Implement FHIR Patch (#1850)

* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup

azure-pipelines.yml

@@ -33,7 +33,7 @@ jobs:
           # These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy
           options: '-P ALLMODULES,JACOCO,CI,ERRORPRONE -nsu -e -B -Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
           # These are JVM options (and don't show up in the build logs)
-          mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
+          mavenOptions: '-Xmx1024m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
           jdkVersionOption: 1.11
       - script: bash <(curl https://codecov.io/bash) -t $(CODECOV_TOKEN)
         displayName: 'codecov'

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

@@ -164,6 +164,9 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
 			}
 			if (theClear) {
 				existingList.clear();
+				if (theValue == null) {
+					return;
+				}
 			}
 			existingList.add(theValue);
 		}

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

@@ -141,10 +141,10 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
 		myChildren.add(theNext);
 	}
 
+	@Override
 	public BaseRuntimeChildDefinition getChildByName(String theName){
 		validateSealed();
-		BaseRuntimeChildDefinition retVal = myNameToChild.get(theName);
+		return myNameToChild.get(theName);
-		return retVal;
 	}
 
 	public BaseRuntimeChildDefinition getChildByNameOrThrowDataFormatException(String theName) throws DataFormatException {
@@ -156,6 +156,7 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
 		return retVal;
 	}
 
+	@Override
 	public List<BaseRuntimeChildDefinition> getChildren() {
 		validateSealed();
 		return myChildren;

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

@@ -66,6 +66,10 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 
 	public abstract ChildTypeEnum getChildType();
 
+	public List<BaseRuntimeChildDefinition> getChildren() {
+		return Collections.emptyList();
+	}
+
 	@SuppressWarnings("unchecked")
 	private Constructor<T> getConstructor(@Nullable Object theArgument) {
 
@@ -225,6 +229,10 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 
 	}
 
+	public BaseRuntimeChildDefinition getChildByName(String theChildName) {
+		return null;
+	}
+
 	public enum ChildTypeEnum {
 		COMPOSITE_DATATYPE,
 		/**

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

@@ -0,0 +1,111 @@
+package ca.uhn.fhir.context;
+
+import com.google.common.collect.Sets;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
+import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class RuntimeChildExt extends BaseRuntimeChildDefinition {
+
+	private Map<String, BaseRuntimeElementDefinition<?>> myNameToChild;
+	private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myDatatypeToChild;
+	private Map<Class<? extends IBase>, String> myDatatypeToChildName;
+
+	@Override
+	public IAccessor getAccessor() {
+		return new IAccessor() {
+			@SuppressWarnings({"unchecked", "rawtypes"})
+			@Override
+			public List<IBase> getValues(IBase theTarget) {
+				List extension = ((IBaseHasExtensions) theTarget).getExtension();
+				return Collections.unmodifiableList(extension);
+			}
+		};
+	}
+
+	@Override
+	public BaseRuntimeElementDefinition<?> getChildByName(String theName) {
+		return myNameToChild.get(theName);
+	}
+
+	@Override
+	public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IBase> theType) {
+		return myDatatypeToChild.get(theType);
+	}
+
+	@Override
+	public String getChildNameByDatatype(Class<? extends IBase> theDatatype) {
+		return myDatatypeToChildName.get(theDatatype);
+	}
+
+	@Override
+	public String getElementName() {
+		return "extension";
+	}
+
+	@Override
+	public int getMax() {
+		return -1;
+	}
+
+	@Override
+	public int getMin() {
+		return 0;
+	}
+
+	@Override
+	public IMutator getMutator() {
+		return new IMutator() {
+			@Override
+			public void addValue(IBase theTarget, IBase theValue) {
+				List extensions = ((IBaseHasExtensions) theTarget).getExtension();
+				IBaseExtension<?, ?> value = (IBaseExtension<?, ?>) theValue;
+				extensions.add(value);
+			}
+
+			@Override
+			public void setValue(IBase theTarget, IBase theValue) {
+				List extensions = ((IBaseHasExtensions) theTarget).getExtension();
+				extensions.clear();
+				if (theValue != null) {
+					IBaseExtension<?, ?> value = (IBaseExtension<?, ?>) theValue;
+					extensions.add(value);
+				}
+			}
+		};
+	}
+
+	@Override
+	public Set<String> getValidChildNames() {
+		return Sets.newHashSet("extension");
+	}
+
+	@Override
+	public boolean isSummary() {
+		return false;
+	}
+
+	@Override
+	void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
+		myNameToChild = new HashMap<>();
+		myDatatypeToChild = new HashMap<>();
+		myDatatypeToChildName = new HashMap<>();
+
+		for (BaseRuntimeElementDefinition<?> next : theClassToElementDefinitions.values()) {
+			if (next.getName().equals("Extension")) {
+				myNameToChild.put("extension", next);
+				myDatatypeToChild.put(next.getImplementingClass(), next);
+				myDatatypeToChildName.put(next.getImplementingClass(), "extension");
+			}
+		}
+
+		Validate.isTrue(!myNameToChild.isEmpty());
+	}
+}

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

@@ -23,10 +23,14 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 
 import java.lang.reflect.ParameterizedType;
 import java.lang.reflect.Type;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 import java.util.Map;
 
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
+import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@@ -38,6 +42,8 @@ public class RuntimePrimitiveDatatypeDefinition extends BaseRuntimeElementDefini
 	private BaseRuntimeElementDefinition<?> myProfileOf;
 	private Class<? extends IBaseDatatype> myProfileOfType;
 	private boolean mySpecialization;
+	private List<BaseRuntimeChildDefinition> myChildren;
+	private RuntimeChildExt myRuntimeChildExt;
 
 	public RuntimePrimitiveDatatypeDefinition(DatatypeDef theDef, Class<? extends IPrimitiveType<?>> theImplementingClass, boolean theStandardType) {
 		super(theDef.name(), theImplementingClass, theStandardType);
@@ -56,6 +62,19 @@ public class RuntimePrimitiveDatatypeDefinition extends BaseRuntimeElementDefini
 		determineNativeType(theImplementingClass);
 	}
 
+	@Override
+	public List<BaseRuntimeChildDefinition> getChildren() {
+		return myChildren;
+	}
+
+	@Override
+	public BaseRuntimeChildDefinition getChildByName(String theChildName) {
+		if ("extension".equals(theChildName)) {
+			return myRuntimeChildExt;
+		}
+		return null;
+	}
+
 	private void determineNativeType(Class<? extends IPrimitiveType<?>> theImplementingClass) {
 		Class<?> clazz = theImplementingClass;
 		while (clazz.equals(Object.class) == false) {
@@ -126,6 +145,14 @@ public class RuntimePrimitiveDatatypeDefinition extends BaseRuntimeElementDefini
 				throw new ConfigurationException(b.toString());
 			}
 		}
+
+		myRuntimeChildExt = new RuntimeChildExt();
+		myRuntimeChildExt.sealAndInitialize(theContext, theClassToElementDefinitions);
+
+		myChildren = new ArrayList<>();
+		myChildren.addAll(super.getChildren());
+		myChildren.add(myRuntimeChildExt);
+		myChildren = Collections.unmodifiableList(myChildren);
 	}
 
 }

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

@@ -20,8 +20,19 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
+import ca.uhn.fhir.context.ConfigurationException;
+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;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
@@ -29,6 +40,7 @@ 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;
@@ -36,9 +48,19 @@ import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
-import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
+import org.hl7.fhir.instance.model.api.IBaseElement;
+import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
+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;
 
 import javax.annotation.Nullable;
 import java.io.IOException;
@@ -49,7 +71,17 @@ import java.io.StringReader;
 import java.io.StringWriter;
 import java.io.Writer;
 import java.lang.reflect.Modifier;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+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;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -73,8 +105,8 @@ public abstract class BaseParser implements IParser {
 	private ContainedResources myContainedResources;
 	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private FhirContext myContext;
-	private List<ElementsPath> myDontEncodeElements;
+	private List<EncodeContextPath> myDontEncodeElements;
-	private List<ElementsPath> myEncodeElements;
+	private List<EncodeContextPath> myEncodeElements;
 	private Set<String> myEncodeElementsAppliesToResourceTypes;
 	private IIdType myEncodeForceResourceId;
 	private IParserErrorHandler myErrorHandler;
@@ -95,7 +127,7 @@ public abstract class BaseParser implements IParser {
 		myErrorHandler = theParserErrorHandler;
 	}
 
-	List<ElementsPath> getDontEncodeElements() {
+	List<EncodeContextPath> getDontEncodeElements() {
 		return myDontEncodeElements;
 	}
 
@@ -106,13 +138,13 @@ public abstract class BaseParser implements IParser {
 		} else {
 			myDontEncodeElements = theDontEncodeElements
 				.stream()
-				.map(ElementsPath::new)
+				.map(EncodeContextPath::new)
 				.collect(Collectors.toList());
 		}
 		return this;
 	}
 
-	List<ElementsPath> getEncodeElements() {
+	List<EncodeContextPath> getEncodeElements() {
 		return myEncodeElements;
 	}
 
@@ -125,7 +157,7 @@ public abstract class BaseParser implements IParser {
 		} else {
 			myEncodeElements = theEncodeElements
 				.stream()
-				.map(ElementsPath::new)
+				.map(EncodeContextPath::new)
 				.collect(Collectors.toList());
 
 			myEncodeElementsAppliesToResourceTypes = new HashSet<>();
@@ -1018,7 +1050,7 @@ public abstract class BaseParser implements IParser {
 
 	protected boolean shouldEncodeResource(String theName) {
 		if (myDontEncodeElements != null) {
-			for (ElementsPath next : myDontEncodeElements) {
+			for (EncodeContextPath next : myDontEncodeElements) {
 				if (next.equalsPath(theName)) {
 					return false;
 				}
@@ -1047,6 +1079,20 @@ public abstract class BaseParser implements IParser {
 
 	}
 
+	/**
+	 * EncodeContext is a shared state object that is passed around the
+	 * encode process
+	 */
+	public class EncodeContext extends EncodeContextPath {
+		private final Map<Key, List<BaseParser.CompositeChildElement>> myCompositeChildrenCache = new HashMap<>();
+
+		public Map<Key, List<BaseParser.CompositeChildElement>> getCompositeChildrenCache() {
+			return myCompositeChildrenCache;
+		}
+
+	}
+
+
 	protected class CompositeChildElement {
 		private final BaseRuntimeChildDefinition myDef;
 		private final CompositeChildElement myParent;
@@ -1127,7 +1173,7 @@ public abstract class BaseParser implements IParser {
 		}
 
 		private boolean checkIfParentShouldBeEncodedAndBuildPath() {
-			List<ElementsPath> encodeElements = myEncodeElements;
+			List<EncodeContextPath> encodeElements = myEncodeElements;
 
 			String currentResourceName = myEncodeContext.getResourcePath().get(myEncodeContext.getResourcePath().size() - 1).getName();
 			if (myEncodeElementsAppliesToResourceTypes != null && !myEncodeElementsAppliesToResourceTypes.contains(currentResourceName)) {
@@ -1158,7 +1204,7 @@ public abstract class BaseParser implements IParser {
 			return checkIfPathMatchesForEncoding(myDontEncodeElements, false);
 		}
 
-		private boolean checkIfPathMatchesForEncoding(List<ElementsPath> theElements, boolean theCheckingForEncodeElements) {
+		private boolean checkIfPathMatchesForEncoding(List<EncodeContextPath> theElements, boolean theCheckingForEncodeElements) {
 
 			boolean retVal = false;
 			if (myDef != null) {
@@ -1172,9 +1218,9 @@ public abstract class BaseParser implements IParser {
 			} else {
 				EncodeContextPath currentResourcePath = myEncodeContext.getCurrentResourcePath();
 				ourLog.trace("Current resource path: {}", currentResourcePath);
-				for (ElementsPath next : theElements) {
+				for (EncodeContextPath next : theElements) {
 
-					if (next.startsWith(currentResourcePath)) {
+					if (next.startsWith(currentResourcePath, true)) {
 						if (theCheckingForEncodeElements || next.getPath().size() == currentResourcePath.getPath().size()) {
 							retVal = true;
 							break;
@@ -1272,225 +1318,13 @@ public abstract class BaseParser implements IParser {
 		}
 	}
 
-	protected class EncodeContextPath {
-		private final List<EncodeContextPathElement> myPath;
-
-		public EncodeContextPath() {
-			myPath = new ArrayList<>(10);
-		}
-
-		public EncodeContextPath(List<EncodeContextPathElement> thePath) {
-			myPath = thePath;
-		}
-
-		@Override
-		public String toString() {
-			return myPath.stream().map(t -> t.toString()).collect(Collectors.joining("."));
-		}
-
-		protected List<EncodeContextPathElement> getPath() {
-			return myPath;
-		}
-
-		public EncodeContextPath getCurrentResourcePath() {
-			EncodeContextPath retVal = null;
-			for (int i = myPath.size() - 1; i >= 0; i--) {
-				if (myPath.get(i).isResource()) {
-					retVal = new EncodeContextPath(myPath.subList(i, myPath.size()));
-					break;
-				}
-			}
-			Validate.isTrue(retVal != null);
-			return retVal;
-		}
-	}
-
-	protected class ElementsPath extends EncodeContextPath {
-
-		protected ElementsPath(String thePath) {
-			StringTokenizer tok = new StringTokenizer(thePath, ".");
-			boolean first = true;
-			while (tok.hasMoreTokens()) {
-				String next = tok.nextToken();
-				if (first && next.equals("*")) {
-					getPath().add(new EncodeContextPathElement("*", true));
-				} else if (isNotBlank(next)) {
-					getPath().add(new EncodeContextPathElement(next, Character.isUpperCase(next.charAt(0))));
-				}
-				first = false;
-			}
-		}
-
-		public boolean startsWith(EncodeContextPath theCurrentResourcePath) {
-			for (int i = 0; i < getPath().size(); i++) {
-				if (theCurrentResourcePath.getPath().size() == i) {
-					return true;
-				}
-				EncodeContextPathElement expected = getPath().get(i);
-				EncodeContextPathElement actual = theCurrentResourcePath.getPath().get(i);
-				if (!expected.matches(actual)) {
-					return false;
-				}
-			}
-			return true;
-		}
-
-		public boolean equalsPath(String thePath) {
-			ElementsPath parsedPath = new ElementsPath(thePath);
-			return getPath().equals(parsedPath.getPath());
-		}
-	}
-
-	/**
-	 * EncodeContext is a shared state object that is passed around the
-	 * encode process
-	 */
-	protected class EncodeContext extends EncodeContextPath {
-		private final ArrayList<EncodeContextPathElement> myResourcePath = new ArrayList<>(10);
-		private final Map<Key, List<CompositeChildElement>> myCompositeChildrenCache = new HashMap<>();
-
-		public Map<Key, List<CompositeChildElement>> getCompositeChildrenCache() {
-			return myCompositeChildrenCache;
-		}
-
-		protected ArrayList<EncodeContextPathElement> getResourcePath() {
-			return myResourcePath;
-		}
-
-		public String getLeafElementName() {
-			return getPath().get(getPath().size() - 1).getName();
-		}
-
-		public String getLeafResourceName() {
-			return myResourcePath.get(myResourcePath.size() - 1).getName();
-		}
-
-		public String getLeafResourcePathFirstField() {
-			String retVal = null;
-			for (int i = getPath().size() - 1; i >= 0; i--) {
-				if (getPath().get(i).isResource()) {
-					break;
-				} else {
-					retVal = getPath().get(i).getName();
-				}
-			}
-			return retVal;
-		}
-
-
-		/**
-		 * Add an element at the end of the path
-		 */
-		protected void pushPath(String thePathElement, boolean theResource) {
-			assert isNotBlank(thePathElement);
-			assert !thePathElement.contains(".");
-			assert theResource ^ Character.isLowerCase(thePathElement.charAt(0));
-
-			EncodeContextPathElement element = new EncodeContextPathElement(thePathElement, theResource);
-			getPath().add(element);
-			if (theResource) {
-				myResourcePath.add(element);
-			}
-		}
-
-		/**
-		 * Remove the element at the end of the path
-		 */
-		public void popPath() {
-			EncodeContextPathElement removed = getPath().remove(getPath().size() - 1);
-			if (removed.isResource()) {
-				myResourcePath.remove(myResourcePath.size() - 1);
-			}
-		}
-
-
-	}
-
-	protected class EncodeContextPathElement {
-		private final String myName;
-		private final boolean myResource;
-
-		public EncodeContextPathElement(String theName, boolean theResource) {
-			Validate.notBlank(theName);
-			myName = theName;
-			myResource = theResource;
-		}
-
-
-		public boolean matches(EncodeContextPathElement theOther) {
-			if (myResource != theOther.isResource()) {
-				return false;
-			}
-			String otherName = theOther.getName();
-			if (myName.equals(otherName)) {
-				return true;
-			}
-			/*
-			 * This is here to handle situations where a path like
-			 *    Observation.valueQuantity has been specified as an include/exclude path,
-			 * since we only know that path as
-			 *    Observation.value
-			 * until we get to actually looking at the values there.
-			 */
-			if (myName.length() > otherName.length() && myName.startsWith(otherName)) {
-				char ch = myName.charAt(otherName.length());
-				if (Character.isUpperCase(ch)) {
-					return true;
-				}
-			}
-			return myName.equals("*");
-		}
-
-		@Override
-		public boolean equals(Object theO) {
-			if (this == theO) {
-				return true;
-			}
-
-			if (theO == null || getClass() != theO.getClass()) {
-				return false;
-			}
-
-			EncodeContextPathElement that = (EncodeContextPathElement) theO;
-
-			return new EqualsBuilder()
-				.append(myResource, that.myResource)
-				.append(myName, that.myName)
-				.isEquals();
-		}
-
-		@Override
-		public int hashCode() {
-			return new HashCodeBuilder(17, 37)
-				.append(myName)
-				.append(myResource)
-				.toHashCode();
-		}
-
-		@Override
-		public String toString() {
-			if (myResource) {
-				return myName + "(res)";
-			}
-			return myName;
-		}
-
-		public String getName() {
-			return myName;
-		}
-
-		public boolean isResource() {
-			return myResource;
-		}
-	}
-
 	private static class Key {
 		private final BaseRuntimeElementCompositeDefinition<?> resDef;
 		private final boolean theContainedResource;
-		private final CompositeChildElement theParent;
+		private final BaseParser.CompositeChildElement theParent;
-		private final EncodeContext theEncodeContext;
+		private final BaseParser.EncodeContext theEncodeContext;
 
-		public Key(BaseRuntimeElementCompositeDefinition<?> resDef, final boolean theContainedResource, final CompositeChildElement theParent, EncodeContext theEncodeContext) {
+		public Key(BaseRuntimeElementCompositeDefinition<?> resDef, final boolean theContainedResource, final BaseParser.CompositeChildElement theParent, BaseParser.EncodeContext theEncodeContext) {
 			this.resDef = resDef;
 			this.theContainedResource = theContainedResource;
 			this.theParent = theParent;
@@ -1524,6 +1358,7 @@ public abstract class BaseParser implements IParser {
 		}
 	}
 
+
 	static class ContainedResources {
 		private long myNextContainedId = 1;
 

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

@@ -104,12 +104,16 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem,
-													CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theContainingElement) {
+                                        CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theContainingElement) {
 		boolean retVal = false;
 		if (ext.size() > 0) {
 			Boolean encodeExtension = null;
 			for (IBaseExtension<?, ?> next : ext) {
 
+				if (next.isEmpty()) {
+					continue;
+				}
+
 				// Make sure we respect _summary and _elements
 				if (encodeExtension == null) {
 					encodeExtension = isEncodeExtension(theParent, theEncodeContext, theContainedResource, theContainingElement);

