2564 contained resource validation flag (#3225)

* First cut at multithreading bundle validation

* javadoc

* change test to a red-green test

* add daoconfig

* move bundle concurrency config from validationsupport to request validator

* Moved concurrent details from ValidationOptions to FhirValidator

* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)

* validate threadpool prefixes

* FIXME cleanup

* reassign FIXMEs to JB

* only create the threadpool if it will be used

* Add the MdcTaskDectorator to all threadpools

* Add bundle path to concurrently validated bundle resource validation messages.

* Add test to check bundle entry path being added to validation messages

* Threaded validation of contained resources initial checkin

* FHIR validator refactored to maintain correct bundle path and async validation task

* Refactored to use validation complete invoke callback to support raw string resource or resource object

* switch from XML to JSON

* # Conflicts:
#	hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Updated to use new HAPI-FHIR version

* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation

* Updated to use new HAPI-FHIR version

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit 910b7f676b.

* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"

This reverts commit c7d60fc3e6.

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit aa8a7af455.

# Conflicts:
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Fix Test dependencies after reverting changes.

* merge 'validate_contains_change' to 2564-contained-resource-validation-flag

* Disable threadpool prefix name validate check.

* merge master

* fix thread regexp

* pre-review cleanup

* change log

* fix test

* revert to XML as default validation serialization

* fix test

* fix test

Co-authored-by: Jaison B <jaisonb@gmail.com>

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>5.7.0-PRE4-SNAPSHOT</version>
+		 <version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -127,6 +127,7 @@ public class FhirContext {
 	private volatile Boolean myFormatJsonSupported;
 	private volatile Boolean myFormatNDJsonSupported;
 	private volatile Boolean myFormatRdfSupported;
+	private IFhirValidatorFactory myFhirValidatorFactory = fhirContext -> new FhirValidator(fhirContext);
 
 	/**
 	 * @deprecated It is recommended that you use one of the static initializer methods instead
@@ -908,7 +909,7 @@ public class FhirContext {
 	 * </p>
 	 */
 	public FhirValidator newValidator() {
-		return new FhirValidator(this);
+		return myFhirValidatorFactory.newFhirValidator(this);
 	}
 
 	public ViewGenerator newViewGenerator() {
@@ -1072,9 +1073,22 @@ public class FhirContext {
 	 *
 	 * @param theParserErrorHandler The error handler
 	 */
-	public void setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
+	public FhirContext setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
 		Validate.notNull(theParserErrorHandler, "theParserErrorHandler must not be null");
 		myParserErrorHandler = theParserErrorHandler;
+		return this;
+	}
+
+	/**
+	 * Set the factory method used to create FhirValidator instances
+	 *
+	 * @param theFhirValidatorFactory
+	 * @return this
+	 * @since 5.6.0
+	 */
+	public FhirContext setFhirValidatorFactory(IFhirValidatorFactory theFhirValidatorFactory) {
+		myFhirValidatorFactory = theFhirValidatorFactory;
+		return this;
 	}
 
 	@SuppressWarnings({"cast"})

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

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.context;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2021 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.validation.FhirValidator;
+
+public interface IFhirValidatorFactory {
+	FhirValidator newFhirValidator(FhirContext theFhirContext);
+}

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

@@ -380,5 +380,4 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		ArrayList<IBaseResource> retVal = new ArrayList<>(theMap.values());
 		return (List<T>) Collections.unmodifiableList(retVal);
 	}
-
 }

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

@@ -36,7 +36,6 @@ import javax.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 import java.util.function.Supplier;
@@ -340,7 +339,6 @@ public interface IValidationSupport {
 		return null;
 	}
 
-
 	enum IssueSeverity {
 		/**
 		 * The issue caused the action to fail, and no further checking could be performed.

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java

@@ -24,13 +24,25 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.validation.schematron.SchematronProvider;
 import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Future;
+import java.util.function.Consumer;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
 
 
 /**
@@ -46,6 +58,7 @@ import java.util.List;
  * </p>
  */
 public class FhirValidator {
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirValidator.class);
 
 	private static final String I18N_KEY_NO_PH_ERROR = FhirValidator.class.getName() + ".noPhError";
 
@@ -53,6 +66,9 @@ public class FhirValidator {
 	private final FhirContext myContext;
 	private List<IValidatorModule> myValidators = new ArrayList<>();
 	private IInterceptorBroadcaster myInterceptorBroadcaster;
+	private boolean myConcurrentBundleValidation;
+
+	private ExecutorService myExecutorService;
 
