Merge remote-tracking branch 'origin/master' into consent_service_resource_filtering_leads_to_empty_pages_with_next_link

.github/workflows/codeql-analysis.yml

@@ -25,7 +25,7 @@ jobs:
       if: ${{ github.event_name == 'pull_request' }}
 
     - name: Setup java
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v3
       with:
          distribution: zulu
          java-version: 17

.mvn/wrapper/MavenWrapperDownloader.java

@@ -13,9 +13,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import java.net.*;
+
-import java.io.*;
+import java.io.File;
-import java.nio.channels.*;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.Authenticator;
+import java.net.PasswordAuthentication;
+import java.net.URL;
+import java.nio.channels.Channels;
+import java.nio.channels.ReadableByteChannel;
 import java.util.Properties;
 
 public class MavenWrapperDownloader {

.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 
 repos:
 -   repo: https://github.com/ejba/pre-commit-maven
-    rev: v0.3.3
+    rev: v0.3.4
     hooks:
     -   id: maven-spotless-apply
         stages: [pre-push]

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.9.7-SNAPSHOT</version>
+		 <version>6.11.7-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>
@@ -45,7 +45,6 @@
 					<checkRuntimeClasspath>false</checkRuntimeClasspath>
 					<checkTestClasspath>false</checkTestClasspath>
 					<skip>false</skip>
-					<quiet>false</quiet>
 					<preferLocal>true</preferLocal>
 					<useResultFile>true</useResultFile>
 					<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
@@ -103,14 +102,6 @@
 							<groupId>net.bytebuddy</groupId>
 							<artifactId>byte-buddy</artifactId>
 						</dependency>
-						<dependency>
-							<groupId>javax.xml.bind</groupId>
-							<artifactId>jaxb-api</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>com.sun.xml.bind</groupId>
-							<artifactId>jaxb-impl</artifactId>
-						</dependency>
 					</ignoredDependencies>
 					<ignoredResourcePatterns>
 						<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.7-SNAPSHOT</version>
+		<version>6.11.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
@@ -131,12 +131,6 @@
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
 				<configuration>
-					<classFolders>
-						<classFolder>${basedir}/target/classes</classFolder>
-					</classFolders>
-					<sourceFolders>
-						<sourceFolder>${basedir}/src/main/java</sourceFolder>
-					</sourceFolders>
 					<dumpOnExit>true</dumpOnExit>
 				</configuration>
 				<executions>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.7-SNAPSHOT</version>
+		<version>6.11.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
@@ -52,19 +52,13 @@
 
 		<!-- Only required for Schematron Validator Support -->
 		<dependency>
-			<groupId>com.helger</groupId>
+			<groupId>com.helger.schematron</groupId>
-			<artifactId>ph-schematron</artifactId>
+			<artifactId>ph-schematron-api</artifactId>
 			<optional>true</optional>
-			<exclusions>
-				<exclusion>
-					<groupId>org.glassfish.jaxb</groupId>
-					<artifactId>jaxb-core</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.helger</groupId>
+			<groupId>com.helger.schematron</groupId>
-			<artifactId>ph-commons</artifactId>
+			<artifactId>ph-schematron-xslt</artifactId>
 			<optional>true</optional>
 		</dependency>
 
@@ -122,10 +116,16 @@
 		</dependency>
 
 		<!-- @Nonnull annotation -->
+
+		<!-- We need to leave this in because otherwise hapi-fhir-structures-dstu3: will fail to generate javadoc -->
 		<dependency>
 			<groupId>com.google.code.findbugs</groupId>
 			<artifactId>jsr305</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>jakarta.annotation</groupId>
+			<artifactId>jakarta.annotation-api</artifactId>
+		</dependency>
 
 		<dependency>
 			<groupId>org.awaitility</groupId>
@@ -221,7 +221,6 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-checkstyle-plugin</artifactId>
-				<version>${maven_checkstyle_version}</version>
 				<configuration>
 					<!--suppress UnresolvedMavenProperty -->
 					<configLocation>${maven.multiModuleProjectDirectory}/hapi-fhir-checkstyle/src/checkstyle/hapi-base-checkstyle.xml</configLocation>

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

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.context;
 
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.model.api.annotation.Child;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 
@@ -78,6 +79,10 @@ public abstract class BaseRuntimeChildDefinition {
 		this.myReplacedParentDefinition = myReplacedParentDefinition;
 	}
 
+	public boolean isMultipleCardinality() {
+		return this.getMax() > 1 || this.getMax() == Child.MAX_UNLIMITED;
+	}
+
 	public interface IAccessor {
 		List<IBase> getValues(IBase theTarget);
 