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

@@ -0,0 +1,141 @@
+package ca.uhn.fhir.parser.path;
+
+import org.apache.commons.lang3.Validate;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.stream.Collectors;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class EncodeContextPath {
+	private final List<EncodeContextPathElement> myPath;
+	private final ArrayList<EncodeContextPathElement> myResourcePath = new ArrayList<>(10);
+
+	public EncodeContextPath() {
+		this(new ArrayList<>(10));
+	}
+
+	public EncodeContextPath(String thePath) {
+		this();
+
+		StringTokenizer tok = new StringTokenizer(thePath, ".");
+		boolean first = true;
+		while (tok.hasMoreTokens()) {
+			String next = tok.nextToken();
+			if (first && next.equals("*")) {
+				getPath().add(new EncodeContextPathElement("*", true));
+			} else if (isNotBlank(next)) {
+				getPath().add(new EncodeContextPathElement(next, Character.isUpperCase(next.charAt(0))));
+			}
+			first = false;
+		}
+	}
+
+	public EncodeContextPath(List<EncodeContextPathElement> thePath) {
+		myPath = thePath;
+	}
+
+	@Override
+	public String toString() {
+		return myPath.stream().map(t -> t.toString()).collect(Collectors.joining("."));
+	}
+
+	public List<EncodeContextPathElement> getPath() {
+		return myPath;
+	}
+
+	public EncodeContextPath getCurrentResourcePath() {
+		EncodeContextPath retVal = null;
+		for (int i = myPath.size() - 1; i >= 0; i--) {
+			if (myPath.get(i).isResource()) {
+				retVal = new EncodeContextPath(myPath.subList(i, myPath.size()));
+				break;
+			}
+		}
+		Validate.isTrue(retVal != null);
+		return retVal;
+	}
+
+	/**
+	 * Add an element at the end of the path
+	 */
+	public void pushPath(String thePathElement, boolean theResource) {
+		assert isNotBlank(thePathElement);
+		assert !thePathElement.contains(".");
+		assert theResource ^ Character.isLowerCase(thePathElement.charAt(0));
+
+		EncodeContextPathElement element = new EncodeContextPathElement(thePathElement, theResource);
+		getPath().add(element);
+		if (theResource) {
+			myResourcePath.add(element);
+		}
+	}
+
+	/**
+	 * Remove the element at the end of the path
+	 */
+	public void popPath() {
+		EncodeContextPathElement removed = getPath().remove(getPath().size() - 1);
+		if (removed.isResource()) {
+			myResourcePath.remove(myResourcePath.size() - 1);
+		}
+	}
+
+	public ArrayList<EncodeContextPathElement> getResourcePath() {
+		return myResourcePath;
+	}
+
+	public String getLeafElementName() {
+		return getPath().get(getPath().size() - 1).getName();
+	}
+
+	public String getLeafResourceName() {
+		return myResourcePath.get(myResourcePath.size() - 1).getName();
+	}
+
+	public String getLeafResourcePathFirstField() {
+		String retVal = null;
+		for (int i = getPath().size() - 1; i >= 0; i--) {
+			if (getPath().get(i).isResource()) {
+				break;
+			} else {
+				retVal = getPath().get(i).getName();
+			}
+		}
+		return retVal;
+	}
+
+	/**
+	 * Tests and returns whether this path starts with {@literal theCurrentResourcePath}
+	 *
+	 * @param theCurrentResourcePath The path to test
+	 * @param theAllowSymmmetrical   If <code>true</code>, this method will return true if {@literal theCurrentResourcePath} starts with this path as well as testing whether this path starts with {@literal theCurrentResourcePath}
+	 */
+	public boolean startsWith(EncodeContextPath theCurrentResourcePath, boolean theAllowSymmmetrical) {
+		for (int i = 0; i < getPath().size(); i++) {
+			if (theCurrentResourcePath.getPath().size() == i) {
+				return true;
+			}
+			EncodeContextPathElement expected = getPath().get(i);
+			EncodeContextPathElement actual = theCurrentResourcePath.getPath().get(i);
+			if (!expected.matches(actual)) {
+				return false;
+			}
+		}
+
+		if (theAllowSymmmetrical) {
+			return true;
+		}
+
+		return getPath().size() == theCurrentResourcePath.getPath().size();
+	}
+
+	public boolean equalsPath(String thePath) {
+		EncodeContextPath parsedPath = new EncodeContextPath(thePath);
+		return getPath().equals(parsedPath.getPath());
+	}
+
+
+}

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

@@ -0,0 +1,83 @@
+package ca.uhn.fhir.parser.path;
+
+import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+
+public class EncodeContextPathElement {
+    private final String myName;
+    private final boolean myResource;
+
+    public EncodeContextPathElement(String theName, boolean theResource) {
+        Validate.notBlank(theName);
+        myName = theName;
+        myResource = theResource;
+    }
+
+
+    public boolean matches(EncodeContextPathElement theOther) {
+        if (myResource != theOther.isResource()) {
+            return false;
+        }
+        String otherName = theOther.getName();
+        if (myName.equals(otherName)) {
+            return true;
+        }
+        /*
+         * This is here to handle situations where a path like
+         *    Observation.valueQuantity has been specified as an include/exclude path,
+         * since we only know that path as
+         *    Observation.value
+         * until we get to actually looking at the values there.
+         */
+        if (myName.length() > otherName.length() && myName.startsWith(otherName)) {
+            char ch = myName.charAt(otherName.length());
+            if (Character.isUpperCase(ch)) {
+                return true;
+            }
+        }
+        return myName.equals("*") || otherName.equals("*");
+    }
+
+    @Override
+    public boolean equals(Object theO) {
+        if (this == theO) {
+            return true;
+        }
+
+        if (theO == null || getClass() != theO.getClass()) {
+            return false;
+        }
+
+        EncodeContextPathElement that = (EncodeContextPathElement) theO;
+
+        return new EqualsBuilder()
+            .append(myResource, that.myResource)
+            .append(myName, that.myName)
+            .isEquals();
+    }
+
+    @Override
+    public int hashCode() {
+        return new HashCodeBuilder(17, 37)
+            .append(myName)
+            .append(myResource)
+            .toHashCode();
+    }
+
+    @Override
+    public String toString() {
+        if (myResource) {
+            return myName + "(res)";
+        }
+        return myName;
+    }
+
+    public String getName() {
+        return myName;
+    }
+
+    public boolean isResource() {
+        return myResource;
+    }
+}

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

@@ -20,18 +20,29 @@ package ca.uhn.fhir.rest.api;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.annotation.Patch;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.UrlUtil;
 
+import javax.annotation.Nonnull;
+import java.util.HashMap;
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 /**
  * Parameter type for methods annotated with {@link Patch}
  */
 public enum PatchTypeEnum {
 
 	JSON_PATCH(Constants.CT_JSON_PATCH),
-	XML_PATCH(Constants.CT_XML_PATCH);
+	XML_PATCH(Constants.CT_XML_PATCH),
+	FHIR_PATCH_JSON(Constants.CT_FHIR_JSON_NEW),
+	FHIR_PATCH_XML(Constants.CT_FHIR_XML_NEW);
 
+	private static volatile Map<String, PatchTypeEnum> ourContentTypeToPatchType;
 	private final String myContentType;
 
 	PatchTypeEnum(String theContentType) {
@@ -42,19 +53,36 @@ public enum PatchTypeEnum {
 		return myContentType;
 	}
 
-	public static PatchTypeEnum forContentTypeOrThrowInvalidRequestException(String theContentType) {
+	@Nonnull
-		String contentType = theContentType;
+	public static PatchTypeEnum forContentTypeOrThrowInvalidRequestException(FhirContext theContext, String theContentType) {
+		String contentType = defaultString(theContentType);
 		int semiColonIdx = contentType.indexOf(';');
 		if (semiColonIdx != -1) {
 			contentType = theContentType.substring(0, semiColonIdx);
 		}
 		contentType = contentType.trim();
-		if (Constants.CT_JSON_PATCH.equals(contentType)) {
+
-			return JSON_PATCH;
+
-		} else if (Constants.CT_XML_PATCH.equals(contentType)) {
+		Map<String, PatchTypeEnum> map = ourContentTypeToPatchType;
-			return XML_PATCH;
+		if (map == null) {
-		} else {
+			map = new HashMap<>();
-			throw new InvalidRequestException("Invalid Content-Type for PATCH operation: " + UrlUtil.sanitizeUrlPart(theContentType));
+			for (PatchTypeEnum next : values()) {
+				map.put(next.getContentType(), next);
+			}
+			ourContentTypeToPatchType = map;
 		}
+
+		PatchTypeEnum retVal = map.get(contentType);
+		if (retVal == null) {
+			if (isBlank(contentType)) {
+				String msg = theContext.getLocalizer().getMessage(PatchTypeEnum.class, "missingPatchContentType");
+				throw new InvalidRequestException(msg);
+			}
+
+			String msg = theContext.getLocalizer().getMessageSanitized(PatchTypeEnum.class, "invalidPatchContentType", contentType);
+			throw new InvalidRequestException(msg);
+		}
+
+		return retVal;
 	}
 }

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

@@ -20,15 +20,23 @@ package ca.uhn.fhir.rest.gclient;
  * #L%
  */
 
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+
 public interface IPatch {
 
 	/**
 	 * The body of the patch document serialized in either XML or JSON which conforms to
 	 * http://jsonpatch.com/ or http://tools.ietf.org/html/rfc5261
-	 * 
+	 *
-	 * @param thePatchBody
+	 * @param thePatchBody The body of the patch
-	 *           The body of the patch
 	 */
 	IPatchWithBody withBody(String thePatchBody);
 
+	/**
+	 * The body of the patch document using FHIR Patch syntax as described at
+	 * http://hl7.org/fhir/fhirpatch.html
+	 *
+	 * @since 5.1.0
+	 */
+	IPatchWithBody withFhirPatch(IBaseParameters thePatchBody);
 }

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

@@ -28,11 +28,11 @@ public interface IPatchWithBody extends IPatchExecutable {
 
 	/**
 	 * Build a conditional URL using fluent constants on resource types
-	 * 
+	 *
 	 * @param theResourceType
 	 *           The resource type to patch (e.g. "Patient.class")
 	 */
-	IPatchWithQuery conditional(Class<? extends IBaseResource> theClass);
+	IPatchWithQuery conditional(Class<? extends IBaseResource> theResourceType);
 
 	/**
 	 * Build a conditional URL using fluent constants on resource types
@@ -53,12 +53,12 @@ public interface IPatchWithBody extends IPatchExecutable {
 	IPatchExecutable conditionalByUrl(String theSearchUrl);
 
 	/**
-	 * The resource ID to patch
+	 * The resource ID to patch (must include both a resource type and an ID, e.g. <code>Patient/123</code>)
 	 */
 	IPatchExecutable withId(IIdType theId);
 
 	/**
-	 * The resource ID to patch
+	 * The resource ID to patch (must include both a resource type and an ID, e.g. <code>Patient/123</code>)
 	 */
 	IPatchExecutable withId(String theId);
 

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

@@ -267,12 +267,12 @@ public class BundleUtil {
 	 * <code>Bundle.entry.resource</code> is a Binary resource with a patch
 	 * payload type.
 	 */
-	public static boolean isDstu3TransactionPatch(IBaseResource thePayloadResource) {
+	public static boolean isDstu3TransactionPatch(FhirContext theContext, IBaseResource thePayloadResource) {
 		boolean isPatch = false;
 		if (thePayloadResource instanceof IBaseBinary) {
 			String contentType = ((IBaseBinary) thePayloadResource).getContentType();
 			 try {
-				 PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(contentType);
+				 PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(theContext, contentType);
 				 isPatch = true;
 			 } catch (InvalidRequestException e) {
 				 // ignore

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

@@ -1,7 +1,17 @@
 package ca.uhn.fhir.util;
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
+import ca.uhn.fhir.context.RuntimeChildDirectResource;
+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.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
@@ -10,14 +20,30 @@ import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
+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.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
  * #%L
@@ -241,6 +267,11 @@ public class FhirTerser {
 		return retVal.get(0);
 	}
 
+	public <T extends IBase> Optional<T> getSingleValue(IBase theTarget, String thePath, Class<T> theWantedType) {
+		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);
 	}
@@ -471,85 +502,85 @@ public class FhirTerser {
 	 * Returns values stored in an element identified by its path. The list of values is of
 	 * type {@link Object}.
 	 *
-	 * @param theResource The resource instance to be accessed. Must not be null.
+	 * @param theElement The element to be accessed. Must not be null.
-	 * @param thePath     The path for the element to be accessed.
+	 * @param thePath    The path for the element to be accessed.@param theElement The resource instance to be accessed. Must not be null.
 	 * @return A list of values of type {@link Object}.
 	 */
-	public List<IBase> getValues(IBaseResource theResource, String thePath) {
+	public List<IBase> getValues(IBase theElement, String thePath) {
 		Class<IBase> wantedClass = IBase.class;
 
-		return getValues(theResource, thePath, wantedClass);
+		return getValues(theElement, thePath, wantedClass);
 	}
 
 	/**
 	 * Returns values stored in an element identified by its path. The list of values is of
 	 * type {@link Object}.
 	 *
-	 * @param theResource The resource instance to be accessed. Must not be null.
+	 * @param theElement The element to be accessed. Must not be null.
-	 * @param thePath     The path for the element to be accessed.
+	 * @param thePath    The path for the element to be accessed.
-	 * @param theCreate   When set to <code>true</code>, the terser will create a null-valued element where none exists.
+	 * @param theCreate  When set to <code>true</code>, the terser will create a null-valued element where none exists.
 	 * @return A list of values of type {@link Object}.
 	 */
-	public List<IBase> getValues(IBaseResource theResource, String thePath, boolean theCreate) {
+	public List<IBase> getValues(IBase theElement, String thePath, boolean theCreate) {
 		Class<IBase> wantedClass = IBase.class;
 
-		return getValues(theResource, thePath, wantedClass, theCreate);
+		return getValues(theElement, thePath, wantedClass, theCreate);
 	}
 
 	/**
 	 * Returns values stored in an element identified by its path. The list of values is of
 	 * type {@link Object}.
 	 *
-	 * @param theResource     The resource instance to be accessed. Must not be null.
+	 * @param theElement      The element to be accessed. Must not be null.
 	 * @param thePath         The path for the element to be accessed.
 	 * @param theCreate       When set to <code>true</code>, the terser will create a null-valued element where none exists.
 	 * @param theAddExtension When set to <code>true</code>, the terser will add a null-valued extension where one or more such extensions already exist.
 	 * @return A list of values of type {@link Object}.
 	 */
-	public List<IBase> getValues(IBaseResource theResource, String thePath, boolean theCreate, boolean theAddExtension) {
+	public List<IBase> getValues(IBase theElement, String thePath, boolean theCreate, boolean theAddExtension) {
 		Class<IBase> wantedClass = IBase.class;
 
-		return getValues(theResource, thePath, wantedClass, theCreate, theAddExtension);
+		return getValues(theElement, thePath, wantedClass, theCreate, theAddExtension);
 	}
 
 	/**
 	 * Returns values stored in an element identified by its path. The list of values is of
 	 * type <code>theWantedClass</code>.
 	 *
-	 * @param theResource    The resource instance to be accessed. Must not be null.
+	 * @param theElement     The element to be accessed. Must not be null.
 	 * @param thePath        The path for the element to be accessed.
 	 * @param theWantedClass The desired class to be returned in a list.
 	 * @param <T>            Type declared by <code>theWantedClass</code>
 	 * @return A list of values of type <code>theWantedClass</code>.
 	 */
-	public <T extends IBase> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass) {
+	public <T extends IBase> List<T> getValues(IBase theElement, String thePath, Class<T> theWantedClass) {
-		RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
+		BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theElement.getClass());
 		List<String> parts = parsePath(def, thePath);
-		return getValues(def, theResource, parts, theWantedClass);
+		return getValues(def, theElement, parts, theWantedClass);
 	}
 
 	/**
 	 * Returns values stored in an element identified by its path. The list of values is of
 	 * type <code>theWantedClass</code>.
 	 *
-	 * @param theResource    The resource instance to be accessed. Must not be null.
+	 * @param theElement     The element to be accessed. Must not be null.
 	 * @param thePath        The path for the element to be accessed.
 	 * @param theWantedClass The desired class to be returned in a list.
 	 * @param theCreate      When set to <code>true</code>, the terser will create a null-valued element where none exists.
 	 * @param <T>            Type declared by <code>theWantedClass</code>
 	 * @return A list of values of type <code>theWantedClass</code>.
 	 */
-	public <T extends IBase> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate) {
+	public <T extends IBase> List<T> getValues(IBase theElement, String thePath, Class<T> theWantedClass, boolean theCreate) {
-		RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
+		BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theElement.getClass());
 		List<String> parts = parsePath(def, thePath);
-		return getValues(def, theResource, parts, theWantedClass, theCreate, false);
+		return getValues(def, theElement, parts, theWantedClass, theCreate, false);
 	}
 
 	/**
 	 * Returns values stored in an element identified by its path. The list of values is of
 	 * type <code>theWantedClass</code>.
 	 *
-	 * @param theResource     The resource instance to be accessed. Must not be null.
+	 * @param theElement      The element to be accessed. Must not be null.
 	 * @param thePath         The path for the element to be accessed.
 	 * @param theWantedClass  The desired class to be returned in a list.
 	 * @param theCreate       When set to <code>true</code>, the terser will create a null-valued element where none exists.
@@ -557,10 +588,10 @@ public class FhirTerser {
 	 * @param <T>             Type declared by <code>theWantedClass</code>
 	 * @return A list of values of type <code>theWantedClass</code>.
 	 */
-	public <T extends IBase> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
+	public <T extends IBase> List<T> getValues(IBase theElement, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
-		RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
+		BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theElement.getClass());
 		List<String> parts = parsePath(def, thePath);
-		return getValues(def, theResource, parts, theWantedClass, theCreate, theAddExtension);
+		return getValues(def, theElement, parts, theWantedClass, theCreate, theAddExtension);
 	}
 
 	private List<String> parsePath(BaseRuntimeElementCompositeDefinition<?> theElementDef, String thePath) {
@@ -801,7 +832,7 @@ public class FhirTerser {
 	}
 
 	/**
-	 * Visit all elements in a given resource
+	 * Visit all elements in a given resource or element
 	 * <p>
 	 * <b>THIS ALTERNATE METHOD IS STILL EXPERIMENTAL! USE WITH CAUTION</b>
 	 * </p>
@@ -810,12 +841,19 @@ public class FhirTerser {
 	 * {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
 	 * </p>
 	 *
-	 * @param theResource The resource to visit
+	 * @param theElement The element to visit
-	 * @param theVisitor  The visitor
+	 * @param theVisitor The visitor
 	 */
-	public void visit(IBaseResource theResource, IModelVisitor2 theVisitor) {
+	public void visit(IBase theElement, IModelVisitor2 theVisitor) {
-		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
+		BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
-		visit(theResource, null, def, theVisitor, new ArrayList<>(), new ArrayList<>(), new ArrayList<>());
+		if (def instanceof BaseRuntimeElementCompositeDefinition) {
+			BaseRuntimeElementCompositeDefinition<?> defComposite = (BaseRuntimeElementCompositeDefinition<?>) def;
+			visit(theElement, null, def, theVisitor, new ArrayList<>(), new ArrayList<>(), new ArrayList<>());
+		} else if (theElement instanceof IBaseExtension) {
+			theVisitor.acceptUndeclaredExtension((IBaseExtension<?, ?>) theElement, Collections.emptyList(), Collections.emptyList(), Collections.emptyList());
+		} else {
+			theVisitor.acceptElement(theElement, Collections.emptyList(), Collections.emptyList(), Collections.emptyList());
+		}
 	}
 
 	private void visit(Map<Object, Object> theStack, IBaseResource theResource, IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition,
@@ -971,4 +1009,5 @@ public class FhirTerser {
 
 		});
 	}
+
 }

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

@@ -20,17 +20,26 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.primitive.StringDt;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Function;
+import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
 
@@ -45,7 +54,7 @@ public class ParametersUtil {
 	}
 
 	public static List<Integer> getNamedParameterValuesAsInteger(FhirContext theCtx, IBaseParameters theParameters, String theParameterName) {
-		Function<IPrimitiveType<?>, Integer> mapper = t -> (Integer)t.getValue();
+		Function<IPrimitiveType<?>, Integer> mapper = t -> (Integer) t.getValue();
 		return extractNamedParameters(theCtx, theParameters, theParameterName, mapper);
 	}
 
@@ -53,33 +62,72 @@ public class ParametersUtil {
 		return getNamedParameterValuesAsInteger(theCtx, theParameters, theParameterName).stream().findFirst();
 	}
 
-	private static <T> List<T> extractNamedParameters(FhirContext theCtx, IBaseParameters theParameters, String theParameterName, Function<IPrimitiveType<?>, T> theMapper) {
+	public static List<IBase> getNamedParameters(FhirContext theCtx, IBaseResource theParameters, String theParameterName) {
 		Validate.notNull(theParameters, "theParameters must not be null");
 		RuntimeResourceDefinition resDef = theCtx.getResourceDefinition(theParameters.getClass());
 		BaseRuntimeChildDefinition parameterChild = resDef.getChildByName("parameter");
 		List<IBase> parameterReps = parameterChild.getAccessor().getValues(theParameters);
 
