactionService(HapiTransactionService theTransactionService) {
+		myTransactionService = theTransactionService;
+	}
+
 	@Override
 	public DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing, @Nonnull TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
 		return myTransactionService.execute(theRequestDetails, tx -> doCreateForPost(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails));
 	}
 
+	@VisibleForTesting
+	public void setRequestPartitionHelperService(IRequestPartitionHelperSvc theRequestPartitionHelperService) {
+		myRequestPartitionHelperService = theRequestPartitionHelperService;
+	}
+
 	/**
 	 * Called for FHIR create (POST) operations
 	 */
@@ -1709,6 +1720,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 	}
 
+	@VisibleForTesting
+	public void setDaoConfig(DaoConfig theDaoConfig) {
+		myDaoConfig = theDaoConfig;
+	}
+
 	private static class IdChecker implements IValidatorModule {
 
 		private final ValidationModeEnum myMode;

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

@@ -54,6 +54,7 @@ import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
+import com.google.common.annotations.VisibleForTesting;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseReference;
@@ -89,6 +90,11 @@ public abstract class BaseStorageDao {
 	@Autowired
 	protected ModelConfig myModelConfig;
 
+	@VisibleForTesting
+	public void setSearchParamRegistry(ISearchParamRegistry theSearchParamRegistry) {
+		mySearchParamRegistry = theSearchParamRegistry;
+	}
+
 	/**
 	 * May be overridden by subclasses to validate resources prior to storage
 	 *
@@ -176,7 +182,7 @@ public abstract class BaseStorageDao {
 
 	/**
 	 * Handle {@link ModelConfig#getAutoVersionReferenceAtPaths() auto-populate-versions}
-	 *
+	 * <p>
 	 * We only do this if thePerformIndexing is true because if it's false, that means
 	 * we're in a FHIR transaction during the first phase of write operation processing,
 	 * meaning that the versions of other resources may not have need updated yet. For example
@@ -184,7 +190,7 @@ public abstract class BaseStorageDao {
 	 * is also being updated in the same transaction, during the first "no index" phase,
 	 * the Patient will not yet have its version number incremented, so it would be wrong
 	 * to use that value. During the second phase it is correct.
-	 *
+	 * <p>
 	 * Also note that {@link BaseTransactionProcessor} also has code to do auto-versioning
 	 * and it is the one that takes care of the placeholder IDs. Look for the other caller of
 	 * {@link #extractReferencesToAutoVersion(FhirContext, ModelConfig, IBaseResource)}

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

@@ -69,6 +69,7 @@ import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.UrlUtil;
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
 import org.apache.commons.lang3.Validate;
@@ -278,6 +279,16 @@ public abstract class BaseTransactionProcessor {
 		}
 	}
 
+	@VisibleForTesting
+	public void setVersionAdapter(ITransactionProcessorVersionAdapter theVersionAdapter) {
+		myVersionAdapter = theVersionAdapter;
+	}
+
+	@VisibleForTesting
+	public void setTxManager(PlatformTransactionManager theTxManager) {
+		myTxManager = theTxManager;
+	}
+
 	private IBaseBundle batch(final RequestDetails theRequestDetails, IBaseBundle theRequest) {
 		ourLog.info("Beginning batch with {} resources", myVersionAdapter.getEntries(theRequest).size());
 		long start = System.currentTimeMillis();
@@ -335,6 +346,11 @@ public abstract class BaseTransactionProcessor {
 		return resp;
 	}
 
+	@VisibleForTesting
+	public void setHapiTransactionService(HapiTransactionService theHapiTransactionService) {
+		myHapiTransactionService = theHapiTransactionService;
+	}
+
 	private IBaseBundle processTransaction(final RequestDetails theRequestDetails, final IBaseBundle theRequest, final String theActionName) {
 		validateDependencies();
 
@@ -549,6 +565,10 @@ public abstract class BaseTransactionProcessor {
 		return myContext.getVersion().newIdType().setValue(theValue);
 	}
 
+	@VisibleForTesting
+	public void setModelConfig(ModelConfig theModelConfig) {
+		myModelConfig = theModelConfig;
+	}
 
 	private Map<IBase, IBasePersistedResource> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
 																									Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
@@ -612,16 +632,16 @@ public abstract class BaseTransactionProcessor {
 							String existingUuid = keyToUuid.get(key);
 							for (IBase nextEntry : theEntries) {
 								IBaseResource nextResource = myVersionAdapter.getResource(nextEntry);
-								for (ResourceReferenceInfo nextReference : myContext.newTerser().getAllResourceReferences(nextResource)) {
+								for (IBaseReference nextReference : myContext.newTerser().getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class)) {
 									// We're interested in any references directly to the placeholder ID, but also
 									// references that have a resource target that has the placeholder ID.
-									String nextReferenceId = nextReference.getResourceReference().getReferenceElement().getValue();
+									String nextReferenceId = nextReference.getReferenceElement().getValue();
-									if (isBlank(nextReferenceId) && nextReference.getResourceReference().getResource() != null) {
+									if (isBlank(nextReferenceId) && nextReference.getResource() != null) {
-										nextReferenceId = nextReference.getResourceReference().getResource().getIdElement().getValue();
+										nextReferenceId = nextReference.getResource().getIdElement().getValue();
 									}
 									if (entryUrl.equals(nextReferenceId)) {
-										nextReference.getResourceReference().setReference(existingUuid);
+										nextReference.setReference(existingUuid);
-										nextReference.getResourceReference().setResource(null);
+										nextReference.setResource(null);
 									}
 								}
 							}
@@ -923,7 +943,6 @@ public abstract class BaseTransactionProcessor {
 						IIdType newId = theIdSubstitutions.get(nextId);
 						ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
 						if (referencesToVersion.contains(resourceReference)) {
-							DaoMethodOutcome outcome = theIdToPersistedOutcome.get(newId);
 							resourceReference.setReference(newId.getValue());
 						} else {
 							resourceReference.setReference(newId.toVersionless().getValue());
@@ -1042,6 +1061,11 @@ public abstract class BaseTransactionProcessor {
 		return newIdType(theToResourceName, theIdPart, null);
 	}
 
+	@VisibleForTesting
+	public void setDaoRegistry(DaoRegistry theDaoRegistry) {
+		myDaoRegistry = theDaoRegistry;
+	}
+
 	private IFhirResourceDao getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
 		IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDaoOrNull(theClass);
 		if (dao == null) {
@@ -1113,6 +1137,11 @@ public abstract class BaseTransactionProcessor {
 		return null;
 	}
 
+	@VisibleForTesting
+	public void setDaoConfig(DaoConfig theDaoConfig) {
+		myDaoConfig = theDaoConfig;
+	}
+
 	public interface ITransactionProcessorVersionAdapter<BUNDLE extends IBaseBundle, BUNDLEENTRY extends IBase> {
 
 		void setResponseStatus(BUNDLEENTRY theBundleEntry, String theStatus);

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

@@ -62,9 +62,16 @@ public class TransactionProcessor extends BaseTransactionProcessor {
 	@Override
 	protected void flushSession(Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome) {
 		try {
+			int insertionCount;
+			int updateCount;
 			SessionImpl session = myEntityManager.unwrap(SessionImpl.class);
-			int insertionCount = session.getActionQueue().numberOfInsertions();
+			if (session != null) {
-			int updateCount = session.getActionQueue().numberOfUpdates();
+				insertionCount = session.getActionQueue().numberOfInsertions();
+				updateCount = session.getActionQueue().numberOfUpdates();
+			} else {
+				insertionCount = -1;
+				updateCount = -1;
+			}
 
 			StopWatch sw = new StopWatch();
 			myEntityManager.flush();

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

@@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
 import ca.uhn.fhir.jpa.util.AddRemoveCount;
+import com.google.common.annotations.VisibleForTesting;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -68,6 +69,11 @@ public class DaoSearchParamSynchronizer {
 		return retVal;
 	}
 
+	@VisibleForTesting
+	public void setEntityManager(EntityManager theEntityManager) {
+		myEntityManager = theEntityManager;
+	}
+
 	private <T extends BaseResourceIndex> void synchronize(ResourceTable theEntity, AddRemoveCount theAddRemoveCount, Collection<T> theNewParams, Collection<T> theExistingParams) {
 		Collection<T> newParams = theNewParams;
 		for (T next : newParams) {

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

@@ -47,6 +47,7 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.UrlUtil;
+import com.google.common.annotations.VisibleForTesting;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -95,6 +96,21 @@ public class SearchParamWithInlineReferencesExtractor {
 	@Autowired
 	private PartitionSettings myPartitionSettings;
 
+	@VisibleForTesting
+	public void setPartitionSettings(PartitionSettings thePartitionSettings) {
+		myPartitionSettings = thePartitionSettings;
+	}
+
+	@VisibleForTesting
+	public void setSearchParamExtractorService(SearchParamExtractorService theSearchParamExtractorService) {
+		mySearchParamExtractorService = theSearchParamExtractorService;
+	}
+
+	@VisibleForTesting
+	public void setSearchParamRegistry(ISearchParamRegistry theSearchParamRegistry) {
+		mySearchParamRegistry = theSearchParamRegistry;
+	}
+
 	public void populateFromResource(ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest) {
 		extractInlineReferences(theResource, theRequest);
 
@@ -214,6 +230,16 @@ public class SearchParamWithInlineReferencesExtractor {
 	}
 
 
+	@VisibleForTesting
+	public void setDaoConfig(DaoConfig theDaoConfig) {
+		myDaoConfig = theDaoConfig;
+	}
+
+	@VisibleForTesting
+	public void setContext(FhirContext theContext) {
+		myContext = theContext;
+	}
+
 	/**
 	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
 	 * matching resource.
@@ -276,6 +302,11 @@ public class SearchParamWithInlineReferencesExtractor {
 		}
 	}
 
+	@VisibleForTesting
+	public void setDaoSearchParamSynchronizer(DaoSearchParamSynchronizer theDaoSearchParamSynchronizer) {
+		myDaoSearchParamSynchronizer = theDaoSearchParamSynchronizer;
+	}
+
 	public void storeCompositeStringUniques(ResourceIndexedSearchParams theParams, ResourceTable theEntity, ResourceIndexedSearchParams existingParams) {
 
 		// Store composite string uniques

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java

@@ -27,9 +27,9 @@ import ca.uhn.fhir.jpa.model.entity.TagDefinition;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
+import com.google.common.annotations.VisibleForTesting;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Meta;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Propagation;
@@ -42,11 +42,14 @@ import java.util.List;
 
 public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoR4.class);
-
 	@Autowired
 	private TransactionProcessor myTransactionProcessor;
 
+	@VisibleForTesting
+	public void setTransactionProcessorForUnitTest(TransactionProcessor theTransactionProcessor) {
+		myTransactionProcessor = theTransactionProcessor;
+	}
+
 	@Override
 	@PostConstruct
 	public void start() {

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

@@ -29,6 +29,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import com.google.common.annotations.VisibleForTesting;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -47,6 +48,16 @@ public class HapiTransactionService {
 	private PlatformTransactionManager myTransactionManager;
 	private TransactionTemplate myTxTemplate;
 
+	@VisibleForTesting
+	public void setInterceptorBroadcaster(IInterceptorBroadcaster theInterceptorBroadcaster) {
+		myInterceptorBroadcaster = theInterceptorBroadcaster;
+	}
+
+	@VisibleForTesting
+	public void setTransactionManager(PlatformTransactionManager theTransactionManager) {
+		myTransactionManager = theTransactionManager;
+	}
+
 	@PostConstruct
 	public void start() {
 		myTxTemplate = new TransactionTemplate(myTransactionManager);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java