 	/**
 	 * Constructor (this should not be called directly, but rather {@link FhirContext#newValidator()} should be called to obtain an instance of {@link FhirValidator})
@@ -72,8 +88,7 @@ public class FhirValidator {
 				registerValidatorModule(theInstance);
 			}
 		} else {
-			for (Iterator<IValidatorModule> iter = myValidators.iterator(); iter.hasNext(); ) {
+			for (IValidatorModule next : myValidators) {
-				IValidatorModule next = iter.next();
 				if (next.getClass().equals(type)) {
 					unregisterValidatorModule(next);
 				}
@@ -86,6 +101,7 @@ public class FhirValidator {
 		for (IValidatorModule next : myValidators) {
 			if (next.getClass().equals(type)) {
 				found = true;
+				break;
 			}
 		}
 		return found;
@@ -202,6 +218,21 @@ public class FhirValidator {
 		return validateWithResult(theResource, null);
 	}
 
+	/**
+	 * Validates a resource instance returning a {@link ValidationResult} which contains the results.
+	 *
+	 * @param theResource the resource to validate
+	 * @param theOptions  Optionally provides options to the validator
+	 * @return the results of validation
+	 * @since 4.0.0
+	 */
+	public ValidationResult validateWithResult(String theResource, ValidationOptions theOptions) {
+		Validate.notNull(theResource, "theResource must not be null");
+		IValidationContext<IBaseResource> validationContext = ValidationContext.forText(myContext, theResource, theOptions);
+		Function<ValidationResult, ValidationResult> callback = result -> invokeValidationCompletedHooks(null, theResource, result);
+		return doValidate(validationContext, theOptions, callback);
+	}
+
 	/**
 	 * Validates a resource instance returning a {@link ValidationResult} which contains the results.
 	 *
@@ -212,18 +243,65 @@ public class FhirValidator {
 	 */
 	public ValidationResult validateWithResult(IBaseResource theResource, ValidationOptions theOptions) {
 		Validate.notNull(theResource, "theResource must not be null");
+		IValidationContext<IBaseResource> validationContext = ValidationContext.forResource(myContext, theResource, theOptions);
+		Function<ValidationResult, ValidationResult> callback = result -> invokeValidationCompletedHooks(theResource, null, result);
+		return doValidate(validationContext, theOptions, callback);
+	}
 
+	private ValidationResult doValidate(IValidationContext<IBaseResource> theValidationContext, ValidationOptions theOptions,
+													Function<ValidationResult, ValidationResult> theValidationCompletionCallback) {
 		applyDefaultValidators();
 
-		IValidationContext<IBaseResource> ctx = ValidationContext.forResource(myContext, theResource, theOptions);
+		ValidationResult result;
-
+		if (myConcurrentBundleValidation && theValidationContext.getResource() instanceof IBaseBundle
-		for (IValidatorModule next : myValidators) {
+			&& myExecutorService != null) {
-			next.validateResource(ctx);
+			result = validateBundleEntriesConcurrently(theValidationContext, theOptions);
+		} else {
+			result = validateResource(theValidationContext);
 		}
 
-		ValidationResult result = ctx.toResult();
+		return theValidationCompletionCallback.apply(result);
-		result = invokeValidationCompletedHooks(theResource, null, result);
+	}
-		return result;
+
+	private ValidationResult validateBundleEntriesConcurrently(IValidationContext<IBaseResource> theValidationContext, ValidationOptions theOptions) {
+		List<IBaseResource> entries = BundleUtil.toListOfResources(myContext, (IBaseBundle) theValidationContext.getResource());
+		// Async validation tasks
+		List<ConcurrentValidationTask> validationTasks = IntStream.range(0, entries.size())
+			.mapToObj(index -> {
+				IBaseResource entry = entries.get(index);
+				String entryPathPrefix = String.format("Bundle.entry[%d].resource.ofType(%s)", index, entry.fhirType());
+				Future<ValidationResult> future = myExecutorService.submit(() -> {
+					IValidationContext<IBaseResource> entryValidationContext = ValidationContext.forResource(theValidationContext.getFhirContext(), entry, theOptions);
+					return validateResource(entryValidationContext);
+				});
+				return new ConcurrentValidationTask(entryPathPrefix, future);
+			}).collect(Collectors.toList());
+
+		List<SingleValidationMessage> validationMessages = new ArrayList<>();
+		try {
+			for (ConcurrentValidationTask validationTask : validationTasks) {
+				ValidationResult result = validationTask.getFuture().get();
+				final String bundleEntryPathPrefix = validationTask.getResourcePathPrefix();
+				List<SingleValidationMessage> messages = result.getMessages().stream()
+					.map(message -> {
+						String currentPath = message.getLocationString().substring(message.getLocationString().indexOf('.'));
+						message.setLocationString(bundleEntryPathPrefix + currentPath);
+						return message;
+					})
+					.collect(Collectors.toList());
+				validationMessages.addAll(messages);
+			}
+		} catch (InterruptedException | ExecutionException exp) {
+			throw new InternalErrorException(exp);
+		}
+		return new ValidationResult(myContext, new ArrayList<>(validationMessages));
+	}
+
+	private ValidationResult validateResource(IValidationContext<IBaseResource> theValidationContext) {
+		for (IValidatorModule next : myValidators) {
+			next.validateResource(theValidationContext);
+		}
+		return theValidationContext.toResult();
 	}
 
