merge master

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.3.0-PRE5-SNAPSHOT</version>
+		 <version>6.3.2-SNAPSHOT</version>
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -22,10 +22,13 @@ package ca.uhn.fhir.context.support;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.parser.LenientErrorHandler;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.ClasspathUtil;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
@@ -321,6 +324,19 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		} else {
 			ourLog.warn("Unable to load resource: {}", theClasspath);
 		}
+
+		// Load built-in system
+
+		if (myCtx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
+			String storageCodeEnum = ClasspathUtil.loadResource("org/hl7/fhir/common/hapi/validation/support/HapiFhirStorageResponseCode.json");
+			IBaseResource storageCodeCodeSystem = myCtx.newJsonParser().setParserErrorHandler(new LenientErrorHandler()).parseResource(storageCodeEnum);
+			String url = myCtx.newTerser().getSinglePrimitiveValueOrNull(storageCodeCodeSystem, "url");
+			theCodeSystems.put(url, storageCodeCodeSystem);
+		}
+
+
+
+
 	}
 
 	private void loadStructureDefinitions(Map<String, IBaseResource> theCodeSystems, String theClasspath) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ICodingEnum.java

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.model.api;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 interface ICodingEnum {
+
+	String getCode();
+	String getSystem();
+	String getDisplay();
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.io.Serializable;
@@ -64,6 +65,23 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  */
 public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
+	// TODO: JA - Replace all of the various other get/put methods in subclasses with just using the two that are here
+	public T get(IBaseResource theResource) {
+		if (theResource instanceof IAnyResource) {
+			return (T) theResource.getUserData(name());
+		} else {
+			return (T) ((IResource)theResource).getResourceMetadata().get(this);
+		}
+	}
+
+	public void put(IBaseResource theResource, T theValue) {
+		if (theResource instanceof IAnyResource) {
+			theResource.setUserData(name(), theValue);
+		} else {
+			((IResource)theResource).getResourceMetadata().put(this, theValue);
+		}
+	}
+
 	/**
 	 * If present and populated with a date/time (as an instance of {@link InstantDt}), this value is an indication that the resource is in the deleted state. This key is only used in a limited number
 	 * of scenarios, such as POSTing transaction bundles to a server, or returning resource history.
@@ -71,29 +89,19 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 * Values for this key are of type <b>{@link InstantDt}</b>
 	 * </p>
 	 */
-	public static final ResourceMetadataKeySupportingAnyResource<InstantDt, IPrimitiveType<Date>> DELETED_AT = new ResourceMetadataKeySupportingAnyResource<InstantDt, IPrimitiveType<Date>>("DELETED_AT") {
+	public static final ResourceMetadataKeyEnum<IPrimitiveType<Date>> DELETED_AT = new ResourceMetadataKeyEnum<>("DELETED_AT") {
 		private static final long serialVersionUID = 1L;
 
 		@Override
-		public InstantDt get(IResource theResource) {
+		public IPrimitiveType<Date> get(IResource theResource) {
-			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), DELETED_AT);
+			return (IPrimitiveType<Date>) theResource.getResourceMetadata().get(this);
-		}
-
-		@SuppressWarnings("unchecked")
-		@Override
-		public IPrimitiveType<Date> get(IAnyResource theResource) {
-			return (IPrimitiveType<Date>) theResource.getUserData(DELETED_AT.name());
 		}
 
 		@Override
-		public void put(IResource theResource, InstantDt theObject) {
+		public void put(IResource theResource, IPrimitiveType<Date> theObject) {
-			theResource.getResourceMetadata().put(DELETED_AT, theObject);
+			theResource.getResourceMetadata().put(this, theObject);
 		}
 
-		@Override
-		public void put(IAnyResource theResource, IPrimitiveType<Date> theObject) {
-			theResource.setUserData(DELETED_AT.name(), theObject);
-		}
 	};
 
 	/**

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/StorageResponseCodeEnum.java

@@ -0,0 +1,72 @@
+package ca.uhn.fhir.model.api;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+
+/**
+ * This enum contains the allowable codes in the HAPI FHIR defined
+ * codesystem: https://hapifhir.io/fhir/CodeSystem/hapi-fhir-storage-response-code
+ *
+ * This is used in CRUD response OperationOutcome resources.
+ */
+public enum StorageResponseCodeEnum implements ICodingEnum {
+
+	SUCCESSFUL_CREATE("Create succeeded."),
+	SUCCESSFUL_CREATE_NO_CONDITIONAL_MATCH("Conditional create succeeded: no existing resource matched the conditional URL."),
+	SUCCESSFUL_CREATE_WITH_CONDITIONAL_MATCH("Conditional create succeeded: an existing resource matched the conditional URL so no action was taken."),
+	SUCCESSFUL_UPDATE("Update succeeded."),
+	SUCCESSFUL_UPDATE_AS_CREATE("Update as create succeeded."),
+	SUCCESSFUL_UPDATE_NO_CHANGE("Update succeeded: No changes were detected so no action was taken."),
+	SUCCESSFUL_UPDATE_NO_CONDITIONAL_MATCH("Conditional update succeeded: no existing resource matched the conditional URL so a new resource was created."),
+	SUCCESSFUL_UPDATE_WITH_CONDITIONAL_MATCH("Conditional update succeeded: an existing resource matched the conditional URL and was updated."),
+	SUCCESSFUL_UPDATE_WITH_CONDITIONAL_MATCH_NO_CHANGE("Conditional update succeeded: an existing resource matched the conditional URL and was updated, but no changes were detected so no action was taken."),
+	SUCCESSFUL_DELETE("Delete succeeded."),
+	SUCCESSFUL_DELETE_ALREADY_DELETED("Delete succeeded: Resource was already deleted so no action was taken."),
+	SUCCESSFUL_DELETE_NOT_FOUND("Delete succeeded: No existing resource was found so no action was taken."),
+
+	SUCCESSFUL_PATCH("Patch succeeded."),
+
+	SUCCESSFUL_PATCH_NO_CHANGE("Patch succeeded: No changes were detected so no action was taken."),
+	SUCCESSFUL_CONDITIONAL_PATCH("Conditional patch succeeded."),
+	SUCCESSFUL_CONDITIONAL_PATCH_NO_CHANGE("Conditional patch succeeded: No changes were detected so no action was taken.");
+
+	public static final String SYSTEM = "https://hapifhir.io/fhir/CodeSystem/hapi-fhir-storage-response-code";
+
+	private final String myDisplay;
+
+	StorageResponseCodeEnum(String theDisplay) {
+		myDisplay = theDisplay;
+	}
+
+	@Override
+	public String getCode() {
+		return name();
+	}
+
+	@Override
+	public String getSystem() {
+		return SYSTEM;
+	}
+
+	@Override
+	public String getDisplay() {
+		return myDisplay;
+	}
+}

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

@@ -29,9 +29,12 @@ import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
+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 javax.annotation.Nonnull;
 import java.util.Objects;
 
 /**
@@ -40,7 +43,7 @@ import java.util.Objects;
  * (method and search).
  *
  * <p>
- *
+ * <p>
  * This is not yet complete, and doesn't support all FHIR features. <b>USE WITH CAUTION</b> as the API
  * may change.
  *
@@ -101,10 +104,8 @@ public class BundleBuilder {
 	/**
 	 * Sets the specified primitive field on the bundle with the value provided.
 	 *
-	 * @param theFieldName
+	 * @param theFieldName  Name of the primitive field.
-	 * 		Name of the primitive field.
+	 * @param theFieldValue Value of the field to be set.
-	 * @param theFieldValue
-	 * 		Value of the field to be set.
 	 */
 	public BundleBuilder setBundleField(String theFieldName, String theFieldValue) {
 		BaseRuntimeChildDefinition typeChild = myBundleDef.getChildByName(theFieldName);
@@ -119,12 +120,9 @@ public class BundleBuilder {
 	/**
 	 * Sets the specified primitive field on the search entry with the value provided.
 	 *
-	 * @param theSearch
+	 * @param theSearch     Search part of the entry
-	 * 		Search part of the entry
+	 * @param theFieldName  Name of the primitive field.
-	 * @param theFieldName
+	 * @param theFieldValue Value of the field to be set.
-	 * 		Name of the primitive field.
-	 * @param theFieldValue
-	 * 		Value of the field to be set.
 	 */
 	public BundleBuilder setSearchField(IBase theSearch, String theFieldName, String theFieldValue) {
 		BaseRuntimeChildDefinition typeChild = mySearchDef.getChildByName(theFieldName);
@@ -144,6 +142,37 @@ public class BundleBuilder {
 		return this;
 	}
 
+	/**
+	 * Adds a FHIRPatch patch bundle to the transaction
+	 * @param theTarget The target resource ID to patch
+	 * @param thePatch The FHIRPath Parameters resource
+	 * @since 6.3.0
+	 */
+	public PatchBuilder addTransactionFhirPatchEntry(IIdType theTarget, IBaseParameters thePatch) {
+		Validate.notNull(theTarget, "theTarget must not be null");
+		Validate.notBlank(theTarget.getResourceType(), "theTarget must contain a resource type");
+		Validate.notBlank(theTarget.getIdPart(), "theTarget must contain an ID");
+
+		IPrimitiveType<?> url = addAndPopulateTransactionBundleEntryRequest(thePatch, theTarget.getValue(), theTarget.toUnqualifiedVersionless().getValue(), "PATCH");
+
+		return new PatchBuilder(url);
+	}
+
+	/**
+	 * Adds a FHIRPatch patch bundle to the transaction. This method is intended for conditional PATCH operations. If you
+	 * know the ID of the resource you wish to patch, use {@link #addTransactionFhirPatchEntry(IIdType, IBaseParameters)}
+	 * instead.
+	 * 
+	 * @param thePatch The FHIRPath Parameters resource
+	 * @since 6.3.0
+	 * @see #addTransactionFhirPatchEntry(IIdType, IBaseParameters)
+	 */
+	public PatchBuilder addTransactionFhirPatchEntry(IBaseParameters thePatch) {
+		IPrimitiveType<?> url = addAndPopulateTransactionBundleEntryRequest(thePatch, null, null, "PATCH");
+
+		return new PatchBuilder(url);
+	}
+
 	/**
 	 * Adds an entry containing an update (PUT) request.
 	 * Also sets the Bundle.type value to "transaction" if it is not already set.
@@ -151,22 +180,39 @@ public class BundleBuilder {
 	 * @param theResource The resource to update
 	 */
 	public UpdateBuilder addTransactionUpdateEntry(IBaseResource theResource) {
+		Validate.notNull(theResource, "theResource must not be null");
+
+		IIdType id = theResource.getIdElement();
+		if (id.hasIdPart() && !id.hasResourceType()) {
+			String resourceType = myContext.getResourceType(theResource);
+			id = id.withResourceType(resourceType);
+		}
+
+		String requestUrl = id.toUnqualifiedVersionless().getValue();
+		String fullUrl = id.getValue();
+		String verb = "PUT";
+
+		IPrimitiveType<?> url = addAndPopulateTransactionBundleEntryRequest(theResource, fullUrl, requestUrl, verb);
+
+		return new UpdateBuilder(url);
+	}
+
+	@Nonnull
+	private IPrimitiveType<?> addAndPopulateTransactionBundleEntryRequest(IBaseResource theResource, String theFullUrl, String theRequestUrl, String theHttpVerb) {
 		setBundleField("type", "transaction");
 
-		IBase request = addEntryAndReturnRequest(theResource);
+		IBase request = addEntryAndReturnRequest(theResource, theFullUrl);
 
 		// Bundle.entry.request.url
 		IPrimitiveType<?> url = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		String resourceType = myContext.getResourceType(theResource);
+		url.setValueAsString(theRequestUrl);
-		url.setValueAsString(theResource.getIdElement().toUnqualifiedVersionless().withResourceType(resourceType).getValue());
 		myEntryRequestUrlChild.getMutator().setValue(request, url);
 
-		// Bundle.entry.request.url
+		// Bundle.entry.request.method
 		IPrimitiveType<?> method = (IPrimitiveType<?>) myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
-		method.setValueAsString("PUT");
+		method.setValueAsString(theHttpVerb);
 		myEntryRequestMethodChild.getMutator().setValue(request, method);
-
+		return url;
-		return new UpdateBuilder(url);
 	}
 
 	/**
@@ -178,7 +224,7 @@ public class BundleBuilder {
 	public CreateBuilder addTransactionCreateEntry(IBaseResource theResource) {
 		setBundleField("type", "transaction");
 
-		IBase request = addEntryAndReturnRequest(theResource);
+		IBase request = addEntryAndReturnRequest(theResource, theResource.getIdElement().getValue());
 
 		String resourceType = myContext.getResourceType(theResource);
 
@@ -198,15 +244,30 @@ public class BundleBuilder {
 	/**
 	 * Adds an entry containing a delete (DELETE) request.
 	 * Also sets the Bundle.type value to "transaction" if it is not already set.
-	 *
+	 * <p>
 	 * Note that the resource is only used to extract its ID and type, and the body of the resource is not included in the entry,
 	 *
 	 * @param theResource The resource to delete.
 	 */
-	public void addTransactionDeleteEntry(IBaseResource theResource) {
+	public DeleteBuilder addTransactionDeleteEntry(IBaseResource theResource) {
 		String resourceType = myContext.getResourceType(theResource);
 		String idPart = theResource.getIdElement().toUnqualifiedVersionless().getIdPart();
-		addTransactionDeleteEntry(resourceType, idPart);
+		return addTransactionDeleteEntry(resourceType, idPart);
+	}
+
+	/**
+	 * Adds an entry containing a delete (DELETE) request.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 * <p>
+	 * Note that the resource is only used to extract its ID and type, and the body of the resource is not included in the entry,
+	 *
+	 * @param theResourceId The resource ID to delete.
+	 * @return
+	 */
+	public DeleteBuilder addTransactionDeleteEntry(IIdType theResourceId) {
+		String resourceType = theResourceId.getResourceType();
+		String idPart = theResourceId.getIdPart();
+		return addTransactionDeleteEntry(resourceType, idPart);
 	}
 
 	/**
@@ -214,24 +275,45 @@ public class BundleBuilder {
 	 * Also sets the Bundle.type value to "transaction" if it is not already set.
 	 *
 	 * @param theResourceType The type resource to delete.
-	 * @param theIdPart  the ID of the resource to delete.
+	 * @param theIdPart       the ID of the resource to delete.
 	 */
-	public void addTransactionDeleteEntry(String theResourceType, String theIdPart) {
+	public DeleteBuilder addTransactionDeleteEntry(String theResourceType, String theIdPart) {
 		setBundleField("type", "transaction");
-		IBase request = addEntryAndReturnRequest();
 		IdDt idDt = new IdDt(theIdPart);
-		
+
+		String deleteUrl = idDt.toUnqualifiedVersionless().withResourceType(theResourceType).getValue();
+
+		return addDeleteEntry(deleteUrl);
+	}
+
+	/**
+	 * Adds an entry containing a delete (DELETE) request.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 *
+	 * @param theMatchUrl The match URL, e.g. <code>Patient?identifier=http://foo|123</code>
+	 * @since 6.3.0
+	 */
+	public BaseOperationBuilder addTransactionDeleteEntryConditional(String theMatchUrl) {
+		Validate.notBlank(theMatchUrl, "theMatchUrl must not be null or blank");
+		return addDeleteEntry(theMatchUrl);
+	}
+
+	@Nonnull
+	private DeleteBuilder addDeleteEntry(String theDeleteUrl) {
+		IBase request = addEntryAndReturnRequest();
+
 		// Bundle.entry.request.url
 		IPrimitiveType<?> url = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		url.setValueAsString(idDt.toUnqualifiedVersionless().withResourceType(theResourceType).getValue());
+		url.setValueAsString(theDeleteUrl);
 		myEntryRequestUrlChild.getMutator().setValue(request, url);
 
 		// Bundle.entry.request.method
 		IPrimitiveType<?> method = (IPrimitiveType<?>) myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
 		method.setValueAsString("DELETE");
 		myEntryRequestMethodChild.getMutator().setValue(request, method);
-	}
 
+		return new DeleteBuilder();
+	}
 
 
 	/**
@@ -239,14 +321,13 @@ public class BundleBuilder {
 	 */
 	public void addCollectionEntry(IBaseResource theResource) {
 		setType("collection");
-		addEntryAndReturnRequest(theResource);
+		addEntryAndReturnRequest(theResource, theResource.getIdElement().getValue());
 	}
 
 	/**
 	 * Creates new entry and adds it to the bundle
 	 *
-	 * @return
+	 * @return Returns the new entry.
-	 * 		Returns the new entry.
 	 */
 	public IBase addEntry() {
 		IBase entry = myEntryDef.newInstance();
@@ -258,8 +339,7 @@ public class BundleBuilder {
 	 * Creates new search instance for the specified entry
 	 *
 	 * @param entry Entry to create search instance for
-	 * @return
+	 * @return Returns the search instance
-	 * 		Returns the search instance
 	 */
 	public IBaseBackboneElement addSearch(IBase entry) {
 		IBase searchInstance = mySearchDef.newInstance();
@@ -267,19 +347,14 @@ public class BundleBuilder {
 		return (IBaseBackboneElement) searchInstance;
 	}
 
-	/**
+	private IBase addEntryAndReturnRequest(IBaseResource theResource, String theFullUrl) {
-	 *
-	 * @param theResource
-	 * @return
-	 */
-	public IBase addEntryAndReturnRequest(IBaseResource theResource) {
 		Validate.notNull(theResource, "theResource must not be null");
 
 		IBase entry = addEntry();
 
 		// Bundle.entry.fullUrl
 		IPrimitiveType<?> fullUrl = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		fullUrl.setValueAsString(theResource.getIdElement().getValue());
+		fullUrl.setValueAsString(theFullUrl);
 		myEntryFullUrlChild.getMutator().setValue(entry, fullUrl);
 
 		// Bundle.entry.resource
@@ -306,6 +381,15 @@ public class BundleBuilder {
 		return myBundle;
 	}
 
+	/**
+	 * Convenience method which auto-casts the results of {@link #getBundle()}
+	 *
+	 * @since 6.3.0
+	 */
+	public <T extends IBaseBundle> T getBundleTyped() {
+		return (T) myBundle;
+	}
+
 	public BundleBuilder setMetaField(String theFieldName, IBase theFieldValue) {
 		BaseRuntimeChildDefinition.IMutator mutator = myMetaDef.getChildByName(theFieldName).getMutator();
 		mutator.setValue(myBundle.getMeta(), theFieldValue);
@@ -315,12 +399,9 @@ public class BundleBuilder {
 	/**
 	 * Sets the specified entry field.
 	 *
-	 * @param theEntry
+	 * @param theEntry          The entry instance to set values on
-	 * 		The entry instance to set values on
+	 * @param theEntryChildName The child field name of the entry instance to be set
-	 * @param theEntryChildName
+	 * @param theValue          The field value to set
-	 * 		The child field name of the entry instance to be set
-	 * @param theValue
-	 * 		The field value to set
 	 */
 	public void addToEntry(IBase theEntry, String theEntryChildName, IBase theValue) {
 		addToBase(theEntry, theEntryChildName, theValue, myEntryDef);
@@ -329,12 +410,9 @@ public class BundleBuilder {
 	/**
 	 * Sets the specified search field.
 	 *
-	 * @param theSearch
+	 * @param theSearch           The search instance to set values on
-	 * 		The search instance to set values on
+	 * @param theSearchFieldName  The child field name of the search instance to be set
-	 * @param theSearchFieldName
+	 * @param theSearchFieldValue The field value to set
-	 * 		The child field name of the search instance to be set
-	 * @param theSearchFieldValue
-	 * 		The field value to set
 	 */
 	public void addToSearch(IBase theSearch, String theSearchFieldName, IBase theSearchFieldValue) {
 		addToBase(theSearch, theSearchFieldName, theSearchFieldValue, mySearchDef);
@@ -349,12 +427,9 @@ public class BundleBuilder {
 	/**
 	 * Creates a new primitive.
 	 *
-	 * @param theTypeName
+	 * @param theTypeName The element type for the primitive
-	 * 		The element type for the primitive
+	 * @param <T>         Actual type of the parameterized primitive type interface
-	 * @param <T>
+	 * @return Returns the new empty instance of the element definition.
-	 *    	Actual type of the parameterized primitive type interface
-	 * @return
-	 * 		Returns the new empty instance of the element definition.
 	 */
 	public <T> IPrimitiveType<T> newPrimitive(String theTypeName) {
 		BaseRuntimeElementDefinition primitiveDefinition = myContext.getElementDefinition(theTypeName);
@@ -365,14 +440,10 @@ public class BundleBuilder {
 	/**
 	 * Creates a new primitive instance of the specified element type.
 	 *
-	 * @param theTypeName
+	 * @param theTypeName     Element type to create
-	 * 		Element type to create
+	 * @param theInitialValue Initial value to be set on the new instance
-	 * @param theInitialValue
+	 * @param <T>             Actual type of the parameterized primitive type interface
-	 * 		Initial value to be set on the new instance
+	 * @return Returns the newly created instance
-	 * @param <T>
-	 *    	Actual type of the parameterized primitive type interface
-	 * @return
-	 * 		Returns the newly created instance
 	 */
 	public <T> IPrimitiveType<T> newPrimitive(String theTypeName, T theInitialValue) {
 		IPrimitiveType<T> retVal = newPrimitive(theTypeName);
@@ -389,38 +460,84 @@ public class BundleBuilder {
 		setBundleField("type", theType);
 	}
 
-	public static class UpdateBuilder {
 
-		private final IPrimitiveType<?> myUrl;
+	public class DeleteBuilder extends BaseOperationBuilder {
 
-		public UpdateBuilder(IPrimitiveType<?> theUrl) {
+		// nothing yet
-			myUrl = theUrl;
-		}
 
-		/**
-		 * Make this update a Conditional Update
-		 */
-		public void conditional(String theConditionalUrl) {
-			myUrl.setValueAsString(theConditionalUrl);
-		}
 	}
 
-	public class CreateBuilder {
+
+	public class PatchBuilder extends BaseOperationBuilderWithConditionalUrl<PatchBuilder> {
+
+		PatchBuilder(IPrimitiveType<?> theUrl) {
+			super(theUrl);
+		}
+
+	}
+
+	public class UpdateBuilder extends BaseOperationBuilderWithConditionalUrl<UpdateBuilder> {
+		UpdateBuilder(IPrimitiveType<?> theUrl) {
+			super(theUrl);
+		}
+
+	}
+
+	public class CreateBuilder extends BaseOperationBuilder {
 		private final IBase myRequest;
 
-		public CreateBuilder(IBase theRequest) {
+		 CreateBuilder(IBase theRequest) {
 			myRequest = theRequest;
 		}
 
 		/**
 		 * Make this create a Conditional Create
 		 */
-		public void conditional(String theConditionalUrl) {
+		public CreateBuilder conditional(String theConditionalUrl) {
 			BaseRuntimeElementDefinition<?> stringDefinition = Objects.requireNonNull(myContext.getElementDefinition("string"));
 			IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) stringDefinition.newInstance();
 			ifNoneExist.setValueAsString(theConditionalUrl);
 
 			myEntryRequestIfNoneExistChild.getMutator().setValue(myRequest, ifNoneExist);
+
+			return this;
+		}
+
+	}
+
+	public abstract class BaseOperationBuilder {
+
+		/**
+		 * Returns a reference to the BundleBuilder instance.
+		 *
+		 * Calling this method has no effect at all, it is only
+		 * provided for easy method chaning if you want to build
+		 * your bundle as a single fluent call.
+		 *
+		 * @since 6.3.0
+		 */
+		public BundleBuilder andThen() {
+			return BundleBuilder.this;
+		}
+
+
+	}
+
+	public abstract class BaseOperationBuilderWithConditionalUrl<T extends BaseOperationBuilder> extends BaseOperationBuilder {
+
+		private final IPrimitiveType<?> myUrl;
+
+		 BaseOperationBuilderWithConditionalUrl(IPrimitiveType<?> theUrl) {
+			myUrl = theUrl;
+		}
+
+		/**
+		 * Make this update a Conditional Update
+		 */
+		@SuppressWarnings("unchecked")
+		public T conditional(String theConditionalUrl) {
+			myUrl.setValueAsString(theConditionalUrl);
+			return (T) this;
 		}
 