+		return parameterReps
+			.stream()
+			.filter(param -> {
+				BaseRuntimeElementCompositeDefinition<?> nextParameterDef = (BaseRuntimeElementCompositeDefinition<?>) theCtx.getElementDefinition(param.getClass());
+				BaseRuntimeChildDefinition nameChild = nextParameterDef.getChildByName("name");
+				List<IBase> nameValues = nameChild.getAccessor().getValues(param);
+				Optional<? extends IPrimitiveType<?>> nameValue = nameValues
+					.stream()
+					.filter(t -> t instanceof IPrimitiveType<?>)
+					.map(t -> ((IPrimitiveType<?>) t))
+					.findFirst();
+				if (!nameValue.isPresent() || !theParameterName.equals(nameValue.get().getValueAsString())) {
+					return false;
+				}
+				return true;
+			})
+			.collect(Collectors.toList());
+
+	}
+
+	public static Optional<IBase> getParameterPart(FhirContext theCtx, IBase theParameter, String theParameterName) {
+		BaseRuntimeElementCompositeDefinition<?> nextParameterDef = (BaseRuntimeElementCompositeDefinition<?>) theCtx.getElementDefinition(theParameter.getClass());
+		BaseRuntimeChildDefinition valueChild = nextParameterDef.getChildByName("part");
+		List<IBase> parts = valueChild.getAccessor().getValues(theParameter);
+
+		for (IBase nextPart : parts) {
+			Optional<IPrimitiveType> name = theCtx.newTerser().getSingleValue(nextPart, "name", IPrimitiveType.class);
+			if (name.isPresent() && theParameterName.equals(name.get().getValueAsString())) {
+				return Optional.of(nextPart);
+			}
+		}
+
+		return Optional.empty();
+	}
+
+	public static Optional<IBase> getParameterPartValue(FhirContext theCtx, IBase theParameter, String theParameterName) {
+		Optional<IBase> part = getParameterPart(theCtx, theParameter, theParameterName);
+		if (part.isPresent()) {
+			return theCtx.newTerser().getSingleValue(part.get(), "value[x]", IBase.class);
+		} else {
+			return Optional.empty();
+		}
+	}
+
+	public static String getParameterPartValueAsString(FhirContext theCtx, IBase theParameter, String theParameterName) {
+		return getParameterPartValue(theCtx, theParameter, theParameterName).map(t -> (IPrimitiveType<?>) t).map(t -> t.getValueAsString()).orElse(null);
+	}
+
+	private static <T> List<T> extractNamedParameters(FhirContext theCtx, IBaseParameters theParameters, String theParameterName, Function<IPrimitiveType<?>, T> theMapper) {
 		List<T> retVal = new ArrayList<>();
 
-		for (IBase nextParameter : parameterReps) {
+		List<IBase> namedParameters = getNamedParameters(theCtx, theParameters, theParameterName);
+		for (IBase nextParameter : namedParameters) {
 			BaseRuntimeElementCompositeDefinition<?> nextParameterDef = (BaseRuntimeElementCompositeDefinition<?>) theCtx.getElementDefinition(nextParameter.getClass());
-			BaseRuntimeChildDefinition nameChild = nextParameterDef.getChildByName("name");
-			List<IBase> nameValues = nameChild.getAccessor().getValues(nextParameter);
-			Optional<? extends IPrimitiveType<?>> nameValue = nameValues
-				.stream()
-				.filter(t -> t instanceof IPrimitiveType<?>)
-				.map(t -> ((IPrimitiveType<?>) t))
-				.findFirst();
-			if (!nameValue.isPresent() || !theParameterName.equals(nameValue.get().getValueAsString())) {
-				continue;
-			}
-
 			BaseRuntimeChildDefinition valueChild = nextParameterDef.getChildByName("value[x]");
 			List<IBase> valueValues = valueChild.getAccessor().getValues(nextParameter);
 			valueValues
 				.stream()
 				.filter(t -> t instanceof IPrimitiveType<?>)
-				.map(t->((IPrimitiveType<?>) t))
+				.map(t -> ((IPrimitiveType<?>) t))
 				.map(theMapper)
 				.filter(t -> t != null)
 				.forEach(retVal::add);
@@ -237,6 +285,13 @@ public class ParametersUtil {
 		addPart(theContext, theParameter, theName, value);
 	}
 
+	public static void addPartInteger(FhirContext theContext, IBase theParameter, String theName, Integer theInteger) {
+		IPrimitiveType<Integer> value = (IPrimitiveType<Integer>) theContext.getElementDefinition("integer").newInstance();
+		value.setValue(theInteger);
+
+		addPart(theContext, theParameter, theName, value);
+	}
+
 	public static void addPartString(FhirContext theContext, IBase theParameter, String theName, String theValue) {
 		IPrimitiveType<String> value = (IPrimitiveType<String>) theContext.getElementDefinition("string").newInstance();
 		value.setValue(theValue);
@@ -267,7 +322,12 @@ public class ParametersUtil {
 		name.setValue(theName);
 		partChildElem.getChildByName("name").getMutator().addValue(part, name);
 
-		partChildElem.getChildByName("value[x]").getMutator().addValue(part, theValue);
+		if (theValue instanceof IBaseResource) {
+			partChildElem.getChildByName("resource").getMutator().addValue(part, theValue);
+		} else {
+			partChildElem.getChildByName("value[x]").getMutator().addValue(part, theValue);
+		}
+
 	}
 
 	public static void addPartResource(FhirContext theContext, IBase theParameter, String theName, IBaseResource theValue) {
@@ -284,4 +344,5 @@ public class ParametersUtil {
 
 		partChildElem.getChildByName("resource").getMutator().addValue(part, theValue);
 	}
+
 }

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

@@ -31,16 +31,42 @@ import org.apache.commons.text.StringEscapeUtils;
 import org.codehaus.stax2.XMLOutputFactory2;
 import org.codehaus.stax2.io.EscapingWriterFactory;
 import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.stream.*;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLEventReader;
+import javax.xml.stream.XMLEventWriter;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLOutputFactory;
+import javax.xml.stream.XMLResolver;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamWriter;
 import javax.xml.stream.events.XMLEvent;
-import java.io.*;
+import javax.xml.transform.OutputKeys;
-import java.util.*;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
@@ -1513,8 +1539,11 @@ public class XmlUtil {
 		VALID_ENTITY_NAMES = Collections.unmodifiableMap(validEntityNames);
 	}
 
-	/** Non-instantiable */
+	/**
-	private XmlUtil() {}
+	 * Non-instantiable
+	 */
+	private XmlUtil() {
+	}
 
 	private static final class ExtendedEntityReplacingXmlResolver implements XMLResolver {
 		@Override
@@ -1835,7 +1864,7 @@ public class XmlUtil {
 	}
 
 	public static Document parseDocument(String theInput) throws IOException, SAXException {
-		DocumentBuilder builder = null;
+		DocumentBuilder builder;
 		try {
 			DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
 			docBuilderFactory.setNamespaceAware(true);
@@ -1860,4 +1889,13 @@ public class XmlUtil {
 		InputSource src = new InputSource(new StringReader(theInput));
 		return builder.parse(src);
 	}
+
+	public static String encodeDocument(Element theElement) throws TransformerException {
+		TransformerFactory transFactory = TransformerFactory.newInstance();
+		Transformer transformer = transFactory.newTransformer();
+		StringWriter buffer = new StringWriter();
+		transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+		transformer.transform(new DOMSource(theElement), new StreamResult(buffer));
+		return buffer.toString();
+	}
 }

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

@@ -100,11 +100,17 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.unableToDeleteNotFound=Unable to fin
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulCreate=Successfully created resource "{0}" in {1}ms
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully updated resource "{0}" in {1}ms
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulDeletes=Successfully deleted {0} resource(s) in {1}ms
-ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSearchParameter=Unknown search parameter "{0}". Value search parameters for this search are: {1}
+ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSearchParameter=Unknown search parameter "{0}" for resource type "{1}". Valid search parameters for this search are: {2}
 
+ca.uhn.fhir.rest.api.PatchTypeEnum.missingPatchContentType=Missing or invalid content type for PATCH operation
+ca.uhn.fhir.rest.api.PatchTypeEnum.invalidPatchContentType=Invalid Content-Type for PATCH operation: {0}
 ca.uhn.fhir.jpa.dao.TransactionProcessor.missingMandatoryResource=Missing required resource in Bundle.entry[{1}].resource for operation {0}
-ca.uhn.fhir.jpa.dao.TransactionProcessor.missingPatchContentType=Missing or invalid content type for PATCH operation
 ca.uhn.fhir.jpa.dao.TransactionProcessor.missingPatchBody=Unable to determine PATCH body from request
+ca.uhn.fhir.jpa.dao.TransactionProcessor.fhirPatchShouldNotUseBinaryResource=Binary PATCH detected with FHIR content type. FHIR Patch should use Parameters resource.
+
+ca.uhn.fhir.jpa.patch.FhirPatch.invalidInsertIndex=Invalid insert index {0} for path {1} - Only have {2} existing entries
+ca.uhn.fhir.jpa.patch.FhirPatch.invalidMoveSourceIndex=Invalid move source index {0} for path {1} - Only have {2} existing entries
+ca.uhn.fhir.jpa.patch.FhirPatch.invalidMoveDestinationIndex=Invalid move destination index {0} for path {1} - Only have {2} existing entries
 
 ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.externalReferenceNotAllowed=Resource contains external reference to URL "{0}" but this server is not configured to allow external references
 ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.failedToExtractPaths=Failed to extract values from resource using FHIRPath "{0}": {1}
@@ -139,7 +145,7 @@ ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
 
-ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
+ca.uhn.fhir.jpa.patch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
 
 ca.uhn.fhir.jpa.graphql.JpaStorageServices.invalidGraphqlArgument=Unknown GraphQL argument "{0}". Value GraphQL argument for this type are: {1}
 
@@ -165,3 +171,5 @@ ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.cantRenameDefaultPartition=Can
 ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor.unknownTenantName=Unknown tenant: {0}
 
 ca.uhn.fhir.jpa.dao.HistoryBuilder.noSystemOrTypeHistoryForPartitionAwareServer=Type- and Server- level history operation not supported across partitions on partitioned server
+
+ca.uhn.fhir.jpa.provider.DiffProvider.cantDiffDifferentTypes=Unable to diff two resources of different types

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.demo;
  */
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import org.apache.commons.dbcp2.BasicDataSource;
@@ -59,7 +60,7 @@ public class CommonConfig {
 	/**
 	 * The following bean configures the database connection. The 'url' property value of "jdbc:h2:file:target./jpaserver_h2_files" indicates that the server should save resources in a
 	 * directory called "jpaserver_h2_files".
-	 *
+	 * <p>
 	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
 	 */
 	@Bean(destroyMethod = "close")
@@ -94,12 +95,17 @@ public class CommonConfig {
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
 		extraProperties.put("hibernate.search.default.worker.execution", "async");
-		
+
 		if (System.getProperty("lowmem") != null) {
 			extraProperties.put("hibernate.search.autoregister_listeners", "false");
 		}
-		
+
 		return extraProperties;
 	}
 
+	@Bean
+	public PartitionSettings partitionSettings() {
+		return new PartitionSettings();
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -45,6 +45,7 @@ import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
 
@@ -176,6 +177,9 @@ public class JpaServerDemo extends RestfulServer {
 		IInterceptorBroadcaster interceptorBroadcaster = myAppCtx.getBean(IInterceptorBroadcaster.class);
 		CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
 		getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
+
+		getInterceptorService().registerInterceptor(new ResponseHighlighterInterceptor());
+
 	}
 
 }

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/GenericClient.java

@@ -1617,14 +1617,23 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			return this;
 		}
 
+		@Override
+		public IPatchWithBody withFhirPatch(IBaseParameters thePatchBody) {
+			Validate.notNull(thePatchBody, "thePatchBody must not be null");
+
+			myPatchType = PatchTypeEnum.FHIR_PATCH_JSON;
+			myPatchBody = myContext.newJsonParser().encodeResourceToString(thePatchBody);
+
+			return this;
+		}
+
 		@Override
 		public IPatchExecutable withId(IIdType theId) {
 			if (theId == null) {
 				throw new NullPointerException("theId can not be null");
 			}
-			if (theId.hasIdPart() == false) {
+			Validate.notBlank(theId.getIdPart(), "theId must not be blank and must contain a resource type and ID (e.g. \"Patient/123\"), found: %s", UrlUtil.sanitizeUrlPart(theId.getValue()));
-				throw new NullPointerException("theId must not be blank and must contain an ID, found: " + theId.getValue());
+			Validate.notBlank(theId.getResourceType(), "theId must not be blank and must contain a resource type and ID (e.g. \"Patient/123\"), found: %s", UrlUtil.sanitizeUrlPart(theId.getValue()));
-			}
 			myId = theId;
 			return this;
 		}
@@ -1634,11 +1643,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			if (theId == null) {
 				throw new NullPointerException("theId can not be null");
 			}
-			if (isBlank(theId)) {
+			return withId(new IdDt(theId));
-				throw new NullPointerException("theId must not be blank and must contain an ID, found: " + theId);
-			}
-			myId = new IdDt(theId);
-			return this;
 		}
 
 	}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1850-add-diff-operation.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1850
+title: "A new operation has been added to the JPA server called `$diff`. This operation can generate a FHIR Patch diff showing
+   the changes between two versions of a resource, or even two separate resources. See [Diff](/hapi-fhir/docs/server_jpa/diff.html)
+   for more information."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1850-add-fhir-patch-support.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 1850
+title: "The [FHIR Patch](https://www.hl7.org/fhir/fhirpatch.html) format is now supported for patching resources, in addition
+  to the previously supported JSON Patch and XML Patch."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1850-dont-encode-empty-extension.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 1850
+title: When serializing a resource, the JSON Parser will now ignore any extensions that are present on an
+   element if they do not have a URL or any children populated.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/generic_client.md

@@ -209,6 +209,22 @@ FHIR also specifies a type of update called "conditional updates", where instead
 
 **See Also:** See the description of [Update ETags](#update_etags) below for information on specifying a matching version in the client request.
 
+# Patch - Instance
+
+The PATCH operation can be used to modify a resource in place by supplying a delta
+
+The following example shows how to perform a patch using a [FHIR Patch](http://hl7.org/fhir/fhirpatch.html)
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/GenericClientExample.java|patchFhir}}
+```
+
+The following example shows how to perform a patch using a [JSON Patch](https://tools.ietf.org/html/rfc6902.)
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/GenericClientExample.java|patchJson}}
+```
+
 # History - Server/Type/Instance
 
 To retrieve the version history of all resources, or all resources of a given type, or of a specific instance of a resource, you call the [`history()`](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/rest/client/api/IGenericClient.html#history()) method.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties

@@ -46,6 +46,7 @@ page.server_jpa.configuration=Configuration
 page.server_jpa.search=Search
 page.server_jpa.performance=Performance
 page.server_jpa.upgrading=Upgrade Guide
+page.server_jpa.diff=Diff Operation
 
 section.server_jpa_partitioning.title=JPA Server: Partitioning and Multitenancy
 page.server_jpa_partitioning.partitioning=Partitioning and Multitenancy

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/diff.md

@@ -0,0 +1,88 @@
+# Diff Operation
+
+The `$diff` operation can be used to generate a differential between two versions of a resource, or even two different resources of the same type.
+
+Differentials generated by this operation are in [FHIR Patch](https://www.hl7.org/fhir/fhirpatch.html) format.
+
+In generated differentials, where a value has changed (i.e. a **replace** operation), an additional part value will be present on the given operation called `previousValue`. This part shows the value as it was in the *from* version of the resource. 
+
+# Diff Instance
+
+When the $diff operation is invoked at the instance level (meaning it is invoked on a specific resource ID), it will compare two versions of the given resource.
+
+## Parameters
+
+* `[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_FROM_VERSION_PARAMETER}]]=[versionId]`: (*optional*) If specified, compare using this version as the source. If not specified, the immediately previous version will be compared.
+* `[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_INCLUDE_META_PARAMETER}]]=true`: (*optional*) If specified, changes to Resource.meta will be included in the diff. This element is omitted by default.  
+
+To invoke:
+
+```http
+GET http://fhir.example.com/baseR4/Patient/123/$diff
+```
+
+The server will produce a response resembling the following:
+
+```json
+{
+  "resourceType": "Parameters",
+  "parameter": [ {
+    "name": "operation",
+    "part": [ {
+      "name": "type",
+      "valueCode": "replace"
+    }, {
+      "name": "path",
+      "valueString": "Patient.name.family"
+    }, {
+      "name": "previousValue",
+      "valueId": "Smyth"
+    }, {
+      "name": "value",
+      "valueId": "SmithB"
+    } ]
+  } ]
+}
+```
+
+# Diff Instance
+
+When the $diff operation is invoked at the instance level (meaning it is invoked on a specific resource ID), it will compare two versions of the given resource.
+
+## Parameters
+
+* `[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_FROM_PARAMETER}]]=[reference]`: Specifies the source of the comparison. The value must include a resource type and a resource ID, and can optionally include a version, e.g. `Patient/123` or `Patient/123/_history/2`.
+* `[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_TO_PARAMETER}]]=[reference]`: Specifies the target of the comparison. The value must include a resource type and a resource ID, and can optionally include a version, e.g. `Patient/123` or `Patient/123/_history/2`.
+* `[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_INCLUDE_META_PARAMETER}]]=true`: (*optional*) If specified, changes to Resource.meta will be included in the diff. This element is omitted by default.  
+
+To invoke:
+
+```http
+GET http://fhir.example.com/baseR4/$diff?[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_FROM_PARAMETER}]]=Patient/1&[[#{T(ca.uhn.fhir.jpa.model.util.ProviderConstants).DIFF_TO_PARAMETER}]]=Patient/2
+```
+
+The server will produce a response resembling the following:
+
+```json
+{
+  "resourceType": "Parameters",
+  "parameter": [ {
+    "name": "operation",
+    "part": [ {
+      "name": "type",
+      "valueCode": "replace"
+    }, {
+      "name": "path",
+      "valueString": "Patient.id"
+    }, {
+      "name": "previousValue",
+      "valueId": "1"
+    }, {
+      "name": "value",
+      "valueId": "2"
+    } ]
+  } ]
+}
+```
+
+

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDao.java

@@ -42,6 +42,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import org.hl7.fhir.instance.model.api.IBaseMetaType;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 
@@ -153,7 +154,7 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	<MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, RequestDetails theRequestDetails);
 
-	DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails);
+	DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequestDetails);
 
 	/**
 	 * Read a resource - Note that this variant of the method does not take in a {@link RequestDetails} and

hapi-fhir-jpaserver-base/pom.xml

@@ -256,7 +256,6 @@
 		<dependency>
 			<groupId>com.h2database</groupId>
 			<artifactId>h2</artifactId>
-			<version>1.4.199</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -562,6 +561,11 @@
 			<artifactId>embedded-elasticsearch</artifactId>
 			<version>2.10.0</version>
 		</dependency>
+		<dependency>
+			<groupId>org.hl7.fhir.testcases</groupId>
+			<artifactId>fhir-test-cases</artifactId>
+			<scope>test</scope>
+		</dependency>
 
 		<dependency>
 			<groupId>com.github.ben-manes.caffeine</groupId>
@@ -576,8 +580,6 @@
 		<dependency>
 			<groupId>org.jetbrains</groupId>
 			<artifactId>annotations</artifactId>
-			<version>16.0.3</version>
-			<scope>compile</scope>
 		</dependency>
 
     </dependencies>
@@ -669,7 +671,7 @@
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
 					<runOrder>alphabetical</runOrder>
-					<argLine>@{argLine} ${surefire_jvm_args} -XX:+HeapDumpOnOutOfMemoryError -XX:+CrashOnOutOfMemoryError</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 					<forkCount>0.6C</forkCount>
 					<excludes>*StressTest*</excludes>
 				</configuration>
@@ -820,6 +822,21 @@
 				</plugins>
 			</build>
 		</profile>
+		<profile>
+			<id>CI</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-surefire-plugin</artifactId>
+						<configuration>
+							<forkCount>1</forkCount>
+							<runOrder>alphabetical</runOrder>
+						</configuration>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
 		<profile>
 			<!--
 			This profile is used on the Travis CI server because the full test suite

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
 import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
+import ca.uhn.fhir.jpa.provider.DiffProvider;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory;
@@ -251,6 +252,12 @@ public abstract class BaseConfig {
 		return new JpaConsentContextServices();
 	}
 
+	@Bean
+	@Lazy
+	public DiffProvider diffProvider() {
+		return new DiffProvider();
+	}
+
 	@Bean
 	@Lazy
 	public IPartitionLookupSvc partitionConfigSvc() {