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

@@ -21,6 +21,8 @@ package ca.uhn.fhir.context;
 
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.util.UrlUtil;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -31,8 +33,6 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 

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

@@ -49,6 +49,8 @@ import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.VersionUtil;
 import ca.uhn.fhir.validation.FhirValidator;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.apache.jena.riot.Lang;
@@ -77,8 +79,6 @@ import java.util.Optional;
 import java.util.Properties;
 import java.util.Set;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 /**
  * The FHIR context is the central starting point for the use of the HAPI FHIR API. It should be created once, and then

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

@@ -38,6 +38,7 @@ import ca.uhn.fhir.model.primitive.BoundCodeDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.util.ReflectionUtil;
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
@@ -67,7 +68,6 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Properties;
 import java.util.Set;
-import javax.annotation.Nonnull;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
@@ -498,7 +498,7 @@ class ModelScanner {
 			nextElementType = ReflectionUtil.getGenericCollectionTypeOfField(next);
 		} else if (Collection.class.isAssignableFrom(nextElementType)) {
 			throw new ConfigurationException(Msg.code(1722) + "Field '" + next.getName() + "' in type '"
-					+ next.getClass().getCanonicalName()
+					+ nextElementType.getCanonicalName()
 					+ "' is a Collection - Only java.util.List curently supported");
 		}
 		return nextElementType;

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

@@ -21,6 +21,8 @@ package ca.uhn.fhir.context;
 
 import ca.uhn.fhir.context.phonetic.IPhoneticEncoder;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
@@ -37,8 +39,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.StringTokenizer;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.apache.commons.lang3.StringUtils.trim;

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

@@ -23,6 +23,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.util.ILockable;
 import ca.uhn.fhir.util.ReflectionUtil;
+import jakarta.annotation.Nullable;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -32,7 +33,6 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import javax.annotation.Nullable;
 
 /**
  * This class returns the vocabulary that is shipped with the base FHIR
@@ -99,6 +99,11 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		}
 	}
 
+	@Override
+	public String getName() {
+		return myCtx.getVersion().getVersion() + " FHIR Standard Profile Validation Support";
+	}
+
 	@Override
 	public List<IBaseResource> fetchAllConformanceResources() {
 		return myDelegate.fetchAllConformanceResources();

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

@@ -28,6 +28,7 @@ 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 jakarta.annotation.Nullable;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -43,7 +44,6 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 import java.util.Properties;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 

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

@@ -24,9 +24,12 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.ParametersUtil;
 import ca.uhn.fhir.util.UrlUtil;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
@@ -41,8 +44,6 @@ import java.util.List;
 import java.util.Set;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -294,8 +295,8 @@ public interface IValidationSupport {
 	 */
 	@Nullable
 	default CodeValidationResult validateCode(
-			@Nonnull ValidationSupportContext theValidationSupportContext,
+			ValidationSupportContext theValidationSupportContext,
-			@Nonnull ConceptValidationOptions theOptions,
+			ConceptValidationOptions theOptions,
 			String theCodeSystem,
 			String theCode,
 			String theDisplay,
@@ -328,14 +329,16 @@ public interface IValidationSupport {
 	}
 
 	/**
-	 * Look up a code using the system and code value
+	 * Look up a code using the system and code value.
+	 * @deprecated This method has been deprecated in HAPI FHIR 7.0.0. Use {@link IValidationSupport#lookupCode(ValidationSupportContext, LookupCodeRequest)} instead.
 	 *
 	 * @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
 	 *                                    other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
 	 * @param theSystem                   The CodeSystem URL
 	 * @param theCode                     The code
-	 * @param theDisplayLanguage          to filter out the designation by the display language. To return all designation, set this value to <code>null</code>.
+	 * @param theDisplayLanguage          Used to filter out the designation by the display language. To return all designation, set this value to <code>null</code>.
 	 */
+	@Deprecated
 	@Nullable
 	default LookupCodeResult lookupCode(
 			ValidationSupportContext theValidationSupportContext,
@@ -347,12 +350,14 @@ public interface IValidationSupport {
 
 	/**
 	 * Look up a code using the system and code value
+	 * @deprecated This method has been deprecated in HAPI FHIR 7.0.0. Use {@link IValidationSupport#lookupCode(ValidationSupportContext, LookupCodeRequest)} instead.
 	 *
 	 * @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
 	 *                                    other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
 	 * @param theSystem                   The CodeSystem URL
 	 * @param theCode                     The code
 	 */
+	@Deprecated
 	@Nullable
 	default LookupCodeResult lookupCode(
 			ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
@@ -360,7 +365,26 @@ public interface IValidationSupport {
 	}
 