 	private ValidationResult invokeValidationCompletedHooks(IBaseResource theResourceParsed, String theResourceRaw, ValidationResult theValidationResult) {
@@ -242,30 +320,6 @@ public class FhirValidator {
 		return theValidationResult;
 	}
 
-	/**
-	 * Validates a resource instance returning a {@link ValidationResult} which contains the results.
-	 *
-	 * @param theResource the resource to validate
-	 * @param theOptions  Optionally provides options to the validator
-	 * @return the results of validation
-	 * @since 4.0.0
-	 */
-	public ValidationResult validateWithResult(String theResource, ValidationOptions theOptions) {
-		Validate.notNull(theResource, "theResource must not be null");
-
-		applyDefaultValidators();
-
-		IValidationContext<IBaseResource> ctx = ValidationContext.forText(myContext, theResource, theOptions);
-
-		for (IValidatorModule next : myValidators) {
-			next.validateResource(ctx);
-		}
-
-		ValidationResult result = ctx.toResult();
-		result = invokeValidationCompletedHooks(null, theResource, result);
-		return result;
-	}
-
 	/**
 	 * Optionally supplies an interceptor broadcaster that will be used to invoke validation related Pointcut events
 	 *
@@ -274,4 +328,47 @@ public class FhirValidator {
 	public void setInterceptorBroadcaster(IInterceptorBroadcaster theInterceptorBraodcaster) {
 		myInterceptorBroadcaster = theInterceptorBraodcaster;
 	}
+
+	public FhirValidator setExecutorService(ExecutorService theExecutorService) {
+		myExecutorService = theExecutorService;
+		return this;
+	}
+
+	/**
+	 * If this is true, bundles will be validated in parallel threads.  The bundle structure itself will not be validated,
+	 * only the resources in its entries.
+	 */
+
+	public boolean isConcurrentBundleValidation() {
+		return myConcurrentBundleValidation;
+	}
+
+	/**
+	 * If this is true, bundles will be validated in parallel threads.  The bundle structure itself will not be validated,
+	 * only the resources in its entries.
+	 */
+	public FhirValidator setConcurrentBundleValidation(boolean theConcurrentBundleValidation) {
+		myConcurrentBundleValidation = theConcurrentBundleValidation;
+		return this;
+	}
+
+	// Simple Tuple to keep track of bundle path and associate aync future task
+	private static class ConcurrentValidationTask {
+		private final String myResourcePathPrefix;
+		private final Future<ValidationResult> myFuture;
+
+		private ConcurrentValidationTask(String theResourcePathPrefix, Future<ValidationResult> theFuture) {
+			myResourcePathPrefix = theResourcePathPrefix;
+			myFuture = theFuture;
+		}
+
+		public String getResourcePathPrefix() {
+			return myResourcePathPrefix;
+		}
+
+		public Future<ValidationResult> getFuture() {
+			return myFuture;
+		}
+	}
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/ValidationOptions.java

@@ -33,6 +33,9 @@ public class ValidationOptions {
 	private static ValidationOptions ourEmpty;
 	private Set<String> myProfiles;
 
+	public ValidationOptions() {
+	}
+
 	public Set<String> getProfiles() {
 		return myProfiles != null ? Collections.unmodifiableSet(myProfiles) : Collections.emptySet();
 	}

hapi-fhir-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-bom/pom.xml

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommandTest.java

@@ -13,6 +13,7 @@ import org.springframework.jdbc.core.support.AbstractLobCreatingPreparedStatemen
 import org.springframework.jdbc.support.lob.DefaultLobHandler;
 import org.springframework.jdbc.support.lob.LobCreator;
 