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

@@ -35,6 +35,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
 import ca.uhn.fhir.jpa.delete.DeleteConflictService;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.patch.FhirPatch;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.model.entity.BaseTag;
@@ -52,8 +53,8 @@ import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
-import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
+import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
-import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
+import ca.uhn.fhir.jpa.patch.XmlPatchUtils;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
@@ -91,6 +92,7 @@ import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -856,7 +858,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
-	public DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequest) {
+	public DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest) {
 
 		ResourceTable entityToUpdate;
 		if (isNotBlank(theConditionalUrl)) {
@@ -886,10 +888,20 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		IBaseResource resourceToUpdate = toResource(entityToUpdate, false);
 		IBaseResource destination;
-		if (thePatchType == PatchTypeEnum.JSON_PATCH) {
+		switch (thePatchType) {
+			case JSON_PATCH:
 			destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
-		} else {
+				break;
+			case XML_PATCH:
 			destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
+				break;
+			case FHIR_PATCH_XML:
+			case FHIR_PATCH_JSON:
+			default:
+				IBaseParameters fhirPatchJson = theFhirPatchBody;
+				new FhirPatch(getContext()).apply(resourceToUpdate, fhirPatchJson);
+				destination = resourceToUpdate;
+				break;
 		}
 
 		@SuppressWarnings("unchecked")

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

@@ -34,13 +34,16 @@ import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
-import ca.uhn.fhir.rest.api.server.*;
+import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
+import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
+import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import ca.uhn.fhir.rest.param.QualifierDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.FhirTerser;
@@ -51,6 +54,8 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.InstantType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
@@ -58,7 +63,11 @@ import org.springframework.transaction.annotation.Transactional;
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import javax.validation.constraints.NotNull;
-import java.util.*;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
 
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR;
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO;
@@ -66,6 +75,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public abstract class BaseStorageDao {
+	private static final Logger ourLog = LoggerFactory.getLogger(BaseStorageDao.class);
 	@Autowired
 	protected ISearchParamRegistry mySearchParamRegistry;
 
@@ -213,7 +223,6 @@ public abstract class BaseStorageDao {
 	 */
 	protected abstract FhirContext getContext();
 
-
 	@Transactional(propagation = Propagation.SUPPORTS)
 	public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
 		if (theSource == null || theSource.isEmpty()) {

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

@@ -32,10 +32,8 @@ import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.DeleteConflict;
 import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
 import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.jpa.delete.DeleteConflictService;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
@@ -47,6 +45,8 @@ import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.PreferReturnEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import ca.uhn.fhir.rest.server.RestfulServerUtils;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
@@ -74,6 +74,7 @@ import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -350,7 +351,7 @@ public abstract class BaseTransactionProcessor {
 		// Do all entries have a verb?
 		for (int i = 0; i < myVersionAdapter.getEntries(theRequest).size(); i++) {
 			IBase nextReqEntry = requestEntries.get(i);
-			String verb = myVersionAdapter.getEntryRequestVerb(nextReqEntry);
+			String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
 			if (verb == null || !isValidVerb(verb)) {
 				throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", verb, i));
 			}
@@ -372,7 +373,7 @@ public abstract class BaseTransactionProcessor {
 		for (int i = 0; i < requestEntries.size(); i++) {
 			originalRequestOrder.put(requestEntries.get(i), i);
 			myVersionAdapter.addEntry(response);
-			if (myVersionAdapter.getEntryRequestVerb(requestEntries.get(i)).equals("GET")) {
+			if (myVersionAdapter.getEntryRequestVerb(myContext, requestEntries.get(i)).equals("GET")) {
 				getEntries.add(requestEntries.get(i));
 			}
 		}
@@ -544,7 +545,7 @@ public abstract class BaseTransactionProcessor {
 				IBase nextReqEntry = theEntries.get(index);
 				IBaseResource resource = myVersionAdapter.getResource(nextReqEntry);
 				if (resource != null) {
-					String verb = myVersionAdapter.getEntryRequestVerb(nextReqEntry);
+					String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
 					String entryUrl = myVersionAdapter.getFullUrl(nextReqEntry);
 					String requestUrl = myVersionAdapter.getEntryRequestUrl(nextReqEntry);
 					String ifNoneExist = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
@@ -647,7 +648,7 @@ public abstract class BaseTransactionProcessor {
 
 				}
 
-				String verb = myVersionAdapter.getEntryRequestVerb(nextReqEntry);
+				String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
 				String resourceType = res != null ? myContext.getResourceDefinition(res).getName() : null;
 				Integer order = theOriginalRequestOrder.get(nextReqEntry);
 				IBase nextRespEntry = (IBase) myVersionAdapter.getEntries(theResponse).get(order);
@@ -768,6 +769,8 @@ public abstract class BaseTransactionProcessor {
 						matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 						String patchBody = null;
 						String contentType = null;
+						IBaseParameters patchBodyParameters = null;
+						PatchTypeEnum patchType = null;
 
 						if (res instanceof IBaseBinary) {
 							IBaseBinary binary = (IBaseBinary) res;
@@ -775,21 +778,26 @@ public abstract class BaseTransactionProcessor {
 								patchBody = new String(binary.getContent(), Charsets.UTF_8);
 							}
 							contentType = binary.getContentType();
+							patchType = PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(myContext, contentType);
+							if (patchType == PatchTypeEnum.FHIR_PATCH_JSON || patchType == PatchTypeEnum.FHIR_PATCH_XML) {
+								String msg = myContext.getLocalizer().getMessage(TransactionProcessor.class, "fhirPatchShouldNotUseBinaryResource");
+								throw new InvalidRequestException(msg);
+							}
+						} else if (res instanceof IBaseParameters) {
+							patchBodyParameters = (IBaseParameters) res;
+							patchType = PatchTypeEnum.FHIR_PATCH_JSON;
 						}
 
-						if (isBlank(patchBody)) {
+						if (patchBodyParameters == null) {
-							String msg = myContext.getLocalizer().getMessage(TransactionProcessor.class, "missingPatchBody");
+							if (isBlank(patchBody)) {
-							throw new InvalidRequestException(msg);
+								String msg = myContext.getLocalizer().getMessage(TransactionProcessor.class, "missingPatchBody");
-						}
+								throw new InvalidRequestException(msg);
-						if (isBlank(contentType)) {
+							}
-							String msg = myContext.getLocalizer().getMessage(TransactionProcessor.class, "missingPatchContentType");
-							throw new InvalidRequestException(msg);
 						}
 
 						IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb, url);
-						PatchTypeEnum patchType = PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(contentType);
 						IIdType patchId = myContext.getVersion().newIdType().setValue(parts.getResourceId());
-						DaoMethodOutcome outcome = dao.patch(patchId, matchUrl, patchType, patchBody, theRequest);
+						DaoMethodOutcome outcome = dao.patch(patchId, matchUrl, patchType, patchBody, patchBodyParameters, theRequest);
 						updatedEntities.add(outcome.getEntity());
 						if (outcome.getResource() != null) {
 							updatedResources.add(outcome.getResource());
@@ -1030,7 +1038,7 @@ public abstract class BaseTransactionProcessor {
 	}
 
 	private String toMatchUrl(IBase theEntry) {
-		String verb = myVersionAdapter.getEntryRequestVerb(theEntry);
+		String verb = myVersionAdapter.getEntryRequestVerb(myContext, theEntry);
 		if (verb.equals("POST")) {
 			return myVersionAdapter.getEntryIfNoneExist(theEntry);
 		}
@@ -1069,7 +1077,7 @@ public abstract class BaseTransactionProcessor {
 
 		BUNDLEENTRY addEntry(BUNDLE theBundle);
 
-		String getEntryRequestVerb(BUNDLEENTRY theEntry);
+		String getEntryRequestVerb(FhirContext theContext, BUNDLEENTRY theEntry);
 
 		String getFullUrl(BUNDLEENTRY theEntry);
 
@@ -1106,7 +1114,7 @@ public abstract class BaseTransactionProcessor {
 	//@formatter:off
 	public class TransactionSorter implements Comparator<IBase> {
 
-		private Set<String> myPlaceholderIds;
+		private final Set<String> myPlaceholderIds;
 
 		public TransactionSorter(Set<String> thePlaceholderIds) {
 			myPlaceholderIds = thePlaceholderIds;
@@ -1159,8 +1167,8 @@ public abstract class BaseTransactionProcessor {
 
 		private int toOrder(IBase theO1) {
 			int o1 = 0;
-			if (myVersionAdapter.getEntryRequestVerb(theO1) != null) {
+			if (myVersionAdapter.getEntryRequestVerb(myContext, theO1) != null) {
-				switch (myVersionAdapter.getEntryRequestVerb(theO1)) {
+				switch (myVersionAdapter.getEntryRequestVerb(myContext, theO1)) {
 					case "DELETE":
 						o1 = 1;
 						break;
@@ -1206,7 +1214,7 @@ public abstract class BaseTransactionProcessor {
 	}
 
 	private static String toStatusString(int theStatusCode) {
-		return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
+		return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
 	}
 
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/TransactionProcessorVersionAdapterDstu3.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -102,7 +103,7 @@ public class TransactionProcessorVersionAdapterDstu3 implements TransactionProce
 	}
 
 	@Override
-	public String getEntryRequestVerb(Bundle.BundleEntryComponent theEntry) {
+	public String getEntryRequestVerb(FhirContext theContext, Bundle.BundleEntryComponent theEntry) {
 		String retVal = null;
 		Bundle.HTTPVerb value = theEntry.getRequest().getMethodElement().getValue();
 		if (value != null) {
@@ -115,7 +116,7 @@ public class TransactionProcessorVersionAdapterDstu3 implements TransactionProce
 		 */
 		if (isBlank(retVal)) {
 			Resource resource = theEntry.getResource();
-			boolean isPatch = BundleUtil.isDstu3TransactionPatch(resource);
+			boolean isPatch = BundleUtil.isDstu3TransactionPatch(theContext, resource);
 
 			if (isPatch) {
 				retVal = "PATCH";

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

@@ -100,6 +100,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Set;
+import java.util.TreeSet;
 import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -685,9 +686,10 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 							}
 						}
 
-
 					} else {
-						throw new InvalidRequestException("Unknown search parameter " + theParamName + " for resource type " + theResourceName);
+						String validNames = new TreeSet<>(mySearchParamRegistry.getActiveSearchParams(theResourceName).keySet()).toString();
+						String msg = myContext.getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", theParamName, theResourceName, validNames);
+						throw new InvalidRequestException(msg);
 					}
 				}
 				break;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/TransactionProcessorVersionAdapterR4.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -99,7 +100,7 @@ public class TransactionProcessorVersionAdapterR4 implements TransactionProcesso
 	}
 
 	@Override
-	public String getEntryRequestVerb(Bundle.BundleEntryComponent theEntry) {
+	public String getEntryRequestVerb(FhirContext theContext, Bundle.BundleEntryComponent theEntry) {
 		String retVal = null;
 		Bundle.HTTPVerb value = theEntry.getRequest().getMethodElement().getValue();
 		if (value != null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/TransactionProcessorVersionAdapterR5.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -99,7 +100,7 @@ public class TransactionProcessorVersionAdapterR5 implements TransactionProcesso
 	}
 
 	@Override
-	public String getEntryRequestVerb(Bundle.BundleEntryComponent theEntry) {
+	public String getEntryRequestVerb(FhirContext theContext, Bundle.BundleEntryComponent theEntry) {
 		String retVal = null;
 		Bundle.HTTPVerb value = theEntry.getRequest().getMethodElement().getValue();
 		if (value != null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/patch/FhirPatch.java

@@ -0,0 +1,420 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.path.EncodeContextPath;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.IModelVisitor2;
+import ca.uhn.fhir.util.ParametersUtil;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseEnumeration;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.utilities.xhtml.XhtmlNode;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class FhirPatch {
+
+	private final FhirContext myContext;
+	private boolean myIncludePreviousValueInDiff;
+	private Set<EncodeContextPath> myIgnorePaths = Collections.emptySet();
+
+	public FhirPatch(FhirContext theContext) {
+		myContext = theContext;
+	}
+
+	/**
+	 * Adds a path element that will not be included in generated diffs. Values can take the form
+	 * <code>ResourceName.fieldName.fieldName</code> and wildcards are supported, such
+	 * as <code>*.meta</code>.
+	 */
+	public void addIgnorePath(String theIgnorePath) {
+		Validate.notBlank(theIgnorePath, "theIgnorePath must not be null or empty");
+
+		if (myIgnorePaths.isEmpty()) {
+			myIgnorePaths = new HashSet<>();
+		}
+		myIgnorePaths.add(new EncodeContextPath(theIgnorePath));
+	}
+
+	public void setIncludePreviousValueInDiff(boolean theIncludePreviousValueInDiff) {
+		myIncludePreviousValueInDiff = theIncludePreviousValueInDiff;
+	}
+
+	public void apply(IBaseResource theResource, IBaseResource thePatch) {
+
+		List<IBase> opParameters = ParametersUtil.getNamedParameters(myContext, thePatch, "operation");
+		for (IBase nextOp : opParameters) {
+			String type = ParametersUtil.getParameterPartValueAsString(myContext, nextOp, "type");
+			String path = ParametersUtil.getParameterPartValueAsString(myContext, nextOp, "path");
+			Optional<IBase> valuePart = ParametersUtil.getParameterPart(myContext, nextOp, "value");
+			Optional<IBase> valuePartValue = ParametersUtil.getParameterPartValue(myContext, nextOp, "value");
+
+			type = defaultString(type);
+			path = defaultString(path);
+
+			String containingPath;
+			String elementName;
+			Integer removeIndex = null;
+			Integer insertIndex = null;
+			if ("delete".equals(type)) {
+
+				doDelete(theResource, path);
+				return;
+
+			} else if ("add".equals(type)) {
+
+				containingPath = path;
+				elementName = ParametersUtil.getParameterPartValueAsString(myContext, nextOp, "name");
+
+			} else if ("replace".equals(type)) {
+
+				int lastDot = path.lastIndexOf(".");
+				containingPath = path.substring(0, lastDot);
+				elementName = path.substring(lastDot + 1);
+
+			} else if ("insert".equals(type)) {
+
+				int lastDot = path.lastIndexOf(".");
+				containingPath = path.substring(0, lastDot);
+				elementName = path.substring(lastDot + 1);
+				insertIndex = ParametersUtil
+					.getParameterPartValue(myContext, nextOp, "index")
+					.map(t -> (IPrimitiveType<Integer>) t)
+					.map(t -> t.getValue())
+					.orElseThrow(() -> new InvalidRequestException("No index supplied for insert operation"));
+
+			} else if ("move".equals(type)) {
+
+				int lastDot = path.lastIndexOf(".");
+				containingPath = path.substring(0, lastDot);
+				elementName = path.substring(lastDot + 1);
+				insertIndex = ParametersUtil
+					.getParameterPartValue(myContext, nextOp, "destination")
+					.map(t -> (IPrimitiveType<Integer>) t)
+					.map(t -> t.getValue())
+					.orElseThrow(() -> new InvalidRequestException("No index supplied for insert operation"));
+				removeIndex = ParametersUtil
+					.getParameterPartValue(myContext, nextOp, "source")
+					.map(t -> (IPrimitiveType<Integer>) t)
+					.map(t -> t.getValue())
+					.orElseThrow(() -> new InvalidRequestException("No index supplied for insert operation"));
+
+			} else {
+
+				throw new InvalidRequestException("Unknown patch operation type: " + type);
+
+			}
+
+			List<IBase> paths = myContext.newFhirPath().evaluate(theResource, containingPath, IBase.class);
+			for (IBase next : paths) {
+
+				BaseRuntimeElementDefinition<?> elementDef = myContext.getElementDefinition(next.getClass());
+
+				String childName = elementName;
+				BaseRuntimeChildDefinition childDef = elementDef.getChildByName(childName);
+				BaseRuntimeElementDefinition<?> childElement;
+				if (childDef == null) {
+					childName = elementName + "[x]";
+					childDef = elementDef.getChildByName(childName);
+					childElement = childDef.getChildByName(childDef.getValidChildNames().iterator().next());
+				} else {
+					childElement = childDef.getChildByName(childName);
+				}
+
+				if ("move".equals(type)) {
+
+					List<IBase> existingValues = new ArrayList<>(childDef.getAccessor().getValues(next));
+					if (removeIndex == null || removeIndex >= existingValues.size()) {
+						String msg = myContext.getLocalizer().getMessage(FhirPatch.class, "invalidMoveSourceIndex", removeIndex, path, existingValues.size());
+						throw new InvalidRequestException(msg);
+					}
+					IBase newValue = existingValues.remove(removeIndex.intValue());
+
+					if (insertIndex == null || insertIndex > existingValues.size()) {
+						String msg = myContext.getLocalizer().getMessage(FhirPatch.class, "invalidMoveDestinationIndex", insertIndex, path, existingValues.size());
+						throw new InvalidRequestException(msg);
+					}
+					existingValues.add(insertIndex, newValue);
+
+					childDef.getMutator().setValue(next, null);
+					for (IBase nextNewValue : existingValues) {
+						childDef.getMutator().addValue(next, nextNewValue);
+					}
+
+					continue;
+				}
+
+				IBase newValue;
+				if (valuePartValue.isPresent()) {
+					newValue = valuePartValue.get();
+				} else {
+					newValue = childElement.newInstance();
+
+					if (valuePart.isPresent()) {
+						List<IBase> valuePartParts = myContext.newTerser().getValues(valuePart.get(), "part");
+						for (IBase nextValuePartPart : valuePartParts) {
+
+							String name = myContext.newTerser().getSingleValue(nextValuePartPart, "name", IPrimitiveType.class).map(t -> t.getValueAsString()).orElse(null);
+							if (isNotBlank(name)) {
+
+								Optional<IBase> value = myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class);
+								if (value.isPresent()) {
+
+									BaseRuntimeChildDefinition partChildDef = childElement.getChildByName(name);
+									partChildDef.getMutator().addValue(newValue, value.get());
+
+								}
+
+							}
+
+						}
+					}
+
+				}
+
+				if (IBaseEnumeration.class.isAssignableFrom(childElement.getImplementingClass()) || XhtmlNode.class.isAssignableFrom(childElement.getImplementingClass())) {
+					// If the compositeElementDef is an IBaseEnumeration, we will use the actual compositeElementDef definition to build one, since
+					// it needs the right factory object passed to its constructor
+					IPrimitiveType<?> newValueInstance = (IPrimitiveType<?>) childElement.newInstance();
+					newValueInstance.setValueAsString(((IPrimitiveType<?>) newValue).getValueAsString());
+					childDef.getMutator().setValue(next, newValueInstance);
+					newValue = newValueInstance;
+				}
+
+				if ("insert".equals(type)) {
+
+					List<IBase> existingValues = new ArrayList<>(childDef.getAccessor().getValues(next));
+					if (insertIndex == null || insertIndex > existingValues.size()) {
+						String msg = myContext.getLocalizer().getMessage(FhirPatch.class, "invalidInsertIndex", insertIndex, path, existingValues.size());
+						throw new InvalidRequestException(msg);
+					}
+					existingValues.add(insertIndex, newValue);
+
+					childDef.getMutator().setValue(next, null);
+					for (IBase nextNewValue : existingValues) {
+						childDef.getMutator().addValue(next, nextNewValue);
+					}
+
+				} else {
+					childDef.getMutator().setValue(next, newValue);
+				}
+
+			}
+
+
+		}
+
+	}
+
+	private void doDelete(IBaseResource theResource, String thePath) {
+		List<IBase> paths = myContext.newFhirPath().evaluate(theResource, thePath, IBase.class);
+		for (IBase next : paths) {
+			myContext.newTerser().visit(next, new IModelVisitor2() {
+				@Override
+				public boolean acceptElement(IBase theElement, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
+					if (theElement instanceof IPrimitiveType) {
+						((IPrimitiveType<?>) theElement).setValueAsString(null);
+					}
+					return true;
+				}
+
+				@Override
+				public boolean acceptUndeclaredExtension(IBaseExtension<?, ?> theNextExt, List<IBase> theContainingElementPath, List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
+					theNextExt.setUrl(null);
+					theNextExt.setValue(null);
+					return true;
+				}
+			});
+		}
+	}
+
+	public IBaseParameters diff(@Nullable IBaseResource theOldValue, @Nonnull IBaseResource theNewValue) {
+		IBaseParameters retVal = ParametersUtil.newInstance(myContext);
+		String newValueTypeName = myContext.getResourceDefinition(theNewValue).getName();
+
+		if (theOldValue == null) {
+
+			IBase operation = ParametersUtil.addParameterToParameters(myContext, retVal, "operation");
+			ParametersUtil.addPartCode(myContext, operation, "type", "insert");
+			ParametersUtil.addPartString(myContext, operation, "path", newValueTypeName);
+			ParametersUtil.addPart(myContext, operation, "value", theNewValue);
+
+		} else {
+
+			String oldValueTypeName = myContext.getResourceDefinition(theOldValue).getName();
+			Validate.isTrue(oldValueTypeName.equalsIgnoreCase(newValueTypeName), "Resources must be of same type");
+
+
+			BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theOldValue).getBaseDefinition();
+			String path = def.getName();
+
+			EncodeContextPath contextPath = new EncodeContextPath();
+			contextPath.pushPath(path, true);
+
+			compare(retVal, contextPath, def, path, path, theOldValue, theNewValue);
+
+			contextPath.popPath();
+			assert contextPath.getPath().isEmpty();
+		}
+
+		return retVal;
+	}
+
+	private void compare(IBaseParameters theDiff, EncodeContextPath theSourceEncodeContext, BaseRuntimeElementDefinition<?> theDef, String theSourcePath, String theTargetPath, IBase theOldField, IBase theNewField) {
+
+		boolean pathIsIgnored = pathIsIgnored(theSourceEncodeContext);
+		if (pathIsIgnored) {
+			return;
+		}
+
+		BaseRuntimeElementDefinition<?> sourceDef = myContext.getElementDefinition(theOldField.getClass());
+		BaseRuntimeElementDefinition<?> targetDef = myContext.getElementDefinition(theNewField.getClass());
+		if (!sourceDef.getName().equals(targetDef.getName())) {
+			IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, "operation");
+			ParametersUtil.addPartCode(myContext, operation, "type", "replace");
+			ParametersUtil.addPartString(myContext, operation, "path", theTargetPath);
+			addValueToDiff(operation, theOldField, theNewField);
+		} else {
+			if (theOldField instanceof IPrimitiveType) {
+				IPrimitiveType<?> oldPrimitive = (IPrimitiveType<?>) theOldField;
+				IPrimitiveType<?> newPrimitive = (IPrimitiveType<?>) theNewField;
+				String oldValueAsString = toValue(oldPrimitive);
+				String newValueAsString = toValue(newPrimitive);
+				if (!Objects.equals(oldValueAsString, newValueAsString)) {
+					IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, "operation");
+					ParametersUtil.addPartCode(myContext, operation, "type", "replace");
+					ParametersUtil.addPartString(myContext, operation, "path", theTargetPath);
+					addValueToDiff(operation, oldPrimitive, newPrimitive);
+				}
+			}
+
+			List<BaseRuntimeChildDefinition> children = theDef.getChildren();
+			for (BaseRuntimeChildDefinition nextChild : children) {
+				compareField(theDiff, theSourceEncodeContext, theSourcePath, theTargetPath, theOldField, theNewField, nextChild);
+			}
+
+		}
+
+	}
+
+	private void compareField(IBaseParameters theDiff, EncodeContextPath theSourceEncodePath, String theSourcePath, String theTargetPath, IBase theOldField, IBase theNewField, BaseRuntimeChildDefinition theChildDef) {
+		String elementName = theChildDef.getElementName();
+		boolean repeatable = theChildDef.getMax() != 1;
+		theSourceEncodePath.pushPath(elementName, false);
+		if (pathIsIgnored(theSourceEncodePath)) {
+			theSourceEncodePath.popPath();
+			return;
+		}
+
+		List<? extends IBase> sourceValues = theChildDef.getAccessor().getValues(theOldField);
+		List<? extends IBase> targetValues = theChildDef.getAccessor().getValues(theNewField);
+
+		int sourceIndex = 0;
+		int targetIndex = 0;
+		while (sourceIndex < sourceValues.size() && targetIndex < targetValues.size()) {
+
+			IBase sourceChildField = sourceValues.get(sourceIndex);
+			Validate.notNull(sourceChildField); // not expected to happen, but just in case
+			BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(sourceChildField.getClass());
+			IBase targetChildField = targetValues.get(targetIndex);
+			Validate.notNull(targetChildField); // not expected to happen, but just in case
+			String sourcePath = theSourcePath + "." + elementName + (repeatable ? "[" + sourceIndex + "]" : "");
+			String targetPath = theSourcePath + "." + elementName + (repeatable ? "[" + targetIndex + "]" : "");
+
+			compare(theDiff, theSourceEncodePath, def, sourcePath, targetPath, sourceChildField, targetChildField);
+
+			sourceIndex++;
+			targetIndex++;
+		}
+
+		// Find newly inserted items
+		while (targetIndex < targetValues.size()) {
+			String path = theTargetPath + "." + elementName;
+
+
+			IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, "operation");
+			ParametersUtil.addPartCode(myContext, operation, "type", "insert");
+			ParametersUtil.addPartString(myContext, operation, "path", path);
+			ParametersUtil.addPartInteger(myContext, operation, "index", targetIndex);
+			ParametersUtil.addPart(myContext, operation, "value", targetValues.get(targetIndex));
+
+			targetIndex++;
+		}
+
+		// Find deleted items
+		while (sourceIndex < sourceValues.size()) {
+			IBase operation = ParametersUtil.addParameterToParameters(myContext, theDiff, "operation");
+			ParametersUtil.addPartCode(myContext, operation, "type", "delete");
+			ParametersUtil.addPartString(myContext, operation, "path", theTargetPath + "." + elementName + (repeatable ? "[" + targetIndex + "]" : ""));
+
+			sourceIndex++;
+			targetIndex++;
+		}
+
+		theSourceEncodePath.popPath();
+	}
+
+	private void addValueToDiff(IBase theOperationPart, IBase theOldValue, IBase theNewValue) {
+
+		if (myIncludePreviousValueInDiff) {
+			IBase oldValue = massageValueForDiff(theOldValue);
+			ParametersUtil.addPart(myContext, theOperationPart, "previousValue", oldValue);
+		}
+
+		IBase newValue = massageValueForDiff(theNewValue);
+		ParametersUtil.addPart(myContext, theOperationPart, "value", newValue);
+	}
+
+	private boolean pathIsIgnored(EncodeContextPath theSourceEncodeContext) {
+		boolean pathIsIgnored = false;
+		for (EncodeContextPath next : myIgnorePaths) {
+			if (theSourceEncodeContext.startsWith(next, false)) {
+				pathIsIgnored = true;
+				break;
+			}
+		}
+		return pathIsIgnored;
+	}
+
+	private IBase massageValueForDiff(IBase theNewValue) {
+		// XHTML content is dealt with by putting it in a string
+		if (theNewValue instanceof XhtmlNode) {
+			String xhtmlString = ((XhtmlNode) theNewValue).getValueAsString();
+			theNewValue = myContext.getElementDefinition("string").newInstance(xhtmlString);
+		}
+
+		// IIdType can hold a fully qualified ID, but we just want the ID part to show up in diffs
+		if (theNewValue instanceof IIdType) {
+			String idPart = ((IIdType) theNewValue).getIdPart();
+			theNewValue = myContext.getElementDefinition("id").newInstance(idPart);
+		}
+
+		return theNewValue;
+	}
+
+	private String toValue(IPrimitiveType<?> theOldPrimitive) {
+		if (theOldPrimitive instanceof IIdType) {
+			return ((IIdType) theOldPrimitive).getIdPart();
+		}
+		return theOldPrimitive.getValueAsString();
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/patch/JsonPatchUtils.java