 	/**
-	 * Returns <code>true</code> if the given valueset can be validated by the given
+	 * Look up a code using the system, code and other parameters captured in {@link LookupCodeRequest}.
+	 * @since 7.0.0
+	 *
+	 * @param theValidationSupportContext      The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
+	 *                                         other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
+	 * @param theLookupCodeRequest             The parameters used to perform the lookup, including system and code.
+	 */
+	@Nullable
+	default LookupCodeResult lookupCode(
+			ValidationSupportContext theValidationSupportContext, @Nonnull LookupCodeRequest theLookupCodeRequest) {
+		// TODO: can change to return null once the deprecated methods are removed
+		return lookupCode(
+				theValidationSupportContext,
+				theLookupCodeRequest.getSystem(),
+				theLookupCodeRequest.getCode(),
+				theLookupCodeRequest.getDisplayLanguage());
+	}
+
+	/**
+	 * Returns <code>true</code> if the given ValueSet can be validated by the given
 	 * validation support module
 	 *
 	 * @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
@@ -409,6 +433,13 @@ public interface IValidationSupport {
 		return null;
 	}
 
+	/**
+	 * This field is used by the Terminology Troubleshooting Log to log which validation support module was used for the operation being logged.
+	 */
+	default String getName() {
+		return "Unknown " + getFhirContext().getVersion().getVersion() + " Validation Support";
+	}
+
 	enum IssueSeverity {
 		/**
 		 * The issue caused the action to fail, and no further checking could be performed.
@@ -495,8 +526,13 @@ public interface IValidationSupport {
 		public String getPropertyName() {
 			return myPropertyName;
 		}
+
+		public abstract String getType();
 	}
 
+	String TYPE_STRING = "string";
+	String TYPE_CODING = "Coding";
+
 	class StringConceptProperty extends BaseConceptProperty {
 		private final String myValue;
 
@@ -513,6 +549,10 @@ public interface IValidationSupport {
 		public String getValue() {
 			return myValue;
 		}
+
+		public String getType() {
+			return TYPE_STRING;
+		}
 	}
 
 	class CodingConceptProperty extends BaseConceptProperty {
@@ -543,9 +583,18 @@ public interface IValidationSupport {
 		public String getDisplay() {
 			return myDisplay;
 		}
+
+		public String getType() {
+			return TYPE_CODING;
+		}
 	}
 
 	class CodeValidationResult {
+		public static final String SOURCE_DETAILS = "sourceDetails";
+		public static final String RESULT = "result";
+		public static final String MESSAGE = "message";
+		public static final String DISPLAY = "display";
+
 		private String myCode;
 		private String myMessage;
 		private IssueSeverity mySeverity;
@@ -674,6 +723,23 @@ public interface IValidationSupport {
 			setSeverity(IssueSeverity.valueOf(theIssueSeverity.toUpperCase()));
 			return this;
 		}
+
+		public IBaseParameters toParameters(FhirContext theContext) {
+			IBaseParameters retVal = ParametersUtil.newInstance(theContext);
+
+			ParametersUtil.addParameterToParametersBoolean(theContext, retVal, RESULT, isOk());
+			if (isNotBlank(getMessage())) {
+				ParametersUtil.addParameterToParametersString(theContext, retVal, MESSAGE, getMessage());
+			}
+			if (isNotBlank(getDisplay())) {
+				ParametersUtil.addParameterToParametersString(theContext, retVal, DISPLAY, getDisplay());
+			}
+			if (isNotBlank(getSourceDetails())) {
+				ParametersUtil.addParameterToParametersString(theContext, retVal, SOURCE_DETAILS, getSourceDetails());
+			}
+
+			return retVal;
+		}
 	}
 
 	class ValueSetExpansionOutcome {
@@ -806,7 +872,7 @@ public interface IValidationSupport {
 		}
 
 		public IBaseParameters toParameters(
-				FhirContext theContext, List<? extends IPrimitiveType<String>> theProperties) {
+				FhirContext theContext, List<? extends IPrimitiveType<String>> thePropertyNames) {
 
 			IBaseParameters retVal = ParametersUtil.newInstance(theContext);
 			if (isNotBlank(getCodeSystemDisplayName())) {
@@ -821,32 +887,42 @@ public interface IValidationSupport {
 			if (myProperties != null) {
 
 				Set<String> properties = Collections.emptySet();
-				if (theProperties != null) {
+				if (thePropertyNames != null) {
-					properties = theProperties.stream()
+					properties = thePropertyNames.stream()
 							.map(IPrimitiveType::getValueAsString)
 							.collect(Collectors.toSet());
 				}
 
 				for (BaseConceptProperty next : myProperties) {
+					String propertyName = next.getPropertyName();
 