+import javax.annotation.Nonnull;
 import javax.validation.constraints.NotNull;
 import java.io.File;
 import java.io.IOException;
@@ -278,7 +279,7 @@ public class HapiFlywayMigrateDatabaseCommandTest {
 		assertTrue(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_BLK_EXPORT_JOB")); // Late table
 	}
 
-	@NotNull
+	@Nonnull
 	private File getLocation(String theDatabaseName) throws IOException {
 		File directory = new File(DB_DIRECTORY);
 		if (directory.exists()) {

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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/2564-skip-contained-multithreaded-validation.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+title: "New configuration option added to validate bundle resources concurrently.
+Also new configuration added to skip validation of contained resources."

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.binstore;
  * #L%
  */
 
-import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IIdType;
 

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

@@ -125,7 +125,6 @@ import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
 import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
 import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
-import ca.uhn.fhir.jpa.search.reindex.BlockPolicy;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
 import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
@@ -151,6 +150,7 @@ import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
 import ca.uhn.fhir.rest.server.provider.ReindexProvider;
+import ca.uhn.fhir.util.ThreadPoolUtil;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -181,7 +181,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.scheduling.TaskScheduler;
 import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
 import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
-import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
 
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
@@ -426,18 +425,9 @@ public abstract class BaseConfig {
 
 	@Bean(name= BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
 	public TaskExecutor jobLaunchingTaskExecutor() {
-		ThreadPoolTaskExecutor asyncTaskExecutor = new ThreadPoolTaskExecutor();
+		return ThreadPoolUtil.newThreadPool(0, 10, "job-launcher-");
-		asyncTaskExecutor.setCorePoolSize(0);
-		asyncTaskExecutor.setMaxPoolSize(10);
-		asyncTaskExecutor.setQueueCapacity(0);
-		asyncTaskExecutor.setAllowCoreThreadTimeOut(true);
-		asyncTaskExecutor.setThreadNamePrefix("JobLauncher-");
-		asyncTaskExecutor.setRejectedExecutionHandler(new BlockPolicy());
-		asyncTaskExecutor.initialize();
-		return asyncTaskExecutor;
 	}
 
-
 	@Bean
 	public IResourceReindexingSvc resourceReindexingSvc() {
 		return new ResourceReindexingSvcImpl();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfigDstu3Plus.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.config;
 
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
 import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
 import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
@@ -66,7 +67,7 @@ public abstract class BaseConfigDstu3Plus extends BaseConfig {
 	public abstract ITermVersionAdapterSvc terminologyVersionAdapterSvc();
 
 	@Bean(name = "myDefaultProfileValidationSupport")
-	public DefaultProfileValidationSupport defaultProfileValidationSupport() {
+	public DefaultProfileValidationSupport defaultProfileValidationSupport(DaoConfig theDaoConfig) {
 		return new DefaultProfileValidationSupport(fhirContext());
 	}
 

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

@@ -86,7 +86,6 @@ import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
 import ca.uhn.fhir.rest.server.RestfulServerUtils;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
-import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
@@ -1776,7 +1775,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		FhirValidator validator = getContext().newValidator();
-
 		validator.setInterceptorBroadcaster(CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest));
 		validator.registerValidatorModule(getInstanceValidator());
 		validator.registerValidatorModule(new IdChecker(theMode));

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

@@ -40,7 +40,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.MultimapBuilder;
-import org.apache.commons.lang3.Functions;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IAnyResource;

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

@@ -27,7 +27,12 @@ import ca.uhn.fhir.jpa.model.search.ExtendedLuceneIndexData;
 import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
 import org.jetbrains.annotations.NotNull;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
 
 /**
  * Extract search params for advanced lucene indexing.