@@ -26,10 +26,15 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
 import ca.uhn.fhir.jpa.util.AddRemoveCount;
+import com.google.common.annotations.VisibleForTesting;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 import java.util.Map.Entry;
 
 @Service
@@ -40,10 +45,14 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 
 	@Autowired
 	private PartitionSettings myPartitionSettings;
-
 	@Autowired
 	private DaoConfig myDaoConfig;
 
+	@VisibleForTesting
+	public void setDaoConfig(DaoConfig theDaoConfig) {
+		myDaoConfig = theDaoConfig;
+	}
+
 	@Override
 	public AddRemoveCount updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
 		AddRemoveCount retVal = new AddRemoveCount();

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

@@ -5,8 +5,6 @@ import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
 import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
 import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
 import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
-import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
-import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
@@ -16,10 +14,6 @@ import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.hibernate.dialect.H2Dialect;
-import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
-import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
-import org.hibernate.search.engine.cfg.BackendSettings;
-import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java

@@ -1095,14 +1095,18 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 				.stream()
 				.filter(t -> t.getParamName().equals("medicationadministration-ingredient-medication"))
 				.collect(Collectors.toList());
-			ourLog.info("Tokens: {}", tokens);
+			ourLog.info("Tokens:\n * {}", tokens.stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
 			assertEquals(1, tokens.size(), tokens.toString());
+			assertEquals(false, tokens.get(0).isMissing());
 
 		});
 
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("medicationadministration-ingredient-medication", new TokenParam("system","code"));
-		assertEquals(1, myMedicationAdministrationDao.search(map).size().intValue());
+		myCaptureQueriesListener.clear();
+		IBundleProvider search = myMedicationAdministrationDao.search(map);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+		assertEquals(1, search.sizeOrThrowNpe());
 
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java

@@ -25,6 +25,7 @@ import org.hl7.fhir.r4.model.StringType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.springframework.test.annotation.DirtiesContext;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -45,6 +46,7 @@ import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
 @SuppressWarnings({"unchecked", "deprecation", "Duplicates"})
+@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
 public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ConcurrentWriteTest.class);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ContainedTest.java

@@ -32,6 +32,9 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
+import java.util.stream.Collector;
+import java.util.stream.Collectors;
+
 public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ContainedTest.class);
 
@@ -64,6 +67,8 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
 		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
 		
 		runInTransaction(()->{
+			ourLog.info("String indexes:\n * {}", myResourceIndexedSearchParamStringDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+
 			Long i = myEntityManager
 				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'subject.family' AND s.myResourceType = 'Observation'", Long.class)
 				.getSingleResult();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -306,13 +306,17 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 		o.getMeta().addTag("http://foo", "bar", "FOOBAR");
 		p.getManagingOrganization().setResource(o);
 
-		ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info("Input: {}", encoded);
+		assertThat(encoded, containsString("#1"));
 
 		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
 
 		p = myPatientDao.read(id);
 
-		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info("Output: {}", encoded);
+		assertThat(encoded, containsString("#1"));
 
 		Organization org = (Organization) p.getManagingOrganization().getResource();
 		assertEquals("#1", org.getId());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java

@@ -787,7 +787,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
 
 		// Lookup the two existing IDs to make sure they are legit
-		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+		myCaptureQueriesListener.logInsertQueriesForCurrentThread();
+		myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
 		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(3, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(2, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -94,6 +94,7 @@ import org.hl7.fhir.r4.model.OperationOutcome.IssueType;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Period;
+import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Quantity.QuantityComparator;
 import org.hl7.fhir.r4.model.Questionnaire;
@@ -295,6 +296,39 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		});
 	}
 
+	@Test
+	public void testStoreReferenceFromContainedToContainer() {
+		Patient patient = new Patient();
+		patient.setActive(true);
+
+		Provenance provenance = new Provenance();
+		provenance.setId("#1");
+		provenance.addTarget().setReference("#");
+		patient.getContained().add(provenance);
+
+		Observation observation = new Observation();
+		observation.setId("#2");
+		observation.getSubject().setReference("#");
+		patient.getContained().add(observation);
+
+		IIdType id = myPatientDao.create(patient).getId();
+
+		patient = myPatientDao.read(id);
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
+
+		assertEquals(2, patient.getContained().size());
+
+		provenance = (Provenance) patient.getContained().get(0);
+		assertEquals("#1", provenance.getId());
+		assertEquals("#", provenance.getTargetFirstRep().getReference());
+
+		observation = (Observation) patient.getContained().get(1);
+		assertEquals("#2", observation.getId());
+		assertEquals("#", observation.getSubject().getReference());
+	}
+
+
 	@Test
 	public void testTermConceptReindexingDoesntDuplicateData() {
 		myDaoConfig.setSchedulingDisabled(true);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java

@@ -26,6 +26,7 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 	@AfterEach
 	public void afterEach() {
 		myFhirCtx.getParserOptions().setStripVersionsFromReferences(true);
+		myFhirCtx.getParserOptions().getDontStripVersionsFromReferencesAtPaths().clear();
 		myDaoConfig.setDeleteEnabled(new DaoConfig().isDeleteEnabled());
 		myModelConfig.setRespectVersionsForSearchIncludes(new ModelConfig().isRespectVersionsForSearchIncludes());
 		myModelConfig.setAutoVersionReferenceAtPaths(new ModelConfig().getAutoVersionReferenceAtPaths());
@@ -457,6 +458,10 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		observation.getSubject().setReference(patientId.withVersion("1").getValue());
 		IIdType observationId = myObservationDao.create(observation).getId().toUnqualified();
 
+		// Read the observation back
+		observation = myObservationDao.read(observationId);
+		assertEquals(patientId.toVersionless().getValue(), observation.getSubject().getReference());
+
 		// Search - Non Synchronous for *
 		{
 			IBundleProvider outcome = myObservationDao.search(SearchParameterMap.newSynchronous().addInclude(IBaseResource.INCLUDE_ALL));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java

@@ -168,12 +168,11 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 			WebApplicationContext wac = WebApplicationContextUtils.getWebApplicationContext(subsServletHolder.getServlet().getServletConfig().getServletContext());
 			myValidationSupport = wac.getBean(IValidationSupport.class);
 			mySearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
-			SubscriptionMatcherInterceptor ourSubscriptionMatcherInterceptor = wac.getBean(SubscriptionMatcherInterceptor.class);
 
 			confProvider.setSearchParamRegistry(ourSearchParamRegistry);
 
 			myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
-			myFhirCtx.getRestfulClientFactory().setSocketTimeout(20000);
+			myFhirCtx.getRestfulClientFactory().setSocketTimeout(400000);
 
 			PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
 			HttpClientBuilder builder = HttpClientBuilder.create();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -15,6 +15,7 @@ import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.hasItems;
 import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.in;
 import static org.hamcrest.Matchers.lessThan;
 import static org.hamcrest.Matchers.lessThanOrEqualTo;
 import static org.hamcrest.Matchers.matchesPattern;
@@ -47,7 +48,9 @@ import java.util.Set;
 import java.util.TreeSet;
 import java.util.stream.Collectors;
 
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
+import ca.uhn.fhir.util.BundleBuilder;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -849,6 +852,72 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+
+	@Test
+	public void testCreateAndReadBackResourceWithContainedReferenceToContainer() {
+		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+
+		String input = "{\n" +
+			"  \"resourceType\": \"Organization\",\n" +
+			"  \"id\": \"1\",\n" +
+			"  \"meta\": {\n" +
+			"    \"tag\": [\n" +
+			"      {\n" +
+			"        \"system\": \"https://blah.org/deployment\",\n" +
+			"        \"code\": \"e69414dd-b5c2-462d-bcfd-9d04d6b16596\",\n" +
+			"        \"display\": \"DEPLOYMENT\"\n" +
+			"      },\n" +
+			"      {\n" +
+			"        \"system\": \"https://blah.org/region\",\n" +
+			"        \"code\": \"b47d7a5b-b159-4bed-a8f8-3258e6603adb\",\n" +
+			"        \"display\": \"REGION\"\n" +
+			"      },\n" +
+			"      {\n" +
+			"        \"system\": \"https://blah.org/provider\",\n" +
+			"        \"code\": \"28c30004-0333-40cf-9e7f-3f9e080930bd\",\n" +
+			"        \"display\": \"PROVIDER\"\n" +
+			"      }\n" +
+			"    ]\n" +
+			"  },\n" +
+			"  \"contained\": [\n" +
+			"    {\n" +
+			"      \"resourceType\": \"Location\",\n" +
+			"      \"id\": \"2\",\n" +
+			"      \"position\": {\n" +
+			"        \"longitude\": 51.443238301454289,\n" +
+			"        \"latitude\": 7.34196905697293\n" +
+			"      },\n" +
+			"      \"managingOrganization\": {\n" +
+			"        \"reference\": \"#\"\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"type\": [\n" +
+			"    {\n" +
+			"      \"coding\": [\n" +
+			"        {\n" +
+			"          \"system\": \"https://blah.org/fmc/OrganizationType\",\n" +
+			"          \"code\": \"CLINIC\",\n" +
+			"          \"display\": \"Clinic\"\n" +
+			"        }\n" +
+			"      ]\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"name\": \"testOrg\"\n" +
+			"}";
+
+		Organization org = myFhirCtx.newJsonParser().parseResource(Organization.class, input);
+		IIdType id = myOrganizationDao.create(org).getId();
+		org = myOrganizationDao.read(id);
+
+		String output = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(org);
+		ourLog.info(output);
+
+		Location loc = (Location) org.getContained().get(0);
+		assertEquals("#", loc.getManagingOrganization().getReference());
+	}
+
+
 	@Test
 	public void testCountParam() {
 		List<IBaseResource> resources = new ArrayList<>();
@@ -857,7 +926,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			org.setName("rpr4_testCountParam_01");
 			resources.add(org);
 		}
-		myClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
+		List<IBaseResource> outcome = myClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
+
+		runInTransaction(()->{
+			assertEquals(100, myResourceTableDao.count());
+		});
 
 		Bundle found = myClient
 			.search()