 	}

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

@@ -34,6 +34,9 @@ import org.slf4j.LoggerFactory;
 import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.nio.charset.StandardCharsets;
 import java.util.function.Function;
 import java.util.zip.GZIPInputStream;
 
@@ -86,6 +89,10 @@ public class ClasspathUtil {
 		return retVal;
 	}
 
+	public static Reader loadResourceAsReader(String theClasspath) {
+		return new InputStreamReader(loadResourceAsStream(theClasspath), StandardCharsets.UTF_8);
+	}
+
 	/**
 	 * Load a classpath resource, throw an {@link InternalErrorException} if not found
 	 */

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

@@ -29,11 +29,13 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
+import javax.annotation.Nullable;
 import java.util.List;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -53,8 +55,12 @@ public class OperationOutcomeUtil {
 	 * @return Returns the newly added issue
 	 */
 	public static IBase addIssue(FhirContext theCtx, IBaseOperationOutcome theOperationOutcome, String theSeverity, String theDetails, String theLocation, String theCode) {
+		return addIssue(theCtx, theOperationOutcome, theSeverity, theDetails, theLocation, theCode, null, null, null);
+	}
+
+	public static IBase addIssue(FhirContext theCtx, IBaseOperationOutcome theOperationOutcome, String theSeverity, String theDetails, String theLocation, String theCode, @Nullable String theDetailSystem, @Nullable String theDetailCode, @Nullable String theDetailDescription) {
 		IBase issue = createIssue(theCtx, theOperationOutcome);
-		populateDetails(theCtx, issue, theSeverity, theDetails, theLocation, theCode);
+		populateDetails(theCtx, issue, theSeverity, theDetails, theLocation, theCode, theDetailSystem, theDetailCode, theDetailDescription);
 		return issue;
 	}
 
@@ -127,17 +133,17 @@ public class OperationOutcomeUtil {
 		}
 	}
 
-	private static void populateDetails(FhirContext theCtx, IBase theIssue, String theSeverity, String theDetails, String theLocation, String theCode) {
+	private static void populateDetails(FhirContext theCtx, IBase theIssue, String theSeverity, String theDetails, String theLocation, String theCode, String theDetailSystem, String theDetailCode, String theDetailDescription) {
 		BaseRuntimeElementCompositeDefinition<?> issueElement = (BaseRuntimeElementCompositeDefinition<?>) theCtx.getElementDefinition(theIssue.getClass());
-		BaseRuntimeChildDefinition detailsChild;
+		BaseRuntimeChildDefinition diagnosticsChild;
-		detailsChild = issueElement.getChildByName("diagnostics");
+		diagnosticsChild = issueElement.getChildByName("diagnostics");
 
 		BaseRuntimeChildDefinition codeChild = issueElement.getChildByName("code");
 		IPrimitiveType<?> codeElem = (IPrimitiveType<?>) codeChild.getChildByName("code").newInstance(codeChild.getInstanceConstructorArguments());
 		codeElem.setValueAsString(theCode);
 		codeChild.getMutator().addValue(theIssue, codeElem);
 
-		BaseRuntimeElementDefinition<?> stringDef = detailsChild.getChildByName(detailsChild.getElementName());
+		BaseRuntimeElementDefinition<?> stringDef = diagnosticsChild.getChildByName(diagnosticsChild.getElementName());
 		BaseRuntimeChildDefinition severityChild = issueElement.getChildByName("severity");
 
 		IPrimitiveType<?> severityElem = (IPrimitiveType<?>) severityChild.getChildByName("severity").newInstance(severityChild.getInstanceConstructorArguments());
@@ -146,9 +152,27 @@ public class OperationOutcomeUtil {
 
 		IPrimitiveType<?> string = (IPrimitiveType<?>) stringDef.newInstance();
 		string.setValueAsString(theDetails);
-		detailsChild.getMutator().setValue(theIssue, string);
+		diagnosticsChild.getMutator().setValue(theIssue, string);
 
 		addLocationToIssue(theCtx, theIssue, theLocation);
+
+		if (isNotBlank(theDetailSystem)) {
+			BaseRuntimeChildDefinition detailsChild = issueElement.getChildByName("details");
+			if (detailsChild != null) {
+				BaseRuntimeElementDefinition<?> codeableConceptDef = theCtx.getElementDefinition("CodeableConcept");
+				IBase codeableConcept = codeableConceptDef.newInstance();
+
+				BaseRuntimeElementDefinition<?> codingDef = theCtx.getElementDefinition("Coding");
+				IBaseCoding coding = (IBaseCoding) codingDef.newInstance();
+				coding.setSystem(theDetailSystem);
+				coding.setCode(theDetailCode);
+				coding.setDisplay(theDetailDescription);
+
+				codeableConceptDef.getChildByName("coding").getMutator().addValue(codeableConcept, coding);
+
+				detailsChild.getMutator().addValue(theIssue, codeableConcept);
+			}
+		}
 	}
 
 	public static void addLocationToIssue(FhirContext theContext, IBase theIssue, String theLocation) {

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

@@ -107,6 +107,7 @@ public enum VersionEnum {
 	V6_1_4,
 	V6_2_0,
 	V6_2_1,
+	// Dev Build
 	V6_3_0
 	;
 

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

@@ -99,10 +99,22 @@ ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidParameterChain=Invalid parameter chain
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidVersion=Version "{0}" is not valid for resource {1}
 ca.uhn.fhir.jpa.dao.BaseStorageDao.multipleParamsWithSameNameOneIsMissingTrue=This server does not know how to handle multiple "{0}" parameters where one has a value of :missing=true
 ca.uhn.fhir.jpa.dao.BaseStorageDao.missingBody=No body was supplied in request
-ca.uhn.fhir.jpa.dao.BaseStorageDao.unableToDeleteNotFound=Unable to find resource matching URL "{0}". Deletion failed.
+ca.uhn.fhir.jpa.dao.BaseStorageDao.unableToDeleteNotFound=Unable to find resource matching URL "{0}". Nothing has been deleted.
-ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulCreate=Successfully created resource "{0}" in {1}ms
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulCreate=Successfully created resource "{0}".
-ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdate=Successfully updated resource "{0}" in {1}ms
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulCreateConditionalNoMatch=Successfully conditionally created resource "{0}". No existing resources matched URL "{1}".
-ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulDeletes=Successfully deleted {0} resource(s) in {1}ms
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulCreateConditionalWithMatch=Successfully conditionally created resource "{0}". Existing resource matched URL "{1}".
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulPatch=Successfully patched resource "{0}".
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulPatchNoChange=Successfully patched resource "{0}" with no changes detected.
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulPatchConditional=Successfully conditionally patched resource. Existing resource {0} matched URL: {1}. 
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulPatchConditionalNoChange=Successfully conditionally patched resource with no changes detected. Existing resource {0} matched URL: {1}.
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdate=Successfully updated resource "{0}".
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdateNoChange=Successfully updated resource "{0}" with no changes detected.
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdateAsCreate=Successfully created resource "{0}" using update as create (ie. create with client assigned ID).
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdateConditionalWithMatch=Successfully conditionally updated resource "{0}". Existing resource matched URL "{1}".
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdateConditionalNoMatch=Successfully conditionally updated resource "{0}". Created resource because no existing resource matched URL "{1}".
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulUpdateConditionalNoChangeWithMatch=Successfully conditionally updated resource "{0}" with no changes detected. Existing resource matched URL "{1}".
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulDeletes=Successfully deleted {0} resource(s).
+ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulTimingSuffix=Took {0}ms.
 ca.uhn.fhir.jpa.dao.BaseStorageDao.deleteResourceNotExisting=Not deleted, resource {0} does not exist.
 ca.uhn.fhir.jpa.dao.BaseStorageDao.deleteResourceAlreadyDeleted=Not deleted, resource {0} was already deleted.
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSearchParameter=Unknown search parameter "{0}" for resource type "{1}". Valid search parameters for this search are: {2}
@@ -130,7 +142,7 @@ ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder.invalidCodeMissin
 ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.matchesFound=Matches found
 ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.noMatchesFound=No Matches found
 
-ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4.invalidSearchParamExpression=The expression "{0}" can not be evaluated and may be invalid: {1}
+ca.uhn.fhir.jpa.dao.JpaResourceDaoSearchParameter.invalidSearchParamExpression=The expression "{0}" can not be evaluated and may be invalid: {1}
 
 ca.uhn.fhir.jpa.search.builder.QueryStack.textModifierDisabledForSearchParam=The :text modifier is disabled for this search parameter
 ca.uhn.fhir.jpa.search.builder.QueryStack.textModifierDisabledForServer=The :text modifier is disabled on this server

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

@@ -32,6 +32,15 @@ public class ClasspathUtilTest {
 		}
 	}
 
+	@Test
+	public void testLoadResourceAsReaderNotFound() {
+		try {
+			ClasspathUtil.loadResourceAsReader("/FOOOOOO");
+		} catch (InternalErrorException e) {
+			assertEquals(Msg.code(1758) + "Unable to find classpath resource: /FOOOOOO", e.getMessage());
+		}
+	}
+
 	/**
 	 * Should not throw any exception
 	 */

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

@@ -8,6 +8,7 @@ import java.util.stream.Collectors;
 
 import static org.hamcrest.CoreMatchers.hasItem;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class VersionEnumTest {
 
@@ -18,10 +19,25 @@ public class VersionEnumTest {
 			.collect(Collectors.toList());
 
 		String version = VersionUtil.getVersion();
-		version = "V" + version.replace(".", "_");
+
 		version = version.replaceAll("-PRE[0-9]+", "");
 		version = version.replace("-SNAPSHOT", "");
 
+		String[] parts = version.split("\\.");
+		assertEquals(3, parts.length);
+		int major = Integer.parseInt(parts[0]);
+		int minor = Integer.parseInt(parts[1]);
+		int patch = Integer.parseInt(parts[2]);
+
+		if (major >= 6 && minor >= 3) {
+			if (minor % 2 == 1) {
+				patch = 0;
+			}
+		}
+		version = major + "." + minor + "." + patch;
+
+		version = "V" + version.replace(".", "_");
+
 		assertThat(versions, hasItem(version));
 	}
 

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>6.3.0-PRE5-SNAPSHOT</version>
+    <version>6.3.2-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
     

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/canonical/VersionCanonicalizer.java

@@ -47,9 +47,12 @@ import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r5.model.CapabilityStatement;
+import org.hl7.fhir.r5.model.SearchParameter;
 
 import java.util.List;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 /**
  * This class converts versions of various resources to/from a canonical version
  * of the resource. The specific version that is considered canonical is arbitrary
@@ -68,14 +71,13 @@ public class VersionCanonicalizer {
 	private static final BaseAdvisor_10_50 ADVISOR_10_50 = new BaseAdvisor_10_50(false);
 	private static final BaseAdvisor_40_50 ADVISOR_40_50 = new BaseAdvisor_40_50(false);
 	private static final BaseAdvisor_43_50 ADVISOR_43_50 = new BaseAdvisor_43_50(false);
-	@SuppressWarnings("rawtypes")
 	private final IStrategy myStrategy;
 
 	public VersionCanonicalizer(FhirContext theTargetContext) {
 		this(theTargetContext.getVersion().getVersion());
 	}
 
-	@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
+	@SuppressWarnings({"EnumSwitchStatementWhichMissesCases", "EnhancedSwitchMigration"})
 	public VersionCanonicalizer(FhirVersionEnum theTargetVersion) {
 		switch (theTargetVersion) {
 			case DSTU2:
@@ -160,9 +162,13 @@ public class VersionCanonicalizer {
 		return myStrategy.conceptMapToCanonical(theConceptMap);
 	}
 
-	private interface IStrategy<T extends IBaseResource> {
+	public <T extends IBaseResource> SearchParameter searchParameterToCanonical(T theSearchParameter) {
+		return myStrategy.searchParameterToCanonical(theSearchParameter);
+	}
 
-		CapabilityStatement capabilityStatementToCanonical(T theCapabilityStatement);
+	private interface IStrategy {
+
+		CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement);
 
 		Coding codingToCanonical(IBaseCoding theCoding);
 
@@ -175,9 +181,11 @@ public class VersionCanonicalizer {
 		IBaseResource valueSetFromCanonical(ValueSet theValueSet);
 
 		ConceptMap conceptMapToCanonical(IBaseResource theConceptMap);
+
+		SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter);
 	}
 
-	private class Dstu2Strategy implements IStrategy<ca.uhn.fhir.model.dstu2.resource.BaseResource> {
+	private static class Dstu2Strategy implements IStrategy {
 
 		private final FhirContext myDstu2Hl7OrgContext = FhirContext.forDstu2Hl7OrgCached();
 
@@ -189,7 +197,7 @@ public class VersionCanonicalizer {
 		}
 
 		@Override
-		public CapabilityStatement capabilityStatementToCanonical(ca.uhn.fhir.model.dstu2.resource.BaseResource theCapabilityStatement) {
+		public CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement) {
 			org.hl7.fhir.dstu2.model.Resource reencoded = reencodeToHl7Org(theCapabilityStatement);
 			return (CapabilityStatement) VersionConvertorFactory_10_50.convertResource(reencoded, ADVISOR_10_50);
 		}
@@ -224,8 +232,7 @@ public class VersionCanonicalizer {
 		@Override
 		public ValueSet valueSetToCanonical(IBaseResource theValueSet) {
 			org.hl7.fhir.dstu2.model.Resource reencoded = reencodeToHl7Org(theValueSet);
-			ValueSet valueSet = (ValueSet) VersionConvertorFactory_10_40.convertResource(reencoded, ADVISOR_10_40);
+			return (ValueSet) VersionConvertorFactory_10_40.convertResource(reencoded, ADVISOR_10_40);
-			return valueSet;
 		}
 
 		@Override
@@ -275,6 +282,16 @@ public class VersionCanonicalizer {
 			return (ConceptMap) VersionConvertorFactory_10_40.convertResource(reencoded, ADVISOR_10_40);
 		}
 
+		@Override
+		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
+			org.hl7.fhir.dstu2.model.SearchParameter reencoded = (org.hl7.fhir.dstu2.model.SearchParameter) reencodeToHl7Org(theSearchParameter);
+			SearchParameter retVal = (SearchParameter) VersionConvertorFactory_10_50.convertResource(reencoded, ADVISOR_10_50);
+			if (isBlank(retVal.getExpression())) {
+				retVal.setExpression(reencoded.getXpath());
+			}
+			return retVal;
+		}
+
 		private Resource reencodeToHl7Org(IBaseResource theInput) {
 			if (myHl7OrgStructures) {
 				return (Resource) theInput;
@@ -291,11 +308,11 @@ public class VersionCanonicalizer {
 
 	}
 
-	private class Dstu3Strategy implements IStrategy<org.hl7.fhir.dstu3.model.Resource> {
+	private static class Dstu3Strategy implements IStrategy {
 
 		@Override
-		public CapabilityStatement capabilityStatementToCanonical(org.hl7.fhir.dstu3.model.Resource theCapabilityStatement) {
+		public CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement) {
-			return (CapabilityStatement) VersionConvertorFactory_30_50.convertResource(theCapabilityStatement, ADVISOR_30_50);
+			return (CapabilityStatement) VersionConvertorFactory_30_50.convertResource((org.hl7.fhir.dstu3.model.Resource) theCapabilityStatement, ADVISOR_30_50);
 		}
 
 		@Override
@@ -327,12 +344,17 @@ public class VersionCanonicalizer {
 		public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 			return (ConceptMap) VersionConvertorFactory_30_40.convertResource((org.hl7.fhir.dstu3.model.Resource) theConceptMap, ADVISOR_30_40);
 		}
+
+		@Override
+		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
+			return (SearchParameter) VersionConvertorFactory_30_50.convertResource((org.hl7.fhir.dstu3.model.Resource) theSearchParameter, ADVISOR_30_50);
+		}
 	}
 
-	private class R4Strategy implements IStrategy<org.hl7.fhir.r4.model.Resource> {
+	private static class R4Strategy implements IStrategy {
 		@Override
-		public CapabilityStatement capabilityStatementToCanonical(org.hl7.fhir.r4.model.Resource theCapabilityStatement) {
+		public CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement) {
-			return (CapabilityStatement) VersionConvertorFactory_40_50.convertResource(theCapabilityStatement, ADVISOR_40_50);
+			return (CapabilityStatement) VersionConvertorFactory_40_50.convertResource((org.hl7.fhir.r4.model.Resource) theCapabilityStatement, ADVISOR_40_50);
 		}
 
 		@Override
@@ -365,13 +387,18 @@ public class VersionCanonicalizer {
 			return (ConceptMap) theConceptMap;
 		}
 
+		@Override
+		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
+			return (SearchParameter) VersionConvertorFactory_40_50.convertResource((org.hl7.fhir.r4.model.Resource) theSearchParameter, ADVISOR_40_50);
+		}
+
 	}
 
-	private class R4BStrategy implements IStrategy<org.hl7.fhir.r4b.model.Resource> {
+	private static class R4BStrategy implements IStrategy {
 
 		@Override
-		public CapabilityStatement capabilityStatementToCanonical(org.hl7.fhir.r4b.model.Resource theCapabilityStatement) {
+		public CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement) {
-			return (CapabilityStatement) VersionConvertorFactory_43_50.convertResource(theCapabilityStatement, ADVISOR_43_50);
+			return (CapabilityStatement) VersionConvertorFactory_43_50.convertResource((org.hl7.fhir.r4b.model.Resource) theCapabilityStatement, ADVISOR_43_50);
 		}
 
 		@Override
@@ -410,13 +437,18 @@ public class VersionCanonicalizer {
 			return (ConceptMap) VersionConvertorFactory_40_50.convertResource(conceptMapR5, ADVISOR_40_50);
 		}
 
+		@Override
+		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
+			return (SearchParameter) VersionConvertorFactory_43_50.convertResource((org.hl7.fhir.r4b.model.Resource) theSearchParameter, ADVISOR_43_50);
+		}
+
 	}
 
 
-	private class R5Strategy implements IStrategy<org.hl7.fhir.r5.model.Resource> {
+	private static class R5Strategy implements IStrategy {
 
 		@Override
-		public CapabilityStatement capabilityStatementToCanonical(org.hl7.fhir.r5.model.Resource theCapabilityStatement) {
+		public CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement) {
 			return (CapabilityStatement) theCapabilityStatement;
 		}
 
@@ -450,6 +482,11 @@ public class VersionCanonicalizer {
 			return (ConceptMap) VersionConvertorFactory_40_50.convertResource((org.hl7.fhir.r5.model.ConceptMap) theConceptMap, ADVISOR_40_50);
 		}
 
+		@Override
+		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
+			return (SearchParameter) theSearchParameter;
+		}
+
 	}
 
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/BundleBuilderExamples.java

@@ -26,6 +26,11 @@ import ca.uhn.fhir.util.BundleBuilder;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Patient;
 
 import java.math.BigDecimal;
@@ -109,6 +114,53 @@ public class BundleBuilderExamples {
 		//END SNIPPET: createConditional
 	}
 
+	public void patch() throws FHIRException {
+		//START SNIPPET: patch
+
+		// Create a FHIR Patch object
+		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));
+
+		// Create a TransactionBuilder
+		BundleBuilder builder = new BundleBuilder(myFhirContext);
+
+		// Create a target object (this is the ID of the resource that will be patched)
+		IIdType targetId = new IdType("Patient/123");
+
+		// Add the patch to the bundle
+		builder.addTransactionFhirPatchEntry(targetId, patch);
+
+		// Execute the transaction
+		IBaseBundle outcome = myFhirClient.transaction().withBundle(builder.getBundle()).execute();
+		//END SNIPPET: patch
+	}
+
+	public void patchConditional() throws FHIRException {
+		//START SNIPPET: patchConditional
+
+		// Create a FHIR Patch object
+		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));
+
+		// Create a TransactionBuilder
+		BundleBuilder builder = new BundleBuilder(myFhirContext);
+
+		// Add the patch to the bundle with a conditional URL
+		String conditionalUrl = "Patient?identifier=http://foo|123";
+		builder.addTransactionFhirPatchEntry(patch).conditional(conditionalUrl);
+
+
+		// Execute the transaction
+		IBaseBundle outcome = myFhirClient.transaction().withBundle(builder.getBundle()).execute();
+		//END SNIPPET: patchConditional
+	}
+
 	public void customizeBundle() throws FHIRException {
 		//START SNIPPET: customizeBundle
 		// Create a TransactionBuilder

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_7/version.yaml

@@ -1,3 +1,3 @@
 ---
-release-date: "FILL ME"
+release-date: "2022-07-08"
 codename: "Sojourner"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_3_0/4293-add-conditional-delete-to-bundlebuilder.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 4293
+title: "The BundleBuilder now supports adding conditional
+   DELETE operations, PATCH operations, and conditional PATCH 
+   operations to a transaction bundle."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_3_0/4293-improved-operationoutcome-for-jpa-cud.yaml

@@ -0,0 +1,11 @@
+---
+type: add
+issue: 4293
+title: "When performing create/update/patch/delete operations against the JPA server, the response
+   OperationOutcome will now include additional details about the outcome of the operation. This
+   includes:
+   <ul>
+   <li>For updates, the message will indicate the the update did not contain any changes (i.e. a No-op)</li>
+   <li>For conditional creates/updates/deletes, the message will indicate whether the conditional URL matched any existing resources and the outcome of the operation.</li>
+   <li>A new coding has been added to the <code>OperationOutcome.issue.details.coding</code> containing a machine processable equivalent to the outcome.</li>
+   </ul>"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_3_0/4293-include-carried-tags-in-transaction-response.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 4293
+title: "When updating resources using a FHIR transaction in the JPA server, if the
+   client instructs the server to include the resource body in the response, any
+   tags that have been carried forward from previous versions of the resource are
+   now included in the response."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_3_0/changes.yaml

@@ -6,6 +6,7 @@
       <ul>
       <li>SLF4j (All): 1.7.33 -> 2.0.3</li>
       <li>Logback (All): 1.2.10 -> 1.4.4</li>
+      <li>Woodstox-Core (XML Parser): 6.3.1 -> 6.4.0</li>
       <li>log4j-to-slf4j (JPA): 2.17.1 -> 2.19.0</li>
       <li>Jetty (CLI): 9.4.48.v20220622 -> 10.0.12</li>
       <li>Spring Boot: 2.7.4 -> 2.7.5</li>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/interceptors/server_pointcuts.md

@@ -2,13 +2,13 @@
 
 The following diagram shows the request processing pipeline for processing a server request. You may click on the diagram to enlarge it.
 
-<a href="/hapi-fhir/docs/images/interceptors-server-pipeline.svg" target="_blank">Expand</a>
+<a href="server_pointcuts/interceptors-server-pipeline.svg" target="_blank">Expand</a>
-<img src="/hapi-fhir/docs/images/interceptors-server-pipeline.svg" alt="Server Pipeline"/>
+<img src="server_pointcuts/interceptors-server-pipeline.svg" alt="Server Pipeline"/>
 
 # Storage / JPA Server Pointcuts
 
 The following diagram shows the request processing pipeline for processing a server request. You may click on the diagram to enlarge it.
 