-					if (!properties.isEmpty()) {
+					if (!properties.isEmpty() && !properties.contains(propertyName)) {
-						if (!properties.contains(next.getPropertyName())) {
+						continue;
-							continue;
-						}
 					}
 
 					IBase property = ParametersUtil.addParameterToParameters(theContext, retVal, "property");
-					ParametersUtil.addPartCode(theContext, property, "code", next.getPropertyName());
+					ParametersUtil.addPartCode(theContext, property, "code", propertyName);
 
-					if (next instanceof StringConceptProperty) {
+					String propertyType = next.getType();
-						StringConceptProperty prop = (StringConceptProperty) next;
+					switch (propertyType) {
-						ParametersUtil.addPartString(theContext, property, "value", prop.getValue());
+						case TYPE_STRING:
-					} else if (next instanceof CodingConceptProperty) {
+							StringConceptProperty stringConceptProperty = (StringConceptProperty) next;
-						CodingConceptProperty prop = (CodingConceptProperty) next;
+							ParametersUtil.addPartString(
-						ParametersUtil.addPartCoding(
+									theContext, property, "value", stringConceptProperty.getValue());
-								theContext, property, "value", prop.getCodeSystem(), prop.getCode(), prop.getDisplay());
+							break;
-					} else {
+						case TYPE_CODING:
-						throw new IllegalStateException(Msg.code(1739) + "Don't know how to handle " + next.getClass());
+							CodingConceptProperty codingConceptProperty = (CodingConceptProperty) next;
+							ParametersUtil.addPartCoding(
+									theContext,
+									property,
+									"value",
+									codingConceptProperty.getCodeSystem(),
+									codingConceptProperty.getCode(),
+									codingConceptProperty.getDisplay());
+							break;
+						default:
+							throw new IllegalStateException(
+									Msg.code(1739) + "Don't know how to handle " + next.getClass());
 					}
 				}
 			}
@@ -990,6 +1066,16 @@ public interface IValidationSupport {
 		public boolean isReverse() {
 			return myReverse;
 		}
+
+		@Override
+		public String toString() {
+			return new ToStringBuilder(this)
+					.append("sourceValueSetUrl", mySourceValueSetUrl)
+					.append("targetSystemUrl", myTargetSystemUrl)
+					.append("targetValueSetUrl", myTargetValueSetUrl)
+					.append("reverse", myReverse)
+					.toString();
+		}
 	}
 
 	/**

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

@@ -0,0 +1,75 @@
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2023 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%
+ */
+package ca.uhn.fhir.context.support;
+
+import java.util.Collection;
+import java.util.Collections;
+
+/**
+ * Represents parameters which can be passed to the $lookup operation for codes.
+ * @since 7.0.0
+ */
+public class LookupCodeRequest {
+	private final String mySystem;
+	private final String myCode;
+	private String myDisplayLanguage;
+	private Collection<String> myPropertyNames;
+
+	/**
+	 * @param theSystem                    The CodeSystem URL
+	 * @param theCode                      The code
+	 */
+	public LookupCodeRequest(String theSystem, String theCode) {
+		mySystem = theSystem;
+		myCode = theCode;
+	}
+
+	/**
+	 * @param theSystem                    The CodeSystem URL
+	 * @param theCode                      The code
+	 * @param theDisplayLanguage           Used to filter out the designation by the display language. To return all designation, set this value to <code>null</code>.
+	 * @param thePropertyNames             The collection of properties to be returned in the output. If no properties are specified, the implementor chooses what to return.
+	 */
+	public LookupCodeRequest(
+			String theSystem, String theCode, String theDisplayLanguage, Collection<String> thePropertyNames) {
+		this(theSystem, theCode);
+		myDisplayLanguage = theDisplayLanguage;
+		myPropertyNames = thePropertyNames;
+	}
+
+	public String getSystem() {
+		return mySystem;
+	}
+
+	public String getCode() {
+		return myCode;
+	}
+
+	public String getDisplayLanguage() {
+		return myDisplayLanguage;
+	}
+
+	public Collection<String> getPropertyNames() {
+		if (myPropertyNames == null) {
+			return Collections.emptyList();
+		}
+		return myPropertyNames;
+	}
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/fhirpath/IFhirPath.java

@@ -19,11 +19,11 @@
  */
 package ca.uhn.fhir.fhirpath;
 
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBase;
 
 import java.util.List;
 import java.util.Optional;
-import javax.annotation.Nonnull;
 
 public interface IFhirPath {
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/fhirpath/IFhirPathEvaluationContext.java

@@ -19,12 +19,11 @@
  */
 package ca.uhn.fhir.fhirpath;
 
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
-
 public interface IFhirPathEvaluationContext {
 