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java

@@ -0,0 +1,830 @@
+package ca.uhn.fhir.jpa.stresstest;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.interceptor.executor.InterceptorService;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
+import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCache;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheFactory;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheRefresherImpl;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryImpl;
+import ca.uhn.fhir.jpa.cache.ResourceVersionMap;
+import ca.uhn.fhir.jpa.dao.JpaResourceDao;
+import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer;
+import ca.uhn.fhir.jpa.dao.index.SearchParamWithInlineReferencesExtractor;
+import ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4;
+import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
+import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
+import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
+import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.ClasspathUtil;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.validation.IInstanceValidatorModule;
+import com.google.common.collect.Lists;
+import org.hamcrest.Matchers;
+import org.hibernate.Session;
+import org.hibernate.internal.SessionImpl;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.ExplanationOfBenefit;
+import org.junit.Ignore;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Answers;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.quartz.JobKey;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.context.ApplicationContext;
+import org.springframework.data.domain.Example;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Slice;
+import org.springframework.data.domain.Sort;
+import org.springframework.mock.web.MockHttpServletRequest;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.TransactionException;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.SimpleTransactionStatus;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import javax.persistence.EntityGraph;
+import javax.persistence.EntityManager;
+import javax.persistence.EntityManagerFactory;
+import javax.persistence.EntityTransaction;
+import javax.persistence.FlushModeType;
+import javax.persistence.LockModeType;
+import javax.persistence.Query;
+import javax.persistence.StoredProcedureQuery;
+import javax.persistence.TypedQuery;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaDelete;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.CriteriaUpdate;
+import javax.persistence.metamodel.Metamodel;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.Set;
+import java.util.concurrent.TimeUnit;
+import java.util.stream.Collectors;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyLong;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+public class GiantTransactionPerfTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(GiantTransactionPerfTest.class);
+	private final FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
+	private FhirSystemDaoR4 mySystemDao;
+	private IInterceptorBroadcaster myInterceptorSvc;
+	private TransactionProcessor myTransactionProcessor;
+	private PlatformTransactionManager myTransactionManager;
+	private MockEntityManager myEntityManager;
+	private DaoConfig myDaoConfig;
+	private HapiTransactionService myHapiTransactionService;
+	private DaoRegistry myDaoRegistry;
+	private JpaResourceDao<ExplanationOfBenefit> myEobDao;
+	@Mock(answer = Answers.CALLS_REAL_METHODS)
+	private ApplicationContext myAppCtx;
+	@Mock
+	private IInstanceValidatorModule myInstanceValidatorSvc;
+	private SearchParamWithInlineReferencesExtractor mySearchParamWithInlineReferencesExtractor;
+	private PartitionSettings myPartitionSettings;
+	private SearchParamExtractorService mySearchParamExtractorSvc;
+	private SearchParamExtractorR4 mySearchParamExtractor;
+	private SearchParamRegistryImpl mySearchParamRegistry;
+	private ResourceChangeListenerRegistryImpl myResourceChangeListenerRegistry;
+	private InMemoryResourceMatcher myInMemoryResourceMatcher;
+	@Mock
+	private ResourceChangeListenerCacheFactory myResourceChangeListenerCacheFactory;
+	private ResourceChangeListenerCacheRefresherImpl myResourceChangeListenerCacheRefresher;
+	private MockResourceVersionSvc myResourceVersionSvc;
+	private MockResourceHistoryTableDao myResourceHistoryTableDao;
+	private SearchParamPresenceSvcImpl mySearchParamPresenceSvc;
+	private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
+
+	@AfterEach
+	public void afterEach() {
+		myDaoConfig.setEnforceReferenceTargetTypes(new DaoConfig().isEnforceReferenceTargetTypes());
+		myDaoConfig.setAllowInlineMatchUrlReferences(new DaoConfig().isAllowInlineMatchUrlReferences());
+	}
+
+	@BeforeEach
+	public void beforeEach() {
+		myDaoConfig = new DaoConfig();
+
+		mySearchParamPresenceSvc = new SearchParamPresenceSvcImpl();
+		mySearchParamPresenceSvc.setDaoConfig(myDaoConfig);
+
+		myTransactionManager = new MockTransactionManager();
+
+		myResourceHistoryTableDao = new MockResourceHistoryTableDao();
+
+		myEntityManager = new MockEntityManager();
+
+		myInterceptorSvc = new InterceptorService();
+
+		myDaoRegistry = new DaoRegistry(myCtx);
+
+		myPartitionSettings = new PartitionSettings();
+
+		myHapiTransactionService = new HapiTransactionService();
+		myHapiTransactionService.setTransactionManager(myTransactionManager);
+		myHapiTransactionService.setInterceptorBroadcaster(myInterceptorSvc);
+		myHapiTransactionService.start();
+
+		myTransactionProcessor = new TransactionProcessor();
+		myTransactionProcessor.setContext(myCtx);
+		myTransactionProcessor.setDao(mySystemDao);
+		myTransactionProcessor.setTxManager(myTransactionManager);
+		myTransactionProcessor.setEntityManagerForUnitTest(myEntityManager);
+		myTransactionProcessor.setVersionAdapter(new TransactionProcessorVersionAdapterR4());
+		myTransactionProcessor.setDaoConfig(myDaoConfig);
+		myTransactionProcessor.setModelConfig(myDaoConfig.getModelConfig());
+		myTransactionProcessor.setHapiTransactionService(myHapiTransactionService);
+		myTransactionProcessor.setDaoRegistry(myDaoRegistry);
+		myTransactionProcessor.start();
+
+		mySystemDao = new FhirSystemDaoR4();
+		mySystemDao.setTransactionProcessorForUnitTest(myTransactionProcessor);
+		mySystemDao.start();
+
+		when(myAppCtx.getBean(eq(IInstanceValidatorModule.class))).thenReturn(myInstanceValidatorSvc);
+
+		myInMemoryResourceMatcher = new InMemoryResourceMatcher();
+
+		myResourceVersionSvc = new MockResourceVersionSvc();
+
+		myResourceChangeListenerCacheRefresher = new ResourceChangeListenerCacheRefresherImpl();
+		myResourceChangeListenerCacheRefresher.setSchedulerService(new MockSchedulerSvc());
+		myResourceChangeListenerCacheRefresher.setResourceVersionSvc(myResourceVersionSvc);
+
+		when(myResourceChangeListenerCacheFactory.create(any(), any(), any(), anyLong())).thenAnswer(t -> {
+			String resourceName = t.getArgument(0, String.class);
+			SearchParameterMap searchParameterMap = t.getArgument(1, SearchParameterMap.class);
+			IResourceChangeListener changeListener = t.getArgument(2, IResourceChangeListener.class);
+			long refreshInterval = t.getArgument(3, Long.class);
+			ResourceChangeListenerCache retVal = new ResourceChangeListenerCache(resourceName, changeListener, searchParameterMap, refreshInterval);
+			retVal.setResourceChangeListenerCacheRefresher(myResourceChangeListenerCacheRefresher);
+			return retVal;
+		});
+
+		myResourceChangeListenerRegistry = new ResourceChangeListenerRegistryImpl();
+		myResourceChangeListenerRegistry.setFhirContext(myCtx);
+		myResourceChangeListenerRegistry.setInMemoryResourceMatcher(myInMemoryResourceMatcher);
+		myResourceChangeListenerRegistry.setResourceChangeListenerCacheFactory(myResourceChangeListenerCacheFactory);
+		myResourceChangeListenerCacheRefresher.setResourceChangeListenerRegistry(myResourceChangeListenerRegistry);
+
+		mySearchParamRegistry = new SearchParamRegistryImpl();
+		mySearchParamRegistry.setResourceChangeListenerRegistry(myResourceChangeListenerRegistry);
+		mySearchParamRegistry.setFhirContext(myCtx);
+		mySearchParamRegistry.setModelConfig(myDaoConfig.getModelConfig());
+		mySearchParamRegistry.registerListener();
+
+		mySearchParamExtractor = new SearchParamExtractorR4();
+		mySearchParamExtractor.setContext(myCtx);
+		mySearchParamExtractor.setSearchParamRegistry(mySearchParamRegistry);
+		mySearchParamExtractor.setPartitionSettings(myPartitionSettings);
+		mySearchParamExtractor.setModelConfig(myDaoConfig.getModelConfig());
+		mySearchParamExtractor.start();
+
+		mySearchParamExtractorSvc = new SearchParamExtractorService();
+		mySearchParamExtractorSvc.setContext(myCtx);
+		mySearchParamExtractorSvc.setSearchParamExtractor(mySearchParamExtractor);
+		mySearchParamExtractorSvc.setModelConfig(myDaoConfig.getModelConfig());
+
+		myDaoSearchParamSynchronizer = new DaoSearchParamSynchronizer();
+		myDaoSearchParamSynchronizer.setEntityManager(myEntityManager);
+
+		mySearchParamWithInlineReferencesExtractor = new SearchParamWithInlineReferencesExtractor();
+		mySearchParamWithInlineReferencesExtractor.setDaoConfig(myDaoConfig);
+		mySearchParamWithInlineReferencesExtractor.setContext(myCtx);
+		mySearchParamWithInlineReferencesExtractor.setPartitionSettings(myPartitionSettings);
+		mySearchParamWithInlineReferencesExtractor.setSearchParamExtractorService(mySearchParamExtractorSvc);
+		mySearchParamWithInlineReferencesExtractor.setSearchParamRegistry(mySearchParamRegistry);
+		mySearchParamWithInlineReferencesExtractor.setDaoSearchParamSynchronizer(myDaoSearchParamSynchronizer);
+
+		myEobDao = new JpaResourceDao<>();
+		myEobDao.setContext(myCtx);
+		myEobDao.setConfig(myDaoConfig);
+		myEobDao.setResourceType(ExplanationOfBenefit.class);
+		myEobDao.setApplicationContext(myAppCtx);
+		myEobDao.setTransactionService(myHapiTransactionService);
+		myEobDao.setDaoConfig(myDaoConfig);
+		myEobDao.setRequestPartitionHelperService(new MockRequestPartitionHelperSvc());
+		myEobDao.setEntityManager(myEntityManager);
+		myEobDao.setSearchParamWithInlineReferencesExtractor(mySearchParamWithInlineReferencesExtractor);
+		myEobDao.setResourceHistoryTableDao(myResourceHistoryTableDao);
+		myEobDao.setSearchParamRegistry(mySearchParamRegistry);
+		myEobDao.setSearchParamPresenceSvc(mySearchParamPresenceSvc);
+		myEobDao.setDaoSearchParamSynchronizer(myDaoSearchParamSynchronizer);
+		myEobDao.start();
+
+		myDaoRegistry.setResourceDaos(Lists.newArrayList(myEobDao));
+	}
+
+	@Test
+	public void testTransaction() {
+		Bundle input = ClasspathUtil.loadResource(myCtx, Bundle.class, "/r4/large-transaction.json");
+		while (input.getEntry().size() > 1) {
+			input.getEntry().remove(1);
+		}
+
+		ServletRequestDetails requestDetails = new ServletRequestDetails(myInterceptorSvc);
+		requestDetails.setServletRequest(new MockServletRequest());
+
+		mySystemDao.transaction(requestDetails, input);
+
+		assertThat(myEntityManager.myPersistCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.contains("ResourceTable"));
+		assertThat(myEntityManager.myMergeCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.containsInAnyOrder("ResourceTable", "ResourceIndexedSearchParamToken", "ResourceIndexedSearchParamToken"));
+		assertEquals(1, myEntityManager.myFlushCount);
+		assertEquals(1, myResourceVersionSvc.myGetVersionMap);
+		assertEquals(1, myResourceHistoryTableDao.mySaveCount);
+	}
+
+	@Test
+	@Disabled
+	public void testTransactionStressTest() {
+		myDaoConfig.setEnforceReferenceTargetTypes(false);
+		myDaoConfig.setAllowInlineMatchUrlReferences(false);
+
+
+		Bundle input = ClasspathUtil.loadResource(myCtx, Bundle.class, "/r4/large-transaction.json");
+
+		ServletRequestDetails requestDetails = new ServletRequestDetails(myInterceptorSvc);
+		requestDetails.setServletRequest(new MockServletRequest());
+
+		// Pre-warmup
+		ourLog.info("Warming up...");
+		for (int i = 0; i < 10; i++) {
+			mySystemDao.transaction(requestDetails, input);
+		}
+		ourLog.info("Done warming up");
+
+		StopWatch sw = new StopWatch();
+		for (int i = 1; i < 10000; i++) {
+			mySystemDao.transaction(requestDetails, input);
+			if (i % 5 == 0) {
+				ourLog.info("Processed {} - {}/second", i, sw.formatThroughput(i, TimeUnit.SECONDS));
+			}
+
+			myEntityManager.clearCounts();
+		}
+
+		assertThat(myEntityManager.myPersistCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.contains("ResourceTable"));
+		assertThat(myEntityManager.myMergeCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.containsInAnyOrder("ResourceTable", "ResourceIndexedSearchParamToken", "ResourceIndexedSearchParamToken"));
+		assertEquals(1, myEntityManager.myFlushCount);
+		assertEquals(1, myResourceVersionSvc.myGetVersionMap);
+		assertEquals(1, myResourceHistoryTableDao.mySaveCount);
+	}
+
+	private class MockResourceVersionSvc implements IResourceVersionSvc {
+		private int myGetVersionMap;
+
+		@Nonnull
+		@Override
+		public ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap) {
+			myGetVersionMap++;
+			return ResourceVersionMap.fromResources(Lists.newArrayList());
+		}
+	}
+
+	private class MockResourceHistoryTableDao implements IResourceHistoryTableDao {
+		private int mySaveCount;
+
+		@Override
+		public ResourceHistoryTable findForIdAndVersionAndFetchProvenance(long theId, long theVersion) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Slice<Long> findForResourceId(Pageable thePage, Long theId, Long theDontWantVersion) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Slice<Long> findIdsOfPreviousVersionsOfResourceId(Pageable thePage, Long theResourceId) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Slice<Long> findIdsOfPreviousVersionsOfResources(Pageable thePage, String theResourceName) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Slice<Long> findIdsOfPreviousVersionsOfResources(Pageable thePage) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void updateVersion(long theId, long theOldVersion, long theNewVersion) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void deleteByPid(Long theId) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public List<ResourceHistoryTable> findAll() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public List<ResourceHistoryTable> findAll(Sort sort) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Page<ResourceHistoryTable> findAll(Pageable pageable) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public List<ResourceHistoryTable> findAllById(Iterable<Long> ids) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public long count() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void deleteById(Long theLong) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void delete(ResourceHistoryTable entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void deleteAll(Iterable<? extends ResourceHistoryTable> entities) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void deleteAll() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> S save(S entity) {
+			mySaveCount++;
+			return entity;
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> List<S> saveAll(Iterable<S> entities) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Optional<ResourceHistoryTable> findById(Long theLong) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public boolean existsById(Long theLong) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void flush() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> S saveAndFlush(S entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void deleteInBatch(Iterable<ResourceHistoryTable> entities) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void deleteAllInBatch() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public ResourceHistoryTable getOne(Long theLong) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> Optional<S> findOne(Example<S> example) {
+			return Optional.empty();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> List<S> findAll(Example<S> example) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> List<S> findAll(Example<S> example, Sort sort) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> Page<S> findAll(Example<S> example, Pageable pageable) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> long count(Example<S> example) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <S extends ResourceHistoryTable> boolean exists(Example<S> example) {
+			throw new UnsupportedOperationException();
+		}
+	}
+
+	private class MockEntityManager implements EntityManager {
+		private List<Object> myPersistCount = new ArrayList<>();
+		private List<Object> myMergeCount = new ArrayList<>();
+		private long ourNextId = 0L;
+		private int myFlushCount;
+
+		@Override
+		public void persist(Object entity) {
+			myPersistCount.add(entity);
+			if (entity instanceof ResourceTable) {
+				((ResourceTable) entity).setId(ourNextId++);
+			}
+		}
+
+		@Override
+		public <T> T merge(T entity) {
+			myMergeCount.add(entity);
+			return entity;
+		}
+
+		@Override
+		public void remove(Object entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> T find(Class<T> entityClass, Object primaryKey) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> T find(Class<T> entityClass, Object primaryKey, Map<String, Object> properties) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> T find(Class<T> entityClass, Object primaryKey, LockModeType lockMode) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> T find(Class<T> entityClass, Object primaryKey, LockModeType lockMode, Map<String, Object> properties) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> T getReference(Class<T> entityClass, Object primaryKey) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void flush() {
+			myFlushCount++;
+		}
+
+		@Override
+		public FlushModeType getFlushMode() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void setFlushMode(FlushModeType flushMode) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void lock(Object entity, LockModeType lockMode) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void lock(Object entity, LockModeType lockMode, Map<String, Object> properties) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void refresh(Object entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void refresh(Object entity, Map<String, Object> properties) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void refresh(Object entity, LockModeType lockMode) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void refresh(Object entity, LockModeType lockMode, Map<String, Object> properties) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void clear() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void detach(Object entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public boolean contains(Object entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public LockModeType getLockMode(Object entity) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void setProperty(String propertyName, Object value) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Map<String, Object> getProperties() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createQuery(String qlString) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> TypedQuery<T> createQuery(CriteriaQuery<T> criteriaQuery) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createQuery(CriteriaUpdate updateQuery) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createQuery(CriteriaDelete deleteQuery) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> TypedQuery<T> createQuery(String qlString, Class<T> resultClass) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createNamedQuery(String name) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> TypedQuery<T> createNamedQuery(String name, Class<T> resultClass) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createNativeQuery(String sqlString) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createNativeQuery(String sqlString, Class resultClass) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Query createNativeQuery(String sqlString, String resultSetMapping) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public StoredProcedureQuery createNamedStoredProcedureQuery(String name) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public StoredProcedureQuery createStoredProcedureQuery(String procedureName) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public StoredProcedureQuery createStoredProcedureQuery(String procedureName, Class... resultClasses) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public StoredProcedureQuery createStoredProcedureQuery(String procedureName, String... resultSetMappings) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void joinTransaction() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public boolean isJoinedToTransaction() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> T unwrap(Class<T> cls) {
+			if (cls.equals(SessionImpl.class)) {
+				return null;
+			}
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Object getDelegate() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void close() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public boolean isOpen() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public EntityTransaction getTransaction() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public EntityManagerFactory getEntityManagerFactory() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public CriteriaBuilder getCriteriaBuilder() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Metamodel getMetamodel() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> EntityGraph<T> createEntityGraph(Class<T> rootType) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public EntityGraph<?> createEntityGraph(String graphName) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public EntityGraph<?> getEntityGraph(String graphName) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public <T> List<EntityGraph<? super T>> getEntityGraphs(Class<T> entityClass) {
+			throw new UnsupportedOperationException();
+		}
+
+		public void clearCounts() {
+			myMergeCount.clear();
+			myPersistCount.clear();
+		}
+	}
+
+	private static class MockSchedulerSvc implements ISchedulerService {
+		@Override
+		public void purgeAllScheduledJobsForUnitTest() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void logStatusForUnitTest() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void scheduleLocalJob(long theIntervalMillis, ScheduledJobDefinition theJobDefinition) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void scheduleClusteredJob(long theIntervalMillis, ScheduledJobDefinition theJobDefinition) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Set<JobKey> getLocalJobKeysForUnitTest() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public Set<JobKey> getClusteredJobKeysForUnitTest() {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public boolean isStopping() {
+			return false;
+		}
+	}
+
+	private static class MockServletRequest extends MockHttpServletRequest {
+	}
+
+	private static class MockRequestPartitionHelperSvc implements ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc {
+		@Nonnull
+		@Override
+		public RequestPartitionId determineReadPartitionForRequest(@Nullable RequestDetails theRequest, String theResourceType) {
+			return RequestPartitionId.defaultPartition();
+		}
+
+		@Nonnull
+		@Override
+		public RequestPartitionId determineCreatePartitionForRequest(@Nullable RequestDetails theRequest, @Nonnull IBaseResource theResource, @Nonnull String theResourceType) {
+			return RequestPartitionId.defaultPartition();
+		}
+	}
+
+	private static class MockTransactionManager implements PlatformTransactionManager {
+
+
+		@Nonnull
+		@Override
+		public TransactionStatus getTransaction(TransactionDefinition definition) throws TransactionException {
+			return new SimpleTransactionStatus();
+		}
+
+		@Override
+		public void commit(@Nonnull TransactionStatus status) throws TransactionException {
+
+		}
+
+		@Override
+		public void rollback(@Nonnull TransactionStatus status) throws TransactionException {
+
+		}
+	}
+}

hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml

@@ -27,7 +27,7 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 	j
-	<logger name="org.hibernate.event.internal.DefaultPersistEventListener" additivity="true" level="trace">
+	<logger name="org.hibernate.event.internal.DefaultPersistEventListener" additivity="true" level="info">
 		<appender-ref ref="STDOUT" />
 	</logger>
 

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

@@ -72,6 +72,20 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		init510(); // 20200516 - 20201028
 		init520(); // 20201029 -
 		init530(); 
+		init540(); // 20210218 - 
+	}
+
+	private void init540() {
+		
+		Builder version = forVersion(VersionEnum.V5_4_0);
+		
+		//-- add index on HFJ_SPIDX_DATE
+	    version.onTable("HFJ_SPIDX_DATE").addIndex("20210309.1", "IDX_SP_DATE_HASH_HIGH")
+	        .unique(false).withColumns("HASH_IDENTITY", "SP_VALUE_HIGH");
+	    
+		//-- add index on HFJ_FORCED_ID
+	    version.onTable("HFJ_FORCED_ID").addIndex("20210309.2", "IDX_FORCEID_FID")
+	        .unique(false).withColumns("FORCED_ID");   
 	}
 	
 	private void init530() {
@@ -126,6 +140,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		// HFJ_RES_LINK
 		version.onTable("HFJ_RES_LINK")
 			.addColumn("20210126.1", "TARGET_RESOURCE_VERSION").nullable().type(ColumnTypeEnum.LONG);
+
 	}
 
 	protected void init520() {

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ForcedId.java

@@ -31,6 +31,7 @@ import javax.persistence.ForeignKey;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
@@ -48,6 +49,7 @@ import javax.persistence.UniqueConstraint;
 	 * - IDX_FORCEDID_TYPE_RESID
 	 * so don't reuse these names
 	 */
+	@Index(name = "IDX_FORCEID_FID", columnList = "FORCED_ID")
 })
 public class ForcedId extends BasePartitionable {
 

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ModelConfig.java

@@ -98,7 +98,6 @@ public class ModelConfig {
 	private Set<String> myAutoVersionReferenceAtPaths = Collections.emptySet();
 	private Map<String, Set<String>> myTypeToAutoVersionReferenceAtPaths = Collections.emptyMap();
 	private boolean myRespectVersionsForSearchIncludes;
-	
 	private boolean myIndexOnContainedResources = false;
 
 	/**
@@ -732,7 +731,6 @@ public class ModelConfig {
 		myRespectVersionsForSearchIncludes = theRespectVersionsForSearchIncludes;
 	}
 
-	
 	/**
 	 * Should indexing and searching on contained resources be enabled on this server.
 	 * This may have performance impacts, and should be enabled only if it is needed. Default is <code>false</code>.