-<a href="/hapi-fhir/docs/images/interceptors-server-jpa-pipeline.svg" target="_blank">Expand</a>
+<a href="server_pointcuts/interceptors-server-jpa-pipeline.svg" target="_blank">Expand</a>
-<img src="/hapi-fhir/docs/images/interceptors-server-jpa-pipeline.svg" alt="Server Pipeline"/>
+<img src="server_pointcuts/interceptors-server-jpa-pipeline.svg" alt="Server Pipeline"/>
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/model/bundle_builder.md

@@ -36,7 +36,23 @@ If you want to perform a conditional update:
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/BundleBuilderExamples.java|updateConditional}}
 ``` 
 
-# Customizing bundle
+# Transaction Patch
+
+To add a PATCH operation to a transaction bundle:
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/BundleBuilderExamples.java|patch}}
+``` 
+
+## Conditional Patch
+
+If you want to perform a conditional patch:
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/BundleBuilderExamples.java|patchConditional}}
+``` 
+
+# Customizing the Bundle
 
 If you want to manipulate a bundle:
 

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/util/SqlQuery.java

@@ -39,14 +39,16 @@ public class SqlQuery {
 	private final StackTraceElement[] myStackTrace;
 	private final int mySize;
 	private final LanguageEnum myLanguage;
+	private final String myNamespace;
 
 	public SqlQuery(String theSql, List<String> theParams, long theQueryTimestamp, long theElapsedTime, StackTraceElement[] theStackTraceElements, int theSize) {
-		this(theSql,  theParams,  theQueryTimestamp,  theElapsedTime,  theStackTraceElements, theSize, LanguageEnum.SQL);
+		this(null, theSql, theParams, theQueryTimestamp, theElapsedTime, theStackTraceElements, theSize, LanguageEnum.SQL);
 	}
 
-	public SqlQuery(String theSql, List<String> theParams, long theQueryTimestamp, long theElapsedTime, StackTraceElement[] theStackTraceElements, int theSize, LanguageEnum theLanguage) {
+	public SqlQuery(String theNamespace, String theSql, List<String> theParams, long theQueryTimestamp, long theElapsedTime, StackTraceElement[] theStackTraceElements, int theSize, LanguageEnum theLanguage) {
 		Validate.notNull(theLanguage, "theLanguage must not be null");
 
+		myNamespace = theNamespace;
 		mySql = theSql;
 		myParams = Collections.unmodifiableList(theParams);
 		myQueryTimestamp = theQueryTimestamp;
@@ -56,6 +58,10 @@ public class SqlQuery {
 		myLanguage = theLanguage;
 	}
 
+	public String getNamespace() {
+		return myNamespace;
+	}
+
 	public long getQueryTimestamp() {
 		return myQueryTimestamp;
 	}
@@ -118,6 +124,10 @@ public class SqlQuery {
 		return mySize;
 	}
 
+	@Override
+	public String toString() {
+		return getSql(true, true);
+	}
 
 	public enum LanguageEnum {
 
@@ -125,9 +135,4 @@ public class SqlQuery {
 		JSON
 
 	}
-
-	@Override
-	public String toString() {
-		return getSql(true, true);
-	}
 }

hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java

@@ -384,7 +384,7 @@ public class TestUtil {
 	}
 
 	public static void sleepOneClick() {
-		ca.uhn.fhir.util.TestUtil.sleepAtLeast(1);
+		ca.uhn.fhir.util.TestUtil.sleepAtLeast(1, false);
 	}
 
 

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java

@@ -84,7 +84,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.REQUIRES_NEW)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public String storeWorkChunk(BatchWorkChunk theBatchWorkChunk) {
 		Batch2WorkChunkEntity entity = new Batch2WorkChunkEntity();
 		entity.setId(UUID.randomUUID().toString());
@@ -102,7 +102,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.REQUIRES_NEW)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public Optional<WorkChunk> fetchWorkChunkSetStartTimeAndMarkInProgress(String theChunkId) {
 		myWorkChunkRepository.updateChunkStatusForStart(theChunkId, new Date(), StatusEnum.IN_PROGRESS);
 		Optional<Batch2WorkChunkEntity> chunk = myWorkChunkRepository.findById(theChunkId);
@@ -110,7 +110,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.REQUIRES_NEW)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public String storeNewInstance(JobInstance theInstance) {
 		Validate.isTrue(isBlank(theInstance.getInstanceId()));
 
@@ -271,7 +271,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.REQUIRES_NEW)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public boolean canAdvanceInstanceToNextStep(String theInstanceId, String theCurrentStepId) {
 		List<StatusEnum> statusesForStep = myWorkChunkRepository.getDistinctStatusesForStep(theInstanceId, theCurrentStepId);
 		ourLog.debug("Checking whether gated job can advanced to next step. [instanceId={}, currentStepId={}, statusesForStep={}]", theInstanceId, theCurrentStepId, statusesForStep);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/Batch2SupportConfig.java

@@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.dao.index.IJpaIdHelperService;
 import ca.uhn.fhir.jpa.delete.batch2.DeleteExpungeSqlBuilder;
 import ca.uhn.fhir.jpa.delete.batch2.DeleteExpungeSvcImpl;
 import ca.uhn.fhir.jpa.reindex.Batch2DaoSvcImpl;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 
 import javax.persistence.EntityManager;
@@ -43,7 +44,7 @@ public class Batch2SupportConfig {
 	}
 
 	@Bean
-	public IDeleteExpungeSvc deleteExpungeSvc(EntityManager theEntityManager, DeleteExpungeSqlBuilder theDeleteExpungeSqlBuilder, IFulltextSearchSvc theFullTextSearchSvc) {
+	public IDeleteExpungeSvc deleteExpungeSvc(EntityManager theEntityManager, DeleteExpungeSqlBuilder theDeleteExpungeSqlBuilder, @Autowired(required = false) IFulltextSearchSvc theFullTextSearchSvc) {
 		return new DeleteExpungeSvcImpl(theEntityManager, theDeleteExpungeSqlBuilder, theFullTextSearchSvc);
 	}
 

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

@@ -25,8 +25,11 @@ import ca.uhn.fhir.jpa.dao.DaoSearchParamProvider;
 import ca.uhn.fhir.jpa.dao.HistoryBuilder;
 import ca.uhn.fhir.jpa.dao.HistoryBuilderFactory;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.dao.JpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
+import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.expunge.ExpungeEverythingService;
@@ -116,10 +119,14 @@ import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamProvider;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
+import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
 import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
 import ca.uhn.fhir.jpa.term.TermReadSvcImpl;
+import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
 import ca.uhn.fhir.jpa.term.config.TermCodeSystemConfig;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.jpa.validation.ResourceLoaderImpl;
@@ -225,7 +232,6 @@ public class JpaConfig {
 		return new ResponseTerminologyTranslationInterceptor(theValidationSupport, theResponseTerminologyTranslationSvc);
 	}
 
-	@Lazy
 	@Bean
 	public ResponseTerminologyTranslationSvc responseTerminologyTranslationSvc(IValidationSupport theValidationSupport) {
 		return new ResponseTerminologyTranslationSvc(theValidationSupport);
@@ -260,6 +266,11 @@ public class JpaConfig {
 		return new ValueSetOperationProvider();
 	}
 
+	@Bean
+	public IJpaStorageResourceParser jpaStorageResourceParser() {
+		return new JpaStorageResourceParser();
+	}
+
 	@Bean
 	public TransactionProcessor transactionProcessor() {
 		return new TransactionProcessor();
@@ -763,4 +774,22 @@ public class JpaConfig {
 		return new TermReadSvcImpl();
 	}
 
+	@Bean
+	public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
+		return new TermCodeSystemStorageSvcImpl();
+	}
+
+
+
+	@Bean
+	public ITermReindexingSvc termReindexingSvc() {
+		return new TermReindexingSvcImpl();
+	}
+
+	@Bean
+	public ObservationLastNIndexPersistSvc baseObservationLastNIndexpersistSvc() {
+		return new ObservationLastNIndexPersistSvc();
+	}
+
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/SharedConfigDstu3Plus.java

@@ -1,55 +0,0 @@
-package ca.uhn.fhir.jpa.config;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
-import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
-import ca.uhn.fhir.jpa.term.TermConceptDaoSvc;
-import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
-import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
-import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
-import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
-import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-@Configuration
-public class SharedConfigDstu3Plus {
-
-	@Bean
-	public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
-		return new TermCodeSystemStorageSvcImpl();
-	}
-
-
-
-	@Bean
-	public ITermReindexingSvc termReindexingSvc() {
-		return new TermReindexingSvcImpl();
-	}
-
-	@Bean
-	public ObservationLastNIndexPersistSvc baseObservationLastNIndexpersistSvc() {
-		return new ObservationLastNIndexPersistSvc();
-	}
-
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/JpaDstu3Config.java

@@ -6,7 +6,6 @@ import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigDstu3;
 import ca.uhn.fhir.jpa.config.JpaConfig;
-import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@@ -53,7 +52,6 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 @Import({
 	FhirContextDstu3Config.class,
 	GeneratedDaoAndResourceProviderConfigDstu3.class,
-	SharedConfigDstu3Plus.class,
 	JpaConfig.class
 })
 public class JpaDstu3Config {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/JpaR4Config.java

@@ -7,7 +7,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR4;
 import ca.uhn.fhir.jpa.config.JpaConfig;
-import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@@ -22,7 +21,6 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
-import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Consent;
@@ -62,7 +60,6 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 @Import({
 	FhirContextR4Config.class,
 	GeneratedDaoAndResourceProviderConfigR4.class,
-	SharedConfigDstu3Plus.class,
 	JpaConfig.class
 })
 public class JpaR4Config {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4b/JpaR4BConfig.java

@@ -6,7 +6,6 @@ import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR4B;
 import ca.uhn.fhir.jpa.config.JpaConfig;
-import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.r4b.TransactionProcessorVersionAdapterR4B;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@@ -53,7 +52,6 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 @Import({
 	FhirContextR4BConfig.class,
 	GeneratedDaoAndResourceProviderConfigR4B.class,
-	SharedConfigDstu3Plus.class,
 	JpaConfig.class
 })
 public class JpaR4BConfig {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/JpaR5Config.java

@@ -6,7 +6,6 @@ import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR5;
 import ca.uhn.fhir.jpa.config.JpaConfig;
-import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.r5.TransactionProcessorVersionAdapterR5;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@@ -53,7 +52,6 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 @Import({
 	FhirContextR5Config.class,
 	GeneratedDaoAndResourceProviderConfigR5.class,
-	SharedConfigDstu3Plus.class,
 	JpaConfig.class
 })
 public class JpaR5Config {

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

@@ -16,6 +16,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.api.dao.IJpaDao;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
 import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
@@ -29,8 +30,6 @@ import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.delete.DeleteConflictService;
 import ca.uhn.fhir.jpa.entity.PartitionEntity;
 import ca.uhn.fhir.jpa.entity.ResourceSearchView;
-import ca.uhn.fhir.jpa.entity.Search;
-import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
@@ -46,11 +45,9 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTag;
 import ca.uhn.fhir.jpa.model.entity.TagDefinition;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.model.search.ExtendedHSearchIndexData;
-import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
-import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
 import ca.uhn.fhir.jpa.searchparam.extractor.LogicalReferenceHelper;
 import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
 import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryMatchResult;
@@ -61,6 +58,7 @@ import ca.uhn.fhir.jpa.util.AddRemoveCount;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.StorageResponseCodeEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
@@ -72,13 +70,11 @@ import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.LenientErrorHandler;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import ca.uhn.fhir.rest.param.HistorySearchStyleEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
@@ -86,6 +82,8 @@ import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.HapiExtensions;
 import ca.uhn.fhir.util.MetaUtil;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.util.XmlUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
@@ -148,11 +146,9 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.StringTokenizer;
-import java.util.UUID;
 import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.jpa.model.util.JpaConstants.ALL_PARTITIONS_NAME;
-import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -181,9 +177,18 @@ import static org.apache.commons.lang3.StringUtils.trim;
  * #L%
  */
 
+
+/**
+ * TODO: JA - This class has only one subclass now. Historically it was a common
+ * ancestor for BaseHapiFhirSystemDao and BaseHapiFhirResourceDao but I've untangled
+ * the former from this hierarchy in order to simplify moving common functionality
+ * for resource DAOs into the hapi-fhir-storage project. This class should be merged
+ * into BaseHapiFhirResourceDao, but that should be done in its own dedicated PR
+ * since it'll be a noisy change.
+ */
 @SuppressWarnings("WeakerAccess")
 @Repository
-public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStorageDao implements IDao, IJpaDao<T>, ApplicationContextAware {
+public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStorageResourceDao<T> implements IDao, IJpaDao<T>, ApplicationContextAware {
 
 	public static final long INDEX_STATUS_INDEXED = 1L;
 	public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
@@ -233,8 +238,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	@Autowired
 	private PartitionSettings myPartitionSettings;
 	@Autowired
-	private PersistedJpaBundleProviderFactory myPersistedJpaBundleProviderFactory;
-	@Autowired
 	private IPartitionLookupSvc myPartitionLookupSvc;
 	@Autowired
 	private MemoryCacheService myMemoryCacheService;
@@ -243,6 +246,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 	@Autowired
 	private PlatformTransactionManager myTransactionManager;
+	@Autowired
+	protected IJpaStorageResourceParser myJpaStorageResourceParser;
 
 	@VisibleForTesting
 	public void setSearchParamPresenceSvc(ISearchParamPresenceSvc theSearchParamPresenceSvc) {
@@ -371,14 +376,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		myContext = theContext;
 	}
 
-	public FhirContext getContext(FhirVersionEnum theVersion) {
-		Validate.notNull(theVersion, "theVersion must not be null");
-		if (theVersion == myFhirContext.getVersion().getVersion()) {
-			return myFhirContext;
-		}
-		return FhirContext.forCached(theVersion);
-	}
-
 	/**
 	 * <code>null</code> will only be returned if the scheme and tag are both blank
 	 */
@@ -513,27 +510,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		return retVal;
 	}
 
-	protected IBundleProvider history(RequestDetails theRequest, String theResourceType, Long theResourcePid, Date theRangeStartInclusive, Date theRangeEndInclusive, Integer theOffset) {
-		return history(theRequest, theResourceType, theResourcePid, theRangeStartInclusive, theRangeEndInclusive, theOffset, null);
-	}
-
-	protected IBundleProvider history(RequestDetails theRequest, String theResourceType, Long theResourcePid, Date theRangeStartInclusive, Date theRangeEndInclusive, Integer theOffset, HistorySearchStyleEnum searchParameterType) {
-		String resourceName = defaultIfBlank(theResourceType, null);
-
-		Search search = new Search();
-		search.setOffset(theOffset);
-		search.setDeleted(false);
-		search.setCreated(new Date());
-		search.setLastUpdated(theRangeStartInclusive, theRangeEndInclusive);
-		search.setUuid(UUID.randomUUID().toString());
-		search.setResourceType(resourceName);
-		search.setResourceId(theResourcePid);
-		search.setSearchType(SearchTypeEnum.HISTORY);
-		search.setStatus(SearchStatusEnum.FINISHED);
-		search.setHistorySearchStyle(searchParameterType);
-
-		return myPersistedJpaBundleProviderFactory.newInstance(theRequest, search);
-	}
 
 	void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
 		String newVersion;
@@ -796,133 +772,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		return !allTagsOld.equals(allTagsNew);
 	}
 
-	@SuppressWarnings("unchecked")
-	private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res, Long theVersion) {
-		R retVal = (R) res;
-		if (theEntity.getDeleted() != null) {
-			res = (IResource) myContext.getResourceDefinition(theResourceType).newInstance();
-			retVal = (R) res;
-			ResourceMetadataKeyEnum.DELETED_AT.put(res, new InstantDt(theEntity.getDeleted()));
-			if (theForHistoryOperation) {
-				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, BundleEntryTransactionMethodEnum.DELETE);
-			}
-		} else if (theForHistoryOperation) {
-			/*
-			 * If the create and update times match, this was when the resource was created so we should mark it as a POST. Otherwise, it's a PUT.
-			 */
-			Date published = theEntity.getPublished().getValue();
-			Date updated = theEntity.getUpdated().getValue();
-			if (published.equals(updated)) {
-				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, BundleEntryTransactionMethodEnum.POST);
-			} else {
-				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, BundleEntryTransactionMethodEnum.PUT);
-			}
-		}
-
-		res.setId(theEntity.getIdDt().withVersion(theVersion.toString()));
-
-		ResourceMetadataKeyEnum.VERSION.put(res, Long.toString(theEntity.getVersion()));
-		ResourceMetadataKeyEnum.PUBLISHED.put(res, theEntity.getPublished());
-		ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
-		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
-
-		if (theTagList != null) {
-			if (theEntity.isHasTags()) {
-				TagList tagList = new TagList();
-				List<IBaseCoding> securityLabels = new ArrayList<>();
-				List<IdDt> profiles = new ArrayList<>();
-				for (BaseTag next : theTagList) {
-					switch (next.getTag().getTagType()) {
-						case PROFILE:
-							profiles.add(new IdDt(next.getTag().getCode()));
-							break;
-						case SECURITY_LABEL:
-							IBaseCoding secLabel = (IBaseCoding) myContext.getVersion().newCodingDt();
-							secLabel.setSystem(next.getTag().getSystem());
-							secLabel.setCode(next.getTag().getCode());
-							secLabel.setDisplay(next.getTag().getDisplay());
-							securityLabels.add(secLabel);
-							break;
-						case TAG:
-							tagList.add(new Tag(next.getTag().getSystem(), next.getTag().getCode(), next.getTag().getDisplay()));
-							break;
-					}
-				}
-				if (tagList.size() > 0) {
-					ResourceMetadataKeyEnum.TAG_LIST.put(res, tagList);
-				}
-				if (securityLabels.size() > 0) {
-					ResourceMetadataKeyEnum.SECURITY_LABELS.put(res, toBaseCodingList(securityLabels));
-				}
-				if (profiles.size() > 0) {
-					ResourceMetadataKeyEnum.PROFILES.put(res, profiles);
-				}
-			}
-		}
-
-		return retVal;
-	}
-
-	@SuppressWarnings("unchecked")
-	private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res, Long theVersion) {
-		R retVal = (R) res;
-		if (theEntity.getDeleted() != null) {
-			res = (IAnyResource) myContext.getResourceDefinition(theResourceType).newInstance();
-			retVal = (R) res;
-			ResourceMetadataKeyEnum.DELETED_AT.put(res, new InstantDt(theEntity.getDeleted()));
-			if (theForHistoryOperation) {
-				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, HTTPVerb.DELETE.toCode());
-			}
-		} else if (theForHistoryOperation) {
-			/*
-			 * If the create and update times match, this was when the resource was created so we should mark it as a POST. Otherwise, it's a PUT.
-			 */
-			Date published = theEntity.getPublished().getValue();
-			Date updated = theEntity.getUpdated().getValue();
-			if (published.equals(updated)) {
-				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, HTTPVerb.POST.toCode());
-			} else {
-				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, HTTPVerb.PUT.toCode());
-			}
-		}
-
-		res.getMeta().setLastUpdated(null);
-		res.getMeta().setVersionId(null);
-
-		updateResourceMetadata(theEntity, res);
-		res.setId(res.getIdElement().withVersion(theVersion.toString()));
-
-		res.getMeta().setLastUpdated(theEntity.getUpdatedDate());
-		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
-
-		if (theTagList != null) {
-			res.getMeta().getTag().clear();
-			res.getMeta().getProfile().clear();
-			res.getMeta().getSecurity().clear();
-			for (BaseTag next : theTagList) {
-				switch (next.getTag().getTagType()) {
-					case PROFILE:
-						res.getMeta().addProfile(next.getTag().getCode());
-						break;
-					case SECURITY_LABEL:
-						IBaseCoding sec = res.getMeta().addSecurity();
-						sec.setSystem(next.getTag().getSystem());
-						sec.setCode(next.getTag().getCode());
-						sec.setDisplay(next.getTag().getDisplay());
-						break;
-					case TAG:
-						IBaseCoding tag = res.getMeta().addTag();
-						tag.setSystem(next.getTag().getSystem());
-						tag.setCode(next.getTag().getCode());
-						tag.setDisplay(next.getTag().getDisplay());
-						break;
-				}
-			}
-		}
-
-		return retVal;
-	}
-
 	/**
 	 * Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
 	 *
@@ -954,6 +803,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		// nothing
 	}
 
+	@Override
 	@CoverageIgnore
 	public BaseHasResource readEntity(IIdType theValueId, RequestDetails theRequest) {
 		throw new NotImplementedException(Msg.code(927) + "");
@@ -1005,220 +855,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		return metaSnapshotModeTokens.contains(theTag.getTag().getTagType());
 	}
 
-	@Override
-	public IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation) {
-		RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
-		Class<? extends IBaseResource> resourceType = type.getImplementingClass();
-		return toResource(resourceType, theEntity, null, theForHistoryOperation);
-	}
 
-	@SuppressWarnings("unchecked")
-	@Override
-	public <R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation) {
 
-		// 1. get resource, it's encoding and the tags if any
-		byte[] resourceBytes;
-		String resourceText;
-		ResourceEncodingEnum resourceEncoding;
-		@Nullable
-		Collection<? extends BaseTag> tagList = Collections.emptyList();
-		long version;
-		String provenanceSourceUri = null;
-		String provenanceRequestId = null;
-
-		if (theEntity instanceof ResourceHistoryTable) {
-			ResourceHistoryTable history = (ResourceHistoryTable) theEntity;
-			resourceBytes = history.getResource();
-			resourceText = history.getResourceTextVc();
-			resourceEncoding = history.getEncoding();
-			switch (getConfig().getTagStorageMode()) {
-				case VERSIONED:
-				default:
-					if (history.isHasTags()) {
-						tagList = history.getTags();
-					}
-					break;
-				case NON_VERSIONED:
-					if (history.getResourceTable().isHasTags()) {
-						tagList = history.getResourceTable().getTags();
-					}
-					break;
-				case INLINE:
-					tagList = null;
-			}
-			version = history.getVersion();
-			if (history.getProvenance() != null) {
-				provenanceRequestId = history.getProvenance().getRequestId();
-				provenanceSourceUri = history.getProvenance().getSourceUri();
-			}
-		} else if (theEntity instanceof ResourceTable) {
-			ResourceTable resource = (ResourceTable) theEntity;
-			ResourceHistoryTable history;
-			if (resource.getCurrentVersionEntity() != null) {
-				history = resource.getCurrentVersionEntity();
-			} else {
-				version = theEntity.getVersion();
-				history = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), version);
-				((ResourceTable) theEntity).setCurrentVersionEntity(history);
-
-				while (history == null) {
-					if (version > 1L) {
-						version--;
-						history = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), version);
-					} else {
-						return null;
-					}
-				}
-			}
-
-			resourceBytes = history.getResource();
-			resourceEncoding = history.getEncoding();
-			resourceText = history.getResourceTextVc();
-			switch (getConfig().getTagStorageMode()) {
-				case VERSIONED:
-				case NON_VERSIONED:
-					if (resource.isHasTags()) {
-						tagList = resource.getTags();
-					} else {
-						tagList = Collections.emptyList();
-					}
-					break;
-				case INLINE:
-					tagList = null;
-					break;
-			}
-			version = history.getVersion();
-			if (history.getProvenance() != null) {
-				provenanceRequestId = history.getProvenance().getRequestId();
-				provenanceSourceUri = history.getProvenance().getSourceUri();
-			}
-		} else if (theEntity instanceof ResourceSearchView) {
-			// This is the search View
-			ResourceSearchView view = (ResourceSearchView) theEntity;
-			resourceBytes = view.getResource();
-			resourceText = view.getResourceTextVc();
-			resourceEncoding = view.getEncoding();
-			version = view.getVersion();
-			provenanceRequestId = view.getProvenanceRequestId();
-			provenanceSourceUri = view.getProvenanceSourceUri();
-			switch (getConfig().getTagStorageMode()) {
-				case VERSIONED:
-				case NON_VERSIONED:
-					if (theTagList != null) {
-						tagList = theTagList;
-					} else {
-						tagList = Collections.emptyList();
-					}
-					break;
-				case INLINE:
-					tagList = null;
-					break;
-			}
-		} else {
-			// something wrong
-			return null;
-		}
-
-		// 2. get The text
-		String decodedResourceText;
-		if (resourceText != null) {
-			decodedResourceText = resourceText;
-		} else {