 	/**

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.interceptor.api;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Multimaps;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.lang3.Validate;
 
 import java.util.Collection;
@@ -29,7 +30,6 @@ import java.util.Collections;
 import java.util.List;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
 
 public class HookParams {
 

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

@@ -19,10 +19,11 @@
  */
 package ca.uhn.fhir.interceptor.api;
 
+import jakarta.annotation.Nullable;
+
 import java.util.Collection;
 import java.util.List;
 import java.util.function.Predicate;
-import javax.annotation.Nullable;
 
 public interface IBaseInterceptorService<POINTCUT extends IPointcut> extends IBaseInterceptorBroadcaster<POINTCUT> {
 

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

@@ -19,8 +19,9 @@
  */
 package ca.uhn.fhir.interceptor.api;
 
+import jakarta.annotation.Nonnull;
+
 import java.util.List;
-import javax.annotation.Nonnull;
 
 public interface IPointcut {
 	@Nonnull

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.validation.ValidationResult;
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBaseConformance;
 
 import java.io.Writer;
@@ -33,7 +34,6 @@ import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
-import javax.annotation.Nonnull;
 
 /**
  * Value for {@link Hook#value()}
@@ -93,6 +93,10 @@ public enum Pointcut implements IPointcut {
 	 * <li>
 	 *    ca.uhn.fhir.rest.client.api.IRestfulClient - The client object making the request
 	 * </li>
+	 * <li>
+	 *    ca.uhn.fhir.rest.client.api.ClientResponseContext - Contains an IHttpRequest, an IHttpResponse, and an IRestfulClient
+	 *    and also allows the client to mutate the contained IHttpResponse
+	 * </li>
 	 * </ul>
 	 * </p>
 	 * Hook methods must return <code>void</code>.
@@ -101,7 +105,8 @@ public enum Pointcut implements IPointcut {
 			void.class,
 			"ca.uhn.fhir.rest.client.api.IHttpRequest",
 			"ca.uhn.fhir.rest.client.api.IHttpResponse",
-			"ca.uhn.fhir.rest.client.api.IRestfulClient"),
+			"ca.uhn.fhir.rest.client.api.IRestfulClient",
+			"ca.uhn.fhir.rest.client.api.ClientResponseContext"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -153,10 +158,10 @@ public enum Pointcut implements IPointcut {
 	 * Hooks may accept the following parameters:
 	 * <ul>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * </ul>
 	 * </p>
@@ -166,7 +171,7 @@ public enum Pointcut implements IPointcut {
 	 * no further processing will occur and no further interceptors will be called.
 	 */
 	SERVER_INCOMING_REQUEST_PRE_PROCESSED(
-			boolean.class, "javax.servlet.http.HttpServletRequest", "javax.servlet.http.HttpServletResponse"),
+			boolean.class, "jakarta.servlet.http.HttpServletRequest", "jakarta.servlet.http.HttpServletResponse"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -193,10 +198,10 @@ public enum Pointcut implements IPointcut {
 	 * only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * <li>
 	 * ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException - The exception that was thrown
@@ -215,8 +220,8 @@ public enum Pointcut implements IPointcut {
 			boolean.class,
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
-			"javax.servlet.http.HttpServletRequest",
+			"jakarta.servlet.http.HttpServletRequest",
-			"javax.servlet.http.HttpServletResponse",
+			"jakarta.servlet.http.HttpServletResponse",
 			"ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException"),
 