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java

@@ -55,6 +55,7 @@ import java.util.Date;
 	// We previously had an index called IDX_SP_DATE - Dont reuse
 	@Index(name = "IDX_SP_DATE_HASH", columnList = "HASH_IDENTITY,SP_VALUE_LOW,SP_VALUE_HIGH"),
 	@Index(name = "IDX_SP_DATE_HASH_LOW", columnList = "HASH_IDENTITY,SP_VALUE_LOW"),
+	@Index(name = "IDX_SP_DATE_HASH_HIGH", columnList = "HASH_IDENTITY,SP_VALUE_HIGH"),
 	@Index(name = "IDX_SP_DATE_ORD_HASH", columnList = "HASH_IDENTITY,SP_VALUE_LOW_DATE_ORDINAL,SP_VALUE_HIGH_DATE_ORDINAL"),
 	@Index(name = "IDX_SP_DATE_ORD_HASH_LOW", columnList = "HASH_IDENTITY,SP_VALUE_LOW_DATE_ORDINAL"),
 	@Index(name = "IDX_SP_DATE_RESID", columnList = "RES_ID"),

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java

@@ -257,6 +257,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
 		b.append("hashIdentity", myHashIdentity);
 		b.append("hashSystem", myHashSystem);
 		b.append("hashValue", myHashValue);
+		b.append("hashSysAndValue", myHashSystemAndValue);
 		return b.build();
 	}
 

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

@@ -134,6 +134,11 @@ public class ResourceChangeListenerCache implements IResourceChangeListenerCache
 		return retval;
 	}
 
+	@VisibleForTesting
+	public void setResourceChangeListenerCacheRefresher(IResourceChangeListenerCacheRefresher theResourceChangeListenerCacheRefresher) {
+		myResourceChangeListenerCacheRefresher = theResourceChangeListenerCacheRefresher;
+	}
+
 	private ResourceChangeResult refreshCacheAndNotifyListenersWithRetry() {
 		Retrier<ResourceChangeResult> refreshCacheRetrier = new Retrier<>(() -> {
 			synchronized (this) {

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

@@ -103,6 +103,21 @@ public class ResourceChangeListenerCacheRefresherImpl implements IResourceChange
 		return retval;
 	}
 
+	@VisibleForTesting
+	public void setSchedulerService(ISchedulerService theSchedulerService) {
+		mySchedulerService = theSchedulerService;
+	}
+
+	@VisibleForTesting
+	public void setResourceChangeListenerRegistry(ResourceChangeListenerRegistryImpl theResourceChangeListenerRegistry) {
+		myResourceChangeListenerRegistry = theResourceChangeListenerRegistry;
+	}
+
+	@VisibleForTesting
+	public void setResourceVersionSvc(IResourceVersionSvc theResourceVersionSvc) {
+		myResourceVersionSvc = theResourceVersionSvc;
+	}
+
 	@Override
 	public ResourceChangeResult refreshCacheAndNotifyListener(IResourceChangeListenerCache theCache) {
 		ResourceChangeResult retVal = new ResourceChangeResult();

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

@@ -47,28 +47,42 @@ import java.util.concurrent.ConcurrentLinkedQueue;
 @Component
 public class ResourceChangeListenerRegistryImpl implements IResourceChangeListenerRegistry {
 	private static final Logger ourLog = LoggerFactory.getLogger(ResourceChangeListenerRegistryImpl.class);
-
+	private final Queue<ResourceChangeListenerCache> myListenerEntries = new ConcurrentLinkedQueue<>();
+	@Autowired
+	ResourceChangeListenerCacheFactory myResourceChangeListenerCacheFactory;
 	@Autowired
 	private FhirContext myFhirContext;
 	@Autowired
 	private InMemoryResourceMatcher myInMemoryResourceMatcher;
-	@Autowired
-    ResourceChangeListenerCacheFactory myResourceChangeListenerCacheFactory;
 
-	private final Queue<ResourceChangeListenerCache> myListenerEntries = new ConcurrentLinkedQueue<>();
+	@VisibleForTesting
+	public void setResourceChangeListenerCacheFactory(ResourceChangeListenerCacheFactory theResourceChangeListenerCacheFactory) {
+		myResourceChangeListenerCacheFactory = theResourceChangeListenerCacheFactory;
+	}
+
+	@VisibleForTesting
+	public void setFhirContext(FhirContext theFhirContext) {
+		myFhirContext = theFhirContext;
+	}
+
+	@VisibleForTesting
+	public void setInMemoryResourceMatcher(InMemoryResourceMatcher theInMemoryResourceMatcher) {
+		myInMemoryResourceMatcher = theInMemoryResourceMatcher;
+	}
 
 	/**
 	 * Register a listener in order to be notified whenever a resource matching the provided SearchParameterMap
 	 * changes in any way.  If the change happened on the same jvm process where this registry resides, then the listener will be called
 	 * within {@link ResourceChangeListenerCacheRefresherImpl#LOCAL_REFRESH_INTERVAL_MS} of the change happening.  If the change happened
 	 * on a different jvm process, then the listener will be called within theRemoteRefreshIntervalMs.
+	 *
 	 * @param theResourceName            the type of the resource the listener should be notified about (e.g. "Subscription" or "SearchParameter")
 	 * @param theSearchParameterMap      the listener will only be notified of changes to resources that match this map
 	 * @param theResourceChangeListener  the listener that will be called whenever resource changes are detected
 	 * @param theRemoteRefreshIntervalMs the number of milliseconds between checking the database for changed resources that match the search parameter map
+	 * @return RegisteredResourceChangeListener that stores the resource id cache, and the next refresh time
 	 * @throws ca.uhn.fhir.parser.DataFormatException if theResourceName is not a valid resource type in our FhirContext
 	 * @throws IllegalArgumentException               if theSearchParamMap cannot be evaluated in-memory
-	 * @return RegisteredResourceChangeListener that stores the resource id cache, and the next refresh time
 	 */
 	@Override
 	public IResourceChangeListenerCache registerResourceResourceChangeListener(String theResourceName, SearchParameterMap theSearchParameterMap, IResourceChangeListener theResourceChangeListener, long theRemoteRefreshIntervalMs) {

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

@@ -45,8 +45,10 @@ import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.model.primitive.BoundCodeDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.HapiExtensions;
 import ca.uhn.fhir.util.StringUtil;
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Sets;
 import org.apache.commons.lang3.ObjectUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -81,6 +83,7 @@ import java.util.TreeSet;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.apache.commons.lang3.StringUtils.trim;
@@ -532,6 +535,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 
 	protected abstract IValueExtractor getPathValueExtractor(IBaseResource theResource, String theSinglePath);
 
+	@VisibleForTesting
+	public void setContext(FhirContext theContext) {
+		myContext = theContext;
+	}
+
 	protected FhirContext getContext() {
 		return myContext;
 	}
@@ -540,6 +548,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		return myModelConfig;
 	}
 
+	@VisibleForTesting
+	public void setSearchParamRegistry(ISearchParamRegistry theSearchParamRegistry) {
+		mySearchParamRegistry = theSearchParamRegistry;
+	}
+
 	private Collection<RuntimeSearchParam> getSearchParams(IBaseResource theResource) {
 		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
 		Collection<RuntimeSearchParam> retVal = mySearchParamRegistry.getActiveSearchParams(def.getName()).values();
@@ -644,6 +657,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		}
 	}
 
+	@VisibleForTesting
+	public void setModelConfig(ModelConfig theModelConfig) {
+		myModelConfig = theModelConfig;
+	}
+
 	protected boolean shouldIndexTextComponentOfToken(RuntimeSearchParam theSearchParam) {
 		return tokenTextIndexingEnabledForSearchParam(myModelConfig, theSearchParam);
 	}
@@ -938,6 +956,9 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		SearchParamSet<T> retVal = new SearchParamSet<>();
 
 		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
+
+		cleanUpContainedResourceReferences(theResource, theSearchParamType, searchParams);
+
 		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != theSearchParamType) {
 				continue;
@@ -948,6 +969,31 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		return retVal;
 	}
 
+	/**
+	 * HAPI FHIR Reference objects (e.g. {@link org.hl7.fhir.r4.model.Reference}) can hold references either by text
+	 * (e.g. "#3") or by resource (e.g. "new Reference(patientInstance)"). The FHIRPath evaluator only understands the
+	 * first way, so if there is any chance of the FHIRPath evaluator needing to descend across references, we
+	 * have to assign values to those references before indexing.
+	 *
+	 * Doing this cleanup isn't hugely expensive, but it's not completely free either so we only do it
+	 * if we think there's actually a chance
+	 */
+	private void cleanUpContainedResourceReferences(IBaseResource theResource, RestSearchParameterTypeEnum theSearchParamType, Collection<RuntimeSearchParam> searchParams) {
+		boolean havePathWithResolveExpression = myModelConfig.isIndexOnContainedResources();
+		for (RuntimeSearchParam nextSpDef : searchParams) {
+			if (nextSpDef.getParamType() != theSearchParamType) {
+				continue;
+			}
+			if (defaultString(nextSpDef.getPath()).contains("resolve")) {
+				havePathWithResolveExpression = true;
+				break;
+			}
+		}
+		if (havePathWithResolveExpression) {
+			myContext.newTerser().containResources(theResource, FhirTerser.OptionsEnum.MODIFY_RESOURCE, FhirTerser.OptionsEnum.STORE_AND_REUSE_RESULTS);
+		}
+	}
+
 	private <T> void extractSearchParam(RuntimeSearchParam theSearchParameterDef, IBaseResource theResource, IExtractor<T> theExtractor, SearchParamSet<T> theSetToPopulate, boolean theWantLocalReferences) {
 		String nextPathUnsplit = theSearchParameterDef.getPath();
 		if (isBlank(nextPathUnsplit)) {
@@ -1020,6 +1066,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		}
 	}
 
+	@VisibleForTesting
+	public void setPartitionSettings(PartitionSettings thePartitionSettings) {
+		myPartitionSettings = thePartitionSettings;
+	}
+
 	private ResourceIndexedSearchParamToken createTokenIndexIfNotBlank(String theResourceType, RuntimeSearchParam theSearchParam, String theSystem, String theValue) {
 		String system = theSystem;
 		String value = theValue;

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

@@ -74,10 +74,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class SearchParamExtractorService {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamExtractorService.class);
-
 	@Autowired
 	private ISearchParamExtractor mySearchParamExtractor;
-
 	@Autowired
 	private IInterceptorBroadcaster myInterceptorBroadcaster;
 	@Autowired
@@ -91,22 +89,25 @@ public class SearchParamExtractorService {
 	@Autowired(required = false)
 	private IResourceLinkResolver myResourceLinkResolver;
 
+	@VisibleForTesting
+	public void setSearchParamExtractor(ISearchParamExtractor theSearchParamExtractor) {
+		mySearchParamExtractor = theSearchParamExtractor;
+	}
 
 	/**
 	 * This method is responsible for scanning a resource for all of the search parameter instances. I.e. for all search parameters defined for
 	 * a given resource type, it extracts the associated indexes and populates {@literal theParams}.
 	 */
 	public void extractFromResource(RequestPartitionId theRequestPartitionId, RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, TransactionDetails theTransactionDetails, boolean theFailOnInvalidReference) {
-		IBaseResource resource = normalizeResource(theResource);
 
 		// All search parameter types except Reference
 		ResourceIndexedSearchParams normalParams = new ResourceIndexedSearchParams();
-		extractSearchIndexParameters(theRequestDetails, normalParams, resource, theEntity);
+		extractSearchIndexParameters(theRequestDetails, normalParams, theResource, theEntity);
 		mergeParams(normalParams, theParams);
 
 		if (myModelConfig.isIndexOnContainedResources()) {
 			ResourceIndexedSearchParams containedParams = new ResourceIndexedSearchParams();
-			extractSearchIndexParametersForContainedResources(theRequestDetails, containedParams, resource, theEntity);
+			extractSearchIndexParametersForContainedResources(theRequestDetails, containedParams, theResource, theEntity);
 			mergeParams(containedParams, theParams);
 		}
 		
@@ -114,11 +115,16 @@ public class SearchParamExtractorService {
 		populateResourceTables(theParams, theEntity);
 		
 		// Reference search parameters
-		extractResourceLinks(theRequestPartitionId, theParams, theEntity, resource, theTransactionDetails, theFailOnInvalidReference, theRequestDetails);
+		extractResourceLinks(theRequestPartitionId, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference, theRequestDetails);
 
 		theParams.setUpdatedTime(theTransactionDetails.getTransactionDate());
 	}
 
+	@VisibleForTesting
+	public void setModelConfig(ModelConfig theModelConfig) {
+		myModelConfig = theModelConfig;
+	}
+
 	private void extractSearchIndexParametersForContainedResources(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {		
 		
 		FhirTerser terser = myContext.newTerser();
@@ -247,19 +253,9 @@ public class SearchParamExtractorService {
 		populateResourceTable(theParams.myCoordsParams, theEntity);
 	}
 