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

@@ -23,7 +23,18 @@ package ca.uhn.fhir.jpa.entity;
 import ca.uhn.fhir.util.ValidateUtil;
 
 import javax.annotation.Nonnull;
-import javax.persistence.*;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ForeignKey;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Index;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
 import java.io.Serializable;
 
 import static org.apache.commons.lang3.StringUtils.left;

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

@@ -22,7 +22,20 @@ package ca.uhn.fhir.jpa.entity;
 
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
 
-import javax.persistence.*;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.ForeignKey;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Index;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
 import java.io.Serializable;
 
 @Entity

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

@@ -41,15 +41,10 @@ import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
 import ca.uhn.fhir.util.VersionEnum;
 
 import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-import static java.util.stream.Collectors.toSet;
 
 @SuppressWarnings({"SqlNoDataSourceInspection", "SpellCheckingInspection"})
 public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {

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

@@ -390,21 +390,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		return Optional.empty();
 	}
 
-	@NotNull
+	@Nonnull
 	private PersistedJpaSearchFirstPageBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString, RequestPartitionId theRequestPartitionId, Search theSearch) {
 		StopWatch w = new StopWatch();
-//		Search search = new Search();
-		//TODO GGG MOVE THIS POPULATE AND ALSO THE HOOK CALL HIGHER UP IN THE STACK.
-//		populateSearchEntity(theParams, theResourceType, theSearchUuid, theQueryString, search, theRequestPartitionId);
-
-//		 Interceptor call: STORAGE_PRESEARCH_REGISTERED
-//		HookParams params = new HookParams()
-//			.add(ICachedSearchDetails.class, search)
-//			.add(RequestDetails.class, theRequestDetails)
-//			.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
-//			.add(SearchParameterMap.class, theParams);
-//		CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
-
 		SearchTask task = new SearchTask(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails, theRequestPartitionId);
 		myIdToSearchTask.put(theSearch.getUuid(), task);
 		task.call();
@@ -841,7 +829,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 			txTemplate.execute(new TransactionCallbackWithoutResult() {
 				@Override
-				protected void doInTransactionWithoutResult(@Nonnull @NotNull TransactionStatus theArg0) {
+				protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theArg0) {
 					doSaveSearch();
 				}
 
@@ -853,7 +841,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
 			txTemplate.execute(new TransactionCallbackWithoutResult() {
 				@Override
-				protected void doInTransactionWithoutResult(@Nonnull @NotNull TransactionStatus theArg0) {
+				protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theArg0) {
 					if (mySearch.getId() == null) {
 						doSaveSearch();
 					}

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

@@ -2266,7 +2266,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	@Nullable
 	protected abstract CodeableConcept toCanonicalCodeableConcept(@Nullable IBaseDatatype theCodeableConcept);
 
-	@NotNull
+	@Nonnull
 	private FhirVersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theCodeSystemIdentifierType, IBaseCoding theCodingType) {
 		String code = theCodeType != null ? theCodeType.getValueAsString() : null;
 		String system = theCodeSystemIdentifierType != null ? getUrlFromIdentifier(theCodeSystemIdentifierType.getValueAsString()) : null;

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

@@ -413,7 +413,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 	}
 
 	@VisibleForTesting
-	@NotNull
+	@Nonnull
 	Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
 		Properties retVal = new Properties();
 

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

@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.term.api;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;

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

@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.term.api;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;

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

@@ -22,10 +22,6 @@ package ca.uhn.fhir.jpa.term.job;
 
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
-import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
-import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
-import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
-import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import org.slf4j.Logger;
@@ -34,7 +30,6 @@ import org.springframework.batch.item.ItemWriter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import java.text.DecimalFormat;
 import java.util.List;
 import java.util.Optional;
 

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

@@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.term.job;
 
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
-import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

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

@@ -32,6 +32,8 @@ import org.springframework.batch.repeat.RepeatStatus;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
+import javax.annotation.Nonnull;
+
 import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
 
 /**
@@ -49,7 +51,7 @@ public class TermConceptDeleteTasklet implements Tasklet {
 	private ITermCodeSystemVersionDao myCodeSystemVersionDao;
 
 	@Override
-	public RepeatStatus execute(@NotNull StepContribution contribution, ChunkContext context) throws Exception {
+	public RepeatStatus execute(@Nonnull StepContribution contribution, ChunkContext context) throws Exception {
 		long codeSystemPid = (Long) context.getStepContext().getJobParameters().get(JOB_PARAM_CODE_SYSTEM_ID);
 		ourLog.info("Deleting code system {}", codeSystemPid);
 

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

@@ -5,6 +5,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
 
 import java.util.List;
 
+import javax.annotation.Nonnull;
 import javax.validation.constraints.NotNull;
 
 import org.apache.commons.csv.CSVRecord;
@@ -73,7 +74,7 @@ public class LoincLinguisticVariantsHandler implements IZipContentsHandlerCsv {
 		private String myIsoCountry;
 		private String myLanguageName;
 