 	/**
@@ -239,10 +244,10 @@ public enum Pointcut implements IPointcut {
 	 * only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * </ul>
 	 * <p>
@@ -263,8 +268,8 @@ public enum Pointcut implements IPointcut {
 			boolean.class,
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
-			"javax.servlet.http.HttpServletRequest",
+			"jakarta.servlet.http.HttpServletRequest",
-			"javax.servlet.http.HttpServletResponse"),
+			"jakarta.servlet.http.HttpServletResponse"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -286,10 +291,10 @@ public enum Pointcut implements IPointcut {
 	 * only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * </ul>
 	 * <p>
@@ -308,8 +313,8 @@ public enum Pointcut implements IPointcut {
 			boolean.class,
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
-			"javax.servlet.http.HttpServletRequest",
+			"jakarta.servlet.http.HttpServletRequest",
-			"javax.servlet.http.HttpServletResponse"),
+			"jakarta.servlet.http.HttpServletResponse"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -411,10 +416,10 @@ public enum Pointcut implements IPointcut {
 	 * {@link NullPointerException} in the case of a bug being triggered.
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * </ul>
 	 * <p>
@@ -429,8 +434,8 @@ public enum Pointcut implements IPointcut {
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
 			"java.lang.Throwable",
-			"javax.servlet.http.HttpServletRequest",
+			"jakarta.servlet.http.HttpServletRequest",
-			"javax.servlet.http.HttpServletResponse"),
+			"jakarta.servlet.http.HttpServletResponse"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -458,10 +463,10 @@ public enum Pointcut implements IPointcut {
 	 * ca.uhn.fhir.rest.api.server.ResponseDetails - This object contains details about the response, including the contents. Hook methods may modify this object to change or replace the response.
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * </ul>
 	 * </p>
@@ -482,8 +487,8 @@ public enum Pointcut implements IPointcut {
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
 			"org.hl7.fhir.instance.model.api.IBaseResource",
 			"ca.uhn.fhir.rest.api.server.ResponseDetails",
-			"javax.servlet.http.HttpServletRequest",
+			"jakarta.servlet.http.HttpServletRequest",
-			"javax.servlet.http.HttpServletResponse"),
+			"jakarta.servlet.http.HttpServletResponse"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -549,10 +554,10 @@ public enum Pointcut implements IPointcut {
 	 * java.lang.String - The GraphQL response
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
 	 * </li>
 	 * <li>
-	 * javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
+	 * jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
 	 * </li>
 	 * </ul>
 	 * </p>
@@ -573,8 +578,8 @@ public enum Pointcut implements IPointcut {
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
 			"java.lang.String",
 			"java.lang.String",
-			"javax.servlet.http.HttpServletRequest",
+			"jakarta.servlet.http.HttpServletRequest",
-			"javax.servlet.http.HttpServletResponse"),
+			"jakarta.servlet.http.HttpServletResponse"),
 
 	/**
 	 * <b>Server Hook:</b>
@@ -2930,6 +2935,31 @@ public enum Pointcut implements IPointcut {
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"org.hl7.fhir.instance.model.api.IBaseResource"),
 
+	/**
+	 * <b>Storage Hook:</b>
+	 * Invoked before a batch job is persisted to the database.
+	 * <p>
+	 * Hooks will have access to the content of the job being created
+	 * and may choose to make modifications to it. These changes will be
+	 * reflected in permanent storage.
+	 * </p>
+	 * Hooks may accept the following parameters:
+	 * <ul>
+	 * <li>
+	 * ca.uhn.fhir.batch2.model.JobInstance
+	 * </li>
+	 * <li>
+	 * ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that lead to the creation
+	 * of the jobInstance.
+	 * </li>
+	 * </ul>
+	 * <p>
+	 * Hooks should return <code>void</code>.
+	 * </p>
+	 */
+	STORAGE_PRESTORAGE_BATCH_JOB_CREATE(
+			void.class, "ca.uhn.fhir.batch2.model.JobInstance", "ca.uhn.fhir.rest.api.server.RequestDetails"),
+
 	/**
 	 * This pointcut is used only for unit tests. Do not use in production code as it may be changed or
 	 * removed at any time.

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/executor/BaseInterceptorService.java

@@ -31,6 +31,8 @@ import ca.uhn.fhir.util.ReflectionUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
@@ -57,8 +59,6 @@ import java.util.Optional;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 public abstract class BaseInterceptorService<POINTCUT extends Enum<POINTCUT> & IPointcut>
 		implements IBaseInterceptorService<POINTCUT>, IBaseInterceptorBroadcaster<POINTCUT> {
@@ -263,10 +263,14 @@ public abstract class BaseInterceptorService<POINTCUT extends Enum<POINTCUT> & I
 		return myRegisteredPointcuts.contains(thePointcut);
 	}
 
+	protected Class<?> getBooleanReturnType() {
+		return boolean.class;
+	}
+
 	@Override
 	public boolean callHooks(POINTCUT thePointcut, HookParams theParams) {
 		assert haveAppropriateParams(thePointcut, theParams);
-		assert thePointcut.getReturnType() == void.class || thePointcut.getReturnType() == boolean.class;
+		assert thePointcut.getReturnType() == void.class || thePointcut.getReturnType() == getBooleanReturnType();
 