@@ -0,0 +1,85 @@
+package ca.uhn.fhir.jpa.patch;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import com.fasterxml.jackson.core.JsonFactory;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.github.fge.jsonpatch.JsonPatch;
+import com.github.fge.jsonpatch.JsonPatchException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.intellij.lang.annotations.Language;
+
+import java.io.IOException;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
+public class JsonPatchUtils {
+
+	public static <T extends IBaseResource> T apply(FhirContext theCtx, T theResourceToUpdate, @Language("JSON") String thePatchBody) {
+		// Parse the patch
+		ObjectMapper mapper = new ObjectMapper();
+		mapper.configure(JsonParser.Feature.INCLUDE_SOURCE_IN_LOCATION, false);
+
+		JsonFactory factory = mapper.getFactory();
+
+		final JsonPatch patch;
+		try {
+			com.fasterxml.jackson.core.JsonParser parser = factory.createParser(thePatchBody);
+			JsonNode jsonPatchNode = mapper.readTree(parser);
+			patch = JsonPatch.fromJson(jsonPatchNode);
+
+			JsonNode originalJsonDocument = mapper.readTree(theCtx.newJsonParser().encodeResourceToString(theResourceToUpdate));
+			JsonNode after = patch.apply(originalJsonDocument);
+
+			@SuppressWarnings("unchecked")
+			Class<T> clazz = (Class<T>) theResourceToUpdate.getClass();
+
+			String postPatchedContent = mapper.writeValueAsString(after);
+
+			IParser fhirJsonParser = theCtx.newJsonParser();
+			fhirJsonParser.setParserErrorHandler(new StrictErrorHandler());
+
+			T retVal;
+			try {
+				retVal = fhirJsonParser.parseResource(clazz, postPatchedContent);
+			} catch (DataFormatException e) {
+				String resourceId = theResourceToUpdate.getIdElement().toUnqualifiedVersionless().getValue();
+				String resourceType = theCtx.getResourceDefinition(theResourceToUpdate).getName();
+				resourceId = defaultString(resourceId, resourceType);
+				String msg = theCtx.getLocalizer().getMessage(JsonPatchUtils.class, "failedToApplyPatch", resourceId, e.getMessage());
+				throw new InvalidRequestException(msg);
+			}
+			return retVal;
+
+		} catch (IOException | JsonPatchException theE) {
+			throw new InvalidRequestException(theE.getMessage());
+		}
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/patch/XmlPatchUtils.java

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import com.github.dnault.xmlpatch.Patcher;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+public class XmlPatchUtils {
+
+	public static <T extends IBaseResource> T apply(FhirContext theCtx, T theResourceToUpdate, String thePatchBody) {
+		
+		@SuppressWarnings("unchecked")
+		Class<T> clazz = (Class<T>) theResourceToUpdate.getClass();
+		
+		String inputResource = theCtx.newXmlParser().encodeResourceToString(theResourceToUpdate);
+		
+		ByteArrayOutputStream result = new ByteArrayOutputStream();
+		try {
+			Patcher.patch(new ByteArrayInputStream(inputResource.getBytes(Constants.CHARSET_UTF8)), new ByteArrayInputStream(thePatchBody.getBytes(Constants.CHARSET_UTF8)), result);
+		} catch (IOException e) {
+			throw new InternalErrorException(e);
+		}
+		
+		String resultString = new String(result.toByteArray(), Constants.CHARSET_UTF8);
+		T retVal = theCtx.newXmlParser().parseResource(clazz, resultString);
+		
+		return retVal;
+	}
+
+	
+}

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

@@ -38,11 +38,13 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.util.CoverageIgnore;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.Parameters;
 import org.springframework.beans.factory.annotation.Required;
+import org.springframework.web.bind.annotation.RequestBody;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.Date;
@@ -122,10 +124,10 @@ public abstract class BaseJpaResourceProvider<T extends IBaseResource> extends B
 	}
 
 	@Patch
-	public DaoMethodOutcome patch(HttpServletRequest theRequest, @IdParam IIdType theId, @ConditionalUrlParam String theConditionalUrl,  RequestDetails theRequestDetails, @ResourceParam String theBody, PatchTypeEnum thePatchType) {
+	public DaoMethodOutcome patch(HttpServletRequest theRequest, @IdParam IIdType theId, @ConditionalUrlParam String theConditionalUrl, RequestDetails theRequestDetails, @ResourceParam String theBody, PatchTypeEnum thePatchType, @ResourceParam IBaseParameters theRequestBody) {
 		startRequest(theRequest);
 		try {
-			return myDao.patch(theId, theConditionalUrl, thePatchType, theBody, theRequestDetails);
+			return myDao.patch(theId, theConditionalUrl, thePatchType, theBody, theRequestBody, theRequestDetails);
 		} finally {
 			endRequest(theRequest);
 		}

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

@@ -0,0 +1,105 @@
+package ca.uhn.fhir.jpa.provider;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.util.ProviderConstants;
+import ca.uhn.fhir.jpa.patch.FhirPatch;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import com.google.common.base.Objects;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nonnull;
+
+public class DiffProvider {
+	private static final Logger ourLog = LoggerFactory.getLogger(DiffProvider.class);
+	@Autowired
+	private FhirContext myContext;
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
+	@Operation(name = ProviderConstants.DIFF_OPERATION_NAME, global = true, idempotent = true)
+	public IBaseParameters diff(
+		@IdParam IIdType theResourceId,
+		@OperationParam(name = ProviderConstants.DIFF_FROM_VERSION_PARAMETER, typeName = "string", min = 0, max = 1) IPrimitiveType<?> theFromVersion,
+		@OperationParam(name = ProviderConstants.DIFF_INCLUDE_META_PARAMETER, typeName = "boolean", min = 0, max = 1) IPrimitiveType<Boolean> theIncludeMeta,
+		RequestDetails theRequestDetails) {
+
+		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResourceId.getResourceType());
+		IBaseResource targetResource = dao.read(theResourceId, theRequestDetails);
+		IBaseResource sourceResource = null;
+
+		Long versionId = targetResource.getIdElement().getVersionIdPartAsLong();
+
+		if (theFromVersion == null || theFromVersion.getValueAsString() == null) {
+
+			// If no explicit from version is specified, find the next previous existing version
+			while (--versionId > 0L && sourceResource == null) {
+				IIdType nextVersionedId = theResourceId.withVersion(Long.toString(versionId));
+				try {
+					sourceResource = dao.read(nextVersionedId, theRequestDetails);
+				} catch (ResourceNotFoundException e) {
+					ourLog.trace("Resource version {} can not be found, most likely it was expunged", nextVersionedId);
+				}
+			}
+
+		} else {
+
+			long fromVersion = Long.parseLong(theFromVersion.getValueAsString());
+			sourceResource = dao.read(theResourceId.withVersion(Long.toString(fromVersion)), theRequestDetails);
+
+		}
+
+		FhirPatch fhirPatch = newPatch(theIncludeMeta);
+		IBaseParameters diff = fhirPatch.diff(sourceResource, targetResource);
+		return diff;
+
+	}
+
+	@Operation(name = ProviderConstants.DIFF_OPERATION_NAME, idempotent = true)
+	public IBaseParameters diff(
+		@OperationParam(name = ProviderConstants.DIFF_FROM_PARAMETER, typeName = "id", min = 1, max = 1) IIdType theFromVersion,
+		@OperationParam(name = ProviderConstants.DIFF_TO_PARAMETER, typeName = "id", min = 1, max = 1) IIdType theToVersion,
+		@OperationParam(name = ProviderConstants.DIFF_INCLUDE_META_PARAMETER, typeName = "boolean", min = 0, max = 1) IPrimitiveType<Boolean> theIncludeMeta,
+		RequestDetails theRequestDetails) {
+
+		if (!Objects.equal(theFromVersion.getResourceType(), theToVersion.getResourceType())) {
+			String msg = myContext.getLocalizer().getMessage(DiffProvider.class, "cantDiffDifferentTypes");
+			throw new InvalidRequestException(msg);
+		}
+
+		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theFromVersion.getResourceType());
+		IBaseResource sourceResource = dao.read(theFromVersion, theRequestDetails);
+		IBaseResource targetResource = dao.read(theToVersion, theRequestDetails);
+
+		FhirPatch fhirPatch = newPatch(theIncludeMeta);
+		IBaseParameters diff = fhirPatch.diff(sourceResource, targetResource);
+		return diff;
+	}
+
+	@Nonnull
+	public FhirPatch newPatch(IPrimitiveType<Boolean> theIncludeMeta) {
+		FhirPatch fhirPatch = new FhirPatch(myContext);
+		fhirPatch.setIncludePreviousValueInDiff(true);
+
+		if (theIncludeMeta != null && theIncludeMeta.getValue()) {
+			ourLog.trace("Including resource metadata in patch");
+		} else {
+			fhirPatch.addIgnorePath("*.meta");
+		}
+
+		return fhirPatch;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java

@@ -958,7 +958,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter foo for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -995,7 +995,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter foo for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 		// Try with normal gender SP

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -1649,7 +1649,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			found = toList(myPatientDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01"))));
 			assertEquals(0, found.size());
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter birthdateAAAA for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 	}

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

@@ -1007,7 +1007,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter foo for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -1045,7 +1045,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter foo for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 		// Try with normal gender SP

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -2129,7 +2129,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01")).setLoadSynchronous(true)));
 			assertEquals(0, found.size());
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter birthdateAAAA for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 

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

@@ -79,6 +79,7 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.BasePagingProvider;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.test.utilities.ITestDataBuilder;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.validation.FhirValidator;
@@ -89,6 +90,7 @@ import org.hibernate.search.jpa.Search;
 import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.AllergyIntolerance;
 import org.hl7.fhir.r4.model.Appointment;
 import org.hl7.fhir.r4.model.AuditEvent;
@@ -175,7 +177,7 @@ import static org.mockito.Mockito.mock;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(classes = {TestR4Config.class})
-public abstract class BaseJpaR4Test extends BaseJpaTest {
+public abstract class BaseJpaR4Test extends BaseJpaTest  implements ITestDataBuilder {
 	private static IValidationSupport ourJpaValidationSupportChainR4;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
@@ -535,6 +537,23 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
 	}
 
+	@Override
+	public IIdType doCreateResource(IBaseResource theResource) {
+		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
+		return dao.create(theResource, mySrd).getId().toUnqualifiedVersionless();
+	}
+
+	@Override
+	public IIdType doUpdateResource(IBaseResource theResource) {
+		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
+		return dao.update(theResource, mySrd).getId().toUnqualifiedVersionless();
+	}
+
+	@Override
+	public FhirContext getFhirContext() {
+		return myFhirCtx;
+	}
+
 	@Override
 	protected FhirContext getContext() {
 		return myFhirCtx;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -1278,7 +1278,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter foo for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -1316,7 +1316,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter foo for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 		// Try with normal gender SP

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

@@ -2498,7 +2498,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01")).setLoadSynchronous(true)));
 			assertEquals(0, found.size());
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter birthdateAAAA for resource type Patient", e.getMessage());
+			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningR4Test.java

@@ -87,7 +87,7 @@ import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
 @SuppressWarnings("unchecked")
-public class PartitioningR4Test extends BaseJpaR4SystemTest implements ITestDataBuilder {
+public class PartitioningR4Test extends BaseJpaR4SystemTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(PartitioningR4Test.class);
 
@@ -2355,23 +2355,6 @@ public class PartitioningR4Test extends BaseJpaR4SystemTest implements ITestData
 		};
 	}
 
-	@Override
-	public IIdType doCreateResource(IBaseResource theResource) {
-		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
-		return dao.create(theResource, mySrd).getId().toUnqualifiedVersionless();
-	}
-
-	@Override
-	public IIdType doUpdateResource(IBaseResource theResource) {
-		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
-		return dao.update(theResource, mySrd).getId().toUnqualifiedVersionless();
-	}
-
-	@Override
-	public FhirContext getFhirContext() {
-		return myFhirCtx;
-	}
-
 	@Interceptor
 	public static class MyReadWriteInterceptor extends MyWriteInterceptor {
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/patch/BaseFhirPatchCoreTest.java