-		public LinguisticVariant(@NotNull String theId, @NotNull String theIsoLanguage, @NotNull String theIsoCountry, @NotNull String theLanguageName) {
+		public LinguisticVariant(@Nonnull String theId, @Nonnull String theIsoLanguage, @Nonnull String theIsoCountry, @Nonnull String theLanguageName) {
 			this.myId = theId;
 			this.myIsoLanguage = theIsoLanguage;
 			this.myIsoCountry = theIsoCountry;

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

@@ -615,7 +615,7 @@ public abstract class BaseJpaTest extends BaseTest {
 		}
 	}
 
-	@NotNull
+	@Nonnull
 	public static Map<String, String> buildHibernateSearchProperties(boolean enableLucene) {
 		Map<String, String> hibernateSearchProperties;
 		if (enableLucene) {

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

@@ -16,7 +16,6 @@ import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.validation.FhirValidator;

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

@@ -60,7 +60,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
 import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
 import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
 import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
@@ -93,8 +92,6 @@ import ca.uhn.fhir.util.ClasspathUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;
-import org.hibernate.search.mapper.orm.Search;
-import org.hibernate.search.mapper.orm.session.SearchSession;
 import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseResource;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LuceneDisabledStandardQueries.java

@@ -20,8 +20,6 @@ import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 import org.springframework.transaction.PlatformTransactionManager;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
 @ExtendWith(SpringExtension.class)
 @ContextConfiguration(classes = {TestR4WithLuceneDisabledConfig.class})
 @DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)

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

@@ -15,7 +15,6 @@ import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.validation.FhirValidator;

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

@@ -130,7 +130,6 @@ import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 
-import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
 import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
 import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.apache.commons.lang3.StringUtils.defaultString;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java

@@ -49,7 +49,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
 import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
@@ -76,8 +75,6 @@ import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;
 import org.apache.commons.io.IOUtils;
-import org.hibernate.search.mapper.orm.Search;
-import org.hibernate.search.mapper.orm.session.SearchSession;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ExpungeR4Test.java

@@ -32,7 +32,6 @@ import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.DecimalType;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.MedicationRequest;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu2Test.java

@@ -34,6 +34,7 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
 import javax.validation.constraints.NotNull;
 import java.util.ArrayList;
 import java.util.List;
@@ -109,7 +110,7 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
 		return subscription;
 	}
 
-	@NotNull
+	@Nonnull
 	private Subscription newSubscription(String criteria, String payload, String endpoint) {
 		Subscription subscription = new Subscription();
 		subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");

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

@@ -41,6 +41,7 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
 import javax.servlet.http.HttpServletRequest;
 import javax.validation.constraints.NotNull;
 import java.util.ArrayList;
@@ -136,7 +137,7 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
 		return (Subscription) methodOutcome.getResource();
 	}
 
-	@NotNull
+	@Nonnull
 	private Subscription newSubscription(String theCriteria, String thePayload, String theEndpoint, List<StringType> headers) {
 		Subscription subscription = new Subscription();
 		subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");

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

@@ -14,9 +14,7 @@ import org.springframework.batch.core.JobExecution;
 import org.springframework.test.util.ReflectionTestUtils;
 import org.springframework.transaction.PlatformTransactionManager;
 
-import java.util.ArrayList;
 import java.util.Collections;
-import java.util.List;
 import java.util.Optional;
 
 import static org.junit.jupiter.api.Assertions.assertFalse;

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

@@ -13,7 +13,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import java.io.IOException;
 
-import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
 import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java

@@ -27,7 +27,6 @@ import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.mockito.Answers;
@@ -36,7 +35,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.util.ResourceUtils;
 
 import javax.persistence.EntityManager;

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-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>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java

@@ -155,7 +155,7 @@ public class MdmLinkDaoSvc {
 		return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.POSSIBLE_MATCH);
 	}
 
-	@NotNull
+	@Nonnull
 	private Optional<MdmLink> getMdmLinkWithMatchResult(IBaseResource theSourceResource, MdmMatchResultEnum theMatchResult) {
 		Long pid = myIdHelperService.getPidOrNull(theSourceResource);
 		if (pid == null) {

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/BaseProviderR4Test.java

@@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.mdm.provider;
 import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
 import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
 import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
-import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
 import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
 import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
 import ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus;

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -20,7 +20,13 @@ package ca.uhn.fhir.jpa.model.entity;
  * #L%
  */
 
-import javax.persistence.*;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import javax.persistence.Lob;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
 import java.sql.Blob;
 import java.util.Date;
 