-			decodedResourceText = decodeResource(resourceBytes, resourceEncoding);
-		}
-
-		// 3. Use the appropriate custom type if one is specified in the context
-		Class<R> resourceType = theResourceType;
-		if (tagList != null) {
-			if (myContext.hasDefaultTypeForProfile()) {
-				for (BaseTag nextTag : tagList) {
-					if (nextTag.getTag().getTagType() == TagTypeEnum.PROFILE) {
-						String profile = nextTag.getTag().getCode();
-						if (isNotBlank(profile)) {
-							Class<? extends IBaseResource> newType = myContext.getDefaultTypeForProfile(profile);
-							if (newType != null && theResourceType.isAssignableFrom(newType)) {
-								ourLog.debug("Using custom type {} for profile: {}", newType.getName(), profile);
-								resourceType = (Class<R>) newType;
-								break;
-							}
-						}
-					}
-				}
-			}
-		}
-
-		// 4. parse the text to FHIR
-		R retVal;
-		if (resourceEncoding != ResourceEncodingEnum.DEL) {
-
-			LenientErrorHandler errorHandler = new LenientErrorHandler(false).setErrorOnInvalidValue(false);
-			IParser parser = new TolerantJsonParser(getContext(theEntity.getFhirVersion()), errorHandler, theEntity.getId());
-
-			try {
-				retVal = parser.parseResource(resourceType, decodedResourceText);
-			} catch (Exception e) {
-				StringBuilder b = new StringBuilder();
-				b.append("Failed to parse database resource[");
-				b.append(myFhirContext.getResourceType(resourceType));
-				b.append("/");
-				b.append(theEntity.getIdDt().getIdPart());
-				b.append(" (pid ");
-				b.append(theEntity.getId());
-				b.append(", version ");
-				b.append(theEntity.getFhirVersion().name());
-				b.append("): ");
-				b.append(e.getMessage());
-				String msg = b.toString();
-				ourLog.error(msg, e);
-				throw new DataFormatException(Msg.code(928) + msg, e);
-			}
-
-		} else {
-
-			retVal = (R) myContext.getResourceDefinition(theEntity.getResourceType()).newInstance();
-
-		}
-
-		// 5. fill MetaData
-		retVal = populateResourceMetadata(theEntity, theForHistoryOperation, tagList, version, resourceType, retVal);
-
-		// 6. Handle source (provenance)
-		if (isNotBlank(provenanceRequestId) || isNotBlank(provenanceSourceUri)) {
-			String sourceString = cleanProvenanceSourceUri(provenanceSourceUri)
-				+ (isNotBlank(provenanceRequestId) ? "#" : "")
-				+ defaultString(provenanceRequestId);
-
-			MetaUtil.setSource(myContext, retVal, sourceString);
-		}
-
-		// 7. Add partition information
-		if (myPartitionSettings.isPartitioningEnabled()) {
-			PartitionablePartitionId partitionId = theEntity.getPartitionId();
-			if (partitionId != null && partitionId.getPartitionId() != null) {
-				PartitionEntity persistedPartition = myPartitionLookupSvc.getPartitionById(partitionId.getPartitionId());
-				retVal.setUserData(Constants.RESOURCE_PARTITION_ID, persistedPartition.toRequestPartitionId());
-			} else {
-				retVal.setUserData(Constants.RESOURCE_PARTITION_ID, null);
-			}
-		}
-
-		return retVal;
-	}
-
-	protected <R extends IBaseResource> R populateResourceMetadata(IBaseResourceEntity theEntity, boolean theForHistoryOperation, @Nullable Collection<? extends BaseTag> tagList, long theVersion, Class<R> theResourceType, R theResource) {
-		if (theResource instanceof IResource) {
-			IResource res = (IResource) theResource;
-			theResource = populateResourceMetadataHapi(theResourceType, theEntity, tagList, theForHistoryOperation, res, theVersion);
-		} else {
-			IAnyResource res = (IAnyResource) theResource;
-			theResource = populateResourceMetadataRi(theResourceType, theEntity, tagList, theForHistoryOperation, res, theVersion);
-		}
-		return theResource;
-	}
-
-	public String toResourceName(Class<? extends IBaseResource> theResourceType) {
-		return myContext.getResourceType(theResourceType);
-	}
 
 	String toResourceName(IBaseResource theResource) {
 		return myContext.getResourceType(theResource);
@@ -1375,7 +1013,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		if (thePerformIndexing && changed != null && !changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange() && (entity.getVersion() > 1 || theUpdateVersion)) {
 			ourLog.debug("Resource {} has not changed", entity.getIdDt().toUnqualified().getValue());
 			if (theResource != null) {
-				updateResourceMetadata(entity, theResource);
+				myJpaStorageResourceParser.updateResourceMetadata(entity, theResource);
 			}
 			entity.setUnchangedInCurrentOperation(true);
 			return entity;
@@ -1475,7 +1113,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		}
 
 		if (theResource != null) {
-			updateResourceMetadata(entity, theResource);
+			myJpaStorageResourceParser.updateResourceMetadata(entity, theResource);
 		}
 
 
@@ -1498,7 +1136,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			if (getConfig().isMassIngestionMode()) {
 				oldResource = null;
 			} else {
-				oldResource = toResource(entity, false);
+				oldResource = myJpaStorageResourceParser.toResource(entity, false);
 			}
 
 			notifyInterceptors(theRequest, theResource, oldResource, theTransactionDetails, true);
@@ -1510,7 +1148,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			historyEntity = ((ResourceTable) readEntity(theResourceId, theRequest)).getCurrentVersionEntity();
 
 			// Update version/lastUpdated so that interceptors see the correct version
-			updateResourceMetadata(savedEntity, theResource);
+			myJpaStorageResourceParser.updateResourceMetadata(savedEntity, theResource);
 			// Populate the PID in the resource, so it is available to hooks
 			addPidToResource(savedEntity, theResource);
 
@@ -1537,7 +1175,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 			if (!changed && myConfig.isSuppressUpdatesWithNoChange() && (historyEntity.getVersion() > 1)) {
 				ourLog.debug("Resource {} has not changed", historyEntity.getIdDt().toUnqualified().getValue());
-				updateResourceMetadata(historyEntity, theResource);
+				myJpaStorageResourceParser.updateResourceMetadata(historyEntity, theResource);
 				return historyEntity;
 			}
 
@@ -1556,7 +1194,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		historyEntity.setResourceTextVc(encodedResource.getResourceText());
 		myResourceHistoryTableDao.save(historyEntity);
 
-		updateResourceMetadata(historyEntity, theResource);
+		myJpaStorageResourceParser.updateResourceMetadata(historyEntity, theResource);
 
 		return historyEntity;
 	}
@@ -1586,14 +1224,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 	/**
 	 * TODO eventually consider refactoring this to be part of an interceptor.
-	 *
+	 * <p>
 	 * Throws an exception if the partition of the request, and the partition of the existing entity do not match.
+	 *
 	 * @param theRequest the request.
-	 * @param entity the existing entity.
+	 * @param entity     the existing entity.
 	 */
 	private void failIfPartitionMismatch(RequestDetails theRequest, ResourceTable entity) {
 		if (myPartitionSettings.isPartitioningEnabled() && theRequest != null && theRequest.getTenantId() != null && entity.getPartitionId() != null &&
-				theRequest.getTenantId() != ALL_PARTITIONS_NAME) {
+			!ALL_PARTITIONS_NAME.equals(theRequest.getTenantId())) {
 			PartitionEntity partitionEntity = myPartitionLookupSvc.getPartitionByName(theRequest.getTenantId());
 			//partitionEntity should never be null
 			if (partitionEntity != null && !partitionEntity.getId().equals(entity.getPartitionId().getPartitionId())) {
@@ -1668,8 +1307,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	}
 
 	@Override
-	public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
+	public DaoMethodOutcome updateInternal(RequestDetails theRequestDetails, T theResource, String theMatchUrl, boolean thePerformIndexing, boolean theForceUpdateVersion,
-													IBasePersistedResource theEntity, IIdType theResourceId, IBaseResource theOldResource, TransactionDetails theTransactionDetails) {
+														IBasePersistedResource theEntity, IIdType theResourceId, @Nullable IBaseResource theOldResource, RestOperationTypeEnum theOperationType, TransactionDetails theTransactionDetails) {
 
 		ResourceTable entity = (ResourceTable) theEntity;
 
@@ -1696,7 +1335,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		}
 
 		// Update version/lastUpdated so that interceptors see the correct version
-		updateResourceMetadata(savedEntity, theResource);
+		myJpaStorageResourceParser.updateResourceMetadata(savedEntity, theResource);
 
 		// Populate the PID in the resource so it is available to hooks
 		addPidToResource(savedEntity, theResource);
@@ -1706,7 +1345,42 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			notifyInterceptors(theRequestDetails, theResource, theOldResource, theTransactionDetails, false);
 		}
 
-		return savedEntity;
+		Collection<? extends BaseTag> tagList = Collections.emptyList();
+		if (entity.isHasTags()) {
+			tagList = entity.getTags();
+		}
+		long version = entity.getVersion();
+		myJpaStorageResourceParser.populateResourceMetadata(entity, false, tagList, version, theResource);
+
+		boolean wasDeleted = false;
+		// NB If this if-else ever gets collapsed, make sure to account for possible null (will happen in mass-ingestion mode)
+		if (theOldResource instanceof IResource) {
+			wasDeleted = ResourceMetadataKeyEnum.DELETED_AT.get((IResource) theOldResource) != null;
+		} else if (theOldResource instanceof IAnyResource) {
+			wasDeleted = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) theOldResource) != null;
+		}
+
+		DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, theResource, theMatchUrl, theOperationType).setCreated(wasDeleted);
+
+		if (!thePerformIndexing) {
+			IIdType id = getContext().getVersion().newIdType();
+			id.setValue(entity.getIdDt().getValue());
+			outcome.setId(id);
+		}
+
+		// Only include a task timer if we're not in a sub-request (i.e. a transaction)
+		// since individual item times don't actually make much sense in the context
+		// of a transaction
+		StopWatch w = null;
+		if (theRequestDetails != null && !theRequestDetails.isSubRequest()) {
+			if (theTransactionDetails != null && !theTransactionDetails.isFhirTransaction()) {
+				w = new StopWatch(theTransactionDetails.getTransactionDate());
+			}
+		}
+
+		populateOperationOutcomeForUpdate(w, outcome, theMatchUrl, outcome.getOperationType());
+
+		return outcome;
 	}
 
 	private void notifyInterceptors(RequestDetails theRequestDetails, T theResource, IBaseResource theOldResource, TransactionDetails theTransactionDetails, boolean isUnchanged) {
@@ -1735,26 +1409,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		}
 	}
 
-	protected void updateResourceMetadata(IBaseResourceEntity theEntity, IBaseResource theResource) {
-		IIdType id = theEntity.getIdDt();
-		if (getContext().getVersion().getVersion().isRi()) {
-			id = getContext().getVersion().newIdType().setValue(id.getValue());
-		}
 
-		if (id.hasResourceType() == false) {
-			id = id.withResourceType(theEntity.getResourceType());
-		}
-
-		theResource.setId(id);
-		if (theResource instanceof IResource) {
-			ResourceMetadataKeyEnum.VERSION.put((IResource) theResource, id.getVersionIdPart());
-			ResourceMetadataKeyEnum.UPDATED.put((IResource) theResource, theEntity.getUpdated());
-		} else {
-			IBaseMetaType meta = theResource.getMeta();
-			meta.setVersionId(id.getVersionIdPart());
-			meta.setLastUpdated(theEntity.getUpdatedDate());
-		}
-	}
 
 	private void validateChildReferenceTargetTypes(IBase theElement, String thePath) {
 		if (theElement == null) {
@@ -1896,6 +1551,22 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		myPartitionSettings = thePartitionSettings;
 	}
 
+	private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
+
+		private final TagDefinition myTagDefinition;
+		private final MemoryCacheService.TagDefinitionCacheKey myKey;
+
+		public AddTagDefinitionToCacheAfterCommitSynchronization(MemoryCacheService.TagDefinitionCacheKey theKey, TagDefinition theTagDefinition) {
+			myTagDefinition = theTagDefinition;
+			myKey = theKey;
+		}
+
+		@Override
+		public void afterCommit() {
+			myMemoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, myKey, myTagDefinition);
+		}
+	}
+
 	@Nonnull
 	public static MemoryCacheService.TagDefinitionCacheKey toTagDefinitionMemoryCacheKey(TagTypeEnum theTagType, String theScheme, String theTerm) {
 		return new MemoryCacheService.TagDefinitionCacheKey(theTagType, theScheme, theTerm);
@@ -1999,34 +1670,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		ourValidationDisabledForUnitTest = theValidationDisabledForUnitTest;
 	}
 
-	private static List<BaseCodingDt> toBaseCodingList(List<IBaseCoding> theSecurityLabels) {
+	/**
-		ArrayList<BaseCodingDt> retVal = new ArrayList<>(theSecurityLabels.size());
+	 * Do not call this method outside of unit tests
-		for (IBaseCoding next : theSecurityLabels) {
+	 */
-			retVal.add((BaseCodingDt) next);
+	@VisibleForTesting
-		}
+	public void setJpaStorageResourceParserForUnitTest(IJpaStorageResourceParser theJpaStorageResourceParser) {
-		return retVal;
+		myJpaStorageResourceParser = theJpaStorageResourceParser;
-	}
-
-	public static void validateResourceType(BaseHasResource theEntity, String theResourceName) {
-		if (!theResourceName.equals(theEntity.getResourceType())) {
-			throw new ResourceNotFoundException(Msg.code(935) + "Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
-		}
-	}
-
-	private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
-
-		private final TagDefinition myTagDefinition;
-		private final MemoryCacheService.TagDefinitionCacheKey myKey;
-
-		public AddTagDefinitionToCacheAfterCommitSynchronization(MemoryCacheService.TagDefinitionCacheKey theKey, TagDefinition theTagDefinition) {
-			myTagDefinition = theTagDefinition;
-			myKey = theKey;
-		}
-
-		@Override
-		public void afterCommit() {
-			myMemoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, myKey, myTagDefinition);
-		}
 	}
 
 }

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

@@ -58,26 +58,23 @@ import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
-import ca.uhn.fhir.jpa.patch.FhirPatch;
-import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
-import ca.uhn.fhir.jpa.patch.XmlPatchUtils;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
 import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.api.StorageResponseCodeEnum;
 import ca.uhn.fhir.model.dstu2.resource.ListResource;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.parser.DataFormatException;
-import ca.uhn.fhir.parser.StrictErrorHandler;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
@@ -105,9 +102,9 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
 import ca.uhn.fhir.util.ObjectUtil;
-import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
 import ca.uhn.fhir.validation.IValidationContext;
@@ -119,7 +116,6 @@ 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;
@@ -161,7 +157,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	public static final String BASE_RESOURCE_NAME = "resource";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
-
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired(required = false)
@@ -182,18 +177,37 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	private IDeleteExpungeJobSubmitter myDeleteExpungeJobSubmitter;
 	@Autowired
 	private IJobCoordinator myJobCoordinator;
-
 	private IInstanceValidatorModule myInstanceValidator;
 	private String myResourceName;
 	private Class<T> myResourceType;
-
+	@Autowired
+	private PersistedJpaBundleProviderFactory myPersistedJpaBundleProviderFactory;
 	@Autowired
 	private MemoryCacheService myMemoryCacheService;
 	private TransactionTemplate myTxTemplate;
-
 	@Autowired
 	private UrlPartitioner myUrlPartitioner;
 
+	@Override
+	protected HapiTransactionService getTransactionService() {
+		return myTransactionService;
+	}
+
+	@VisibleForTesting
+	public void setTransactionService(HapiTransactionService theTransactionService) {
+		myTransactionService = theTransactionService;
+	}
+
+	@Override
+	protected MatchResourceUrlService getMatchResourceUrlService() {
+		return myMatchResourceUrlService;
+	}
+
+	@Override
+	protected IStorageResourceParser getStorageResourceParser() {
+		return myJpaStorageResourceParser;
+	}
+
 	/**
 	 * @deprecated Use {@link #create(T, RequestDetails)} instead
 	 */
@@ -220,11 +234,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return create(theResource, theIfNoneExist, true, new TransactionDetails(), theRequestDetails);
 	}
 
-	@VisibleForTesting
-	public void setTransactionService(HapiTransactionService theTransactionService) {
-		myTransactionService = theTransactionService;
-	}
-
 	@Override
 	public DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing, @Nonnull TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
 		return myTransactionService.execute(theRequestDetails, theTransactionDetails, tx -> doCreateForPost(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails));
@@ -260,14 +269,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(theRequestDetails, theResource, getResourceName());
-		return doCreateForPostOrPut(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails, requestPartitionId);
+		return doCreateForPostOrPut(theRequestDetails, theResource, theIfNoneExist, true, thePerformIndexing, requestPartitionId, RestOperationTypeEnum.CREATE, theTransactionDetails);
 	}
 
 	/**
 	 * Called both for FHIR create (POST) operations (via {@link #doCreateForPost(IBaseResource, String, boolean, TransactionDetails, RequestDetails)}
 	 * as well as for FHIR update (PUT) where we're doing a create-with-client-assigned-ID (via {@link #doUpdate(IBaseResource, String, boolean, boolean, RequestDetails, TransactionDetails)}.
 	 */
-	private DaoMethodOutcome doCreateForPostOrPut(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
+	private DaoMethodOutcome doCreateForPostOrPut(RequestDetails theRequest, T theResource, String theMatchUrl, boolean theProcessMatchUrl, boolean thePerformIndexing, RequestPartitionId theRequestPartitionId, RestOperationTypeEnum theOperationType, TransactionDetails theTransactionDetails) {
 		StopWatch w = new StopWatch();
 
 		preProcessResourceForStorage(theResource);
@@ -276,22 +285,21 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		ResourceTable entity = new ResourceTable();
 		entity.setResourceType(toResourceName(theResource));
 		entity.setPartitionId(myRequestPartitionHelperService.toStoragePartition(theRequestPartitionId));
-		entity.setCreatedByMatchUrl(theIfNoneExist);
+		entity.setCreatedByMatchUrl(theMatchUrl);
 		entity.setVersion(1);
 
-		if (isNotBlank(theIfNoneExist)) {
+		if (isNotBlank(theMatchUrl) && theProcessMatchUrl) {
-			Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theTransactionDetails, theRequest)
+			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest);
-				.stream().map(id -> (JpaPid) id).collect(Collectors.toSet());
 			if (match.size() > 1) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theMatchUrl, match.size());
 				throw new PreconditionFailedException(Msg.code(958) + msg);
 			} else if (match.size() == 1) {
-				JpaPid pid = match.iterator().next();
+				JpaPid pid = (JpaPid) match.iterator().next();
 
 				Supplier<LazyDaoMethodOutcome.EntityAndResource> entitySupplier = () -> {
 					return myTxTemplate.execute(tx -> {
 						ResourceTable foundEntity = myEntityManager.find(ResourceTable.class, pid.getId());
-						IBaseResource resource = toResource(foundEntity, false);
+						IBaseResource resource = myJpaStorageResourceParser.toResource(foundEntity, false);
 						theResource.setId(resource.getIdElement().getValue());
 						return new LazyDaoMethodOutcome.EntityAndResource(foundEntity, resource);
 					});
@@ -316,7 +324,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 					});
 				};
 
-				return toMethodOutcomeLazy(theRequest, pid, entitySupplier, idSupplier).setCreated(false).setNop(true);
+				DaoMethodOutcome outcome = toMethodOutcomeLazy(theRequest, pid, entitySupplier, idSupplier).setCreated(false).setNop(true);
+				StorageResponseCodeEnum responseCode = StorageResponseCodeEnum.SUCCESSFUL_CREATE_WITH_CONDITIONAL_MATCH;
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulCreateConditionalWithMatch", w.getMillisAndRestart(), UrlUtil.sanitizeUrlPart(theMatchUrl));
+				outcome.setOperationOutcome(createInfoOperationOutcome(msg, responseCode));
+				return outcome;
 			}
 		}
 
@@ -387,15 +399,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		theTransactionDetails.addResolvedResourceId(jpaPid.getAssociatedResourceId(), jpaPid);
 
 		// Pre-cache the match URL
-		if (theIfNoneExist != null) {
+		if (theMatchUrl != null) {
-			myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theIfNoneExist, jpaPid);
+			myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, jpaPid);
 		}
 
 		// Update the version/last updated in the resource so that interceptors get
 		// the correct version
 		// TODO - the above updateEntity calls updateResourceMetadata
 		// 		Maybe we don't need this call here?
-		updateResourceMetadata(entity, theResource);
+		myJpaStorageResourceParser.updateResourceMetadata(entity, theResource);
 
 		// Populate the PID in the resource so it is available to hooks
 		addPidToResource(entity, theResource);
@@ -411,15 +423,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, hookParams);
 		}
 
-		DaoMethodOutcome outcome = toMethodOutcome(theRequest, entity, theResource).setCreated(true);
+		DaoMethodOutcome outcome = toMethodOutcome(theRequest, entity, theResource, theMatchUrl, theOperationType)
+			.setCreated(true);
+
 		if (!thePerformIndexing) {
 			outcome.setId(theResource.getIdElement());
 		}
 
-		String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart());
+		populateOperationOutcomeForUpdate(w, outcome, theMatchUrl, theOperationType);
-		outcome.setOperationOutcome(createInfoOperationOutcome(msg));
 
-		ourLog.debug(msg);
 		return outcome;
 	}
 
@@ -533,8 +545,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			// if not found, return an outcome anyways.
 			// Because no object actually existed, we'll
 			// just set the id and nothing else
-			DaoMethodOutcome outcome = createMethodOutcomeForResourceId(theId.getValue(), MESSAGE_KEY_DELETE_RESOURCE_NOT_EXISTING);
+			return createMethodOutcomeForResourceId(theId.getValue(), MESSAGE_KEY_DELETE_RESOURCE_NOT_EXISTING, StorageResponseCodeEnum.SUCCESSFUL_DELETE_NOT_FOUND);
-			return outcome;
 		}
 
 		if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) {
@@ -543,7 +554,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		// Don't delete again if it's already deleted
 		if (isDeleted(entity)) {
-			DaoMethodOutcome outcome = createMethodOutcomeForResourceId(entity.getIdDt().getValue(), MESSAGE_KEY_DELETE_RESOURCE_ALREADY_DELETED);
+			DaoMethodOutcome outcome = createMethodOutcomeForResourceId(entity.getIdDt().getValue(), MESSAGE_KEY_DELETE_RESOURCE_ALREADY_DELETED, StorageResponseCodeEnum.SUCCESSFUL_DELETE_ALREADY_DELETED);
 
 			// used to exist, so we'll set the persistent id
 			outcome.setPersistentId(new JpaPid(entity.getResourceId()));
@@ -554,7 +565,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		StopWatch w = new StopWatch();
 
-		T resourceToDelete = toResource(myResourceType, entity, null, false);
+		T resourceToDelete = myJpaStorageResourceParser.toResource(myResourceType, entity, null, false);
 		theDeleteConflicts.setResourceIdMarkedForDeletion(theId);
 
 		// Notify IServerOperationInterceptors about pre-action call
@@ -583,14 +594,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		doCallHooks(theTransactionDetails, theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
 
-		DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, resourceToDelete).setCreated(true);
+		DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, resourceToDelete, null, RestOperationTypeEnum.DELETE).setCreated(true);
 
-		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
+		String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulDeletes", 1);
-		String message = getContext().getLocalizer().getMessage(BaseStorageDao.class, "successfulDeletes", 1, w.getMillis());
+		msg += " " + getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulTimingSuffix", w.getMillis());
-		String severity = "information";
+		outcome.setOperationOutcome(createInfoOperationOutcome(msg, StorageResponseCodeEnum.SUCCESSFUL_DELETE));
-		String code = "informational";
-		OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
-		outcome.setOperationOutcome(oo);
 
 		return outcome;
 	}
@@ -671,7 +679,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			ResourceTable entity = myEntityManager.find(ResourceTable.class, ((JpaPid) pid).getId());
 			deletedResources.add(entity);
 
-			T resourceToDelete = toResource(myResourceType, entity, null, false);
+			T resourceToDelete = myJpaStorageResourceParser.toResource(myResourceType, entity, null, false);
 
 			// Notify IServerOperationInterceptors about pre-action call
 			HookParams hooks = new HookParams()
@@ -705,17 +713,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		IBaseOperationOutcome oo;
 		if (deletedResources.isEmpty()) {
-			oo = OperationOutcomeUtil.newInstance(getContext());
+			String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "unableToDeleteNotFound", theUrl);
-			String message = getMessageSanitized("unableToDeleteNotFound", theUrl);
+			oo = createOperationOutcome(OO_SEVERITY_WARN, msg, "not-found", StorageResponseCodeEnum.SUCCESSFUL_DELETE_NOT_FOUND);
-			String severity = "warning";
-			String code = "not-found";
-			OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
 		} else {
-			oo = OperationOutcomeUtil.newInstance(getContext());
+			String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulDeletes", deletedResources.size());
-			String message = getContext().getLocalizer().getMessage(BaseStorageDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
+			msg += " " + getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulTimingSuffix", w.getMillis());