-	/**
+	@VisibleForTesting
-	 * This is a bit hacky, but if someone has manually populated a resource (ie. my working directly with the model
+	public void setContext(FhirContext theContext) {
-	 * as opposed to by parsing a serialized instance) it's possible that they have put in contained resources
+		myContext = theContext;
-	 * using {@link IBaseReference#setResource(IBaseResource)}, and those contained resources have not yet
-	 * ended up in the Resource.contained array, meaning that FHIRPath expressions won't be able to find them.
-	 *
-	 * As a result, we to a serialize-and-parse to normalize the object. This really only affects people who
-	 * are calling the JPA DAOs directly, but there are a few of those...
-	 */
-	private IBaseResource normalizeResource(IBaseResource theResource) {
-		IParser parser = myContext.newJsonParser().setPrettyPrint(false);
-		theResource = parser.parseResource(parser.encodeResourceToString(theResource));
-		return theResource;
 	}
 
 	private void extractResourceLinks(RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, TransactionDetails theTransactionDetails, boolean theFailOnInvalidReference, RequestDetails theRequest) {
@@ -291,6 +287,10 @@ public class SearchParamExtractorService {
 			nextId = nextReference.getResource().getIdElement();
 		}
 
+		if (myContext.getParserOptions().isStripVersionsFromReferences() && !myContext.getParserOptions().getDontStripVersionsFromReferencesAtPaths().contains(thePathAndRef.getPath()) && nextId.hasVersionIdPart()) {
+			nextId = nextId.toVersionless();
+		}
+
 		theParams.myPopulatedResourceLinkParameters.add(thePathAndRef.getSearchParamName());
 
 		boolean canonical = thePathAndRef.isCanonical();
@@ -431,24 +431,6 @@ public class SearchParamExtractorService {
 		return ResourceLink.forLocalReference(nextPathAndRef.getPath(), theEntity, targetResourceType, targetResourcePid, targetResourceIdPart, theUpdateTime, targetVersion);
 	}
 
-
-	static void handleWarnings(RequestDetails theRequestDetails, IInterceptorBroadcaster theInterceptorBroadcaster, ISearchParamExtractor.SearchParamSet<?> theSearchParamSet) {
-		if (theSearchParamSet.getWarnings().isEmpty()) {
-			return;
-		}
-
-		// If extraction generated any warnings, broadcast an error
-		for (String next : theSearchParamSet.getWarnings()) {
-			StorageProcessingMessage messageHolder = new StorageProcessingMessage();
-			messageHolder.setMessage(next);
-			HookParams params = new HookParams()
-				.add(RequestDetails.class, theRequestDetails)
-				.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
-				.add(StorageProcessingMessage.class, messageHolder);
-			JpaInterceptorBroadcaster.doCallHooks(theInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_WARNING, params);
-		}
-	}
-
 	private void populateResourceTable(Collection<? extends BaseResourceIndexedSearchParam> theParams, ResourceTable theResourceTable) {
 		for (BaseResourceIndexedSearchParam next : theParams) {
 			if (next.getResourcePid() == null) {
@@ -498,5 +480,22 @@ public class SearchParamExtractorService {
 	public List<String> extractParamValuesAsStrings(RuntimeSearchParam theActiveSearchParam, IBaseResource theResource) {
 		return mySearchParamExtractor.extractParamValuesAsStrings(theActiveSearchParam, theResource);
 	}
+
+	static void handleWarnings(RequestDetails theRequestDetails, IInterceptorBroadcaster theInterceptorBroadcaster, ISearchParamExtractor.SearchParamSet<?> theSearchParamSet) {
+		if (theSearchParamSet.getWarnings().isEmpty()) {
+			return;
+		}
+
+		// If extraction generated any warnings, broadcast an error
+		for (String next : theSearchParamSet.getWarnings()) {
+			StorageProcessingMessage messageHolder = new StorageProcessingMessage();
+			messageHolder.setMessage(next);
+			HookParams params = new HookParams()
+				.add(RequestDetails.class, theRequestDetails)
+				.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
+				.add(StorageProcessingMessage.class, messageHolder);
+			JpaInterceptorBroadcaster.doCallHooks(theInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_WARNING, params);
+		}
+	}
 }
 

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

@@ -148,6 +148,11 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
 		ourLog.debug("Refreshed search parameter cache in {}ms", sw.getMillis());
 	}
 
+	@VisibleForTesting
+	public void setFhirContext(FhirContext theFhirContext) {
+		myFhirContext = theFhirContext;
+	}
+
 	private ReadOnlySearchParamCache getBuiltInSearchParams() {
 		if (myBuiltInSearchParams == null) {
 			myBuiltInSearchParams = ReadOnlySearchParamCache.fromFhirContext(myFhirContext);
@@ -162,6 +167,11 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
 		}
 	}
 
+	@VisibleForTesting
+	public void setModelConfig(ModelConfig theModelConfig) {
+		myModelConfig = theModelConfig;
+	}
+
 	private long overrideBuiltinSearchParamsWithActiveJpaSearchParams(RuntimeSearchParamCache theSearchParamCache, Collection<IBaseResource> theSearchParams) {
 		if (!myModelConfig.isDefaultSearchParamsCanBeOverridden() || theSearchParams == null) {
 			return 0;
@@ -228,6 +238,11 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
 		return myResourceChangeListenerCache.refreshCacheIfNecessary();
 	}
 
+	@VisibleForTesting
+	public void setResourceChangeListenerRegistry(IResourceChangeListenerRegistry theResourceChangeListenerRegistry) {
+		myResourceChangeListenerRegistry = theResourceChangeListenerRegistry;
+	}
+
 	@PostConstruct
 	public void registerListener() {
 		myResourceChangeListenerCache = myResourceChangeListenerRegistry.registerResourceResourceChangeListener("SearchParameter", SearchParameterMap.newSynchronous(), this, REFRESH_INTERVAL);

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

@@ -1090,6 +1090,7 @@ public class XmlParserDstu3Test {
 	 * See #103
 	 */
 	@Test
+	@Disabled
 	public void testEncodeAndReEncodeContainedJson() {
 		Composition comp = new Composition();
 		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section0_Allergy0")));
@@ -1115,6 +1116,7 @@ public class XmlParserDstu3Test {
 	 * See #103
 	 */
 	@Test
+	@Disabled
 	public void testEncodeAndReEncodeContainedXml() {
 		Composition comp = new Composition();
 		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section0_Allergy0")));

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

@@ -2,10 +2,7 @@ package ca.uhn.fhir.parser;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
-import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.test.BaseTest;
 import ca.uhn.fhir.util.StopWatch;
@@ -22,7 +19,6 @@ import org.hl7.fhir.r4.model.Composition;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Device;
 import org.hl7.fhir.r4.model.DocumentReference;
-import org.hl7.fhir.r4.model.Dosage;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Medication;
@@ -39,7 +35,6 @@ import org.hl7.fhir.r4.model.QuestionnaireResponse;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Type;
-import org.hl7.fhir.r4.model.UuidType;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Disabled;
@@ -473,8 +468,8 @@ public class JsonParserR4Test extends BaseTest {
 		ourLog.info(encoded);
 		mr = ourCtx.newJsonParser().parseResource(MedicationRequest.class, encoded);
 
-		assertEquals("#2", mr.getContained().get(0).getId());
+		assertEquals("#1", mr.getContained().get(0).getId());
-		assertEquals("#1", mr.getContained().get(1).getId());
+		assertEquals("#2", mr.getContained().get(1).getId());
 
 	}
 
@@ -929,6 +924,50 @@ public class JsonParserR4Test extends BaseTest {
 	}
 
 
+	/**
+	 * Ensure that a contained bundle doesn't cause a crash
+	 */
+	@Test
+	public void testParseAndEncodePreservesContainedResourceOrder() {
+		String auditEvent = "{\n" +
+			"  \"resourceType\": \"AuditEvent\",\n" +
+			"  \"contained\": [ {\n" +
+			"    \"resourceType\": \"Observation\",\n" +
+			"    \"id\": \"A\",\n" +
+			"    \"identifier\": [ {\n" +
+			"      \"value\": \"A\"\n" +
+			"    } ]\n" +
+			"  }, {\n" +
+			"    \"resourceType\": \"Observation\",\n" +
+			"    \"id\": \"B\",\n" +
+			"    \"identifier\": [ {\n" +
+			"      \"value\": \"B\"\n" +
+			"    } ]\n" +
+			"  } ],\n" +
+			"  \"entity\": [ {\n" +
+			"    \"what\": {\n" +
+			"      \"reference\": \"#B\"\n" +
+			"    }\n" +
+			"  }, {\n" +
+			"    \"what\": {\n" +
+			"      \"reference\": \"#A\"\n" +
+			"    }\n" +
+			"  } ]\n" +
+			"}";
+
+		ourLog.info("Input: {}", auditEvent);
+		AuditEvent ae = ourCtx.newJsonParser().parseResource(AuditEvent.class, auditEvent);
+		assertEquals("#A", ae.getContained().get(0).getId());
+		assertEquals("#B", ae.getContained().get(1).getId());
+		assertEquals("#B", ae.getEntity().get(0).getWhat().getReference());
+		assertEquals("#A", ae.getEntity().get(1).getWhat().getReference());
+
+		String serialized = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(ae);
+		assertEquals(auditEvent, serialized);
+
+	}
+
+
 	@DatatypeDef(
 		name = "UnknownPrimitiveType"
 	)

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java

@@ -44,6 +44,55 @@ public class XmlParserR4Test extends BaseTest {
 		return c;
 	}
 
+
+	/**
+	 * Ensure that a contained bundle doesn't cause a crash
+	 */
+	@Test
+	public void testParseAndEncodePreservesContainedResourceOrder() {
+		String auditEvent = "<AuditEvent xmlns=\"http://hl7.org/fhir\">\n" +
+			"   <contained>\n" +
+			"      <Observation xmlns=\"http://hl7.org/fhir\">\n" +
+			"         <id value=\"A\"/>\n" +
+			"         <identifier>\n" +
+			"            <value value=\"A\"/>\n" +
+			"         </identifier>\n" +
+			"      </Observation>\n" +
+			"   </contained>\n" +
+			"   <contained>\n" +
+			"      <Observation xmlns=\"http://hl7.org/fhir\">\n" +
+			"         <id value=\"B\"/>\n" +
+			"         <identifier>\n" +
+			"            <value value=\"B\"/>\n" +
+			"         </identifier>\n" +
+			"      </Observation>\n" +
+			"   </contained>\n" +
+			"   <entity>\n" +
+			"      <what>\n" +
+			"         <reference value=\"#B\"/>\n" +
+			"      </what>\n" +
+			"   </entity>\n" +
+			"   <entity>\n" +
+			"      <what>\n" +
+			"         <reference value=\"#A\"/>\n" +
+			"      </what>\n" +
+			"   </entity>\n" +
+			"</AuditEvent>";
+
+		ourLog.info("Input: {}", auditEvent);
+		AuditEvent ae = ourCtx.newXmlParser().parseResource(AuditEvent.class, auditEvent);
+		assertEquals("#A", ae.getContained().get(0).getId());
+		assertEquals("#B", ae.getContained().get(1).getId());
+		assertEquals("#B", ae.getEntity().get(0).getWhat().getReference());
+		assertEquals("#A", ae.getEntity().get(1).getWhat().getReference());
+
+		String serialized = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(ae);
+		assertEquals(auditEvent, serialized);
+
+	}
+
+
+
 	/**
 	 * See #402 section.text is overwritten by composition.text
 	 */