 		Object retValObj = doCallHooks(thePointcut, theParams, true);
 		return (Boolean) retValObj;
@@ -282,14 +286,16 @@ public abstract class BaseInterceptorService<POINTCUT extends Enum<POINTCUT> & I
 		for (BaseInvoker nextInvoker : invokers) {
 			Object nextOutcome = nextInvoker.invoke(theParams);
 			Class<?> pointcutReturnType = thePointcut.getReturnType();
-			if (pointcutReturnType.equals(boolean.class)) {
+			if (pointcutReturnType.equals(getBooleanReturnType())) {
 				Boolean nextOutcomeAsBoolean = (Boolean) nextOutcome;
 				if (Boolean.FALSE.equals(nextOutcomeAsBoolean)) {
 					ourLog.trace("callHooks({}) for invoker({}) returned false", thePointcut, nextInvoker);
 					theRetVal = false;
 					break;
+				} else {
+					theRetVal = true;
 				}
-			} else if (pointcutReturnType.equals(void.class) == false) {
+			} else if (!pointcutReturnType.equals(void.class)) {
 				if (nextOutcome != null) {
 					theRetVal = nextOutcome;
 					break;
@@ -349,7 +355,7 @@ public abstract class BaseInterceptorService<POINTCUT extends Enum<POINTCUT> & I
 
 		List<BaseInvoker> retVal;
 
-		if (haveMultiple == false) {
+		if (!haveMultiple) {
 
 			// The global list doesn't need to be sorted every time since it's sorted on
 			// insertion each time. Doing so is a waste of cycles..
@@ -485,9 +491,9 @@ public abstract class BaseInterceptorService<POINTCUT extends Enum<POINTCUT> & I
 			myMethod = theHookMethod;
 
 			Class<?> returnType = theHookMethod.getReturnType();
-			if (myPointcut.getReturnType().equals(boolean.class)) {
+			if (myPointcut.getReturnType().equals(getBooleanReturnType())) {
 				Validate.isTrue(
-						boolean.class.equals(returnType) || void.class.equals(returnType),
+						getBooleanReturnType().equals(returnType) || void.class.equals(returnType),
 						"Method does not return boolean or void: %s",
 						theHookMethod);
 			} else if (myPointcut.getReturnType().equals(void.class)) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/model/RequestPartitionId.java

@@ -24,6 +24,8 @@ import ca.uhn.fhir.util.JsonUtil;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
@@ -37,8 +39,6 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
 

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

@@ -24,7 +24,11 @@ import ca.uhn.fhir.model.api.annotation.Description;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 public abstract class BaseElement implements /*IElement, */ ISupportsUndeclaredExtensions {
 

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

@@ -19,10 +19,15 @@
  */
 package ca.uhn.fhir.model.api;
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.fhirpath.IFhirPath;
 import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.io.InputStream;
 import java.util.Date;

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/BaseNarrativeGenerator.java

@@ -28,6 +28,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.Logs;
+import jakarta.annotation.Nullable;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.INarrative;
@@ -37,7 +38,6 @@ import java.util.EnumSet;
 import java.util.List;
 import java.util.Set;
 import java.util.stream.Collectors;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.defaultIfEmpty;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/INarrativeTemplateManifest.java

@@ -20,12 +20,12 @@
 package ca.uhn.fhir.narrative2;
 
 import ca.uhn.fhir.context.FhirContext;
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBase;
 
 import java.util.Collection;
 import java.util.EnumSet;
 import java.util.List;
-import javax.annotation.Nonnull;
 
 public interface INarrativeTemplateManifest {
 	List<INarrativeTemplate> getTemplateByResourceName(

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/NarrativeTemplateManifest.java

@@ -28,6 +28,7 @@ import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Multimaps;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -41,10 +42,18 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Properties;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
-import java.util.*;
-import javax.annotation.Nonnull;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 

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

@@ -45,6 +45,7 @@ import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
+import jakarta.annotation.Nullable;
 import org.apache.commons.io.output.StringBuilderWriter;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -78,7 +79,6 @@ import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
 import java.util.stream.Collectors;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;

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

@@ -39,7 +39,6 @@ import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -659,9 +658,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 						theEventWriter.endArray();
 					}
 					BaseRuntimeChildDefinition replacedParentDefinition = nextChild.getReplacedParentDefinition();
-					if (isMultipleCardinality(nextChild.getMax())
+					if (nextChild.isMultipleCardinality()
-							|| (replacedParentDefinition != null
+							|| (replacedParentDefinition != null && replacedParentDefinition.isMultipleCardinality())) {
-									&& isMultipleCardinality(replacedParentDefinition.getMax()))) {
 						beginArray(theEventWriter, nextChildSpecificName);
 						inArray = true;
 						encodeChildElementToStreamWriter(
@@ -728,14 +726,14 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					List<HeldExtension> heldModExts = Collections.emptyList();
 					if (extensions.size() > i
 							&& extensions.get(i) != null
-							&& extensions.get(i).isEmpty() == false) {
+							&& !extensions.get(i).isEmpty()) {
 						haveContent = true;
 						heldExts = extensions.get(i);
 					}
 
 					if (modifierExtensions.size() > i
 							&& modifierExtensions.get(i) != null
-							&& modifierExtensions.get(i).isEmpty() == false) {
+							&& !modifierExtensions.get(i).isEmpty()) {
 						haveContent = true;
 						heldModExts = modifierExtensions.get(i);
 					}
@@ -746,7 +744,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					} else {
 						nextComments = null;
 					}
-					if (nextComments != null && nextComments.isEmpty() == false) {
+					if (nextComments != null && !nextComments.isEmpty()) {
 						haveContent = true;
 					}
 