-			String severity = "information";
+			oo = createInfoOperationOutcome(msg, StorageResponseCodeEnum.SUCCESSFUL_DELETE);
-			String code = "informational";
-			OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
 		}
 
 		ourLog.debug("Processed delete on {} (matched {} resource(s)) in {}ms", theUrl, deletedResources.size(), w.getMillis());
@@ -747,7 +750,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	private <MT extends IBaseMetaType> void doMetaAdd(MT theMetaAdd, BaseHasResource theEntity, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
-		IBaseResource oldVersion = toResource(theEntity, false);
+		IBaseResource oldVersion = myJpaStorageResourceParser.toResource(theEntity, false);
 
 		List<TagDefinition> tags = toTagList(theMetaAdd);
 		for (TagDefinition nextDef : tags) {
@@ -780,7 +783,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		myEntityManager.merge(theEntity);
 
 		// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
-		IBaseResource newVersion = toResource(theEntity, false);
+		IBaseResource newVersion = myJpaStorageResourceParser.toResource(theEntity, false);
 		HookParams preStorageParams = new HookParams()
 			.add(IBaseResource.class, oldVersion)
 			.add(IBaseResource.class, newVersion)
@@ -804,7 +807,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	private <MT extends IBaseMetaType> void doMetaDelete(MT theMetaDel, BaseHasResource theEntity, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
 
 		// todo mb update hibernate search index if we are storing resources - it assumes inline tags.
-		IBaseResource oldVersion = toResource(theEntity, false);
+		IBaseResource oldVersion = myJpaStorageResourceParser.toResource(theEntity, false);
 
 		List<TagDefinition> tags = toTagList(theMetaDel);
 
@@ -826,7 +829,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		theEntity = myEntityManager.merge(theEntity);
 
 		// Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
-		IBaseResource newVersion = toResource(theEntity, false);
+		IBaseResource newVersion = myJpaStorageResourceParser.toResource(theEntity, false);
 		HookParams preStorageParams = new HookParams()
 			.add(IBaseResource.class, oldVersion)
 			.add(IBaseResource.class, newVersion)
@@ -891,6 +894,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
+	@Nonnull
 	public String getResourceName() {
 		return myResourceName;
 	}
@@ -910,7 +914,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Transactional
 	public IBundleProvider history(Date theSince, Date theUntil, Integer theOffset, RequestDetails theRequestDetails) {
 		StopWatch w = new StopWatch();
-		IBundleProvider retVal = super.history(theRequestDetails, myResourceName, null, theSince, theUntil, theOffset);
+		IBundleProvider retVal = myPersistedJpaBundleProviderFactory.history(theRequestDetails, myResourceName, null, theSince, theUntil, theOffset);
 		ourLog.debug("Processed history on {} in {}ms", myResourceName, w.getMillisAndRestart());
 		return retVal;
 	}
@@ -926,7 +930,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		IIdType id = theId.withResourceType(myResourceName).toUnqualifiedVersionless();
 		BaseHasResource entity = readEntity(id, theRequest);
 
-		IBundleProvider retVal = super.history(theRequest, myResourceName, entity.getId(), theSince, theUntil, theOffset);
+		IBundleProvider retVal = myPersistedJpaBundleProviderFactory.history(theRequest, myResourceName, entity.getId(), theSince, theUntil, theOffset);
 
 		ourLog.debug("Processed history on {} in {}ms", id, w.getMillisAndRestart());
 		return retVal;
@@ -941,7 +945,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		IIdType id = theId.withResourceType(myResourceName).toUnqualifiedVersionless();
 		BaseHasResource entity = readEntity(id, theRequest);
 
-		IBundleProvider retVal = super.history(theRequest, myResourceName, entity.getId(),
+		IBundleProvider retVal = myPersistedJpaBundleProviderFactory.history(theRequest, myResourceName, entity.getId(),
 			theHistorySearchDateRangeParam.getLowerBoundAsInstant(),
 			theHistorySearchDateRangeParam.getUpperBoundAsInstant(),
 			theHistorySearchDateRangeParam.getOffset(),
@@ -1098,68 +1102,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return toMetaDt(theType, tagDefinitions);
 	}
 
-	@Override
-	public DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest) {
-		TransactionDetails transactionDetails = new TransactionDetails();
-		return myTransactionService.execute(theRequest, transactionDetails, tx -> doPatch(theId, theConditionalUrl, thePatchType, thePatchBody, theFhirPatchBody, theRequest, transactionDetails));
-	}
-
-	private DaoMethodOutcome doPatch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
-		ResourceTable entityToUpdate;
-		if (isNotBlank(theConditionalUrl)) {
-
-			Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(theConditionalUrl, myResourceType, theTransactionDetails, theRequest)
-				.stream().map(id -> (JpaPid) id).collect(Collectors.toSet());
-			if (match.size() > 1) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "PATCH", theConditionalUrl, match.size());
-				throw new PreconditionFailedException(Msg.code(972) + msg);
-			} else if (match.size() == 1) {
-				JpaPid pid = match.iterator().next();
-				entityToUpdate = myEntityManager.find(ResourceTable.class, pid.getId());
-			} else {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidMatchUrlNoMatches", theConditionalUrl);
-				throw new ResourceNotFoundException(Msg.code(973) + msg);
-			}
-
-		} else {
-			entityToUpdate = readEntityLatestVersion(theId, theRequest, theTransactionDetails);
-			if (theId.hasVersionIdPart()) {
-				if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) {
-					throw new ResourceVersionConflictException(Msg.code(974) + "Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch");
-				}
-			}
-		}
-
-		validateResourceType(entityToUpdate);
-
-		if (isDeleted(entityToUpdate)) {
-			throw createResourceGoneException(entityToUpdate);
-		}
-
-		IBaseResource resourceToUpdate = toResource(entityToUpdate, false);
-		IBaseResource destination;
-		switch (thePatchType) {
-			case JSON_PATCH:
-				destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
-				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")
-		T destinationCasted = (T) destination;
-		myFhirContext.newJsonParser().setParserErrorHandler(new StrictErrorHandler()).encodeResourceToString(destinationCasted);
-		return update(destinationCasted, null, true, theRequest);
-	}
-
 	private boolean isDeleted(BaseHasResource entityToUpdate) {
 		return entityToUpdate.getDeleted() != null;
 	}
@@ -1209,7 +1151,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			throw createResourceGoneException(entity.get());
 		}
 
-		T retVal = toResource(myResourceType, entity.get(), null, false);
+		T retVal = myJpaStorageResourceParser.toResource(myResourceType, entity.get(), null, false);
 
 		ourLog.debug("Processed read on {} in {}ms", jpaPid, w.getMillis());
 		return retVal;
@@ -1243,7 +1185,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		BaseHasResource entity = readEntity(theId, theRequest);
 		validateResourceType(entity);
 
-		T retVal = toResource(myResourceType, entity, null, false);
+		T retVal = myJpaStorageResourceParser.toResource(myResourceType, entity, null, false);
 
 		if (theDeletedOk == false) {
 			if (isDeleted(entity)) {
@@ -1297,7 +1239,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		ResourceTable entity = entityOpt.get();
 		try {
-			T resource = (T) toResource(entity, false);
+			T resource = (T) myJpaStorageResourceParser.toResource(entity, false);
 			reindex(resource, entity);
 		} catch (BaseServerResponseException | DataFormatException e) {
 			myResourceTableDao.updateIndexStatus(entity.getId(), INDEX_STATUS_INDEXING_FAILED);
@@ -1379,6 +1321,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return entity;
 	}
 
+	@Override
+	protected IBasePersistedResource readEntityLatestVersion(ResourcePersistentId thePersistentId, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
+		return myEntityManager.find(ResourceTable.class, thePersistentId.getIdAsLong());
+	}
+
+
+	@Override
 	@Nonnull
 	protected ResourceTable readEntityLatestVersion(IIdType theId, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
 		RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForRead(theRequestDetails, getResourceName(), theId);
@@ -1695,8 +1644,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	private DaoMethodOutcome doUpdate(T theResource, String theMatchUrl, boolean thePerformIndexing, boolean theForceUpdateVersion, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
-		StopWatch w = new StopWatch();
-
 		T resource = theResource;
 
 		preProcessResourceForStorage(resource);
@@ -1705,6 +1652,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		ResourceTable entity = null;
 
 		IIdType resourceId;
+		RestOperationTypeEnum update = RestOperationTypeEnum.UPDATE;
 		if (isNotBlank(theMatchUrl)) {
 			Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest, theResource)
 				.stream().map(id -> (JpaPid) id).collect(Collectors.toSet());
@@ -1716,7 +1664,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				entity = myEntityManager.find(ResourceTable.class, pid.getId());
 				resourceId = entity.getIdDt();
 			} else {
-				DaoMethodOutcome outcome = create(resource, null, thePerformIndexing, theTransactionDetails, theRequest);
+				RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(theRequest, theResource, getResourceName());
+				DaoMethodOutcome outcome = doCreateForPostOrPut(theRequest, resource, theMatchUrl, false, thePerformIndexing, requestPartitionId, update, theTransactionDetails);
 
 				// Pre-cache the match URL
 				if (outcome.getPersistentId() != null) {
@@ -1755,86 +1704,17 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 
 			if (create) {
-				return doCreateForPostOrPut(resource, null, thePerformIndexing, theTransactionDetails, theRequest, requestPartitionId);
+				return doCreateForPostOrPut(theRequest, resource, null, false, thePerformIndexing, requestPartitionId, update, theTransactionDetails);
 			}
 		}
 
-		if (resourceId.hasVersionIdPart() && Long.parseLong(resourceId.getVersionIdPart()) != entity.getVersion()) {
+		// Start
-			throw new ResourceVersionConflictException(Msg.code(989) + "Trying to update " + resourceId + " but this is not the current version");
-		}
 
-		if (resourceId.hasResourceType() && !resourceId.getResourceType().equals(getResourceName())) {
+		return doUpdateForUpdateOrPatch(theRequest, resourceId, theMatchUrl, thePerformIndexing, theForceUpdateVersion, resource, entity, update, theTransactionDetails);
-			throw new UnprocessableEntityException(Msg.code(990) + "Invalid resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] of type[" + entity.getResourceType() + "] - Does not match expected [" + getResourceName() + "]");
-		}
-
-		IBaseResource oldResource;
-		if (getConfig().isMassIngestionMode()) {
-			oldResource = null;
-		} else {
-			oldResource = toResource(entity, false);
-		}
-
-		/*
-		 * Mark the entity as not deleted - This is also done in the actual updateInternal()
-		 * method later on so it usually doesn't matter whether we do it here, but in the
-		 * case of a transaction with multiple PUTs we don't get there until later so
-		 * having this here means that a transaction can have a reference in one
-		 * resource to another resource in the same transaction that is being
-		 * un-deleted by the transaction. Wacky use case, sure. But it's real.
-		 *
-		 * See SystemProviderR4Test#testTransactionReSavesPreviouslyDeletedResources
-		 * for a test that needs this.
-		 */
-		boolean wasDeleted = isDeleted(entity);
-		entity.setDeleted(null);
-
-		/*
-		 * If we aren't indexing, that means we're doing this inside a transaction.
-		 * The transaction will do the actual storage to the database a bit later on,
-		 * after placeholder IDs have been replaced, by calling {@link #updateInternal}
-		 * directly. So we just bail now.
-		 */
-		if (!thePerformIndexing) {
-			resource.setId(entity.getIdDt().getValue());
-			DaoMethodOutcome outcome = toMethodOutcome(theRequest, entity, resource).setCreated(wasDeleted);
-			outcome.setPreviousResource(oldResource);
-			if (!outcome.isNop()) {
-				// Technically this may not end up being right since we might not increment if the
-				// contents turn out to be the same
-				outcome.setId(outcome.getId().withVersion(Long.toString(outcome.getId().getVersionIdPartAsLong() + 1)));
-			}
-			return outcome;
-		}
-
-		/*
-		 * Otherwise, we're not in a transaction
-		 */
-		ResourceTable savedEntity = updateInternal(theRequest, resource, thePerformIndexing, theForceUpdateVersion, entity, resourceId, oldResource, theTransactionDetails);
-
-		if (thePerformIndexing) {
-			Collection<? extends BaseTag> tagList = Collections.emptyList();
-			if (entity.isHasTags()) {
-				tagList = entity.getTags();
-			}
-			long version = entity.getVersion();
-			populateResourceMetadata(entity, false, tagList, version, getResourceType(), resource);
-		}
-
-		DaoMethodOutcome outcome = toMethodOutcome(theRequest, savedEntity, resource).setCreated(wasDeleted);
-
-		if (!thePerformIndexing) {
-			IIdType id = getContext().getVersion().newIdType();
-			id.setValue(entity.getIdDt().getValue());
-			outcome.setId(id);
-		}
-
-		String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulUpdate", outcome.getId(), w.getMillisAndRestart());
-		outcome.setOperationOutcome(createInfoOperationOutcome(msg));
-
-		ourLog.debug(msg);
-		return outcome;
 	}
 
+
+
 	/**
 	 * Method for updating the historical version of the resource when a history version id is included in the request.
 	 *
@@ -1849,8 +1729,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		// No need for indexing as this will update a non-current version of the resource which will not be searchable
 		preProcessResourceForStorage(theResource, theRequest, theTransactionDetails, false);
 
-		BaseHasResource entity = null;
+		BaseHasResource entity;
-		BaseHasResource currentEntity = null;
+		BaseHasResource currentEntity;
 
 		IIdType resourceId;
 
@@ -1879,12 +1759,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		entity.setDeleted(null);
 		boolean isUpdatingCurrent = resourceId.hasVersionIdPart() && Long.parseLong(resourceId.getVersionIdPart()) == currentEntity.getVersion();
 		IBasePersistedResource savedEntity = updateHistoryEntity(theRequest, theResource, currentEntity, entity, resourceId, theTransactionDetails, isUpdatingCurrent);
-		DaoMethodOutcome outcome = toMethodOutcome(theRequest, savedEntity, theResource).setCreated(wasDeleted);
+		DaoMethodOutcome outcome = toMethodOutcome(theRequest, savedEntity, theResource, null, RestOperationTypeEnum.UPDATE).setCreated(wasDeleted);
 
-		String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulUpdate", outcome.getId(), w.getMillisAndRestart());
+		populateOperationOutcomeForUpdate(w, outcome, null, RestOperationTypeEnum.UPDATE);
-		outcome.setOperationOutcome(createInfoOperationOutcome(msg));
 
-		ourLog.debug(msg);
 		return outcome;
 	}
 

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

@@ -1,13 +1,21 @@
 package ca.uhn.fhir.jpa.dao;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
+import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
+import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
 import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
 import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
@@ -26,6 +34,9 @@ import org.springframework.transaction.annotation.Transactional;
 
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.PersistenceContextType;
 import javax.persistence.TypedQuery;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -59,25 +70,36 @@ import java.util.stream.Collectors;
  * #L%
  */
 
-public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends BaseHapiFhirDao<IBaseResource> implements IFhirSystemDao<T, MT> {
+public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends BaseStorageDao implements IFhirSystemDao<T, MT> {
 
 	public static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[0];
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirSystemDao.class);
 	public ResourceCountCache myResourceCountsCache;
+
+	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
+	protected EntityManager myEntityManager;
 	@Autowired
 	private TransactionProcessor myTransactionProcessor;
 	@Autowired
 	private ApplicationContext myApplicationContext;
+	@Autowired
+	private ExpungeService myExpungeService;
+	@Autowired
+	private IResourceTableDao myResourceTableDao;
+	@Autowired
+	private PersistedJpaBundleProviderFactory myPersistedJpaBundleProviderFactory;
+	@Autowired
+	private IResourceTagDao myResourceTagDao;
+	@Autowired
+	private IInterceptorBroadcaster myInterceptorBroadcaster;
 
 	@VisibleForTesting
 	public void setTransactionProcessorForUnitTest(TransactionProcessor theTransactionProcessor) {
 		myTransactionProcessor = theTransactionProcessor;
 	}
 
-	@Override
 	@PostConstruct
 	public void start() {
-		super.start();
 		myTransactionProcessor.setDao(this);
 	}
 
@@ -125,7 +147,7 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
 	@Override
 	public IBundleProvider history(Date theSince, Date theUntil, Integer theOffset, RequestDetails theRequestDetails) {
 		StopWatch w = new StopWatch();
-		IBundleProvider retVal = super.history(theRequestDetails, null, null, theSince, theUntil, theOffset);
+		IBundleProvider retVal = myPersistedJpaBundleProviderFactory.history(theRequestDetails, null, null, theSince, theUntil, theOffset);
 		ourLog.info("Processed global history in {}ms", w.getMillisAndRestart());
 		return retVal;
 	}
@@ -260,4 +282,25 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
 		return null;
 	}
 
+
+	@Override
+	protected IInterceptorBroadcaster getInterceptorBroadcaster() {
+		return myInterceptorBroadcaster;
+	}
+
+	@Override
+	protected DaoConfig getConfig() {
+		return myDaoConfig;
+	}
+
+	@Override
+	public FhirContext getContext() {
+		return myFhirContext;
+	}
+
+	@VisibleForTesting
+	public void setDaoConfigForUnitTest(DaoConfig theDaoConfig) {
+		myDaoConfig = theDaoConfig;
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoCompositionDstu2.java

@@ -1,42 +0,0 @@
-package ca.uhn.fhir.jpa.dao;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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.i18n.Msg;
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoComposition;
-import ca.uhn.fhir.model.dstu2.resource.Composition;
-import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-
-import javax.servlet.http.HttpServletRequest;
-
-public class FhirResourceDaoCompositionDstu2 extends BaseHapiFhirResourceDao<Composition>implements IFhirResourceDaoComposition<Composition> {
-
-	@Override
-	public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
-		throw new NotImplementedOperationException(Msg.code(955) + "$document not implemented in DSTU2");
-	}
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSearchParameterDstu2.java

@@ -1,89 +0,0 @@
-package ca.uhn.fhir.jpa.dao;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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.jpa.api.dao.IFhirResourceDaoSearchParameter;
-import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
-import ca.uhn.fhir.model.dstu2.resource.SearchParameter;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import com.google.common.collect.Lists;
-import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_40;
-import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_40;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import java.util.List;
-
-import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-public class FhirResourceDaoSearchParameterDstu2 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
-
-	@Autowired
-	private ISearchParamExtractor mySearchParamExtractor;
-	private FhirContext myDstu2Hl7OrgContext = FhirContext.forDstu2Hl7Org();
-
-	protected void reindexAffectedResources(SearchParameter theResource, RequestDetails theRequestDetails) {
-		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
-		String expression = theResource != null ? theResource.getXpath() : null;
-		List<String> base = theResource != null ? Lists.newArrayList(theResource.getBase()) : null;
-		requestReindexForRelatedResources(reindex, base, theRequestDetails);
-	}
-
-	@Override
-	protected void postPersist(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postPersist(theEntity, theResource, theRequestDetails);
-		reindexAffectedResources(theResource, theRequestDetails);
-
-	}
-
-	@Override
-	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postUpdate(theEntity, theResource, theRequestDetails);
-		reindexAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void preDelete(SearchParameter theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
-		super.preDelete(theResourceToDelete, theEntityToDelete, theRequestDetails);
-		reindexAffectedResources(theResourceToDelete, theRequestDetails);
-	}
-
-	@Override
-	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
-		super.validateResourceForStorage(theResource, theEntityToSave);
-
-		String encoded = getContext().newJsonParser().encodeResourceToString(theResource);
-		org.hl7.fhir.dstu2.model.SearchParameter hl7Org = myDstu2Hl7OrgContext.newJsonParser().parseResource(org.hl7.fhir.dstu2.model.SearchParameter.class, encoded);
-
-		org.hl7.fhir.r4.model.SearchParameter convertedSp = (org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_10_40.convertResource(hl7Org, new BaseAdvisor_10_40(false));
-		if (isBlank(convertedSp.getExpression()) && isNotBlank(hl7Org.getXpath())) {
-			convertedSp.setExpression(hl7Org.getXpath());
-		}
-
-		FhirResourceDaoSearchParameterR4.validateSearchParam(convertedSp, getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
-
-	}
-
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.jpa.model.entity.TagDefinition;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;

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

@@ -0,0 +1,52 @@
+package ca.uhn.fhir.jpa.dao;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.model.entity.BaseTag;
+import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
+import ca.uhn.fhir.jpa.model.entity.ResourceTag;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import javax.annotation.Nullable;
+import java.util.Collection;
+
+public interface IJpaStorageResourceParser extends IStorageResourceParser {
+
+	/**
+	 * Convert a storage entity into a FHIR resource model instance
+	 */
+	<R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation);
+
+	/**
+	 * Populate the metadata (Resource.meta.*) from a storage entity and other related
+	 * objects pulled from the database
+	 */
+	<R extends IBaseResource> R populateResourceMetadata(IBaseResourceEntity theEntitySource, boolean theForHistoryOperation, @Nullable Collection<? extends BaseTag> tagList, long theVersion, R theResourceTarget);
+
+	/**
+	 * Populates a resource model object's metadata (Resource.meta.*) based on the
+	 * values from a stroage entity.
+	 *
+	 * @param theEntitySource The source
+	 * @param theResourceTarget The target
+	 */
+	void updateResourceMetadata(IBaseResourceEntity theEntitySource, IBaseResource theResourceTarget);
+}

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao.r4;
+package ca.uhn.fhir.jpa.dao;
 
 /*
  * #%L
@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.r4;
  */
 
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoComposition;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.rest.api.SortSpec;
@@ -29,14 +28,14 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringParam;
+import 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.Composition;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.Collections;
 
-public class FhirResourceDaoCompositionR4 extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
+public class JpaResourceDaoComposition<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> implements IFhirResourceDaoComposition<T> {
 
 	@Override
 	public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {

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

@@ -29,29 +29,70 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.api.CacheControlDirective;
+import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.param.ReferenceOrListParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Observation;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.PersistenceContextType;
+import javax.servlet.http.HttpServletResponse;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.TreeMap;
 
-public abstract class BaseHapiFhirResourceDaoObservation<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> implements IFhirResourceDaoObservation<T> {
+public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> implements IFhirResourceDaoObservation<T> {
 
+	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
+	protected EntityManager myEntityManager;
 	@Autowired
 	ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
-
 	@Autowired
 	private IRequestPartitionHelperSvc myRequestPartitionHelperService;
 
+	@Override
+	public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
+		updateSearchParamsForLastn(theSearchParameterMap, theRequestDetails);
+
+		RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(theRequestDetails, getResourceName(), theSearchParameterMap, null);
+		return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails, requestPartitionId);
+	}
+
+	private String getEffectiveParamName() {
+		return Observation.SP_DATE;
+	}
+
+	private String getCodeParamName() {
+		return Observation.SP_CODE;
+	}
+
+	private String getSubjectParamName() {
+		return Observation.SP_SUBJECT;
+	}
+
+	private String getPatientParamName() {
+		return Observation.SP_PATIENT;
+	}
+
+	@Override