@@ -0,0 +1,115 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.test.BaseTest;
+import ca.uhn.fhir.util.ClasspathUtil;
+import ca.uhn.fhir.util.XmlUtil;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Parameters;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
+import javax.annotation.Nonnull;
+import javax.xml.transform.TransformerException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+@RunWith(Parameterized.class)
+public abstract class BaseFhirPatchCoreTest extends BaseTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(BaseFhirPatchCoreTest.class);
+	private final String myName;
+	private final String myMode;
+	private final IBaseResource myInput;
+	private final IBaseResource myPatch;
+	private final IBaseResource myOutput;
+
+	public BaseFhirPatchCoreTest(String theName, String theMode, IBaseResource theInput, IBaseResource thePatch, IBaseResource theOutput) {
+		myName = theName;
+		myMode = theMode;
+		myInput = theInput;
+		myPatch = thePatch;
+		myOutput = theOutput;
+	}
+
+	@Test
+	public void testApply() {
+		ourLog.info("Testing diff in {} mode: {}", myMode, myName);
+
+		if (myMode.equals("both") || myMode.equals("forwards")) {
+
+			FhirPatch patch = new FhirPatch(getContext());
+			patch.apply(myInput, myPatch);
+
+			String expected = getContext().newJsonParser().setPrettyPrint(true).encodeResourceToString(myOutput);
+			String actual = getContext().newJsonParser().setPrettyPrint(true).encodeResourceToString(myInput);
+			assertEquals(expected, actual);
+
+		} else {
+			fail("Unknown mode: " + myMode);
+		}
+
+	}
+
+	protected abstract FhirContext getContext();
+
+
+	@Nonnull
+	public static Collection<Object[]> loadTestSpec(FhirContext theContext, String theTestSpec) throws IOException, SAXException, TransformerException {
+		List<Object[]> retVal = new ArrayList<>();
+
+		String testsString = ClasspathUtil.loadResource(theTestSpec);
+		Document doc = XmlUtil.parseDocument(testsString);
+		Element tests = (Element) doc.getElementsByTagName("tests").item(0);
+		NodeList cases = tests.getElementsByTagName("case");
+
+		for (int i = 0; i < cases.getLength(); i++) {
+			Element next = (Element) cases.item(i);
+
+			String name = next.getAttribute("name");
+			String mode = next.getAttribute("mode");
+
+			Element diffElement = (Element) next.getElementsByTagName("diff").item(0);
+			Element diffParametersElement = getFirstChildElement(diffElement);
+			String encoded = XmlUtil.encodeDocument(diffParametersElement);
+			IBaseResource diff = theContext.newXmlParser().parseResource(encoded);
+
+			Element inputElement = (Element) next.getElementsByTagName("input").item(0);
+			Element inputResourceElement = getFirstChildElement(inputElement);
+			String inputEncoded = XmlUtil.encodeDocument(inputResourceElement);
+			IBaseResource input = theContext.newXmlParser().parseResource(inputEncoded);
+
+			Element outputElement = (Element) next.getElementsByTagName("output").item(0);
+			Element outputResourceElement = getFirstChildElement(outputElement);
+			String outputEncoded = XmlUtil.encodeDocument(outputResourceElement);
+			IBaseResource output = theContext.newXmlParser().parseResource(outputEncoded);
+
+			retVal.add(new Object[]{name, mode, input, diff, output});
+
+		}
+
+		return retVal;
+	}
+
+	private static Element getFirstChildElement(Element theInput) {
+		for (int i = 0; i < theInput.getChildNodes().getLength(); i++) {
+			if (theInput.getChildNodes().item(i) instanceof Element) {
+				return (Element) theInput.getChildNodes().item(i);
+			}
+		}
+		fail("No child of type Element");
+		throw new Error();
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/patch/FhirPatchApplyR4Test.java

@@ -0,0 +1,185 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.IntegerType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.Test;
+
+import java.util.stream.Collectors;
+
+import static org.junit.Assert.assertEquals;
+
+public class FhirPatchApplyR4Test {
+
+	private static final FhirContext ourCtx = FhirContext.forR4();
+
+	@Test
+	public void testInvalidOperation() {
+		FhirPatch svc = new FhirPatch(ourCtx);
+
+		Patient patient = new Patient();
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent operation = patch.addParameter();
+		operation.setName("operation");
+		operation
+			.addPart()
+			.setName("type")
+			.setValue(new CodeType("foo"));
+
+		try {
+			svc.apply(patient, patch);
+		} catch (InvalidRequestException e) {
+			assertEquals("Unknown patch operation type: foo", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testInsertToInvalidIndex() {
+		FhirPatch svc = new FhirPatch(ourCtx);
+
+		Patient patient = new Patient();
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent operation = patch.addParameter();
+		operation.setName("operation");
+		operation
+			.addPart()
+			.setName("type")
+			.setValue(new CodeType("insert"));
+		operation
+			.addPart()
+			.setName("path")
+			.setValue(new StringType("Patient.identifier"));
+		operation
+			.addPart()
+			.setName("index")
+			.setValue(new IntegerType(2));
+
+		try {
+			svc.apply(patient, patch);
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid insert index 2 for path Patient.identifier - Only have 0 existing entries", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testMoveFromInvalidIndex() {
+		FhirPatch svc = new FhirPatch(ourCtx);
+
+		Patient patient = new Patient();
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent operation = patch.addParameter();
+		operation.setName("operation");
+		operation
+			.addPart()
+			.setName("type")
+			.setValue(new CodeType("move"));
+		operation
+			.addPart()
+			.setName("path")
+			.setValue(new StringType("Patient.identifier"));
+		operation
+			.addPart()
+			.setName("source")
+			.setValue(new IntegerType(2));
+		operation
+			.addPart()
+			.setName("destination")
+			.setValue(new IntegerType(1));
+
+		try {
+			svc.apply(patient, patch);
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid move source index 2 for path Patient.identifier - Only have 0 existing entries", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testMoveToInvalidIndex() {
+		FhirPatch svc = new FhirPatch(ourCtx);
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("sys");
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent operation = patch.addParameter();
+		operation.setName("operation");
+		operation
+			.addPart()
+			.setName("type")
+			.setValue(new CodeType("move"));
+		operation
+			.addPart()
+			.setName("path")
+			.setValue(new StringType("Patient.identifier"));
+		operation
+			.addPart()
+			.setName("source")
+			.setValue(new IntegerType(0));
+		operation
+			.addPart()
+			.setName("destination")
+			.setValue(new IntegerType(1));
+
+		try {
+			svc.apply(patient, patch);
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid move destination index 1 for path Patient.identifier - Only have 0 existing entries", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testDeleteItemWithExtension() {
+		FhirPatch svc = new FhirPatch(ourCtx);
+
+		Patient patient = new Patient();
+		patient.setActive(true);
+		patient.addIdentifier().addExtension("http://foo", new StringType("abc"));
+		patient.addIdentifier().setSystem("sys").setValue("val");
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent operation = patch.addParameter();
+		operation.setName("operation");
+		operation
+			.addPart()
+			.setName("type")
+			.setValue(new CodeType("delete"));
+		operation
+			.addPart()
+			.setName("path")
+			.setValue(new StringType("Patient.identifier[0]"));
+
+		svc.apply(patient, patch);
+
+		assertEquals("{\"resourceType\":\"Patient\",\"identifier\":[{\"system\":\"sys\",\"value\":\"val\"}],\"active\":true}", ourCtx.newJsonParser().encodeResourceToString(patient));
+
+	}
+
+	public static String extractPartValuePrimitive(Parameters theDiff, int theIndex, String theParameterName, String thePartName) {
+		Parameters.ParametersParameterComponent component = theDiff.getParameter().stream().filter(t -> t.getName().equals(theParameterName)).collect(Collectors.toList()).get(theIndex);
+		Parameters.ParametersParameterComponent part = component.getPart().stream().filter(t -> t.getName().equals(thePartName)).findFirst().orElseThrow(() -> new IllegalArgumentException());
+		return ((IPrimitiveType) part.getValue()).getValueAsString();
+	}
+
+	public static <T extends IBase> T extractPartValue(Parameters theDiff, int theIndex, String theParameterName, String thePartName, Class<T> theExpectedType) {
+		Parameters.ParametersParameterComponent component = theDiff.getParameter().stream().filter(t -> t.getName().equals(theParameterName)).collect(Collectors.toList()).get(theIndex);
+		Parameters.ParametersParameterComponent part = component.getPart().stream().filter(t -> t.getName().equals(thePartName)).findFirst().orElseThrow(() -> new IllegalArgumentException());
+
+		if (IBaseResource.class.isAssignableFrom(theExpectedType)) {
+			return (T) part.getResource();
+		} else {
+			assert theExpectedType.isAssignableFrom(part.getValue().getClass());
+			return (T) part.getValue();
+		}
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/patch/FhirPatchDiffR4Test.java

@@ -0,0 +1,443 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.Identifier;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static ca.uhn.fhir.jpa.patch.FhirPatchApplyR4Test.extractPartValue;
+import static ca.uhn.fhir.jpa.patch.FhirPatchApplyR4Test.extractPartValuePrimitive;
+import static org.junit.Assert.assertEquals;
+
+public class FhirPatchDiffR4Test {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirPatchDiffR4Test.class);
+	private static final FhirContext ourCtx = FhirContext.forR4();
+
+	@Test
+	public void testReplaceIdentifier() {
+		Patient oldValue = new Patient();
+		oldValue.addIdentifier().setSystem("system-0").setValue("value-0");
+
+		Patient newValue = new Patient();
+		newValue.addIdentifier().setSystem("system-1").setValue("value-1");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(2, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.identifier[0].system", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("system-1", extractPartValuePrimitive(diff, 0, "operation", "value"));
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.identifier[0].value", extractPartValuePrimitive(diff, 1, "operation", "path"));
+		assertEquals("value-1", extractPartValuePrimitive(diff, 1, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testReplaceChoice() {
+		Patient oldValue = new Patient();
+		oldValue.setDeceased(new BooleanType(true));
+
+		Patient newValue = new Patient();
+		newValue.setDeceased(new DateTimeType("2020-05-16"));
+
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.deceased", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("2020-05-16", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testReplaceChoice2() {
+		Patient oldValue = new Patient();
+		oldValue.setDeceased(new DateTimeType("2020-05-16"));
+
+		Patient newValue = new Patient();
+		newValue.setDeceased(new BooleanType(true));
+
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.deceased", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("true", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testAddExtensionOnPrimitive() {
+		Patient oldValue = new Patient();
+		oldValue.setActive(true);
+
+		Patient newValue = new Patient();
+		newValue.setActive(true);
+		newValue.getActiveElement().addExtension("http://foo", new StringType("a value"));
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("insert", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active.extension", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("0", extractPartValuePrimitive(diff, 0, "operation", "index"));
+		assertEquals("http://foo", extractPartValue(diff, 0, "operation", "value", Extension.class).getUrl());
+		assertEquals("a value", extractPartValue(diff, 0, "operation", "value", Extension.class).getValueAsPrimitive().getValueAsString());
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testRemoveExtensionOnPrimitive() {
+		Patient oldValue = new Patient();
+		oldValue.setActive(true);
+		oldValue.getActiveElement().addExtension("http://foo", new StringType("a value"));
+
+		Patient newValue = new Patient();
+		newValue.setActive(true);
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("delete", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active.extension[0]", extractPartValuePrimitive(diff, 0, "operation", "path"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testModifyExtensionOnPrimitive() {
+		Patient oldValue = new Patient();
+		oldValue.setActive(true);
+		oldValue.getActiveElement().addExtension("http://foo", new StringType("a value"));
+
+		Patient newValue = new Patient();
+		newValue.setActive(true);
+		newValue.getActiveElement().addExtension("http://foo", new StringType("a new value"));
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active.extension[0].value", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("a new value", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+
+	@Test
+	public void testAddExtensionOnComposite() {
+		Patient oldValue = new Patient();
+		oldValue.addName().setFamily("Family");
+
+		Patient newValue = new Patient();
+		newValue.addName().setFamily("Family");
+		newValue.getNameFirstRep().addExtension("http://foo", new StringType("a value"));
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("insert", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.name[0].extension", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("0", extractPartValuePrimitive(diff, 0, "operation", "index"));
+		assertEquals("http://foo", extractPartValue(diff, 0, "operation", "value", Extension.class).getUrl());
+		assertEquals("a value", extractPartValue(diff, 0, "operation", "value", Extension.class).getValueAsPrimitive().getValueAsString());
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testRemoveExtensionOnComposite() {
+		Patient oldValue = new Patient();
+		oldValue.addName().setFamily("Family");
+		oldValue.getNameFirstRep().addExtension("http://foo", new StringType("a value"));
+
+		Patient newValue = new Patient();
+		newValue.addName().setFamily("Family");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("delete", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.name[0].extension[0]", extractPartValuePrimitive(diff, 0, "operation", "path"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testModifyExtensionOnComposite() {
+		Patient oldValue = new Patient();
+		oldValue.addName().setFamily("Family");
+		oldValue.getNameFirstRep().addExtension("http://foo", new StringType("a value"));
+
+		Patient newValue = new Patient();
+		newValue.addName().setFamily("Family");
+		newValue.getNameFirstRep().addExtension("http://foo", new StringType("a new value"));
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.name[0].extension[0].value", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("a new value", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testModifyId() {
+		Patient oldValue = new Patient();
+		oldValue.setId("http://foo/Patient/123/_history/2");
+		oldValue.getMeta().setVersionId("2");
+		oldValue.addName().setFamily("Family");
+
+		Patient newValue = new Patient();
+		newValue.setId("http://bar/Patient/456/_history/667");
+		newValue.getMeta().setVersionId("667");
+		newValue.addName().setFamily("Family");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(2, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.id", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("456", extractPartValuePrimitive(diff, 0, "operation", "value"));
+		assertEquals("replace", extractPartValuePrimitive(diff, 1, "operation", "type"));
+		assertEquals("Patient.meta.versionId", extractPartValuePrimitive(diff, 1, "operation", "path"));
+		assertEquals("667", extractPartValuePrimitive(diff, 1, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testModifyId_OnlyVersionDifferent() {
+		Patient oldValue = new Patient();
+		oldValue.setId("http://foo/Patient/123/_history/2");
+		oldValue.getMeta().setVersionId("2");
+		oldValue.addName().setFamily("Family");
+
+		Patient newValue = new Patient();
+		newValue.setId("http://foo/Patient/123/_history/3");
+		newValue.getMeta().setVersionId("3");
+		newValue.addName().setFamily("Family");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.meta.versionId", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("3", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testModifyNarrative() {
+		Patient oldValue = new Patient();
+		oldValue.getText().getDiv().setValue("<div>123</div>");
+		oldValue.addName().setFamily("Family");
+
+		Patient newValue = new Patient();
+		newValue.getText().getDiv().setValue("<div>456</div>");
+		newValue.addName().setFamily("Family");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.text.div", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">456</div>", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testInsertIdentifier() {
+		Patient oldValue = new Patient();
+		oldValue.addIdentifier().setSystem("system-0").setValue("value-0");
+
+		Patient newValue = new Patient();
+		newValue.addIdentifier().setSystem("system-0").setValue("value-0");
+		newValue.addIdentifier().setSystem("system-1").setValue("value-1");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("insert", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("1", extractPartValuePrimitive(diff, 0, "operation", "index"));
+		assertEquals("Patient.identifier", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("system-1", extractPartValue(diff, 0, "operation", "value", Identifier.class).getSystem());
+		assertEquals("value-1", extractPartValue(diff, 0, "operation", "value", Identifier.class).getValue());
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	@Test
+	public void testIgnoreElementComposite_Resource() {
+		Patient oldValue = new Patient();
+		oldValue.setActive(true);
+		oldValue.getMeta().setSource("123");
+
+		Patient newValue = new Patient();
+		newValue.setActive(false);
+		newValue.getMeta().setSource("456");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		svc.addIgnorePath("Patient.meta");
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("false", extractPartValuePrimitive(diff, 0, "operation", "value"));
+	}
+
+	@Test
+	public void testIgnoreElementComposite_Star() {
+		Patient oldValue = new Patient();
+		oldValue.setActive(true);
+		oldValue.getMeta().setSource("123");
+
+		Patient newValue = new Patient();
+		newValue.setActive(false);
+		newValue.getMeta().setSource("456");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		svc.addIgnorePath("*.meta");
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("false", extractPartValuePrimitive(diff, 0, "operation", "value"));
+	}
+
+	@Test
+	public void testIgnoreElementPrimitive() {
+		Patient oldValue = new Patient();
+		oldValue.setActive(true);
+		oldValue.getMeta().setSource("123");
+
+		Patient newValue = new Patient();
+		newValue.setActive(false);
+		newValue.getMeta().setSource("456");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		svc.addIgnorePath("Patient.meta.source");
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("false", extractPartValuePrimitive(diff, 0, "operation", "value"));
+	}
+
+	@Test
+	public void testIgnoreId() {
+		Patient oldValue = new Patient();
+		oldValue.setId("1");
+		oldValue.setActive(true);
+
+		Patient newValue = new Patient();
+		newValue.setId("2");
+		newValue.setActive(false);
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		svc.addIgnorePath("*.id");
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.active", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("false", extractPartValuePrimitive(diff, 0, "operation", "value"));
+	}
+
+	@Test
+	public void testDeleteIdentifier() {
+		Patient oldValue = new Patient();
+		oldValue.addIdentifier().setSystem("system-0").setValue("value-0");
+		oldValue.addIdentifier().setSystem("system-1").setValue("value-1");
+
+		Patient newValue = new Patient();
+		newValue.addIdentifier().setSystem("system-0").setValue("value-0");
+
+		FhirPatch svc = new FhirPatch(ourCtx);
+		Parameters diff = (Parameters) svc.diff(oldValue, newValue);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+		assertEquals("delete", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.identifier[1]", extractPartValuePrimitive(diff, 0, "operation", "path"));
+
+		validateDiffProducesSameResults(oldValue, newValue, svc, diff);
+	}
+
+	public void validateDiffProducesSameResults(Patient theOldValue, Patient theNewValue, FhirPatch theSvc, Parameters theDiff) {
+		theSvc.apply(theOldValue, theDiff);
+		String expected = ourCtx.newJsonParser().encodeResourceToString(theNewValue);
+		String actual = ourCtx.newJsonParser().encodeResourceToString(theOldValue);
+		assertEquals(expected, actual);
+
+		expected = ourCtx.newXmlParser().encodeResourceToString(theNewValue);
+		actual = ourCtx.newXmlParser().encodeResourceToString(theOldValue);
+		assertEquals(expected, actual);
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/patch/FhirPatchR4CoreTest.java

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.xml.sax.SAXException;
+
+import javax.xml.transform.TransformerException;
+import java.io.IOException;
+import java.util.Collection;
+
+@RunWith(Parameterized.class)
+public class FhirPatchR4CoreTest extends BaseFhirPatchCoreTest {
+
+	private static final FhirContext ourCtx = FhirContext.forR4();
+
+	public FhirPatchR4CoreTest(String theName, String theMode, IBaseResource theInput, IBaseResource thePatch, IBaseResource theOutput) {
+		super(theName, theMode, theInput, thePatch, theOutput);
+	}
+
+	@Override
+	protected FhirContext getContext() {
+		return ourCtx;
+	}
+
+	@Parameterized.Parameters(name = "{0}")
+	public static Collection<Object[]> parameters() throws IOException, SAXException, TransformerException {
+		String testSpec = "/org/hl7/fhir/testcases/r4/patch/fhir-path-tests.xml";
+		return loadTestSpec(ourCtx, testSpec);
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/patch/FhirPatchR5CoreTest.java

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.jpa.patch;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.xml.sax.SAXException;
+
+import javax.xml.transform.TransformerException;
+import java.io.IOException;
+import java.util.Collection;
+
+@RunWith(Parameterized.class)
+public class FhirPatchR5CoreTest extends BaseFhirPatchCoreTest {
+
+	private static final FhirContext ourCtx = FhirContext.forR5();
+
+	public FhirPatchR5CoreTest(String theName, String theMode, IBaseResource theInput, IBaseResource thePatch, IBaseResource theOutput) {
+		super(theName, theMode, theInput, thePatch, theOutput);
+	}
+
+	@Override
+	protected FhirContext getContext() {
+		return ourCtx;
+	}
+
+	@Parameterized.Parameters(name = "{0}")
+	public static Collection<Object[]> parameters() throws IOException, SAXException, TransformerException {
+		String testSpec = "/org/hl7/fhir/testcases/r5/patch/fhir-path-tests.xml";
+		return loadTestSpec(ourCtx, testSpec);
+	}
+
+}

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

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.provider.DiffProvider;
 import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
@@ -105,6 +106,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 
 			ourRestServer.registerProviders(mySystemProvider, myTerminologyUploaderProvider);
 			ourRestServer.registerProvider(myAppCtx.getBean(GraphQLProvider.class));
+			ourRestServer.registerProvider(myAppCtx.getBean(DiffProvider.class));
 
 			ourPagingProvider = myAppCtx.getBean(DatabaseBackedPagingProvider.class);
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/DiffProviderR4Test.java