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/FhirTerserR4Test.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.util;
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.model.api.annotation.Block;
 import ca.uhn.fhir.parser.DataFormatException;
 import org.hamcrest.Matchers;
@@ -14,12 +15,14 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DocumentReference;
-import org.hl7.fhir.r4.model.Element;
 import org.hl7.fhir.r4.model.Enumeration;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.MarkdownType;
+import org.hl7.fhir.r4.model.Medication;
+import org.hl7.fhir.r4.model.MedicationAdministration;
+import org.hl7.fhir.r4.model.MedicationRequest;
 import org.hl7.fhir.r4.model.Money;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
@@ -29,8 +32,10 @@ import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.PrimitiveType;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.ResourceType;
 import org.hl7.fhir.r4.model.SimpleQuantity;
 import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.Substance;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
@@ -62,14 +67,74 @@ import static org.mockito.Mockito.when;
 public class FhirTerserR4Test {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirTerserR4Test.class);
-	private static FhirContext ourCtx = FhirContext.forR4();
+	private FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
+
+	@Test
+	public void testContainResourcesWithModify() {
+
+		MedicationRequest mr = new MedicationRequest();
+		mr.setMedication(new Reference(new Medication().setStatus(Medication.MedicationStatus.ACTIVE)));
+		mr.getRequester().setResource(new Practitioner().setActive(true));
+
+		FhirTerser.ContainedResources contained = myCtx.newTerser().containResources(mr, FhirTerser.OptionsEnum.MODIFY_RESOURCE, FhirTerser.OptionsEnum.STORE_AND_REUSE_RESULTS);
+
+		assertEquals("#1", mr.getContained().get(0).getId());
+		assertEquals("#2", mr.getContained().get(1).getId());
+		assertEquals(ResourceType.Medication, mr.getContained().get(0).getResourceType());
+		assertEquals(ResourceType.Practitioner, mr.getContained().get(1).getResourceType());
+		assertEquals("#1", mr.getMedicationReference().getReference());
+		assertEquals("#2", mr.getRequester().getReference());
+
+		FhirTerser.ContainedResources secondPass = myCtx.newTerser().containResources(mr, FhirTerser.OptionsEnum.MODIFY_RESOURCE, FhirTerser.OptionsEnum.STORE_AND_REUSE_RESULTS);
+		assertSame(contained, secondPass);
+	}
+
+	@Test
+	public void testContainedResourcesWithModify_DoubleLink() {
+		Substance ingredient = new Substance();
+		ingredient.getCode().addCoding().setSystem("system").setCode("code");
+
+		Medication medication = new Medication();
+		medication.addIngredient().setItem(new Reference(ingredient));
+
+		MedicationAdministration medAdmin = new MedicationAdministration();
+		medAdmin.setMedication(new Reference(medication));
+
+		myCtx.newTerser().containResources(medAdmin, FhirTerser.OptionsEnum.MODIFY_RESOURCE, FhirTerser.OptionsEnum.STORE_AND_REUSE_RESULTS);
+
+		assertEquals("#1", medAdmin.getContained().get(0).getId());
+		assertEquals("#2", medAdmin.getContained().get(1).getId());
+		assertEquals(ResourceType.Medication, medAdmin.getContained().get(0).getResourceType());
+		assertEquals(ResourceType.Substance, medAdmin.getContained().get(1).getResourceType());
+		assertEquals("#1", medAdmin.getMedicationReference().getReference());
+		assertEquals("#2", ((Medication)(medAdmin.getContained().get(0))).getIngredientFirstRep().getItemReference().getReference());
+
+	}
+
+	@Test
+	public void testContainResourcesWithModify_DontTouchEmbeddedResources() {
+
+		MedicationRequest mr = new MedicationRequest();
+		mr.setMedication(new Reference(new Medication().setStatus(Medication.MedicationStatus.ACTIVE)));
+		mr.getRequester().setResource(new Practitioner().setActive(true));
+
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(mr);
+
+		myCtx.newTerser().containResources(bundle, FhirTerser.OptionsEnum.MODIFY_RESOURCE);
+
+		assertEquals(0, mr.getContained().size());
+		assertEquals(null, mr.getRequester().getReference());
+		assertEquals( null, mr.getMedicationReference().getReference());
+
+	}
 
 	@Test
 	public void testGetValuesCreateEnumeration_SetsEnumFactory() {
 
 		Patient patient = new Patient();
 
-		Enumeration<?> enumeration = (Enumeration<?>) ourCtx.newTerser().getValues(patient, "Patient.gender", Enumeration.class, true).get(0);
+		Enumeration<?> enumeration = (Enumeration<?>) myCtx.newTerser().getValues(patient, "Patient.gender", Enumeration.class, true).get(0);
 		assertNotNull(enumeration.getEnumFactory());
 	}
 
@@ -98,9 +163,9 @@ public class FhirTerserR4Test {
 			.setUrl("Observation/obs")
 			.setMethod(Bundle.HTTPVerb.PUT);
 
-		ourCtx.newTerser().clear(input);
+		myCtx.newTerser().clear(input);
 
-		String output = ourCtx.newJsonParser().encodeResourceToString(input);
+		String output = myCtx.newJsonParser().encodeResourceToString(input);
 		ourLog.info(output);
 		assertTrue(input.isEmpty());
 		assertEquals("{\"resourceType\":\"Bundle\"}", output);
@@ -132,7 +197,7 @@ public class FhirTerserR4Test {
 			.setMethod(Bundle.HTTPVerb.PUT);
 
 		Bundle ionputClone = new Bundle();
-		ourCtx.newTerser().cloneInto(input, ionputClone, false);
+		myCtx.newTerser().cloneInto(input, ionputClone, false);
 	}
 
 	@Test
@@ -141,7 +206,7 @@ public class FhirTerserR4Test {
 		source.setCode("CODE");
 		SimpleQuantity target = new SimpleQuantity();
 
-		ourCtx.newTerser().cloneInto(source, target, true);
+		myCtx.newTerser().cloneInto(source, target, true);
 
 		assertEquals("CODE", target.getCode());
 	}
@@ -153,12 +218,12 @@ public class FhirTerserR4Test {
 		source.setUnit("UNIT");
 		Identifier target = new Identifier();
 
-		ourCtx.newTerser().cloneInto(source, target, true);
+		myCtx.newTerser().cloneInto(source, target, true);
 
 		assertEquals("SYSTEM", target.getSystem());
 
 		try {
-			ourCtx.newTerser().cloneInto(source, target, false);
+			myCtx.newTerser().cloneInto(source, target, false);
 			fail();
 		} catch (DataFormatException e) {
 			// good
@@ -175,7 +240,7 @@ public class FhirTerserR4Test {
 		patient.addExtension(new Extension("http://example.com", new StringType("FOO")));
 
 		Patient target = new Patient();
-		ourCtx.newTerser().cloneInto(patient, target, false);
+		myCtx.newTerser().cloneInto(patient, target, false);
 
 		List<Extension> exts = target.getExtensionsByUrl("http://example.com");
 		assertEquals(1, exts.size());
@@ -189,7 +254,7 @@ public class FhirTerserR4Test {
 
 		DocumentReference target = new DocumentReference();
 
-		ourCtx.newTerser().cloneInto(source, target, true);
+		myCtx.newTerser().cloneInto(source, target, true);
 
 		assertEquals(1, target.getContentFirstRep().getAttachment().getDataElement().getExtension().size());
 		assertEquals("http://foo", target.getContentFirstRep().getAttachment().getDataElement().getExtension().get(0).getUrl());
@@ -204,7 +269,7 @@ public class FhirTerserR4Test {
 		patient.addExtension((Extension) new Extension().setUrl("http://foo").addExtension(ext));
 
 		Patient target = new Patient();
-		ourCtx.newTerser().cloneInto(patient, target, false);
+		myCtx.newTerser().cloneInto(patient, target, false);
 
 		List<Extension> exts = target.getExtensionsByUrl("http://foo");
 		assertEquals(1, exts.size());
@@ -218,7 +283,7 @@ public class FhirTerserR4Test {
 		patient.setGender(Enumerations.AdministrativeGender.MALE);
 
 		Patient target = new Patient();
-		ourCtx.newTerser().cloneInto(patient, target, false);
+		myCtx.newTerser().cloneInto(patient, target, false);
 
 		assertEquals("http://hl7.org/fhir/administrative-gender", target.getGenderElement().getSystem());
 	}
@@ -229,7 +294,7 @@ public class FhirTerserR4Test {
 		source.setId("STRING_ID");
 		MarkdownType target = new MarkdownType();
 
-		ourCtx.newTerser().cloneInto(source, target, true);
+		myCtx.newTerser().cloneInto(source, target, true);
 
 		assertEquals("STR", target.getValueAsString());
 		assertEquals("STRING_ID", target.getId());
@@ -241,11 +306,11 @@ public class FhirTerserR4Test {
 		StringType source = new StringType("STR");
 		Money target = new Money();
 
-		ourCtx.newTerser().cloneInto(source, target, true);
+		myCtx.newTerser().cloneInto(source, target, true);
 		assertTrue(target.isEmpty());
 
 		try {
-			ourCtx.newTerser().cloneInto(source, target, false);
+			myCtx.newTerser().cloneInto(source, target, false);
 			fail();
 		} catch (DataFormatException e) {
 			// good
@@ -263,7 +328,7 @@ public class FhirTerserR4Test {
 		obs.addNote().setText("COMMENTS");
 
 		Observation target = new Observation();
-		ourCtx.newTerser().cloneInto(obs, target, false);
+		myCtx.newTerser().cloneInto(obs, target, false);
 
 		assertEquals("AAA", ((StringType) obs.getValue()).getValue());
 		assertEquals("COMMENTS", obs.getNote().get(0).getText());
@@ -278,7 +343,7 @@ public class FhirTerserR4Test {
 		obs.addNote().setText("COMMENTS");
 
 		Observation target = new Observation();
-		ourCtx.newTerser().cloneInto(obs, target, false);
+		myCtx.newTerser().cloneInto(obs, target, false);
 
 		assertEquals("http://foo/base/Observation/_history/123", target.getId());
 	}
@@ -292,7 +357,7 @@ public class FhirTerserR4Test {
 		obs.setValue(string);
 
 		Observation target = new Observation();
-		ourCtx.newTerser().cloneInto(obs, target, false);
+		myCtx.newTerser().cloneInto(obs, target, false);
 
 		assertEquals("BBB", target.getValueStringType().getId());
 	}
@@ -307,7 +372,7 @@ public class FhirTerserR4Test {
 		o.getNameElement().setValue("ORGANIZATION");
 		p.getContained().add(o);
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 		List<StringType> strings = t.getAllPopulatedChildElementsOfType(p, StringType.class);
 
 		assertThat(toStrings(strings), containsInAnyOrder("PATIENT", "ORGANIZATION"));
@@ -323,7 +388,7 @@ public class FhirTerserR4Test {
 		b.addEntry().setResource(p);
 		b.addLink().setRelation("BUNDLE");
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 		List<StringType> strings = t.getAllPopulatedChildElementsOfType(b, StringType.class);
 
 		assertEquals(1, strings.size());
@@ -342,7 +407,7 @@ public class FhirTerserR4Test {
 		Extension ext = new Extension("urn:foo", ref);
 		p.addExtension(ext);
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 		List<IBaseReference> refs = t.getAllPopulatedChildElementsOfType(p, IBaseReference.class);
 		assertEquals(1, refs.size());
 		assertSame(ref, refs.get(0));
@@ -367,29 +432,29 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.active");
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.active");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(0)).getUrl());
 		assertEquals("value", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("modifierValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -426,7 +491,7 @@ public class FhirTerserR4Test {
 		innerPatient1.setActive(true);
 		outerBundle.addEntry().setResource(innerPatient1);
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 
 		Collection<IBaseResource> resources;
 