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+												 boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+		return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
+			thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
+			theCreateNewHistoryEntry);
+	}
+
 	protected ResourceTable updateObservationEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity,
 																	Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
 																	TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
@@ -130,12 +171,4 @@ public abstract class BaseHapiFhirResourceDaoObservation<T extends IBaseResource
 
 	}
 
-	abstract protected String getEffectiveParamName();
-
-	abstract protected String getCodeParamName();
-
-	abstract protected String getSubjectParamName();
-
-	abstract protected String getPatientParamName();
-
 }

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao.r4;
+package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
@@ -6,18 +6,18 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.HapiExtensions;
+import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
+import com.google.common.annotations.VisibleForTesting;
+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.r5.model.CodeType;
-import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r5.model.Enumerations;
-import org.hl7.fhir.r4.model.SearchParameter;
+import org.hl7.fhir.r5.model.SearchParameter;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.List;
@@ -46,60 +46,63 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
  * #L%
  */
 
-public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
+public class JpaResourceDaoSearchParameter<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> implements IFhirResourceDaoSearchParameter<T> {
 
 	private static final Pattern REGEX_SP_EXPRESSION_HAS_PATH = Pattern.compile("[( ]*([A-Z][a-zA-Z]+\\.)?[a-z].*");
 	@Autowired
-	private ISearchParamExtractor mySearchParamExtractor;
+	private VersionCanonicalizer myVersionCanonicalizer;
 
-	protected void reindexAffectedResources(SearchParameter theResource, RequestDetails theRequestDetails) {
+	protected void reindexAffectedResources(T theResource, RequestDetails theRequestDetails) {
+		// N.B. Don't do this on the canonicalized version
 		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
-		String expression = theResource != null ? theResource.getExpression() : null;
+
-		List<String> base = theResource != null ? theResource.getBase().stream().map(CodeType::getCode).collect(Collectors.toList()) : null;
+		org.hl7.fhir.r5.model.SearchParameter searchParameter = myVersionCanonicalizer.searchParameterToCanonical(theResource);
+		List<String> base = theResource != null ? searchParameter.getBase().stream().map(CodeType::getCode).collect(Collectors.toList()) : null;
 		requestReindexForRelatedResources(reindex, base, theRequestDetails);
 	}
 
 
 	@Override
-	protected void postPersist(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
+	protected void postPersist(ResourceTable theEntity, T theResource, RequestDetails theRequestDetails) {
 		super.postPersist(theEntity, theResource, theRequestDetails);
 		reindexAffectedResources(theResource, theRequestDetails);
 	}
 
 	@Override
-	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
+	protected void postUpdate(ResourceTable theEntity, T theResource, RequestDetails theRequestDetails) {
 		super.postUpdate(theEntity, theResource, theRequestDetails);
 		reindexAffectedResources(theResource, theRequestDetails);
 	}
 
 	@Override
-	protected void preDelete(SearchParameter theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
+	protected void preDelete(T theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
 		super.preDelete(theResourceToDelete, theEntityToDelete, theRequestDetails);
 		reindexAffectedResources(theResourceToDelete, theRequestDetails);
 	}
 
 	@Override
-	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
+	protected void validateResourceForStorage(T theResource, ResourceTable theEntityToSave) {
 		super.validateResourceForStorage(theResource, theEntityToSave);
 
-		validateSearchParam(theResource, getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
+		validateSearchParam(theResource, getContext(), getConfig());
 	}
 
-	public static void validateSearchParam(SearchParameter theResource, FhirContext theContext, DaoConfig theDaoConfig, ISearchParamRegistry theSearchParamRegistry, ISearchParamExtractor theSearchParamExtractor) {
+	public void validateSearchParam(IBaseResource theResource, FhirContext theContext, DaoConfig theDaoConfig) {
+		org.hl7.fhir.r5.model.SearchParameter searchParameter = myVersionCanonicalizer.searchParameterToCanonical(theResource);
 
 		/*
 		 * If overriding built-in SPs is disabled on this server, make sure we aren't
 		 * doing that
 		 */
 		if (theDaoConfig.getModelConfig().isDefaultSearchParamsCanBeOverridden() == false) {
-			for (IPrimitiveType<?> nextBaseType : theResource.getBase()) {
+			for (IPrimitiveType<?> nextBaseType : searchParameter.getBase()) {
 				String nextBase = nextBaseType.getValueAsString();
-				RuntimeSearchParam existingSearchParam = theSearchParamRegistry.getActiveSearchParam(nextBase, theResource.getCode());
+				RuntimeSearchParam existingSearchParam = mySearchParamRegistry.getActiveSearchParam(nextBase, searchParameter.getCode());
 				if (existingSearchParam != null) {
 					boolean isBuiltIn = existingSearchParam.getId() == null;
 					isBuiltIn |= existingSearchParam.getUri().startsWith("http://hl7.org/fhir/SearchParameter/");
 					if (isBuiltIn) {
-						throw new UnprocessableEntityException(Msg.code(1111) + "Can not override built-in search parameter " + nextBase + ":" + theResource.getCode() + " because overriding is disabled on this server");
+						throw new UnprocessableEntityException(Msg.code(1111) + "Can not override built-in search parameter " + nextBase + ":" + searchParameter.getCode() + " because overriding is disabled on this server");
 					}
 				}
 			}
@@ -109,34 +112,34 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
 		 * Everything below is validating that the SP is actually valid. We'll only do that if the
 		 * SPO is active, so that we don't block people from uploading works-in-progress
 		 */
-		if (theResource.getStatus() == null) {
+		if (searchParameter.getStatus() == null) {
 			throw new UnprocessableEntityException(Msg.code(1112) + "SearchParameter.status is missing or invalid");
 		}
-		if (!theResource.getStatus().name().equals("ACTIVE")) {
+		if (!searchParameter.getStatus().name().equals("ACTIVE")) {
 			return;
 		}
 
-		if (ElementUtil.isEmpty(theResource.getBase()) && (theResource.getType() == null || !Enumerations.SearchParamType.COMPOSITE.name().equals(theResource.getType().name()))) {
+		if (ElementUtil.isEmpty(searchParameter.getBase()) && (searchParameter.getType() == null || !Enumerations.SearchParamType.COMPOSITE.name().equals(searchParameter.getType().name()))) {
 			throw new UnprocessableEntityException(Msg.code(1113) + "SearchParameter.base is missing");
 		}
 
-		boolean isUnique = hasAnyExtensionUniqueSetTo(theResource, true);
+		boolean isUnique = hasAnyExtensionUniqueSetTo(searchParameter, true);
 
-		if (theResource.getType() != null && theResource.getType().name().equals(Enumerations.SearchParamType.COMPOSITE.name()) && isBlank(theResource.getExpression())) {
+		if (searchParameter.getType() != null && searchParameter.getType().name().equals(Enumerations.SearchParamType.COMPOSITE.name()) && isBlank(searchParameter.getExpression())) {
 
 			// this is ok
 
-		} else if (isBlank(theResource.getExpression())) {
+		} else if (isBlank(searchParameter.getExpression())) {
 
 			throw new UnprocessableEntityException(Msg.code(1114) + "SearchParameter.expression is missing");
 
 		} else {
 
 			if (isUnique) {
-				if (theResource.getComponent().size() == 0) {
+				if (searchParameter.getComponent().size() == 0) {
 					throw new UnprocessableEntityException(Msg.code(1115) + "SearchParameter is marked as unique but has no components");
 				}
-				for (SearchParameter.SearchParameterComponentComponent next : theResource.getComponent()) {
+				for (SearchParameter.SearchParameterComponentComponent next : searchParameter.getComponent()) {
 					if (isBlank(next.getDefinition())) {
 						throw new UnprocessableEntityException(Msg.code(1116) + "SearchParameter is marked as unique but is missing component.definition");
 					}
@@ -146,14 +149,13 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
 			FhirVersionEnum fhirVersion = theContext.getVersion().getVersion();
 			if (fhirVersion.isOlderThan(FhirVersionEnum.DSTU3)) {
 				// omitting validation for DSTU2_HL7ORG, DSTU2_1 and DSTU2
-			}
+			} else {
-			else {
 
 				if (theDaoConfig.isValidateSearchParameterExpressionsOnSave()) {
 
-					validateExpressionPath(theResource);
+					validateExpressionPath(searchParameter);
 
-					String expression = getExpression(theResource);
+					String expression = getExpression(searchParameter);
 
 					try {
 						theContext.newFhirPath().parse(expression);
@@ -166,7 +168,12 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
 
 	}
 
-	private static void validateExpressionPath(SearchParameter theSearchParameter){
+	@VisibleForTesting
+	void setVersionCanonicalizerForUnitTest(VersionCanonicalizer theVersionCanonicalizer) {
+		myVersionCanonicalizer = theVersionCanonicalizer;
+	}
+
+	private static void validateExpressionPath(SearchParameter theSearchParameter) {
 		String expression = getExpression(theSearchParameter);
 
 		boolean isResourceOfTypeComposite = theSearchParameter.getType() == Enumerations.SearchParamType.COMPOSITE;
@@ -175,23 +182,23 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
 
 		boolean isUnique = hasAnyExtensionUniqueSetTo(theSearchParameter, true);
 
-		if ( !isUnique && !isResourceOfTypeComposite && !isResourceOfTypeSpecial && !expressionHasPath ) {
+		if (!isUnique && !isResourceOfTypeComposite && !isResourceOfTypeSpecial && !expressionHasPath) {
 			throw new UnprocessableEntityException(Msg.code(1120) + "SearchParameter.expression value \"" + expression + "\" is invalid due to missing/incorrect path");
 		}
 
 	}
 
-	private static String getExpression(SearchParameter theSearchParameter){
+	private static String getExpression(SearchParameter theSearchParameter) {
 		return theSearchParameter.getExpression().trim();
 	}
 
-	private static boolean hasAnyExtensionUniqueSetTo(SearchParameter theSearchParameter, boolean theValue){
+	private static boolean hasAnyExtensionUniqueSetTo(SearchParameter theSearchParameter, boolean theValue) {
 		String theValueAsString = Boolean.toString(theValue);
 
 		return theSearchParameter
 			.getExtensionsByUrl(HapiExtensions.EXT_SP_UNIQUE)
 			.stream()
-			.anyMatch(t-> theValueAsString.equals(t.getValueAsPrimitive().getValueAsString()));
+			.anyMatch(t -> theValueAsString.equals(t.getValueAsPrimitive().getValueAsString()));
 	}
 
 }

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

@@ -0,0 +1,490 @@
+package ca.uhn.fhir.jpa.dao;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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.context.FhirVersionEnum;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.IDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.entity.PartitionEntity;
+import ca.uhn.fhir.jpa.entity.ResourceSearchView;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.entity.BaseTag;
+import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
+import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
+import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.entity.ResourceTag;
+import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.model.base.composite.BaseCodingDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.parser.LenientErrorHandler;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.util.MetaUtil;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nullable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+
+import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.cleanProvenanceSourceUri;
+import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.decodeResource;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class JpaStorageResourceParser implements IJpaStorageResourceParser {
+	public static final LenientErrorHandler LENIENT_ERROR_HANDLER = new LenientErrorHandler(false).setErrorOnInvalidValue(false);
+	private static final Logger ourLog = LoggerFactory.getLogger(JpaStorageResourceParser.class);
+	@Autowired
+	private FhirContext myContext;
+	@Autowired
+	private DaoConfig myDaoConfig;
+	@Autowired
+	private IResourceHistoryTableDao myResourceHistoryTableDao;
+	@Autowired
+	private PartitionSettings myPartitionSettings;
+	@Autowired
+	private IPartitionLookupSvc myPartitionLookupSvc;
+
+	@Override
+	public IBaseResource toResource(IBasePersistedResource theEntity, boolean theForHistoryOperation) {
+		RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
+		Class<? extends IBaseResource> resourceType = type.getImplementingClass();
+		return toResource(resourceType, (IBaseResourceEntity) theEntity, null, theForHistoryOperation);
+	}
+
+	@Override
+	public <R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation) {
+
+		// 1. get resource, it's encoding and the tags if any
+		byte[] resourceBytes;
+		String resourceText;
+		ResourceEncodingEnum resourceEncoding;
+		@Nullable
+		Collection<? extends BaseTag> tagList = Collections.emptyList();
+		long version;
+		String provenanceSourceUri = null;
+		String provenanceRequestId = null;
+
+		if (theEntity instanceof ResourceHistoryTable) {
+			ResourceHistoryTable history = (ResourceHistoryTable) theEntity;
+			resourceBytes = history.getResource();
+			resourceText = history.getResourceTextVc();
+			resourceEncoding = history.getEncoding();
+			switch (myDaoConfig.getTagStorageMode()) {
+				case VERSIONED:
+				default:
+					if (history.isHasTags()) {
+						tagList = history.getTags();
+					}
+					break;
+				case NON_VERSIONED:
+					if (history.getResourceTable().isHasTags()) {
+						tagList = history.getResourceTable().getTags();
+					}
+					break;
+				case INLINE:
+					tagList = null;
+			}
+			version = history.getVersion();
+			if (history.getProvenance() != null) {
+				provenanceRequestId = history.getProvenance().getRequestId();
+				provenanceSourceUri = history.getProvenance().getSourceUri();
+			}
+		} else if (theEntity instanceof ResourceTable) {
+			ResourceTable resource = (ResourceTable) theEntity;
+			ResourceHistoryTable history;
+			if (resource.getCurrentVersionEntity() != null) {
+				history = resource.getCurrentVersionEntity();
+			} else {
+				version = theEntity.getVersion();
+				history = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), version);
+				((ResourceTable) theEntity).setCurrentVersionEntity(history);
+
+				while (history == null) {
+					if (version > 1L) {
+						version--;
+						history = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), version);
+					} else {
+						return null;
+					}
+				}
+			}
+
+			resourceBytes = history.getResource();
+			resourceEncoding = history.getEncoding();
+			resourceText = history.getResourceTextVc();
+			switch (myDaoConfig.getTagStorageMode()) {
+				case VERSIONED:
+				case NON_VERSIONED:
+					if (resource.isHasTags()) {
+						tagList = resource.getTags();
+					}
+					break;
+				case INLINE:
+					tagList = null;
+					break;
+			}
+			version = history.getVersion();
+			if (history.getProvenance() != null) {
+				provenanceRequestId = history.getProvenance().getRequestId();
+				provenanceSourceUri = history.getProvenance().getSourceUri();
+			}
+		} else if (theEntity instanceof ResourceSearchView) {
+			// This is the search View
+			ResourceSearchView view = (ResourceSearchView) theEntity;
+			resourceBytes = view.getResource();
+			resourceText = view.getResourceTextVc();
+			resourceEncoding = view.getEncoding();
+			version = view.getVersion();
+			provenanceRequestId = view.getProvenanceRequestId();
+			provenanceSourceUri = view.getProvenanceSourceUri();
+			switch (myDaoConfig.getTagStorageMode()) {
+				case VERSIONED:
+				case NON_VERSIONED:
+					if (theTagList != null) {
+						tagList = theTagList;
+					}
+					break;
+				case INLINE:
+					tagList = null;
+					break;
+			}
+		} else {
+			// something wrong
+			return null;
+		}
+
+		// 2. get The text
+		String decodedResourceText = decodedResourceText(resourceBytes, resourceText, resourceEncoding);
+
+		// 3. Use the appropriate custom type if one is specified in the context
+		Class<R> resourceType = determineTypeToParse(theResourceType, tagList);
+
+		// 4. parse the text to FHIR
+		R retVal = parseResource(theEntity, resourceEncoding, decodedResourceText, resourceType);
+
+		// 5. fill MetaData
+		retVal = populateResourceMetadata(theEntity, theForHistoryOperation, tagList, version, retVal);
+
+		// 6. Handle source (provenance)
+		populateResourceSource(provenanceSourceUri, provenanceRequestId, retVal);
+
+		// 7. Add partition information
+		populateResourcePartitionInformation(theEntity, retVal);
+
+		return retVal;
+	}
+
+	private <R extends IBaseResource> void populateResourcePartitionInformation(IBaseResourceEntity theEntity, R retVal) {
+		if (myPartitionSettings.isPartitioningEnabled()) {
+			PartitionablePartitionId partitionId = theEntity.getPartitionId();
+			if (partitionId != null && partitionId.getPartitionId() != null) {
+				PartitionEntity persistedPartition = myPartitionLookupSvc.getPartitionById(partitionId.getPartitionId());
+				retVal.setUserData(Constants.RESOURCE_PARTITION_ID, persistedPartition.toRequestPartitionId());
+			} else {
+				retVal.setUserData(Constants.RESOURCE_PARTITION_ID, null);
+			}
+		}
+	}
+
+	private <R extends IBaseResource> void populateResourceSource(String provenanceSourceUri, String provenanceRequestId, R retVal) {
+		if (isNotBlank(provenanceRequestId) || isNotBlank(provenanceSourceUri)) {
+			String sourceString = cleanProvenanceSourceUri(provenanceSourceUri)
+				+ (isNotBlank(provenanceRequestId) ? "#" : "")
+				+ defaultString(provenanceRequestId);
+
+			MetaUtil.setSource(myContext, retVal, sourceString);
+		}
+	}
+
+	@SuppressWarnings("unchecked")
+	private <R extends IBaseResource> R parseResource(IBaseResourceEntity theEntity, ResourceEncodingEnum resourceEncoding, String decodedResourceText, Class<R> resourceType) {
+		R retVal;
+		if (resourceEncoding != ResourceEncodingEnum.DEL) {
+
+			IParser parser = new TolerantJsonParser(getContext(theEntity.getFhirVersion()), LENIENT_ERROR_HANDLER, theEntity.getId());
+
+			try {
+				retVal = parser.parseResource(resourceType, decodedResourceText);
+			} catch (Exception e) {
+				StringBuilder b = new StringBuilder();
+				b.append("Failed to parse database resource[");
+				b.append(myContext.getResourceType(resourceType));
+				b.append("/");
+				b.append(theEntity.getIdDt().getIdPart());
+				b.append(" (pid ");
+				b.append(theEntity.getId());
+				b.append(", version ");
+				b.append(theEntity.getFhirVersion().name());
+				b.append("): ");
+				b.append(e.getMessage());
+				String msg = b.toString();
+				ourLog.error(msg, e);
+				throw new DataFormatException(Msg.code(928) + msg, e);
+			}
+
+		} else {
+
+			retVal = (R) myContext.getResourceDefinition(theEntity.getResourceType()).newInstance();
+
+		}
+		return retVal;
+	}
+
+	@SuppressWarnings("unchecked")
+	private <R extends IBaseResource> Class<R> determineTypeToParse(Class<R> theResourceType, @Nullable Collection<? extends BaseTag> tagList) {
+		Class<R> resourceType = theResourceType;
+		if (tagList != null) {
+			if (myContext.hasDefaultTypeForProfile()) {
+				for (BaseTag nextTag : tagList) {
+					if (nextTag.getTag().getTagType() == TagTypeEnum.PROFILE) {
+						String profile = nextTag.getTag().getCode();
+						if (isNotBlank(profile)) {
+							Class<? extends IBaseResource> newType = myContext.getDefaultTypeForProfile(profile);
+							if (newType != null && theResourceType.isAssignableFrom(newType)) {
+								ourLog.debug("Using custom type {} for profile: {}", newType.getName(), profile);
+								resourceType = (Class<R>) newType;
+								break;
+							}
+						}
+					}
+				}
+			}
+		}
+		return resourceType;
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public <R extends IBaseResource> R populateResourceMetadata(IBaseResourceEntity theEntitySource, boolean theForHistoryOperation, @Nullable Collection<? extends BaseTag> tagList, long theVersion, R theResourceTarget) {
+		if (theResourceTarget instanceof IResource) {
+			IResource res = (IResource) theResourceTarget;
+			theResourceTarget = (R) populateResourceMetadataHapi(theEntitySource, tagList, theForHistoryOperation, res, theVersion);
+		} else {
+			IAnyResource res = (IAnyResource) theResourceTarget;
+			theResourceTarget = populateResourceMetadataRi(theEntitySource, tagList, theForHistoryOperation, res, theVersion);
+		}
+		return theResourceTarget;
+	}
+
+	@SuppressWarnings("unchecked")
+	private <R extends IResource> R populateResourceMetadataHapi(IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, R res, Long theVersion) {
+		R retVal = res;
+		if (theEntity.getDeleted() != null) {
+			res = (R) myContext.getResourceDefinition(res).newInstance();
+			retVal = res;
+			ResourceMetadataKeyEnum.DELETED_AT.put(res, new InstantDt(theEntity.getDeleted()));
+			if (theForHistoryOperation) {
+				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, BundleEntryTransactionMethodEnum.DELETE);
+			}
+		} else if (theForHistoryOperation) {
+			/*
+			 * If the create and update times match, this was when the resource was created so we should mark it as a POST. Otherwise, it's a PUT.
+			 */
+			Date published = theEntity.getPublished().getValue();
+			Date updated = theEntity.getUpdated().getValue();
+			if (published.equals(updated)) {
+				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, BundleEntryTransactionMethodEnum.POST);
+			} else {
+				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, BundleEntryTransactionMethodEnum.PUT);
+			}
+		}
+
+		res.setId(theEntity.getIdDt().withVersion(theVersion.toString()));
+
+		ResourceMetadataKeyEnum.VERSION.put(res, Long.toString(theEntity.getVersion()));
+		ResourceMetadataKeyEnum.PUBLISHED.put(res, theEntity.getPublished());
+		ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
+		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
+
+		if (theTagList != null) {
+			if (theEntity.isHasTags()) {
+				TagList tagList = new TagList();
+				List<IBaseCoding> securityLabels = new ArrayList<>();
+				List<IdDt> profiles = new ArrayList<>();
+				for (BaseTag next : theTagList) {
+					switch (next.getTag().getTagType()) {
+						case PROFILE:
+							profiles.add(new IdDt(next.getTag().getCode()));
+							break;
+						case SECURITY_LABEL:
+							IBaseCoding secLabel = (IBaseCoding) myContext.getVersion().newCodingDt();
+							secLabel.setSystem(next.getTag().getSystem());
+							secLabel.setCode(next.getTag().getCode());
+							secLabel.setDisplay(next.getTag().getDisplay());
+							securityLabels.add(secLabel);
+							break;
+						case TAG:
+							tagList.add(new Tag(next.getTag().getSystem(), next.getTag().getCode(), next.getTag().getDisplay()));
+							break;
+					}
+				}
+				if (tagList.size() > 0) {
+					ResourceMetadataKeyEnum.TAG_LIST.put(res, tagList);
+				}
+				if (securityLabels.size() > 0) {
+					ResourceMetadataKeyEnum.SECURITY_LABELS.put(res, toBaseCodingList(securityLabels));
+				}
+				if (profiles.size() > 0) {
+					ResourceMetadataKeyEnum.PROFILES.put(res, profiles);
+				}
+			}
+		}
+
+		return retVal;
+	}
+
+	@SuppressWarnings("unchecked")
+	private <R extends IBaseResource> R populateResourceMetadataRi(IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res, Long theVersion) {
+		R retVal = (R) res;
+		if (theEntity.getDeleted() != null) {
+			res = (IAnyResource) myContext.getResourceDefinition(res).newInstance();
+			retVal = (R) res;
+			ResourceMetadataKeyEnum.DELETED_AT.put(res, new InstantDt(theEntity.getDeleted()));
+			if (theForHistoryOperation) {
+				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, Bundle.HTTPVerb.DELETE.toCode());
+			}
+		} else if (theForHistoryOperation) {
+			/*
+			 * If the create and update times match, this was when the resource was created so we should mark it as a POST. Otherwise, it's a PUT.
+			 */
+			Date published = theEntity.getPublished().getValue();
+			Date updated = theEntity.getUpdated().getValue();
+			if (published.equals(updated)) {
+				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, Bundle.HTTPVerb.POST.toCode());
+			} else {
+				ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(res, Bundle.HTTPVerb.PUT.toCode());
+			}
+		}
+
+		res.getMeta().setLastUpdated(null);
+		res.getMeta().setVersionId(null);
+
+		updateResourceMetadata(theEntity, res);
+		res.setId(res.getIdElement().withVersion(theVersion.toString()));
+
+		res.getMeta().setLastUpdated(theEntity.getUpdatedDate());
+		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
+
+		if (theTagList != null) {
+			res.getMeta().getTag().clear();
+			res.getMeta().getProfile().clear();
+			res.getMeta().getSecurity().clear();
+			for (BaseTag next : theTagList) {
+				switch (next.getTag().getTagType()) {
+					case PROFILE:
+						res.getMeta().addProfile(next.getTag().getCode());
+						break;
+					case SECURITY_LABEL:
+						IBaseCoding sec = res.getMeta().addSecurity();
+						sec.setSystem(next.getTag().getSystem());
+						sec.setCode(next.getTag().getCode());
+						sec.setDisplay(next.getTag().getDisplay());
+						break;
+					case TAG:
+						IBaseCoding tag = res.getMeta().addTag();
+						tag.setSystem(next.getTag().getSystem());
+						tag.setCode(next.getTag().getCode());
+						tag.setDisplay(next.getTag().getDisplay());