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/ExtendedLuceneIndexData.java

@@ -21,11 +21,9 @@ package ca.uhn.fhir.jpa.model.search;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.param.TokenParam;
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.SetMultimap;
-import org.apache.commons.lang3.StringUtils;
 import org.hibernate.search.engine.backend.document.DocumentElement;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -290,7 +290,7 @@ public class SearchParamExtractorService {
 		theEntity.setHasLinks(theParams.myLinks.size() > 0);
 	}
 
-	private void extractResourceLinks(@NotNull RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, TransactionDetails theTransactionDetails, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest) {
+	private void extractResourceLinks(@Nonnull RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, TransactionDetails theTransactionDetails, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest) {
 		IBaseReference nextReference = thePathAndRef.getRef();
 		IIdType nextId = nextReference.getReferenceElement();
 		String path = thePathAndRef.getPath();

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/websocket/WebsocketConnectionValidator.java

@@ -29,6 +29,8 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
+
 public class WebsocketConnectionValidator {
 	private static Logger ourLog = LoggerFactory.getLogger(WebsocketConnectionValidator.class);
 
@@ -43,7 +45,7 @@ public class WebsocketConnectionValidator {
 		super();
 	}
 
-	public WebsocketValidationResponse validate(@NotNull IdType id) {
+	public WebsocketValidationResponse validate(@Nonnull IdType id) {
 		if (!id.hasIdPart() || !id.isIdPartValid()) {
 			return WebsocketValidationResponse.INVALID_RESPONSE("Invalid bind request - No ID included: " + id.getValue());
 		}

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaDstu3Config.java

@@ -22,8 +22,6 @@ package ca.uhn.fhir.jpa.config;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
-import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
-import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderDstu3Plus.java

@@ -22,10 +22,8 @@ package ca.uhn.fhir.mdm.provider;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
-import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
-import ca.uhn.fhir.mdm.api.MatchedTarget;
 import ca.uhn.fhir.mdm.api.MdmConstants;
 import ca.uhn.fhir.mdm.api.MdmLinkJson;
 import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
@@ -39,30 +37,20 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.provider.ProviderConstants;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
-import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.util.ParametersUtil;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
-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.IBaseDatatype;
-import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.slf4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 
-import javax.annotation.Nonnull;
 import java.math.BigDecimal;
 import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.Date;
 import java.util.List;
-import java.util.UUID;
 import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.rest.api.Constants.PARAM_OFFSET;

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderLoader.java

@@ -23,7 +23,6 @@ package ca.uhn.fhir.mdm.provider;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
-import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;

hapi-fhir-server-openapi/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -20,20 +20,19 @@ package ca.uhn.fhir.rest.server.interceptor;
  * #L%
  */
 
-import java.util.HashSet;
-import java.util.Set;
-
 import ca.uhn.fhir.interceptor.api.Hook;
 import ca.uhn.fhir.interceptor.api.Pointcut;
-import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhir.validation.ValidationResult;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.util.HashSet;
+import java.util.Set;
 
 /**
  * This interceptor intercepts each outgoing response and if it contains a FHIR resource, validates that resource. The interceptor may be configured to run any validator modules, and will then add

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

@@ -21,21 +21,15 @@ package ca.uhn.fhir.rest.server.method;
  */
 
 import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.parser.json.JsonLikeObject;
-import ca.uhn.fhir.parser.json.JsonLikeStructure;
-import ca.uhn.fhir.parser.json.JsonLikeValue;
-import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
 import ca.uhn.fhir.rest.annotation.Count;
 import ca.uhn.fhir.rest.api.Constants;
 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 com.fasterxml.jackson.core.JsonFactory;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.io.IOUtils;
 
-import javax.annotation.Nullable;
 import java.io.IOException;
 import java.io.Reader;
 import java.lang.reflect.Method;

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-samples</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml

@@ -5,7 +5,7 @@
    <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>5.7.0-PRE4-SNAPSHOT</version>
+      <version>5.7.0-PRE5-SNAPSHOT</version>
       <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
 

hapi-fhir-spring-boot/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-sql-migrate/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-storage/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
 import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
 import ca.uhn.fhir.util.HapiExtensions;
+import ca.uhn.fhir.validation.FhirValidator;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Sets;
 import org.apache.commons.lang3.StringUtils;
@@ -286,6 +287,12 @@ public class DaoConfig {
 	 */
 	private int myInlineResourceTextBelowSize = 0;
 