@@ -0,0 +1,252 @@
+package ca.uhn.fhir.jpa.provider.r4;
+
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.model.util.ProviderConstants;
+import ca.uhn.fhir.model.primitive.BooleanDt;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.HumanName;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static ca.uhn.fhir.jpa.patch.FhirPatchApplyR4Test.extractPartValue;
+import static ca.uhn.fhir.jpa.patch.FhirPatchApplyR4Test.extractPartValuePrimitive;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
+public class DiffProviderR4Test extends BaseResourceProviderR4Test {
+
+
+	private static final Logger ourLog = LoggerFactory.getLogger(DiffProviderR4Test.class);
+
+	@Test
+	public void testMetaIgnoredByDefault() {
+		// Create and 2 updates
+		IIdType id = createPatient(withActiveFalse()).toUnqualifiedVersionless();
+		createPatient(withId(id), withActiveTrue());
+		createPatient(withId(id), withActiveTrue(), withFamily("SMITH"));
+
+		Parameters diff = ourClient
+			.operation()
+			.onInstance(id)
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withNoParameters(Parameters.class)
+			.useHttpGet()
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(2, diff.getParameter().size());
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.text.div", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>", extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody/></table></div>", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		assertEquals("insert", extractPartValuePrimitive(diff, 1, "operation", "type"));
+		assertEquals("Patient.name", extractPartValuePrimitive(diff, 1, "operation", "path"));
+		assertEquals("0", extractPartValuePrimitive(diff, 1, "operation", "index"));
+		assertEquals("SMITH", extractPartValue(diff, 1, "operation", "value", HumanName.class).getFamily());
+	}
+
+	
+	@Test
+	public void testLatestVersion_2_to_3() {
+		// Create and 2 updates
+		IIdType id = createPatient(withActiveFalse()).toUnqualifiedVersionless();
+		createPatient(withId(id), withActiveTrue());
+		createPatient(withId(id), withActiveTrue(), withFamily("SMITH"));
+
+		Parameters diff = ourClient
+			.operation()
+			.onInstance(id)
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withParameter(Parameters.class, ProviderConstants.DIFF_INCLUDE_META_PARAMETER, new BooleanType(true))
+			.useHttpGet()
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(4, diff.getParameter().size());
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.meta.versionId", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("2", extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		assertEquals("3", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 1, "operation", "type"));
+		assertEquals("Patient.meta.lastUpdated", extractPartValuePrimitive(diff, 1, "operation", "path"));
+		
+		assertEquals("replace", extractPartValuePrimitive(diff, 2, "operation", "type"));
+		assertEquals("Patient.text.div", extractPartValuePrimitive(diff, 2, "operation", "path"));
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>", extractPartValuePrimitive(diff, 2, "operation", "previousValue"));
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody/></table></div>", extractPartValuePrimitive(diff, 2, "operation", "value"));
+
+		assertEquals("insert", extractPartValuePrimitive(diff, 3, "operation", "type"));
+		assertEquals("Patient.name", extractPartValuePrimitive(diff, 3, "operation", "path"));
+		assertEquals("0", extractPartValuePrimitive(diff, 3, "operation", "index"));
+		assertEquals("SMITH", extractPartValue(diff, 3, "operation", "value", HumanName.class).getFamily());
+	}
+
+
+	@Test
+	public void testLatestVersion_PreviousVersionExpunged() {
+		// Create and 2 updates
+		IIdType id = createPatient(withActiveFalse()).toUnqualifiedVersionless();
+		createPatient(withId(id), withActiveTrue());
+		createPatient(withId(id), withActiveTrue(), withFamily("SMITH"));
+
+		runInTransaction(()->{
+			ResourceHistoryTable version2 = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id.getIdPartAsLong(), 2);
+			myResourceHistoryTableDao.deleteByPid(version2.getId());
+		});
+
+		Parameters diff = ourClient
+			.operation()
+			.onInstance(id)
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withParameter(Parameters.class, ProviderConstants.DIFF_INCLUDE_META_PARAMETER, new BooleanType(true))
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(5, diff.getParameter().size());
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.meta.versionId", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("1", extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		assertEquals("3", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+	}
+
+
+	@Test
+	public void testLatestVersion_OnlyOneVersionExists() {
+		// Create only
+		IIdType id = createPatient(withActiveTrue()).toUnqualifiedVersionless();
+
+		Parameters diff = ourClient
+			.operation()
+			.onInstance(id)
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withNoParameters(Parameters.class)
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(1, diff.getParameter().size());
+
+		assertEquals("insert", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals(true, extractPartValue(diff, 0, "operation", "value", Patient.class).getActive());
+
+	}
+
+
+	@Test
+	public void testExplicitFromVersion() {
+		// Create and 2 updates
+		IIdType id = createPatient(withActiveFalse()).toUnqualifiedVersionless();
+		createPatient(withId(id), withActiveTrue());
+		createPatient(withId(id), withActiveTrue(), withFamily("SMITH"));
+
+		Parameters diff = ourClient
+			.operation()
+			.onInstance(id)
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withParameter(Parameters.class, ProviderConstants.DIFF_FROM_VERSION_PARAMETER, new StringType("1"))
+			.andParameter(ProviderConstants.DIFF_INCLUDE_META_PARAMETER, new BooleanType(true))
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(5, diff.getParameter().size());
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.meta.versionId", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("1", extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		assertEquals("3", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+	}
+
+
+
+	@Test
+	public void testDifferentResources_Versionless() {
+		// Create and 2 updates
+		IIdType id1 = createPatient(withId("A"), withActiveFalse()).toUnqualifiedVersionless();
+		IIdType id2 = createPatient(withId("B"), withActiveTrue()).toUnqualifiedVersionless();
+
+		Parameters diff = ourClient
+			.operation()
+			.onServer()
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withParameter(Parameters.class, ProviderConstants.DIFF_FROM_PARAMETER, id1)
+			.andParameter(ProviderConstants.DIFF_TO_PARAMETER, id2)
+			.andParameter(ProviderConstants.DIFF_INCLUDE_META_PARAMETER, new BooleanType(true))
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(3, diff.getParameter().size());
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.id", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("A", extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		assertEquals("B", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+	}
+
+	@Test
+	public void testDifferentResources_Versioned() {
+		// Create and 2 updates
+		IIdType id1 = createPatient(withId("A"), withActiveTrue()).toUnqualifiedVersionless();
+		id1 = createPatient(withId(id1), withActiveTrue(), withFamily("SMITH")).toUnqualified();
+
+		IIdType id2 = createPatient(withId("B"), withActiveFalse()).toUnqualifiedVersionless();
+		id2 = createPatient(withId(id2), withActiveTrue(), withFamily("JONES")).toUnqualified();
+
+		Parameters diff = ourClient
+			.operation()
+			.onServer()
+			.named(ProviderConstants.DIFF_OPERATION_NAME)
+			.withParameter(Parameters.class, ProviderConstants.DIFF_FROM_PARAMETER, id1.withVersion("1"))
+			.andParameter(ProviderConstants.DIFF_TO_PARAMETER, id2.withVersion("1"))
+			.andParameter(ProviderConstants.DIFF_INCLUDE_META_PARAMETER, new BooleanType(true))
+			.execute();
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(diff));
+
+		assertEquals(3, diff.getParameter().size());
+
+		assertEquals("replace", extractPartValuePrimitive(diff, 0, "operation", "type"));
+		assertEquals("Patient.id", extractPartValuePrimitive(diff, 0, "operation", "path"));
+		assertEquals("A", extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		assertEquals("B", extractPartValuePrimitive(diff, 0, "operation", "value"));
+
+	}
+
+	@Test
+	public void testDifferentResources_DifferentTypes() {
+		try {
+			ourClient
+				.operation()
+				.onServer()
+				.named(ProviderConstants.DIFF_OPERATION_NAME)
+				.withParameter(Parameters.class, ProviderConstants.DIFF_FROM_PARAMETER, new IdType("Patient/123"))
+				.andParameter(ProviderConstants.DIFF_TO_PARAMETER, new IdType("Observation/456"))
+				.execute();
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("HTTP 400 Bad Request: Unable to diff two resources of different types", e.getMessage());
+		}
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/PatchProviderR4Test.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.MethodOutcome;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -8,6 +9,7 @@ import org.apache.http.client.methods.HttpPatch;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
 import org.junit.Test;
@@ -26,6 +28,81 @@ public class PatchProviderR4Test extends BaseResourceProviderR4Test {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(PatchProviderR4Test.class);
 
+	@Test
+	public void testFhirPatch() {
+		Patient patient = new Patient();
+		patient.setActive(true);
+		patient.addIdentifier().addExtension("http://foo", new StringType("abc"));
+		patient.addIdentifier().setSystem("sys").setValue("val");
+		IIdType id = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent operation = patch.addParameter();
+		operation.setName("operation");
+		operation
+			.addPart()
+			.setName("type")
+			.setValue(new CodeType("delete"));
+		operation
+			.addPart()
+			.setName("path")
+			.setValue(new StringType("Patient.identifier[0]"));
+
+		MethodOutcome outcome = ourClient
+			.patch()
+			.withFhirPatch(patch)
+			.withId(id)
+			.execute();
+
+		Patient resultingResource = (Patient) outcome.getResource();
+		assertEquals(1, resultingResource.getIdentifier().size());
+
+		resultingResource = ourClient.read().resource(Patient.class).withId(id).execute();
+		assertEquals(1, resultingResource.getIdentifier().size());
+	}
+
+	@Test
+	public void testFhirPatch_Transaction() throws Exception {
+		String methodName = "testFhirPatch_Transaction";
+		IIdType pid1;
+		{
+			Patient patient = new Patient();
+			patient.setActive(true);
+			patient.addIdentifier().setSystem("urn:system").setValue("0");
+			patient.addName().setFamily(methodName).addGiven("Joe");
+			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		Parameters patch = new Parameters();
+		Parameters.ParametersParameterComponent op = patch.addParameter().setName("operation");
+		op.addPart().setName("type").setValue(new CodeType("replace"));
+		op.addPart().setName("path").setValue(new CodeType("Patient.active"));
+		op.addPart().setName("value").setValue(new BooleanType(false));
+
+		Bundle input = new Bundle();
+		input.setType(Bundle.BundleType.TRANSACTION);
+		input.addEntry()
+			.setFullUrl(pid1.getValue())
+			.setResource(patch)
+			.getRequest().setUrl(pid1.getValue())
+			.setMethod(Bundle.HTTPVerb.PATCH);
+
+		HttpPost post = new HttpPost(ourServerBase);
+		String encodedRequest = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
+		ourLog.info("Request:\n{}", encodedRequest);
+		post.setEntity(new StringEntity(encodedRequest, ContentType.parse(Constants.CT_FHIR_JSON_NEW+ Constants.CHARSET_UTF8_CTSUFFIX)));
+		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			assertThat(responseString, containsString("\"resourceType\":\"Bundle\""));
+		}
+
+		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
+		assertEquals("2", newPt.getIdElement().getVersionIdPart());
+		assertEquals(false, newPt.getActive());
+	}
+
+
 	@Test
 	public void testPatchAddArray() throws IOException {
 		IIdType id;
@@ -121,7 +198,7 @@ public class PatchProviderR4Test extends BaseResourceProviderR4Test {
 
 		HttpPost post = new HttpPost(ourServerBase);
 		String encodedRequest = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
-		ourLog.info("Requet:\n{}", encodedRequest);
+		ourLog.info("Request:\n{}", encodedRequest);
 		post.setEntity(new StringEntity(encodedRequest, ContentType.parse(Constants.CT_FHIR_JSON_NEW+ Constants.CHARSET_UTF8_CTSUFFIX)));
 		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
 			assertEquals(200, response.getStatusLine().getStatusCode());
@@ -465,7 +542,45 @@ public class PatchProviderR4Test extends BaseResourceProviderR4Test {
 
 
 	@Test
-	public void testPatchInTransaction_InvalidContentType() throws Exception {
+	public void testPatchInTransaction_InvalidContentType_NonFhir() throws Exception {
+		String methodName = "testPatchUsingJsonPatch_Transaction";
+		IIdType pid1;
+		{
+			Patient patient = new Patient();
+			patient.setActive(true);
+			patient.addIdentifier().setSystem("urn:system").setValue("0");
+			patient.addName().setFamily(methodName).addGiven("Joe");
+			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String patchString = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
+		Binary patch = new Binary();
+		patch.setContentType("application/octet-stream");
+		patch.setContent(patchString.getBytes(Charsets.UTF_8));
+
+		Bundle input = new Bundle();
+		input.setType(Bundle.BundleType.TRANSACTION);
+		input.addEntry()
+			.setFullUrl(pid1.getValue())
+			.setResource(patch)
+			.getRequest().setUrl(pid1.getValue())
+			.setMethod(Bundle.HTTPVerb.PATCH);
+
+		HttpPost post = new HttpPost(ourServerBase);
+		post.setEntity(new StringEntity(myFhirCtx.newJsonParser().encodeResourceToString(input), ContentType.parse(Constants.CT_FHIR_JSON_NEW+ Constants.CHARSET_UTF8_CTSUFFIX)));
+		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
+			assertEquals(400, response.getStatusLine().getStatusCode());
+			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			assertThat(responseString, containsString("Invalid Content-Type for PATCH operation: application/octet-stream"));
+		}
+
+		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
+		assertEquals("1", newPt.getIdElement().getVersionIdPart());
+		assertEquals(true, newPt.getActive());
+	}
+
+	@Test
+	public void testPatchInTransaction_InvalidContentType_Fhir() throws Exception {
 		String methodName = "testPatchUsingJsonPatch_Transaction";
 		IIdType pid1;
 		{
@@ -494,12 +609,11 @@ public class PatchProviderR4Test extends BaseResourceProviderR4Test {
 		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-			assertThat(responseString, containsString("Invalid Content-Type for PATCH operation: application/fhir+json"));
+			assertThat(responseString, containsString("Binary PATCH detected with FHIR content type. FHIR Patch should use Parameters resource."));
 		}
 
 		Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
 		assertEquals("1", newPt.getIdElement().getVersionIdPart());
 		assertEquals(true, newPt.getActive());
 	}
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java

@@ -50,6 +50,7 @@ import java.time.Duration;
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.apache.commons.lang3.time.DateUtils.MILLIS_PER_SECOND;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.Assert.*;
@@ -152,7 +153,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		 * Server Interceptor
 		 */
 
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
 		assertEquals(RestOperationTypeEnum.TRANSACTION, myParamsCaptor.getAllValues().get(0).get(RestOperationTypeEnum.class));
 
 		verify(interceptor, times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_POST_PROCESSED), myParamsCaptor.capture());
@@ -182,7 +183,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 			assertThat(newIdString, startsWith(ourServerBase + "/Patient/"));
 		}
 
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
 		assertEquals(RestOperationTypeEnum.CREATE, myParamsCaptor.getValue().get(RestOperationTypeEnum.class));
 		assertEquals("Patient", myParamsCaptor.getValue().get(RequestDetails.class).getResource().getIdElement().getResourceType());
 
@@ -210,11 +211,11 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 
 		transaction(bundle);
 
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(2)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(2)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
 		assertEquals(RestOperationTypeEnum.CREATE, myParamsCaptor.getValue().get(RestOperationTypeEnum.class));
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_POST_PROCESSED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_POST_PROCESSED), myParamsCaptor.capture());
 
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(1)).invoke(eq(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(1)).invoke(eq(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED), myParamsCaptor.capture());
 	}
 
 	@Test
@@ -276,7 +277,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 			assertThat(newIdString, startsWith(ourServerBase + "/Patient/"));
 		}
 
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(1)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
 		assertEquals(RestOperationTypeEnum.CREATE, myParamsCaptor.getValue().get(RestOperationTypeEnum.class));
 
 		Patient patient = (Patient) myParamsCaptor.getValue().get(RequestDetails.class).getResource();
@@ -312,7 +313,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		entry.getRequest().setIfNoneExist("Patient?name=" + methodName);
 		transaction(bundle);
 
-		verify(interceptor, timeout(Duration.ofSeconds(10)).times(2)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10 * MILLIS_PER_SECOND).times(2)).invoke(eq(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED), myParamsCaptor.capture());
 		assertEquals(RestOperationTypeEnum.TRANSACTION, myParamsCaptor.getAllValues().get(0).get(RestOperationTypeEnum.class));
 		assertEquals(RestOperationTypeEnum.UPDATE, myParamsCaptor.getAllValues().get(1).get(RestOperationTypeEnum.class));
 		verify(interceptor, times(0)).invoke(eq(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED), any());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImplTest.java

@@ -84,7 +84,7 @@ public class SchedulerServiceImplTest {
 		ourLog.info("Fired {} times", CountingJob.ourCount);
 
 		await().until(() -> CountingJob.ourCount, greaterThan(3));
-		assertThat(CountingJob.ourCount, lessThan(20));
+		assertThat(CountingJob.ourCount, lessThan(50));
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/jsonpatch/JsonPatchUtilsTest.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.util.jsonpatch;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.BaseJpaTest;
+import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import org.hl7.fhir.r4.model.Observation;
 import org.junit.Test;

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

@@ -44,6 +44,9 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 
+	<logger name="org.springframework.test.context.cache" additivity="false" level="debug">
+		<appender-ref ref="STDOUT" />
+	</logger>
 
 	<root level="info">
 		<appender-ref ref="STDOUT" />

hapi-fhir-jpaserver-base/src/test/resources/spring.properties

@@ -0,0 +1 @@
+spring.test.context.cache.maxSize=2

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/ProviderConstants.java

@@ -48,4 +48,13 @@ public class ProviderConstants {
 	public static final String PARTITION_MANAGEMENT_PARTITION_NAME = "name";
 	public static final String PARTITION_MANAGEMENT_PARTITION_DESC = "description";
 
+	/**
+	 * Operation name: diff
+	 */
+	public static final String DIFF_OPERATION_NAME = "$diff";
+	public static final String DIFF_FROM_VERSION_PARAMETER = "fromVersion";
+
+	public static final String DIFF_FROM_PARAMETER = "from";
+	public static final String DIFF_TO_PARAMETER = "to";
+	public static final String DIFF_INCLUDE_META_PARAMETER = "includeMeta";
 }

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

@@ -248,11 +248,14 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry {
 			StopWatch sw = new StopWatch();
 
 			Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
-			for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
+			Set<Map.Entry<String, Map<String, RuntimeSearchParam>>> builtInSps = getBuiltInSearchParams().entrySet();
+			for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : builtInSps) {
 				for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
 					String nextResourceName = nextBuiltInEntry.getKey();
 					getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
 				}
+
+				ourLog.trace("Have {} built-in SPs for: {}", nextBuiltInEntry.getValue().size(), nextBuiltInEntry.getKey());
 			}
 
 			SearchParameterMap params = new SearchParameterMap();

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionActivatingSubscriber.java

@@ -83,7 +83,7 @@ public class SubscriptionActivatingSubscriber extends BaseSubscriberForSubscript
 		switch (payload.getOperationType()) {
 			case CREATE:
 			case UPDATE:
-				activateOrRegisterSubscriptionIfRequired(payload.getNewPayload(myFhirContext));
+				activateSubscriptionIfRequired(payload.getNewPayload(myFhirContext));
 				break;
 			case DELETE:
 			case MANUALLY_TRIGGERED:
@@ -93,7 +93,7 @@ public class SubscriptionActivatingSubscriber extends BaseSubscriberForSubscript
 
 	}
 
-	public boolean activateOrRegisterSubscriptionIfRequired(final IBaseResource theSubscription) {
+	public boolean activateSubscriptionIfRequired(final IBaseResource theSubscription) {
 		// Grab the value for "Subscription.channel.type" so we can see if this
 		// subscriber applies..
 		CanonicalSubscriptionChannelType subscriptionChannelType = mySubscriptionCanonicalizer.getChannelType(theSubscription);

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionLoader.java

@@ -20,13 +20,13 @@ package ca.uhn.fhir.jpa.subscription.match.registry;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.model.sched.HapiJob;
 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.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.retry.Retrier;
 import ca.uhn.fhir.jpa.subscription.match.matcher.subscriber.SubscriptionActivatingSubscriber;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -61,6 +61,8 @@ public class SubscriptionLoader {
 	private ISchedulerService mySchedulerService;
 	@Autowired
 	private SubscriptionActivatingSubscriber mySubscriptionActivatingInterceptor;
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
 
 	/**
 	 * Constructor
@@ -122,9 +124,12 @@ public class SubscriptionLoader {
 		synchronized (mySyncSubscriptionsLock) {
 			ourLog.debug("Starting sync subscriptions");
 			SearchParameterMap map = new SearchParameterMap();
-			map.add(Subscription.SP_STATUS, new TokenOrListParam()
+
-				.addOr(new TokenParam(null, Subscription.SubscriptionStatus.REQUESTED.toCode()))
+			if (mySearchParamRegistry.getActiveSearchParam("Subscription", "status") != null) {
-				.addOr(new TokenParam(null, Subscription.SubscriptionStatus.ACTIVE.toCode())));
+				map.add(Subscription.SP_STATUS, new TokenOrListParam()
+					.addOr(new TokenParam(null, Subscription.SubscriptionStatus.REQUESTED.toCode()))
+					.addOr(new TokenParam(null, Subscription.SubscriptionStatus.ACTIVE.toCode())));
+			}
 			map.setLoadSynchronousUpTo(SubscriptionConstants.MAX_SUBSCRIPTION_RESULTS);
 
 			IFhirResourceDao subscriptionDao = myDaoRegistry.getSubscriptionDao();
@@ -146,7 +151,7 @@ public class SubscriptionLoader {
 				String nextId = resource.getIdElement().getIdPart();
 				allIds.add(nextId);
 