+						break;
+				}
+			}
+		}
+
+		return retVal;
+	}
+
+	@Override
+	public void updateResourceMetadata(IBaseResourceEntity theEntitySource, IBaseResource theResourceTarget) {
+		IIdType id = theEntitySource.getIdDt();
+		if (myContext.getVersion().getVersion().isRi()) {
+			id = myContext.getVersion().newIdType().setValue(id.getValue());
+		}
+
+		if (id.hasResourceType() == false) {
+			id = id.withResourceType(theEntitySource.getResourceType());
+		}
+
+		theResourceTarget.setId(id);
+		if (theResourceTarget instanceof IResource) {
+			ResourceMetadataKeyEnum.VERSION.put((IResource) theResourceTarget, id.getVersionIdPart());
+			ResourceMetadataKeyEnum.UPDATED.put((IResource) theResourceTarget, theEntitySource.getUpdated());
+		} else {
+			IBaseMetaType meta = theResourceTarget.getMeta();
+			meta.setVersionId(id.getVersionIdPart());
+			meta.setLastUpdated(theEntitySource.getUpdatedDate());
+		}
+	}
+
+	private FhirContext getContext(FhirVersionEnum theVersion) {
+		Validate.notNull(theVersion, "theVersion must not be null");
+		if (theVersion == myContext.getVersion().getVersion()) {
+			return myContext;
+		}
+		return FhirContext.forCached(theVersion);
+	}
+
+	private static String decodedResourceText(byte[] resourceBytes, String resourceText, ResourceEncodingEnum resourceEncoding) {
+		String decodedResourceText;
+		if (resourceText != null) {
+			decodedResourceText = resourceText;
+		} else {
+			decodedResourceText = decodeResource(resourceBytes, resourceEncoding);
+		}
+		return decodedResourceText;
+	}
+
+	private static List<BaseCodingDt> toBaseCodingList(List<IBaseCoding> theSecurityLabels) {
+		ArrayList<BaseCodingDt> retVal = new ArrayList<>(theSecurityLabels.size());
+		for (IBaseCoding next : theSecurityLabels) {
+			retVal.add((BaseCodingDt) next);
+		}
+		return retVal;
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCompositionDstu3.java

@@ -1,59 +0,0 @@
-package ca.uhn.fhir.jpa.dao.dstu3;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoComposition;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import org.hl7.fhir.dstu3.model.Composition;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-
-import javax.servlet.http.HttpServletRequest;
-import java.util.Collections;
-
-public class FhirResourceDaoCompositionDstu3 extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
-
-	@Override
-	public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
-		SearchParameterMap paramMap = new SearchParameterMap();
-		if (theCount != null) {
-			paramMap.setCount(theCount.getValue());
-		}
-		if (theOffset != null) {
-			paramMap.setOffset(theOffset.getValue());
-		}
-		paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
-		paramMap.setSort(theSort);
-		paramMap.setLastUpdated(theLastUpdate);
-		if (theId != null) {
-			paramMap.add("_id", new StringParam(theId.getIdPart()));
-		}
-		return search(paramMap, theRequestDetails);
-	}
-}
-

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoObservationDstu3.java

@@ -1,83 +0,0 @@
-package ca.uhn.fhir.jpa.dao.dstu3;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
-import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.CacheControlDirective;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import org.hl7.fhir.dstu3.model.Observation;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import javax.servlet.http.HttpServletResponse;
-import java.util.Date;
-
-public class FhirResourceDaoObservationDstu3 extends BaseHapiFhirResourceDaoObservation<Observation> {
-
-	@Autowired
-	private IRequestPartitionHelperSvc myPartitionHelperSvc;
-
-	@Override
-	public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap,  RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
-
-		updateSearchParamsForLastn(theSearchParameterMap, theRequestDetails);
-
-		RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(theRequestDetails, getResourceName(), theSearchParameterMap, null);
-		return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails, requestPartitionId);
-	}
-
-	@Override
-	protected String getEffectiveParamName() {
-		return Observation.SP_DATE;
-	}
-
-	@Override
-	protected String getCodeParamName() {
-		return Observation.SP_CODE;
-	}
-
-	@Override
-	protected String getSubjectParamName() {
-		return Observation.SP_SUBJECT;
-	}
-
-	@Override
-	protected String getPatientParamName() {
-		return Observation.SP_PATIENT;
-	}
-
-	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
-												 boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
-		return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
-			thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
-			theCreateNewHistoryEntry);
-	}
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -1,80 +0,0 @@
-package ca.uhn.fhir.jpa.dao.dstu3;
-
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
-import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
-import org.hl7.fhir.dstu3.model.PrimitiveType;
-import org.hl7.fhir.dstu3.model.SearchParameter;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import java.util.List;
-import java.util.stream.Collectors;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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 FhirResourceDaoSearchParameterDstu3 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
-
-	@Autowired
-	private ISearchParamExtractor mySearchParamExtractor;
-
-	protected void reindexAffectedResources(SearchParameter theResource, RequestDetails theRequestDetails) {
-		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
-		String expression = theResource != null ? theResource.getExpression() : null;
-		List<String> base = theResource != null ? theResource.getBase().stream().map(PrimitiveType::asStringValue).collect(Collectors.toList()) : null;
-		requestReindexForRelatedResources(reindex, base, theRequestDetails);
-	}
-
-
-	@Override
-	protected void postPersist(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postPersist(theEntity, theResource, theRequestDetails);
-		reindexAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postUpdate(theEntity, theResource, theRequestDetails);
-		reindexAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void preDelete(SearchParameter theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
-		super.preDelete(theResourceToDelete, theEntityToDelete, theRequestDetails);
-		reindexAffectedResources(theResourceToDelete, theRequestDetails);
-	}
-
-	@Override
-	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
-		super.validateResourceForStorage(theResource, theEntityToSave);
-
-		org.hl7.fhir.r4.model.SearchParameter resource = (org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_30_40.convertResource(theResource, new BaseAdvisor_30_40(false));
-
-		FhirResourceDaoSearchParameterR4.validateSearchParam(
-			resource,
-			getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
-	}
-
-}

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

@@ -25,10 +25,10 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
-import ca.uhn.fhir.jpa.model.dao.JpaPid;
+import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboStringUniqueDao;
@@ -42,10 +42,10 @@ import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamTokenDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
+import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -124,11 +124,13 @@ public class ResourceExpungeService implements IResourceExpungeService {
 	private DaoConfig myDaoConfig;
 	@Autowired
 	private MemoryCacheService myMemoryCacheService;
+	@Autowired
+	private IJpaStorageResourceParser myJpaStorageResourceParser;
 
 	@Override
 	@Transactional
 	public List<ResourcePersistentId> findHistoricalVersionsOfNonDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theRemainingCount) {
-		if(isEmptyQuery(theRemainingCount)){
+		if (isEmptyQuery(theRemainingCount)) {
 			return Collections.EMPTY_LIST;
 		}
 
@@ -156,7 +158,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
 	@Override
 	@Transactional
 	public List<ResourcePersistentId> findHistoricalVersionsOfDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theRemainingCount) {
-		if(isEmptyQuery(theRemainingCount)){
+		if (isEmptyQuery(theRemainingCount)) {
 			return Collections.EMPTY_LIST;
 		}
 
@@ -194,7 +196,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
 		 * be optimized, but expunge is hopefully not frequently called on busy servers
 		 * so it shouldn't be too big a deal.
 		 */
-		TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronization(){
+		TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronization() {
 			@Override
 			public void afterCommit() {
 				myMemoryCacheService.invalidateAllCaches();
@@ -222,8 +224,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
 	private void callHooks(RequestDetails theRequestDetails, AtomicInteger theRemainingCount, ResourceHistoryTable theVersion, IdDt theId) {
 		final AtomicInteger counter = new AtomicInteger();
 		if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, myInterceptorBroadcaster, theRequestDetails)) {
-			IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(theId.getResourceType());
+			IBaseResource resource = myJpaStorageResourceParser.toResource(theVersion, false);
-			IBaseResource resource = resourceDao.toResource(theVersion, false);
 			HookParams params = new HookParams()
 				.add(AtomicInteger.class, counter)
 				.add(IIdType.class, theId)
@@ -327,7 +328,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
 
 	private void expungeHistoricalVersionsOfId(RequestDetails theRequestDetails, Long myResourceId, AtomicInteger theRemainingCount) {
 		Pageable page;
-		synchronized (theRemainingCount){
+		synchronized (theRemainingCount) {
 			if (expungeLimitReached(theRemainingCount)) {
 				return;
 			}
@@ -351,7 +352,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
 		return new SliceImpl<>(Collections.singletonList(myVersion.getId()));
 	}
 
-	private boolean isEmptyQuery(int theCount){
+	private boolean isEmptyQuery(int theCount) {
 		return theCount <= 0;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoObservationR4.java

@@ -1,88 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r4;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
-import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.CacheControlDirective;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Observation;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.PersistenceContextType;
-import javax.servlet.http.HttpServletResponse;
-import java.util.Date;
-
-public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDaoObservation<Observation> {
-
-
-	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
-	protected EntityManager myEntityManager;
-	@Autowired
-	private IRequestPartitionHelperSvc myRequestPartitionHelperService;
-
-	@Override
-	public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap,  RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
-		updateSearchParamsForLastn(theSearchParameterMap, theRequestDetails);
-
-		RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(theRequestDetails, getResourceName(), theSearchParameterMap, null);
-		return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails, requestPartitionId);
-	}
-
-	@Override
-	protected String getEffectiveParamName() {
-		return Observation.SP_DATE;
-	}
-
-	@Override
-	protected String getCodeParamName() {
-		return Observation.SP_CODE;
-	}
-
-	@Override
-	protected String getSubjectParamName() {
-		return Observation.SP_SUBJECT;
-	}
-
-	@Override
-	protected String getPatientParamName() {
-		return Observation.SP_PATIENT;
-	}
-
-	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
-												 boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
-		return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
-			thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
-			theCreateNewHistoryEntry);
-	}
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4b/FhirResourceDaoCompositionR4B.java

@@ -1,59 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r4b;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoComposition;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import 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.r4b.model.Composition;
-
-import javax.servlet.http.HttpServletRequest;
-import java.util.Collections;
-
-public class FhirResourceDaoCompositionR4B extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
-
-	@Override
-	public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
-		SearchParameterMap paramMap = new SearchParameterMap();
-		if (theCount != null) {
-			paramMap.setCount(theCount.getValue());
-		}
-		if (theOffset != null) {
-			paramMap.setOffset(theOffset.getValue());
-		}
-		paramMap.setIncludes(Collections.singleton(IBaseResource.INCLUDE_ALL.asRecursive()));
-		paramMap.setSort(theSort);
-		paramMap.setLastUpdated(theLastUpdate);
-		if (theId != null) {
-			paramMap.add("_id", new StringParam(theId.getIdPart()));
-		}
-		return search(paramMap, theRequestDetails);
-	}
-}
-

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4b/FhirResourceDaoObservationR4B.java

@@ -1,83 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r4b;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
-import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.CacheControlDirective;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4b.model.Observation;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import javax.servlet.http.HttpServletResponse;
-import java.util.Date;
-
-public class FhirResourceDaoObservationR4B extends BaseHapiFhirResourceDaoObservation<Observation> {
-
-	@Autowired
-	private IRequestPartitionHelperSvc myPartitionHelperSvc;
-
-	@Override
-	public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap,  RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
-
-		updateSearchParamsForLastn(theSearchParameterMap, theRequestDetails);
-
-		RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(theRequestDetails, getResourceName(), theSearchParameterMap, null);
-		return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails, requestPartitionId);
-	}
-
-	@Override
-	protected String getEffectiveParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_DATE;
-	}
-
-	@Override
-	protected String getCodeParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_CODE;
-	}
-
-	@Override
-	protected String getSubjectParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_SUBJECT;
-	}
-
-	@Override
-	protected String getPatientParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_PATIENT;
-	}
-
-	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
-												 boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
-		return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
-			thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
-			theCreateNewHistoryEntry);
-	}
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4b/FhirResourceDaoSearchParameterR4B.java

@@ -1,83 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r4b;
-
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
-import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_43_50;
-import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
-import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
-import org.hl7.fhir.r4b.model.CodeType;
-import org.hl7.fhir.r4b.model.SearchParameter;
-import org.hl7.fhir.r5.model.Resource;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import java.util.List;
-import java.util.stream.Collectors;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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 FhirResourceDaoSearchParameterR4B extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
-
-	@Autowired
-	private ISearchParamExtractor mySearchParamExtractor;
-
-	protected void refactorAffectedResources(SearchParameter theResource, RequestDetails theRequestDetails) {
-		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
-		String expression = theResource != null ? theResource.getExpression() : null;
-		List<String> base = theResource != null ? theResource.getBase().stream().map(CodeType::getCode).collect(Collectors.toList()) : null;
-		requestReindexForRelatedResources(reindex, base, theRequestDetails);
-	}
-
-
-	@Override
-	protected void postPersist(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postPersist(theEntity, theResource, theRequestDetails);
-		refactorAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postUpdate(theEntity, theResource, theRequestDetails);
-		refactorAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void preDelete(SearchParameter theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
-		super.preDelete(theResourceToDelete, theEntityToDelete, theRequestDetails);
-		refactorAffectedResources(theResourceToDelete, theRequestDetails);
-	}
-
-	@Override
-	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
-		super.validateResourceForStorage(theResource, theEntityToSave);
-
-		Resource resR5 = VersionConvertorFactory_43_50.convertResource(theResource, new BaseAdvisor_43_50(false));
-		FhirResourceDaoSearchParameterR4.validateSearchParam(
-			(org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_40_50.convertResource(resR5, new BaseAdvisor_40_50(false)),
-			getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
-	}
-
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCompositionR5.java

@@ -1,59 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r5;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoComposition;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import 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.r5.model.Composition;
-
-import javax.servlet.http.HttpServletRequest;
-import java.util.Collections;
-
-public class FhirResourceDaoCompositionR5 extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
-
-	@Override
-	public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
-		SearchParameterMap paramMap = new SearchParameterMap();
-		if (theCount != null) {
-			paramMap.setCount(theCount.getValue());
-		}
-		if (theOffset != null) {
-			paramMap.setOffset(theOffset.getValue());
-		}
-		paramMap.setIncludes(Collections.singleton(IBaseResource.INCLUDE_ALL.asRecursive()));
-		paramMap.setSort(theSort);
-		paramMap.setLastUpdated(theLastUpdate);
-		if (theId != null) {
-			paramMap.add("_id", new StringParam(theId.getIdPart()));
-		}
-		return search(paramMap, theRequestDetails);
-	}
-}
-

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoObservationR5.java

@@ -1,83 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r5;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
-import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.CacheControlDirective;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r5.model.Observation;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import javax.servlet.http.HttpServletResponse;
-import java.util.Date;
-
-public class FhirResourceDaoObservationR5 extends BaseHapiFhirResourceDaoObservation<Observation> {
-
-	@Autowired
-	private IRequestPartitionHelperSvc myPartitionHelperSvc;
-
-	@Override
-	public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap,  RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
-
-		updateSearchParamsForLastn(theSearchParameterMap, theRequestDetails);
-
-		RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(theRequestDetails, getResourceName(), theSearchParameterMap, null);
-		return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails, requestPartitionId);
-	}
-
-	@Override
-	protected String getEffectiveParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_DATE;
-	}
-
-	@Override
-	protected String getCodeParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_CODE;
-	}
-
-	@Override
-	protected String getSubjectParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_SUBJECT;
-	}
-
-	@Override
-	protected String getPatientParamName() {
-		return org.hl7.fhir.r4.model.Observation.SP_PATIENT;
-	}
-
-	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
-												 boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
-		return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
-			thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
-			theCreateNewHistoryEntry);
-	}
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSearchParameterR5.java

@@ -1,79 +0,0 @@
-package ca.uhn.fhir.jpa.dao.r5;
-
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
-import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
-import org.hl7.fhir.r5.model.CodeType;
-import org.hl7.fhir.r5.model.SearchParameter;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import java.util.List;
-import java.util.stream.Collectors;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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 FhirResourceDaoSearchParameterR5 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
-
-	@Autowired
-	private ISearchParamExtractor mySearchParamExtractor;
-
-	protected void refactorAffectedResources(SearchParameter theResource, RequestDetails theRequestDetails) {
-		Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
-		String expression = theResource != null ? theResource.getExpression() : null;
-		List<String> base = theResource != null ? theResource.getBase().stream().map(CodeType::getCode).collect(Collectors.toList()) : null;
-		requestReindexForRelatedResources(reindex, base, theRequestDetails);
-	}
-
-
-	@Override
-	protected void postPersist(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postPersist(theEntity, theResource, theRequestDetails);
-		refactorAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource, RequestDetails theRequestDetails) {
-		super.postUpdate(theEntity, theResource, theRequestDetails);
-		refactorAffectedResources(theResource, theRequestDetails);
-	}
-
-	@Override
-	protected void preDelete(SearchParameter theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
-		super.preDelete(theResourceToDelete, theEntityToDelete, theRequestDetails);
-		refactorAffectedResources(theResourceToDelete, theRequestDetails);
-	}
-
-	@Override
-	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
-		super.validateResourceForStorage(theResource, theEntityToSave);
-
-		FhirResourceDaoSearchParameterR4.validateSearchParam(
-			(org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_40_50.convertResource(theResource, new BaseAdvisor_40_50(false)),
-			getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
-	}
-
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/batch2/DeleteExpungeSvcImpl.java

@@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 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;
 
@@ -42,7 +43,7 @@ public class DeleteExpungeSvcImpl implements IDeleteExpungeSvc {
 	private final DeleteExpungeSqlBuilder myDeleteExpungeSqlBuilder;
 	private final IFulltextSearchSvc myFullTextSearchSvc;
 
-	public DeleteExpungeSvcImpl(EntityManager theEntityManager, DeleteExpungeSqlBuilder theDeleteExpungeSqlBuilder, IFulltextSearchSvc theFullTextSearchSvc) {
+	public DeleteExpungeSvcImpl(EntityManager theEntityManager, DeleteExpungeSqlBuilder theDeleteExpungeSqlBuilder, @Autowired(required = false) IFulltextSearchSvc theFullTextSearchSvc) {
 		myEntityManager = theEntityManager;
 		myDeleteExpungeSqlBuilder = theDeleteExpungeSqlBuilder;
 		myFullTextSearchSvc = theFullTextSearchSvc;

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

@@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.dao.HistoryBuilder;
 import ca.uhn.fhir.jpa.dao.HistoryBuilderFactory;
+import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.entity.Search;
@@ -104,13 +105,15 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 	private RequestPartitionHelperSvc myRequestPartitionHelperSvc;
 	@Autowired
 	private DaoConfig myDaoConfig;
+	@Autowired
+	private MemoryCacheService myMemoryCacheService;
+	@Autowired
+	private IJpaStorageResourceParser myJpaStorageResourceParser;
 
 	/*
 	 * Non autowired fields (will be different for every instance
 	 * of this class, since it's a prototype
 	 */
-	@Autowired
-	private MemoryCacheService myMemoryCacheService;
 	private Search mySearchEntity;
 	private String myUuid;
 	private SearchCacheStatusEnum myCacheStatus;
@@ -162,7 +165,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 			resource = next;
 
 			IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(next.getResourceType());
-			retVal.add(dao.toResource(resource, true));
+			retVal.add(myJpaStorageResourceParser.toResource(resource, true));
 		}
 
 

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

@@ -23,11 +23,20 @@ package ca.uhn.fhir.jpa.search;
 import ca.uhn.fhir.jpa.config.JpaConfig;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
 import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
+import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.search.builder.tasks.SearchTask;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.HistorySearchStyleEnum;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 
+import java.util.Date;
+import java.util.UUID;
+
+import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+
 public class PersistedJpaBundleProviderFactory {
 
 	@Autowired
@@ -46,4 +55,28 @@ public class PersistedJpaBundleProviderFactory {
 	public PersistedJpaSearchFirstPageBundleProvider newInstanceFirstPage(RequestDetails theRequestDetails, Search theSearch, SearchTask theTask, ISearchBuilder theSearchBuilder) {
 		return (PersistedJpaSearchFirstPageBundleProvider) myApplicationContext.getBean(JpaConfig.PERSISTED_JPA_SEARCH_FIRST_PAGE_BUNDLE_PROVIDER, theRequestDetails, theSearch, theTask, theSearchBuilder);
 	}
+
+
+	public IBundleProvider history(RequestDetails theRequest, String theResourceType, Long theResourcePid, Date theRangeStartInclusive, Date theRangeEndInclusive, Integer theOffset) {
+		return history(theRequest, theResourceType, theResourcePid, theRangeStartInclusive, theRangeEndInclusive, theOffset, null);