+	/**
+	 * @see FhirValidator#isConcurrentBundleValidation()
+	 * @since 5.7.0
+	 */
+	private boolean myConcurrentBundleValidation;
+
 	/**
 	 * Constructor
 	 */
@@ -2724,6 +2731,23 @@ public class DaoConfig {
 		this.myAdvancedLuceneIndexing = theAdvancedLuceneIndexing;
 	}
 
+	/**
+	 * @see FhirValidator#isConcurrentBundleValidation()
+	 * @since 5.7.0
+	 */
+	public boolean isConcurrentBundleValidation() {
+		return myConcurrentBundleValidation;
+	}
+
+	/**
+	 * @see FhirValidator#isConcurrentBundleValidation()
+	 * @since 5.7.0
+	 */
+	public DaoConfig setConcurrentBundleValidation(boolean theConcurrentBundleValidation) {
+		myConcurrentBundleValidation = theConcurrentBundleValidation;
+		return this;
+	}
+
 	public enum StoreMetaSourceInformationEnum {
 		NONE(false, false),
 		SOURCE_URI(true, false),

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

@@ -431,7 +431,7 @@ public abstract class BaseStorageDao {
 		return oo;
 	}
 
-	@NotNull
+	@Nonnull
 	protected ResourceGoneException createResourceGoneException(IBasePersistedResource theResourceEntity) {
 		StringBuilder b = new StringBuilder();
 		b.append("Resource was deleted at ");

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

@@ -80,6 +80,7 @@ import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.ThreadPoolUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ArrayListMultimap;
@@ -102,7 +103,6 @@ import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.task.SyncTaskExecutor;
 import org.springframework.core.task.TaskExecutor;
-import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.support.TransactionCallback;
@@ -193,13 +193,7 @@ public abstract class BaseTransactionProcessor {
 	private TaskExecutor getTaskExecutor() {
 		if (myExecutor == null) {
 			if (myDaoConfig.getBundleBatchPoolSize() > 1) {
-				ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
+				myExecutor = ThreadPoolUtil.newThreadPool(myDaoConfig.getBundleBatchPoolSize(), myDaoConfig.getBundleBatchMaxPoolSize(), "bundle-batch-");
-				executor.setThreadNamePrefix("bundle_batch_");
-				executor.setCorePoolSize(myDaoConfig.getBundleBatchPoolSize());
-				executor.setMaxPoolSize(myDaoConfig.getBundleBatchMaxPoolSize());
-				executor.initialize();
-				myExecutor = executor;
-
 			} else {
 				SyncTaskExecutor executor = new SyncTaskExecutor();
 				myExecutor = executor;

hapi-fhir-storage/src/main/java/ca/uhn/fhir/util/ThreadPoolUtil.java

@@ -0,0 +1,47 @@
+package ca.uhn.fhir.util;
+
+/*-
+ * #%L
+ * HAPI FHIR Storage api
+ * %%
+ * Copyright (C) 2014 - 2021 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.search.reindex.BlockPolicy;
+import org.apache.commons.lang3.Validate;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+
+import javax.annotation.Nonnull;
+
+public final class ThreadPoolUtil {
+	private ThreadPoolUtil() {
+	}
+
+
+	@Nonnull
+	public static ThreadPoolTaskExecutor newThreadPool(int theCorePoolSize, int theMaxPoolSize, String theThreadNamePrefix) {
+		Validate.isTrue(theThreadNamePrefix.endsWith("-"), "Thread pool prefix name must end with a hyphen");
+		ThreadPoolTaskExecutor asyncTaskExecutor = new ThreadPoolTaskExecutor();
+		asyncTaskExecutor.setCorePoolSize(theCorePoolSize);
+		asyncTaskExecutor.setMaxPoolSize(theMaxPoolSize);
+		asyncTaskExecutor.setQueueCapacity(0);
+		asyncTaskExecutor.setAllowCoreThreadTimeOut(true);
+		asyncTaskExecutor.setThreadNamePrefix(theThreadNamePrefix);
+		asyncTaskExecutor.setRejectedExecutionHandler(new BlockPolicy());
+		asyncTaskExecutor.initialize();
+		return asyncTaskExecutor;
+	}
+}

hapi-fhir-structures-dstu2.1/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu2/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu3/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-test-utilities/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-testpage-overlay/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-dstu2.1/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.7.0-PRE4-SNAPSHOT</version>
+		<version>5.7.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>