-				boolean activated = mySubscriptionActivatingInterceptor.activateOrRegisterSubscriptionIfRequired(resource);
+				boolean activated = mySubscriptionActivatingInterceptor.activateSubscriptionIfRequired(resource);
 				if (activated) {
 					activatedCount++;
 				}

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/subscriber/websocket/WebsocketConnectionValidatorTest.java

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
 import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelFactory;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
@@ -63,6 +64,8 @@ public class WebsocketConnectionValidatorTest {
 	ISchedulerService mySchedulerService;
 	@MockBean
 	SubscriptionRegistry mySubscriptionRegistry;
+	@MockBean
+	ISearchParamRegistry mySearchParamRegistry;
 
 	@Autowired
 	WebsocketConnectionValidator myWebsocketConnectionValidator;

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

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
+import ca.uhn.fhir.jpa.provider.DiffProvider;
 import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.provider.GraphQLProvider;
@@ -264,6 +265,11 @@ public class TestRestfulServer extends RestfulServer {
 		 */
 		registerProvider(myAppCtx.getBean(BulkDataExportProvider.class));
 
+		/*
+		 * $diff operation
+		 */
+		registerProvider(myAppCtx.getBean(DiffProvider.class));
+
 	}
 
 	/**

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhirtest.config;
 
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -69,6 +70,11 @@ public class CommonConfig {
 		return retVal;
 	}
 
+	@Bean
+	public PartitionSettings partitionSettings() {
+		return new PartitionSettings();
+	}
+
 	public static boolean isLocalTestMode() {
 		return "true".equalsIgnoreCase(System.getProperty("testmode.local"));
 	}

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -67,6 +67,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setFetchSizeDefaultMaximum(10000);
 		retVal.setWebsocketContextPath("/");
 		retVal.setFilterParameterEnabled(true);
+		retVal.setDefaultSearchParamsCanBeOverridden(false);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -66,6 +66,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setReindexThreadCount(1);
 		retVal.setExpungeEnabled(true);
 		retVal.setFilterParameterEnabled(true);
+		retVal.setDefaultSearchParamsCanBeOverridden(false);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -66,6 +66,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		retVal.setFetchSizeDefaultMaximum(10000);
 		retVal.setExpungeEnabled(true);
 		retVal.setFilterParameterEnabled(true);
+		retVal.setDefaultSearchParamsCanBeOverridden(false);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -66,6 +66,7 @@ public class TestR5Config extends BaseJavaConfigR5 {
 		retVal.setFetchSizeDefaultMaximum(10000);
 		retVal.setExpungeEnabled(true);
 		retVal.setFilterParameterEnabled(true);
+		retVal.setDefaultSearchParamsCanBeOverridden(false);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/test/java/ca/uhn/fhirtest/UhnFhirTestApp.java

@@ -28,6 +28,8 @@ public class UhnFhirTestApp {
 		System.setProperty("fhir.lucene.location.dstu3", "./target/testlucene_dstu3");
 		System.setProperty("fhir.db.location.r4", "./target/fhirtest_r4");
 		System.setProperty("fhir.lucene.location.r4", "./target/testlucene_r4");
+		System.setProperty("fhir.db.location.r5", "./target/fhirtest_r5");
+		System.setProperty("fhir.lucene.location.r5", "./target/testlucene_r5");
 		System.setProperty("fhir.db.location.tdl2", "./target/testdb_tdl2");
 		System.setProperty("fhir.lucene.location.tdl2", "./target/testlucene_tdl2");
 		System.setProperty("fhir.db.location.tdl3", "./target/testdb_tdl3");
@@ -36,6 +38,7 @@ public class UhnFhirTestApp {
 		System.setProperty("fhir.baseurl.dstu1", base.replace("Dstu2", "Dstu1"));
 		System.setProperty("fhir.baseurl.dstu3", base.replace("Dstu2", "Dstu3"));
 		System.setProperty("fhir.baseurl.r4", base.replace("Dstu2", "R4"));
+		System.setProperty("fhir.baseurl.r5", base.replace("Dstu2", "R5"));
 		System.setProperty("fhir.baseurl.tdl2", base.replace("baseDstu2", "testDataLibraryDstu2"));
 		System.setProperty("fhir.baseurl.tdl3", base.replace("baseDstu2", "testDataLibraryStu3"));
 		System.setProperty("fhir.tdlpass", "aa,bb");
@@ -48,8 +51,8 @@ public class UhnFhirTestApp {
 		WebAppContext root = new WebAppContext();
 
 		root.setContextPath("/");
-		root.setDescriptor("src/main/webapp/WEB-INF/web.xml");
+		root.setDescriptor("hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/web.xml");
-		root.setResourceBase("target/hapi-fhir-jpaserver");
+		root.setResourceBase("hapi-fhir-jpaserver-uhnfhirtest/target/hapi-fhir-jpaserver");
 
 		root.setParentLoaderPriority(true);
 

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

@@ -59,6 +59,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import javax.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.io.Writer;
@@ -341,26 +342,21 @@ public class RestfulServerUtils {
 		return b.toString();
 	}
 
-	/**
+	@Nullable
-	 * @TODO: this method is only called from one place and should be removed anyway
+	public static EncodingEnum determineRequestEncodingNoDefault(RequestDetails theReq) {
-	 */
+		return determineRequestEncodingNoDefault(theReq, false);
-	public static EncodingEnum determineRequestEncoding(RequestDetails theReq) {
-		EncodingEnum retVal = determineRequestEncodingNoDefault(theReq);
-		if (retVal != null) {
-			return retVal;
-		}
-		return EncodingEnum.XML;
 	}
 
-	public static EncodingEnum determineRequestEncodingNoDefault(RequestDetails theReq) {
+	@Nullable
-		ResponseEncoding retVal = determineRequestEncodingNoDefaultReturnRE(theReq);
+	public static EncodingEnum determineRequestEncodingNoDefault(RequestDetails theReq, boolean theStrict) {
+		ResponseEncoding retVal = determineRequestEncodingNoDefaultReturnRE(theReq, theStrict);
 		if (retVal == null) {
 			return null;
 		}
 		return retVal.getEncoding();
 	}
 
-	private static ResponseEncoding determineRequestEncodingNoDefaultReturnRE(RequestDetails theReq) {
+	private static ResponseEncoding determineRequestEncodingNoDefaultReturnRE(RequestDetails theReq, boolean theStrict) {
 		ResponseEncoding retVal = null;
 		List<String> headers = theReq.getHeaders(Constants.HEADER_CONTENT_TYPE);
 		if (headers != null) {
@@ -378,7 +374,12 @@ public class RestfulServerUtils {
 								nextPart = nextPart.substring(0, scIdx);
 							}
 							nextPart = nextPart.trim();
-							EncodingEnum encoding = EncodingEnum.forContentType(nextPart);
+							EncodingEnum encoding;
+							if (theStrict) {
+								encoding = EncodingEnum.forContentTypeStrict(nextPart);
+							} else {
+								encoding = EncodingEnum.forContentType(nextPart);
+							}
 							if (encoding != null) {
 								retVal = new ResponseEncoding(theReq.getServer().getFhirContext(), encoding, nextPart);
 								break;
@@ -512,7 +513,7 @@ public class RestfulServerUtils {
 		 * has a Content-Type header but not an Accept header)
 		 */
 		if (retVal == null) {
-			retVal = determineRequestEncodingNoDefaultReturnRE(theReq);
+			retVal = determineRequestEncodingNoDefaultReturnRE(theReq, strict);
 		}
 
 		return retVal;

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

@@ -57,7 +57,7 @@ public class ResponseSizeCapturingInterceptor {
 	public static final String RESPONSE_RESULT_KEY = ResponseSizeCapturingInterceptor.class.getName() + "_RESPONSE_RESULT_KEY";
 
 	private static final String COUNTING_WRITER_KEY = ResponseSizeCapturingInterceptor.class.getName() + "_COUNTING_WRITER_KEY";
-	private List<Consumer<Result>> myConsumers = new ArrayList<>();
+	private final List<Consumer<Result>> myConsumers = new ArrayList<>();
 
 	@Hook(Pointcut.SERVER_OUTGOING_WRITER_CREATED)
 	public Writer capture(RequestDetails theRequestDetails, Writer theWriter) {

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplOp.java

@@ -294,7 +294,7 @@ class RuleImplOp extends BaseRule /* implements IAuthRule */ {
 							operation = RestOperationTypeEnum.DELETE;
 						} else if (nextPart.getRequestType() == RequestTypeEnum.PATCH) {
 							operation = RestOperationTypeEnum.PATCH;
-						} else if (nextPart.getRequestType() == null && theRequestDetails.getServer().getFhirContext().getVersion().getVersion() == FhirVersionEnum.DSTU3 && BundleUtil.isDstu3TransactionPatch(nextPart.getResource())) {
+						} else if (nextPart.getRequestType() == null && theRequestDetails.getServer().getFhirContext().getVersion().getVersion() == FhirVersionEnum.DSTU3 && BundleUtil.isDstu3TransactionPatch(theRequestDetails.getFhirContext(), nextPart.getResource())) {
 							// This is a workaround for the fact that there is no PATCH verb in DSTU3's bundle entry verb type ValueSet.
 							// See BundleUtil#isDstu3TransactionPatch
 							operation = RestOperationTypeEnum.PATCH;

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

@@ -197,7 +197,8 @@ public class MethodUtil {
 							throw new ConfigurationException(b.toString());
 						}
 						boolean methodIsOperation = theMethod.getAnnotation(Operation.class) != null;
-						param = new ResourceParameter((Class<? extends IBaseResource>) parameterType, theProvider, mode, methodIsOperation);
+						boolean methodIsPatch = theMethod.getAnnotation(Patch.class) != null;
+						param = new ResourceParameter((Class<? extends IBaseResource>) parameterType, theProvider, mode, methodIsOperation, methodIsPatch);
 					} else if (nextAnnotation instanceof IdParam) {
 						param = new NullParameter();
 					} else if (nextAnnotation instanceof ServerBase) {

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.rest.server.method;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 /*
  * #%L
@@ -45,7 +46,15 @@ class PatchTypeParameter implements IParameter {
 
 	public static PatchTypeEnum getTypeForRequestOrThrowInvalidRequestException(RequestDetails theRequest) {
 		String contentTypeAll = defaultString(theRequest.getHeader(Constants.HEADER_CONTENT_TYPE));
-		return PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(contentTypeAll);
+
+		int semicolonIndex = contentTypeAll.indexOf(';');
+		if (semicolonIndex > 0) {
+			contentTypeAll = contentTypeAll.substring(0, semicolonIndex);
+		}
+
+		contentTypeAll = trim(contentTypeAll);
+
+		return PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(theRequest.getFhirContext(), contentTypeAll);
 	}
 
 }

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.IResourceProvider;
@@ -53,17 +54,17 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class ResourceParameter implements IParameter {
 
-	private final boolean myMethodIsOperation;
+	private final boolean myMethodIsOperationOrPatch;
 	private Mode myMode;
 	private Class<? extends IBaseResource> myResourceType;
 
-	public ResourceParameter(Class<? extends IBaseResource> theParameterType, Object theProvider, Mode theMode, boolean theMethodIsOperation) {
+	public ResourceParameter(Class<? extends IBaseResource> theParameterType, Object theProvider, Mode theMode, boolean theMethodIsOperation, boolean theMethodIsPatch) {
 		Validate.notNull(theParameterType, "theParameterType can not be null");
 		Validate.notNull(theMode, "theMode can not be null");
 
 		myResourceType = theParameterType;
 		myMode = theMode;
-		myMethodIsOperation = theMethodIsOperation;
+		myMethodIsOperationOrPatch = theMethodIsOperation || theMethodIsPatch;
 
 		Class<? extends IBaseResource> providerResourceType = null;
 		if (theProvider instanceof IResourceProvider) {
@@ -107,7 +108,7 @@ public class ResourceParameter implements IParameter {
 			case RESOURCE:
 			default:
 				Class<? extends IBaseResource> resourceTypeToParse = myResourceType;
-				if (myMethodIsOperation) {
+				if (myMethodIsOperationOrPatch) {
 					// Operations typically have a Parameters resource as the body
 					resourceTypeToParse = null;
 				}
@@ -223,7 +224,15 @@ public class ResourceParameter implements IParameter {
 			}
 		}
 
-		if (retVal == null) {
+		boolean isNonFhirPatch = false;
+		if (theRequest.getRequestType() == RequestTypeEnum.PATCH) {
+			EncodingEnum requestEncoding = RestfulServerUtils.determineRequestEncodingNoDefault(theRequest, true);
+			if (requestEncoding == null) {
+				isNonFhirPatch = true;
+			}
+		}
+
+		if (retVal == null && !isNonFhirPatch) {
 			retVal = loadResourceFromRequest(theRequest, theMethodBinding, theResourceType);
 		}
 

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

@@ -322,7 +322,7 @@ public class SearchParameter extends BaseQueryParameter {
 		} else if (HasParam.class.isAssignableFrom(theType)) {
 			myParamType = RestSearchParameterTypeEnum.STRING;
 		} else {
-			throw new ConfigurationException("Unknown search parameter theType: " + theType);
+			throw new ConfigurationException("Unknown search parameter type: " + theType);
 		}
 
 		// NB: Once this is enabled, we should return true from handlesMissing if

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/rest/server/PatchDstu2_1Test.java

@@ -123,7 +123,7 @@ public class PatchDstu2_1Test {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(400, status.getStatusLine().getStatusCode());
-			assertEquals("<OperationOutcome xmlns=\"http://hl7.org/fhir\"><issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"Invalid Content-Type for PATCH operation: text/plain; charset=UTF-8\"/></issue></OperationOutcome>", responseContent);
+			assertEquals("<OperationOutcome xmlns=\"http://hl7.org/fhir\"><issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"Invalid Content-Type for PATCH operation: text/plain\"/></issue></OperationOutcome>", responseContent);
 		} finally {
 			IOUtils.closeQuietly(status.getEntity().getContent());
 		}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu3Test.java

@@ -201,6 +201,37 @@ public class GenericClientDstu3Test {
 		assertThat(oo.getText().getDivAsString(), containsString("OK!"));
 	}
 
+	@Test
+	public void testPatchByIdNoType() {
+
+		String patch = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+		try {
+			client
+				.patch()
+				.withBody(patch)
+				.withId(new IdType("234"))
+				.execute();
+			fail();
+		} catch (NullPointerException e) {
+			assertEquals("theId must not be blank and must contain a resource type and ID (e.g. \"Patient/123\"), found: 234", e.getMessage());
+		}
+
+		try {
+			client
+				.patch()
+				.withBody(patch)
+				.withId("234")
+				.execute();
+			fail();
+		} catch (NullPointerException e) {
+			assertEquals("theId must not be blank and must contain a resource type and ID (e.g. \"Patient/123\"), found: 234", e.getMessage());
+		}
+
+	}
+
+
 	@Test
 	public void testPatchJsonByConditionalString() throws Exception {
 		OperationOutcome conf = new OperationOutcome();

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/PatchServerDstu3Test.java

@@ -157,7 +157,7 @@ public class PatchServerDstu3Test {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(400, status.getStatusLine().getStatusCode());
-			assertEquals("<OperationOutcome xmlns=\"http://hl7.org/fhir\"><issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"Invalid Content-Type for PATCH operation: text/plain; charset=UTF-8\"/></issue></OperationOutcome>", responseContent);
+			assertEquals("<OperationOutcome xmlns=\"http://hl7.org/fhir\"><issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"Invalid Content-Type for PATCH operation: text/plain\"/></issue></OperationOutcome>", responseContent);
 		} finally {
 			IOUtils.closeQuietly(status.getEntity().getContent());
 		}

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

@@ -17,30 +17,18 @@ import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
-import org.mockito.Mockito;
 import org.mockito.junit.MockitoJUnitRunner;
 
-import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Consumer;
-import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
-import static org.awaitility.Awaitility.await;
+import static org.apache.commons.lang3.time.DateUtils.MILLIS_PER_SECOND;
-import static org.awaitility.Awaitility.waitAtMost;
-import static org.hamcrest.CoreMatchers.not;
-import static org.hamcrest.Matchers.hasSize;
-import static org.hamcrest.Matchers.matchesPattern;
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
 import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.atMost;
 import static org.mockito.Mockito.doAnswer;
 import static org.mockito.Mockito.timeout;
-import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
 @RunWith(MockitoJUnitRunner.class)
@@ -97,7 +85,7 @@ public class ResponseSizeCapturingInterceptorTest {
 		resource = ourServerRule.getFhirClient().read().resource(Patient.class).withId(id).execute();
 		assertEquals(true, resource.getActive());
 
-		verify(myConsumer, timeout(Duration.ofSeconds(10)).times(1)).accept(myResultCaptor.capture());
+		verify(myConsumer, timeout(10 * MILLIS_PER_SECOND).times(1)).accept(myResultCaptor.capture());
 		assertEquals(100, myResultCaptor.getValue().getWrittenChars());
 	}
 

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java

@@ -106,13 +106,15 @@ public interface ITestDataBuilder {
 		};
 	}
 
-	default <T extends IBaseResource> Consumer<T> withId(String theId) {
+	default Consumer<IBaseResource> withId(String theId) {
-		assertThat(theId, matchesPattern("[a-zA-Z0-9-]+"));
+		return t -> {
-		return t -> t.setId(theId);
+			assertThat(theId, matchesPattern("[a-zA-Z0-9]+"));
+			t.setId(theId);
+		};
 	}
 
-	default <T extends IBaseResource> Consumer<T> withId(IIdType theId) {
+	default Consumer<IBaseResource> withId(IIdType theId) {
-		return withId(theId.getIdPart());
+		return t -> t.setId(theId.toUnqualifiedVersionless());
 	}
 
 	default Consumer<IBaseResource> withTag(String theSystem, String theCode) {
@@ -153,19 +155,6 @@ public interface ITestDataBuilder {
 		};
 	}
 
-
-	/**
-	 * Name chosen to avoid potential for conflict. This is an internal API to this interface.
-	 */
-	static void __setPrimitiveChild(FhirContext theFhirContext, IBaseResource theTarget, String theElementName, String theElementType, String theValue) {
-		RuntimeResourceDefinition def = theFhirContext.getResourceDefinition(theTarget.getClass());
-		BaseRuntimeChildDefinition activeChild = def.getChildByName(theElementName);
-
-		IPrimitiveType<?> booleanType = (IPrimitiveType<?>) activeChild.getChildByName(theElementName).newInstance();
-		booleanType.setValueAsString(theValue);
-		activeChild.getMutator().addValue(theTarget, booleanType);
-	}
-
 	/**
 	 * Users of this API must implement this method
 	 */
@@ -181,5 +170,17 @@ public interface ITestDataBuilder {
 	 */
 	FhirContext getFhirContext();
 
+	/**
+	 * Name chosen to avoid potential for conflict. This is an internal API to this interface.
+	 */
+	static void __setPrimitiveChild(FhirContext theFhirContext, IBaseResource theTarget, String theElementName, String theElementType, String theValue) {
+		RuntimeResourceDefinition def = theFhirContext.getResourceDefinition(theTarget.getClass());
+		BaseRuntimeChildDefinition activeChild = def.getChildByName(theElementName);
+
+		IPrimitiveType<?> booleanType = (IPrimitiveType<?>) activeChild.getChildByName(theElementName).newInstance();
+		booleanType.setValueAsString(theValue);
+		activeChild.getMutator().addValue(theTarget, booleanType);
+	}
+
 
 }

pom.xml

@@ -870,10 +870,15 @@
 				<artifactId>commons-csv</artifactId>
 				<version>1.7</version>
 			</dependency>
+			<dependency>
+				<groupId>org.hl7.fhir.testcases</groupId>
+				<artifactId>fhir-test-cases</artifactId>
+				<version>1.1.14-SNAPSHOT</version> 
+			</dependency>
 			<dependency>
 				<groupId>org.jetbrains</groupId>
 				<artifactId>annotations</artifactId>
-				<version>17.0.0</version>
+				<version>19.0.0</version>
 			</dependency>
 			<dependency>
 				<groupId>commons-io</groupId>
@@ -1377,12 +1382,12 @@
 			<dependency>
 				<groupId>org.mockito</groupId>
 				<artifactId>mockito-core</artifactId>
-				<version>3.2.0</version>
+				<version>3.3.3</version>
 			</dependency>
 			<dependency>
 				<groupId>org.postgresql</groupId>
 				<artifactId>postgresql</artifactId>
-				<version>42.2.10</version>
+				<version>42.2.12</version>
 			</dependency>
 			<dependency>
 				<groupId>org.quartz-scheduler</groupId>