+	}
+
+	public IBundleProvider history(RequestDetails theRequest, String theResourceType, Long theResourcePid, Date theRangeStartInclusive, Date theRangeEndInclusive, Integer theOffset, HistorySearchStyleEnum searchParameterType) {
+		String resourceName = defaultIfBlank(theResourceType, null);
+
+		Search search = new Search();
+		search.setOffset(theOffset);
+		search.setDeleted(false);
+		search.setCreated(new Date());
+		search.setLastUpdated(theRangeStartInclusive, theRangeEndInclusive);
+		search.setUuid(UUID.randomUUID().toString());
+		search.setResourceType(resourceName);
+		search.setResourceId(theResourcePid);
+		search.setSearchType(SearchTypeEnum.HISTORY);
+		search.setStatus(SearchStatusEnum.FINISHED);
+		search.setHistorySearchStyle(searchParameterType);
+
+		return newInstance(theRequest, search);
+	}
+
 }

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

@@ -39,15 +39,16 @@ import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
 import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
 import ca.uhn.fhir.jpa.dao.BaseStorageDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.IResultIterator;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
-import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
 import ca.uhn.fhir.jpa.dao.search.ResourceNotFoundInIndexException;
 import ca.uhn.fhir.jpa.entity.ResourceSearchView;
 import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceTag;
@@ -145,20 +146,34 @@ public class SearchBuilder implements ISearchBuilder {
 	@Deprecated
 	public static final int MAXIMUM_PAGE_SIZE = SearchConstants.MAX_PAGE_SIZE;
 	public static final int MAXIMUM_PAGE_SIZE_FOR_TESTING = 50;
+	public static final String RESOURCE_ID_ALIAS = "resource_id";
+	public static final String RESOURCE_VERSION_ALIAS = "resource_version";
 	private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
 	private static final JpaPid NO_MORE = new JpaPid(-1L);
 	private static final String MY_TARGET_RESOURCE_PID = "myTargetResourcePid";
 	private static final String MY_SOURCE_RESOURCE_PID = "mySourceResourcePid";
 	private static final String MY_TARGET_RESOURCE_TYPE = "myTargetResourceType";
-
 	private static final String MY_SOURCE_RESOURCE_TYPE = "mySourceResourceType";
 	private static final String MY_TARGET_RESOURCE_VERSION = "myTargetResourceVersion";
-	public static final String RESOURCE_ID_ALIAS = "resource_id";
-	public static final String RESOURCE_VERSION_ALIAS = "resource_version";
 	public static boolean myUseMaxPageSize50ForTest = false;
+	protected final IInterceptorBroadcaster myInterceptorBroadcaster;
+	protected final IResourceTagDao myResourceTagDao;
 	private final String myResourceName;
 	private final Class<? extends IBaseResource> myResourceType;
-
+	private final HapiFhirLocalContainerEntityManagerFactoryBean myEntityManagerFactory;
+	private final SqlObjectFactory mySqlBuilderFactory;
+	private final HibernatePropertiesProvider myDialectProvider;
+	private final ModelConfig myModelConfig;
+	private final ISearchParamRegistry mySearchParamRegistry;
+	private final PartitionSettings myPartitionSettings;
+	private final DaoRegistry myDaoRegistry;
+	private final IResourceSearchViewDao myResourceSearchViewDao;
+	private final FhirContext myContext;
+	private final IIdHelperService myIdHelperService;
+	private final DaoConfig myDaoConfig;
+	private final IDao myCallingDao;
+	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
+	protected EntityManager myEntityManager;
 	private List<ResourcePersistentId> myAlsoIncludePids;
 	private CriteriaBuilder myCriteriaBuilder;
 	private SearchParameterMap myParams;
@@ -168,30 +183,12 @@ public class SearchBuilder implements ISearchBuilder {
 	private Set<ResourcePersistentId> myPidSet;
 	private boolean myHasNextIteratorQuery = false;
 	private RequestPartitionId myRequestPartitionId;
-
-	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
-	protected EntityManager myEntityManager;
 	@Autowired(required = false)
 	private IFulltextSearchSvc myFulltextSearchSvc;
 	@Autowired(required = false)
 	private IElasticsearchSvc myIElasticsearchSvc;
-
+	@Autowired
-	private final HapiFhirLocalContainerEntityManagerFactoryBean myEntityManagerFactory;
+	private IJpaStorageResourceParser myJpaStorageResourceParser;
-	private final SqlObjectFactory mySqlBuilderFactory;
-	private final HibernatePropertiesProvider myDialectProvider;
-	private final ModelConfig myModelConfig;
-	private final ISearchParamRegistry mySearchParamRegistry;
-	private final PartitionSettings myPartitionSettings;
-	protected final IInterceptorBroadcaster myInterceptorBroadcaster;
-	protected final IResourceTagDao myResourceTagDao;
-	private final DaoRegistry myDaoRegistry;
-	private final IResourceSearchViewDao myResourceSearchViewDao;
-	private final FhirContext myContext;
-	private final IIdHelperService myIdHelperService;
-
-	private final DaoConfig myDaoConfig;
-
-	private final IDao myCallingDao;
 
 	/**
 	 * Constructor
@@ -894,7 +891,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 			IBaseResource resource = null;
 			if (next != null) {
-				resource = myCallingDao.toResource(resourceType, next, tagMap.get(next.getId()), theForHistoryOperation);
+				resource = myJpaStorageResourceParser.toResource(resourceType, next, tagMap.get(next.getId()), theForHistoryOperation);
 			}
 			if (resource == null) {
 				ourLog.warn("Unable to find resource {}/{}/_history/{} in database", next.getResourceType(), next.getIdDt().getIdPart(), next.getVersion());

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

@@ -38,7 +38,7 @@ import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
 import ca.uhn.fhir.jpa.config.util.ConnectionPoolInfoProvider;
 import ca.uhn.fhir.jpa.config.util.IConnectionPoolInfoProvider;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
-import ca.uhn.fhir.jpa.model.dao.JpaPid;
+import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
@@ -61,6 +61,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
+import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.sched.HapiJob;
@@ -265,6 +266,8 @@ public class TermReadSvcImpl implements ITermReadSvc {
 	private CachingValidationSupport myCachingValidationSupport;
 	@Autowired
 	private VersionCanonicalizer myVersionCanonicalizer;
+	@Autowired
+	private IJpaStorageResourceParser myJpaStorageResourceParser;
 
 	@Override
 	public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
@@ -2437,7 +2440,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
 				+ ForcedId.IDX_FORCEDID_TYPE_FID + " removed?");
 
 		IFhirResourceDao<CodeSystem> csDao = myDaoRegistry.getResourceDao("CodeSystem");
-		IBaseResource cs = csDao.toResource(resultList.get(0), false);
+		IBaseResource cs = myJpaStorageResourceParser.toResource(resultList.get(0), false);
 		return Optional.of(cs);
 	}
 
@@ -2526,7 +2529,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
 
 	private org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
 		Class<? extends IBaseResource> type = getFhirContext().getResourceDefinition("ValueSet").getImplementingClass();
-		IBaseResource valueSet = myDaoRegistry.getResourceDao("ValueSet").toResource(type, theResourceTable, null, false);
+		IBaseResource valueSet = myJpaStorageResourceParser.toResource(type, theResourceTable, null, false);
 		return myVersionCanonicalizer.valueSetToCanonical(valueSet);
 	}
 

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-cql/src/test/java/ca/uhn/fhir/cql/BaseCqlR4Test.java

@@ -44,12 +44,6 @@ public class BaseCqlR4Test extends BaseJpaR4Test implements CqlProviderTestBase
 	@RegisterExtension
 	protected PartitionHelper myPartitionHelper;
 
-	// FIXME: restore?
-//	@Override
-//	public void beforeResetInterceptors() {
-//		myInterceptorRegistry.unregisterInterceptorsIf(t->!(t instanceof PartitionHelper.MyTestInterceptor));
-//	}
-
 	@Autowired
 	protected
 	DaoRegistry myDaoRegistry;

hapi-fhir-jpaserver-elastic-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/cross/IBasePersistedResource.java

@@ -20,14 +20,15 @@ package ca.uhn.fhir.jpa.model.cross;
  * #L%
  */
 
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import java.util.Date;
-
 public interface IBasePersistedResource extends IResourceLookup {
 
 	IIdType getIdDt();
 
+	long getVersion();
+
+	boolean isDeleted();
+
+	void setNotDeleted();
 }

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

@@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.model.entity;
  * #L%
  */
 
-import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.ParserOptions;
+import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc;
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu2.model.Subscription;
@@ -79,6 +80,30 @@ public class ModelConfig {
 	private boolean myDefaultSearchParamsCanBeOverridden = true;
 	private Set<Subscription.SubscriptionChannelType> mySupportedSubscriptionTypes = new HashSet<>();
 	private boolean myCrossPartitionSubscription = false;
+
+	/**
+	 * If set to true, attempt to map terminology for bulk export jobs using the
+	 * logic in
+	 * {@link ResponseTerminologyTranslationSvc}. Default is <code>false</code>.
+	 *
+	 * @since 6.3.0
+	 */
+	public boolean isNormalizeTerminologyForBulkExportJobs() {
+		return myNormalizeTerminologyForBulkExportJobs;
+	}
+
+	/**
+	 * If set to true, attempt to map terminology for bulk export jobs using the
+	 * logic in
+	 * {@link ResponseTerminologyTranslationSvc}. Default is <code>false</code>.
+	 *
+	 * @since 6.3.0
+	 */
+	public void setNormalizeTerminologyForBulkExportJobs(boolean theNormalizeTerminologyForBulkExportJobs) {
+		myNormalizeTerminologyForBulkExportJobs = theNormalizeTerminologyForBulkExportJobs;
+	}
+
+	private boolean myNormalizeTerminologyForBulkExportJobs = false;
 	private String myEmailFromAddress = "noreply@unknown.com";
 	private String myWebsocketContextPath = DEFAULT_WEBSOCKET_CONTEXT_PATH;
 	/**

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

@@ -213,6 +213,16 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return myResourceVersion;
 	}
 
+	@Override
+	public boolean isDeleted() {
+		return getDeleted() != null;
+	}
+
+	@Override
+	public void setNotDeleted() {
+		setDeleted(null);
+	}
+
 	public void setVersion(long theVersion) {
 		myResourceVersion = theVersion;
 	}

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

@@ -549,6 +549,16 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		return myVersion;
 	}
 
+	@Override
+	public boolean isDeleted() {
+		return getDeleted() != null;
+	}
+
+	@Override
+	public void setNotDeleted() {
+		setDeleted(null);
+	}
+
 	public void setVersion(long theVersion) {
 		myVersion = theVersion;
 	}

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -20,11 +20,11 @@ package ca.uhn.fhir.jpa.searchparam.registry;
  * #L%
  */
 
-import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.ComboSearchParamType;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.phonetic.IPhoneticEncoder;
+import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -179,33 +179,35 @@ public class SearchParameterCanonicalizer {
 		String path = theNextSp.getExpression();
 		RestSearchParameterTypeEnum paramType = null;
 		RuntimeSearchParam.RuntimeSearchParamStatusEnum status = null;
-		switch (theNextSp.getType()) {
+		if (theNextSp.getType() != null) {
-			case COMPOSITE:
+			switch (theNextSp.getType()) {
-				paramType = RestSearchParameterTypeEnum.COMPOSITE;
+				case COMPOSITE:
-				break;
+					paramType = RestSearchParameterTypeEnum.COMPOSITE;
-			case DATE:
+					break;
-				paramType = RestSearchParameterTypeEnum.DATE;
+				case DATE:
-				break;
+					paramType = RestSearchParameterTypeEnum.DATE;
-			case NUMBER:
+					break;
-				paramType = RestSearchParameterTypeEnum.NUMBER;
+				case NUMBER:
-				break;
+					paramType = RestSearchParameterTypeEnum.NUMBER;
-			case QUANTITY:
+					break;
-				paramType = RestSearchParameterTypeEnum.QUANTITY;
+				case QUANTITY:
-				break;
+					paramType = RestSearchParameterTypeEnum.QUANTITY;
-			case REFERENCE:
+					break;
-				paramType = RestSearchParameterTypeEnum.REFERENCE;
+				case REFERENCE:
-				break;
+					paramType = RestSearchParameterTypeEnum.REFERENCE;
-			case STRING:
+					break;
-				paramType = RestSearchParameterTypeEnum.STRING;
+				case STRING:
-				break;
+					paramType = RestSearchParameterTypeEnum.STRING;
-			case TOKEN:
+					break;
-				paramType = RestSearchParameterTypeEnum.TOKEN;
+				case TOKEN:
-				break;
+					paramType = RestSearchParameterTypeEnum.TOKEN;
-			case URI:
+					break;
-				paramType = RestSearchParameterTypeEnum.URI;
+				case URI:
-				break;
+					paramType = RestSearchParameterTypeEnum.URI;
-			case NULL:
+					break;
-				break;
+				case NULL:
+					break;
+			}
 		}
 		if (theNextSp.getStatus() != null) {
 			switch (theNextSp.getStatus()) {

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/submit/interceptor/SubscriptionValidatingInterceptor.java

@@ -39,6 +39,7 @@ import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.HapiExtensions;
@@ -94,7 +95,12 @@ public class SubscriptionValidatingInterceptor {
 			return;
 		}
 
-		CanonicalSubscription subscription = mySubscriptionCanonicalizer.canonicalize(theSubscription);
+		CanonicalSubscription subscription;
+		try {
+			subscription = mySubscriptionCanonicalizer.canonicalize(theSubscription);
+		} catch (InternalErrorException e) {
+			throw new UnprocessableEntityException(Msg.code(955) + e.getMessage());
+		}
 		boolean finished = false;
 		if (subscription.getStatus() == null) {
 			throw new UnprocessableEntityException(Msg.code(8) + "Can not process submitted Subscription - Subscription.status must be populated on this server");

hapi-fhir-jpaserver-test-dstu2/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -22,6 +22,7 @@ import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistryController;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionLoader;
 import ca.uhn.fhir.jpa.test.BaseJpaTest;
+import ca.uhn.fhir.jpa.test.PreventDanglingInterceptorsExtension;
 import ca.uhn.fhir.jpa.test.config.TestDstu2Config;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@@ -60,6 +61,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.extension.RegisterExtension;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.ApplicationContext;
@@ -213,6 +215,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	private ValidationSupportChain myJpaValidationSupportChain;
 
+	@RegisterExtension
+	private final PreventDanglingInterceptorsExtension myPreventDanglingInterceptorsExtension = new PreventDanglingInterceptorsExtension(()-> myInterceptorRegistry);
+
 	@BeforeEach
 	public void beforeFlushFT() {
 		purgeHibernateSearch(myEntityManager);
@@ -232,13 +237,6 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
 	}
 
-	@Override
-	@AfterEach
-	public void afterResetInterceptors() {
-		super.afterResetInterceptors();
-		myInterceptorRegistry.unregisterAllInterceptors();
-	}
-
 	@Override
 	public FhirContext getFhirContext() {
 		return myFhirContext;

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/provider/SubscriptionsDstu2Test.java

@@ -58,6 +58,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 		Subscription subs = new Subscription();
 		subs.getChannel().setType(SubscriptionChannelTypeEnum.REST_HOOK);
 		subs.setCriteria("Observation?identifier=123");
+		subs.getChannel().setEndpoint("http://localhost");
 		try {
 			myClient.create().resource(subs).execute();
 			fail();
@@ -105,6 +106,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 	public void testCreateWithPopulatedButInvalidStatue() {
 		Subscription subs = new Subscription();
 		subs.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
+		subs.getChannel().setEndpoint("http://localhost");
 		subs.setCriteria("Observation?identifier=123");
 		subs.getStatusElement().setValue("aaaaa");
 
@@ -112,7 +114,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 			myClient.create().resource(subs).execute();
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertThat(e.getMessage(), containsString("Subscription.status must be populated on this server"));
+			assertThat(e.getMessage(), containsString("Unknown SubscriptionStatus code 'aaaaa'"));
 		}
 	}
 
@@ -152,6 +154,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 		Subscription subs = new Subscription();
 		subs.getChannel().setType(SubscriptionChannelTypeEnum.REST_HOOK);
 		subs.setCriteria("Observation?identifier=123");
+		subs.getChannel().setEndpoint("http://localhost");
 		subs.setStatus(SubscriptionStatusEnum.REQUESTED);
 		IIdType id = myClient.create().resource(subs).execute().getId();
 		subs.setId(id);

hapi-fhir-jpaserver-test-dstu3/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -93,7 +93,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 	}
 
 	@Test
-	public void testCreateSpWithMultiplePaths(){
+	public void testCreateSpWithMultiplePaths() {
 		SearchParameter sp = new SearchParameter();
 		sp.setCode("telephone-unformatted");
 		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
@@ -101,18 +101,56 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		sp.getBase().add(new CodeType("Patient"));
 		sp.setType(Enumerations.SearchParamType.TOKEN);
 
-		DaoMethodOutcome daoMethodOutcome = mySearchParameterDao.create(sp);
+		DaoMethodOutcome daoMethodOutcome;
+
+		daoMethodOutcome = mySearchParameterDao.create(sp);
 		assertThat(daoMethodOutcome.getId(), is(notNullValue()));
+	}
+
+	@Test
+	public void testCreateSpWithMultiplePaths2() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("telephone-unformatted");
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		sp.setExpression("Patient.telecom.where(system='phone' or system='email')");
+		sp.getBase().add(new CodeType("Patient"));
+		sp.setType(Enumerations.SearchParamType.TOKEN);
+
+		DaoMethodOutcome daoMethodOutcome;
 
 		sp.setExpression("Patient.telecom.where(system='phone') or Patient.telecome.where(system='email')");
 		sp.setCode("telephone-unformatted-2");
 		daoMethodOutcome = mySearchParameterDao.create(sp);
 		assertThat(daoMethodOutcome.getId(), is(notNullValue()));
+	}
+
+	@Test
+	public void testCreateSpWithMultiplePaths3() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("telephone-unformatted");
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		sp.setExpression("Patient.telecom.where(system='phone' or system='email')");
+		sp.getBase().add(new CodeType("Patient"));
+		sp.setType(Enumerations.SearchParamType.TOKEN);
+
+		DaoMethodOutcome daoMethodOutcome;
 
 		sp.setExpression("Patient.telecom.where(system='phone' or system='email') | Patient.telecome.where(system='email')");
 		sp.setCode("telephone-unformatted-3");
 		daoMethodOutcome = mySearchParameterDao.create(sp);
 		assertThat(daoMethodOutcome.getId(), is(notNullValue()));
+	}
+
+	@Test
+	public void testCreateSpWithMultiplePaths4() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("telephone-unformatted");
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		sp.setExpression("Patient.telecom.where(system='phone' or system='email')");
+		sp.getBase().add(new CodeType("Patient"));
+		sp.setType(Enumerations.SearchParamType.TOKEN);
+
+		DaoMethodOutcome daoMethodOutcome;
 
 		sp.setExpression("Patient.telecom.where(system='phone' or system='email') | Patient.telecom.where(system='email') or Patient.telecom.where(system='mail' | system='phone')");
 		sp.setCode("telephone-unformatted-3");
@@ -120,7 +158,6 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		assertThat(daoMethodOutcome.getId(), is(notNullValue()));
 	}
 
-
 	@Test
 	public void testCreateInvalidParamNoPath() {
 		SearchParameter fooSp = new SearchParameter();
@@ -1110,21 +1147,21 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		medAdmin.setMedication(new Reference(medication));
 
 		myMedicationAdministrationDao.create(medAdmin);
-		
+
-		runInTransaction(()->{
+		runInTransaction(() -> {
 			List<ResourceIndexedSearchParamToken> tokens = myResourceIndexedSearchParamTokenDao
 				.findAll()
 				.stream()
 				.filter(t -> t.getParamName().equals("medicationadministration-ingredient-medication"))
 				.collect(Collectors.toList());
-			ourLog.info("Tokens:\n * {}", tokens.stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+			ourLog.info("Tokens:\n * {}", tokens.stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
 			assertEquals(1, tokens.size(), tokens.toString());
 			assertEquals(false, tokens.get(0).isMissing());
 
 		});
 
 		SearchParameterMap map = SearchParameterMap.newSynchronous();
-		map.add("medicationadministration-ingredient-medication", new TokenParam("system","code"));
+		map.add("medicationadministration-ingredient-medication", new TokenParam("system", "code"));
 		myCaptureQueriesListener.clear();
 		IBundleProvider search = myMedicationAdministrationDao.search(map);
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
@@ -1133,5 +1170,4 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 	}
 
 
-
 }

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java

@@ -49,14 +49,16 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl("http://foo");
-		IIdType id = myCodeSystemDao.create(codeSystem).getId().toUnqualifiedVersionless();
+		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualifiedVersionless();
 
-		myCodeSystemDao.delete(id);
+		myCodeSystemDao.delete(id, mySrd);
 
 		codeSystem = new CodeSystem();
 		codeSystem.setUrl("http://foo");
-		myCodeSystemDao.update(codeSystem, "Patient?name=FAM").getId().toUnqualifiedVersionless();
+		IIdType id2 = myCodeSystemDao.update(codeSystem, "CodeSystem?url=http://foo", mySrd).getId();
 
+		assertNotEquals(id.getIdPart(), id2.getIdPart());
+		assertEquals("1", id2.getVersionIdPart());
 	}
 
 	@Test

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -1117,7 +1117,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		String encoded = myFhirContext.newXmlParser().encodeResourceToString(response.getOperationOutcome());
 		ourLog.info(encoded);
 		assertThat(encoded, containsString(
-			"<issue><severity value=\"information\"/><code value=\"informational\"/><diagnostics value=\"Successfully deleted 2 resource(s) in "));
+			"<diagnostics value=\"Successfully deleted 2 resource(s)"));
 		try {
 			myClient.read().resource("Patient").withId(id1).execute();
 			fail();
@@ -1144,7 +1144,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info(response);
 			assertEquals(200, resp.getStatusLine().getStatusCode());
 			assertThat(response, containsString(
-				"<issue><severity value=\"warning\"/><code value=\"not-found\"/><diagnostics value=\"Unable to find resource matching URL &quot;Patient?identifier=testDeleteConditionalNoMatches&quot;. Deletion failed.\"/></issue>"));
+				"<diagnostics value=\"Unable to find resource matching URL &quot;Patient?identifier=testDeleteConditionalNoMatches&quot;. Nothing has been deleted.\"/>"));
 		} finally {
 			IOUtils.closeQuietly(resp);
 		}
@@ -1214,7 +1214,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			OperationOutcome oo = myFhirContext.newXmlParser().parseResource(OperationOutcome.class, resp);
-			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s) in "));
+			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s). Took "));
 		} finally {
 			response.close();
 		}
@@ -1241,7 +1241,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			OperationOutcome oo = myFhirContext.newXmlParser().parseResource(OperationOutcome.class, resp);
-			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Unable to find resource matching URL \"Patient?name=testDeleteResourceConditional1\". Deletion failed."));
+			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Unable to find resource matching URL \"Patient?name=testDeleteResourceConditional1\". Nothing has been deleted."));
 		} finally {
 			response.close();
 		}
@@ -1322,7 +1322,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 
 		MethodOutcome resp = myClient.delete().resourceById(id).execute();
 		OperationOutcome oo = (OperationOutcome) resp.getOperationOutcome();
-		assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s) in "));
+		assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s). Took"));
 	}
 
 	/**

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

@@ -192,14 +192,11 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 
 
 	@Test
-	public void testPatchUsingJsonPatch_Transaction() throws Exception {
+	public void testPatchUsingJsonPatch_Transaction() {
-		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();
 		}
 
@@ -224,6 +221,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 			.getRequest().setUrl(pid1.getValue()).setMethod(HTTPVerb.PUT);
 
 		Bundle bundle = ourClient.transaction().withBundle(input).execute();
+		ourLog.info("Response: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
 
 		//Validate over all bundle response entry contents.
 		assertThat(bundle.getType(), is(equalTo(Bundle.BundleType.TRANSACTIONRESPONSE)));

hapi-fhir-jpaserver-test-r4/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.3.0-PRE5-SNAPSHOT</version>
+		<version>6.3.2-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/batch2/Batch2CoordinatorIT.java

@@ -404,18 +404,6 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
 
 	@Test
 	public void testStepRunFailure_continuouslyThrows_marksJobFailed() {
-		// FIXME: remove
-//		AtomicInteger interceptorCounter = new AtomicInteger();
-//		myWorkChannel.addInterceptor(new ExecutorChannelInterceptor() {
-//			@Override
-//			public void afterMessageHandled(Message<?> message, MessageChannel channel, MessageHandler handler, Exception ex) {
-//				if (ex != null) {
-//					interceptorCounter.incrementAndGet();
-//					ourLog.info("Work Channel Exception thrown: {}.  Resending message", ex.getMessage());
-//					channel.send(message);
-//				}
-//			}
-//		});
 
 		// setup
 		AtomicInteger counter = new AtomicInteger();