@@ -452,7 +517,7 @@ public class FhirTerserR4Test {
 		patient.getContained().add(practitioner1);
 		patient.addGeneralPractitioner().setReference("#practitioner1");
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 
 		Collection<IBaseResource> resources;
 
@@ -489,9 +554,9 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.active");
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.active");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
@@ -499,15 +564,15 @@ public class FhirTerserR4Test {
 
 		((BooleanType) values.get(0)).setValue(Boolean.FALSE);
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		values = ourCtx.newTerser().getValues(p, "Patient.active");
+		values = myCtx.newTerser().getValues(p, "Patient.active");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertFalse(((BooleanType) values.get(0)).booleanValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -516,16 +581,16 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(0)).setValue(new StringType("modifiedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(0)).getUrl());
 		assertEquals("modifiedValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -534,16 +599,16 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(0)).setValue(new StringType("modifiedModifierValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("modifiedModifierValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -552,9 +617,9 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(0)).setValue(new StringType("modifiedNestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -591,9 +656,9 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue2"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -604,7 +669,7 @@ public class FhirTerserR4Test {
 		assertEquals("http://acme.org/extension", ((Extension) values.get(1)).getUrl());
 		assertEquals("value2", ((StringType) ((Extension) values.get(1)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -615,7 +680,7 @@ public class FhirTerserR4Test {
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(1)).getUrl());
 		assertEquals("modifierValue2", ((StringType) ((Extension) values.get(1)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -646,26 +711,26 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<PrimitiveType> values = ourCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class);
+		List<PrimitiveType> values = myCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
-		List<Extension> extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class);
+		List<Extension> extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/extension", extValues.get(0).getUrl());
 		assertEquals("value", ((StringType) (extValues.get(0).getValue())).getValueAsString());
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/modifierExtension", extValues.get(0).getUrl());
 		assertEquals("modifierValue", ((StringType) (extValues.get(0).getValue())).getValueAsString());
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/childExtension", extValues.get(0).getUrl());
@@ -691,23 +756,23 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<PrimitiveType> values = ourCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class);
+		List<PrimitiveType> values = myCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
 		((BooleanType) values.get(0)).setValue(Boolean.FALSE);
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		values = ourCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class);
+		values = myCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertFalse(((BooleanType) values.get(0)).booleanValue());
 
-		List<Extension> extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class);
+		List<Extension> extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/extension", extValues.get(0).getUrl());
@@ -715,15 +780,15 @@ public class FhirTerserR4Test {
 
 		extValues.get(0).setValue(new StringType("modifiedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/extension", extValues.get(0).getUrl());
 		assertEquals("modifiedValue", ((StringType) (extValues.get(0).getValue())).getValueAsString());
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/modifierExtension", extValues.get(0).getUrl());
@@ -731,15 +796,15 @@ public class FhirTerserR4Test {
 
 		extValues.get(0).setValue(new StringType("modifiedModifierValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/modifierExtension", extValues.get(0).getUrl());
 		assertEquals("modifiedModifierValue", ((StringType) (extValues.get(0).getValue())).getValueAsString());
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/childExtension", extValues.get(0).getUrl());
@@ -747,9 +812,9 @@ public class FhirTerserR4Test {
 
 		extValues.get(0).setValue(new StringType("modifiedNestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class);
+		extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class);
 		assertEquals(1, extValues.size());
 		assertTrue(extValues.get(0).getValue() instanceof StringType);
 		assertEquals("http://acme.org/childExtension", extValues.get(0).getUrl());
@@ -760,24 +825,24 @@ public class FhirTerserR4Test {
 	public void testGetValuesWithWantedClassAndTheCreate() {
 		Patient p = new Patient();
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<PrimitiveType> values = ourCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class, true);
+		List<PrimitiveType> values = myCtx.newTerser().getValues(p, "Patient.active", PrimitiveType.class, true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertNull(((BooleanType) values.get(0)).getValue());
 
-		List<Extension> extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class, true);
+		List<Extension> extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", Extension.class, true);
 		assertEquals(1, extValues.size());
 		assertEquals("http://acme.org/extension", extValues.get(0).getUrl());
 		assertNull(extValues.get(0).getValue());
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class, true);
+		extValues = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", Extension.class, true);
 		assertEquals(1, extValues.size());
 		assertEquals("http://acme.org/modifierExtension", extValues.get(0).getUrl());
 		assertNull(extValues.get(0).getValue());
 
-		extValues = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class, true);
+		extValues = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", Extension.class, true);
 		assertEquals(1, extValues.size());
 		assertEquals("http://acme.org/childExtension", extValues.get(0).getUrl());
 		assertNull(extValues.get(0).getValue());
@@ -802,29 +867,29 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.active");
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.active");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
 		// No change.
-		values = ourCtx.newTerser().getValues(p, "Patient.active", false, true);
+		values = myCtx.newTerser().getValues(p, "Patient.active", false, true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(0)).getUrl());
 		assertEquals("value", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", false, true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", false, true);
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -837,21 +902,21 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(1)).setValue(new StringType("addedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
 		assertTrue(values.get(1) instanceof IBaseExtension);
 		assertTrue(values.get(1) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(1)).getUrl());
 		assertEquals("addedValue", ((StringType) ((Extension) values.get(1)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("modifierValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", false, true);
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", false, true);
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -864,23 +929,23 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(1)).setValue(new StringType("addedModifierValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
 		assertTrue(values.get(1) instanceof IBaseExtension);
 		assertTrue(values.get(1) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(1)).getUrl());
 		assertEquals("addedModifierValue", ((StringType) ((Extension) values.get(1)).getValue()).getValueAsString());
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/childExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("nestedValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", false, true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", false, true);
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -893,7 +958,7 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(1)).setValue(new StringType("addedNestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
 		assertTrue(values.get(1) instanceof IBaseExtension);
 		assertTrue(values.get(1) instanceof Extension);
@@ -905,27 +970,27 @@ public class FhirTerserR4Test {
 	public void testGetValuesWithTheCreate() {
 		Patient p = new Patient();
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.active", true);
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.active", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertNull(((BooleanType) values.get(0)).getValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(0)).getUrl());
 		assertNull(((Extension) values.get(0)).getValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", true);
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(0)).getUrl());
 		assertNull(((Extension) values.get(0)).getValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -952,29 +1017,29 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.active");
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.active");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
 		// No change.
-		values = ourCtx.newTerser().getValues(p, "Patient.active", true, true);
+		values = myCtx.newTerser().getValues(p, "Patient.active", true, true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(0)).getUrl());
 		assertEquals("value", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", true, true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", true, true);
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -987,21 +1052,21 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(1)).setValue(new StringType("addedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
 		assertTrue(values.get(1) instanceof IBaseExtension);
 		assertTrue(values.get(1) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(1)).getUrl());
 		assertEquals("addedValue", ((StringType) ((Extension) values.get(1)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("modifierValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", true, true);
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", true, true);
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -1014,21 +1079,21 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(1)).setValue(new StringType("addedModifierValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
 		assertTrue(values.get(1) instanceof IBaseExtension);
 		assertTrue(values.get(1) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(1)).getUrl());
 		assertEquals("addedModifierValue", ((StringType) ((Extension) values.get(1)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')");
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/childExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("nestedValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", true, true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", true, true);
 		assertEquals(2, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -1041,7 +1106,7 @@ public class FhirTerserR4Test {
 
 		((Extension) values.get(1)).setValue(new StringType("addedNestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
 		assertTrue(values.get(1) instanceof IBaseExtension);
 		assertTrue(values.get(1) instanceof Extension);
@@ -1068,29 +1133,29 @@ public class FhirTerserR4Test {
 			.setUrl("http://acme.org/childExtension")
 			.setValue(new StringType("nestedValue"));
 
-		System.out.println(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+		System.out.println(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
 
-		List<IBase> values = ourCtx.newTerser().getValues(p, "Patient.active", true);
+		List<IBase> values = myCtx.newTerser().getValues(p, "Patient.active", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof PrimitiveType);
 		assertTrue(values.get(0) instanceof BooleanType);
 		assertTrue(((BooleanType) values.get(0)).booleanValue());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/extension')", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/extension", ((Extension) values.get(0)).getUrl());
 		assertEquals("value", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", true);
+		values = myCtx.newTerser().getValues(p, "Patient.modifierExtension('http://acme.org/modifierExtension')", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
 		assertEquals("http://acme.org/modifierExtension", ((Extension) values.get(0)).getUrl());
 		assertEquals("modifierValue", ((StringType) ((Extension) values.get(0)).getValue()).getValueAsString());
 
-		values = ourCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", true);
+		values = myCtx.newTerser().getValues(p, "Patient.extension('http://acme.org/parentExtension').extension('http://acme.org/childExtension')", true);
 		assertEquals(1, values.size());
 		assertTrue(values.get(0) instanceof IBaseExtension);
 		assertTrue(values.get(0) instanceof Extension);
@@ -1107,7 +1172,7 @@ public class FhirTerserR4Test {
 		vs.getExpansion().setIdentifier("http://foo");
 
 		Set<String> strings = new HashSet<>();
-		ourCtx.newTerser().visit(vs, new IModelVisitor() {
+		myCtx.newTerser().visit(vs, new IModelVisitor() {
 			@Override
 			public void acceptElement(IBaseResource theResource, IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
 				if (theElement instanceof IPrimitiveType) {
@@ -1118,7 +1183,7 @@ public class FhirTerserR4Test {
 		assertThat(strings, Matchers.contains("http://foo"));
 
 		strings.clear();
-		ourCtx.newTerser().visit(vs, new IModelVisitor2() {
+		myCtx.newTerser().visit(vs, new IModelVisitor2() {
 			@Override
 			public boolean acceptElement(IBase theElement, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
 				if (theElement instanceof IPrimitiveType) {
@@ -1148,7 +1213,7 @@ public class FhirTerserR4Test {
 
 		Patient p = new Patient();
 		p.addLink().getTypeElement().setValue(LinkType.REFER);
-		ourCtx.newTerser().visit(p, visitor);
+		myCtx.newTerser().visit(p, visitor);
 
 		assertEquals(3, element.getAllValues().size());
 		assertSame(p, element.getAllValues().get(0));
@@ -1172,7 +1237,7 @@ public class FhirTerserR4Test {
 		p.addAddress().addLine("Line2");
 		p.addName().setFamily("Line3");
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 		List<StringType> strings = t.getAllPopulatedChildElementsOfType(p, StringType.class);
 
 		assertEquals(3, strings.size());
@@ -1192,7 +1257,7 @@ public class FhirTerserR4Test {
 		Observation obs = new Observation();
 		obs.setValue(new Quantity(123L));
 
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 
 		// As string
 		{
@@ -1243,8 +1308,8 @@ public class FhirTerserR4Test {
 			"</Observation>";
 		//@formatter:on
 
-		Observation parsed = ourCtx.newXmlParser().parseResource(Observation.class, msg);
+		Observation parsed = myCtx.newXmlParser().parseResource(Observation.class, msg);
-		FhirTerser t = ourCtx.newTerser();
+		FhirTerser t = myCtx.newTerser();
 
 		List<Reference> elems = t.getAllPopulatedChildElementsOfType(parsed, Reference.class);
 		assertEquals(2, elems.size());

pom.xml

@@ -984,7 +984,7 @@
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-csv</artifactId>
-				<version>1.7</version>
+				<version>1.8</version>
 			</dependency>
 			<dependency>
 				<groupId>org.aspectj</groupId>