@@ -804,10 +802,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		return myIsSupportsFhirComment;
 	}
 
-	private boolean isMultipleCardinality(int maxCardinality) {
-		return maxCardinality > 1 || maxCardinality == Child.MAX_UNLIMITED;
-	}
-
 	private void encodeCompositeElementToStreamWriter(
 			RuntimeResourceDefinition theResDef,
 			IBaseResource theResource,
@@ -917,10 +911,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			// Undeclared extensions
 			extractUndeclaredExtensions(
 					theResourceId, extensions, modifierExtensions, null, null, theEncodeContext, theContainedResource);
-			boolean haveExtension = false;
+			boolean haveExtension = !extensions.isEmpty();
-			if (!extensions.isEmpty()) {
-				haveExtension = true;
-			}
 
 			if (theResourceId.hasFormatComment() || haveExtension) {
 				beginObject(theEventWriter, "_id");

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonStructure.java

@@ -28,6 +28,7 @@ import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
 import ca.uhn.fhir.parser.json.JsonLikeStructure;
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.core.StreamReadConstraints;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.JsonNode;
@@ -114,14 +115,38 @@ public class JacksonStructure implements JsonLikeStructure {
 				setNativeArray((ArrayNode) OBJECT_MAPPER.readTree(pbr));
 			}
 		} catch (Exception e) {
-			if (e.getMessage().startsWith("Unexpected char 39")) {
+			String message;
+			if (e instanceof JsonProcessingException) {
+				/*
+				 * Currently there is no way of preventing Jackson from adding this
+				 * annoying REDACTED message from certain messages we get back from
+				 * the parser, so we just manually strip them. Hopefully Jackson
+				 * will accept this request at some point:
+				 * https://github.com/FasterXML/jackson-core/issues/1158
+				 */
+				JsonProcessingException jpe = (JsonProcessingException) e;
+				StringBuilder messageBuilder = new StringBuilder();
+				String originalMessage = jpe.getOriginalMessage();
+				originalMessage = originalMessage.replace(
+						"Source: REDACTED (`StreamReadFeature.INCLUDE_SOURCE_IN_LOCATION` disabled); ", "");
+				messageBuilder.append(originalMessage);
+				if (jpe.getLocation() != null) {
+					messageBuilder.append("\n at [");
+					jpe.getLocation().appendOffsetDescription(messageBuilder);
+					messageBuilder.append("]");
+				}
+				message = messageBuilder.toString();
+			} else {
+				message = e.getMessage();
+			}
+
+			if (message.startsWith("Unexpected char 39")) {
 				throw new DataFormatException(
-						Msg.code(1860) + "Failed to parse JSON encoded FHIR content: " + e.getMessage() + " - "
+						Msg.code(1860) + "Failed to parse JSON encoded FHIR content: " + message + " - "
 								+ "This may indicate that single quotes are being used as JSON escapes where double quotes are required",
 						e);
 			}
-			throw new DataFormatException(
+			throw new DataFormatException(Msg.code(1861) + "Failed to parse JSON encoded FHIR content: " + message, e);
-					Msg.code(1861) + "Failed to parse JSON encoded FHIR content: " + e.getMessage(), e);
 		}
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonWriter.java

@@ -45,29 +45,15 @@ public class JacksonWriter extends BaseJsonLikeWriter {
 	@Override
 	public BaseJsonLikeWriter init() {
 		if (isPrettyPrint()) {
-			DefaultPrettyPrinter prettyPrinter = new DefaultPrettyPrinter() {
+			DefaultPrettyPrinter prettyPrinter = new DefaultPrettyPrinter()
-
+					.withSeparators(new Separators(
-				/**
+							Separators.DEFAULT_ROOT_VALUE_SEPARATOR,
-				 * Objects should serialize as
+							':',
-				 * <pre>
+							Separators.Spacing.AFTER,
-				 * {
+							',',
-				 *    "key": "value"
+							Separators.Spacing.NONE,
-				 * }
+							',',
-				 * </pre>
+							Separators.Spacing.NONE));
-				 * in order to be consistent with Gson behaviour, instead of the jackson default
-				 * <pre>
-				 * {
-				 *    "key" : "value"
-				 * }
-				 * </pre>
-				 */
-				@Override
-				public DefaultPrettyPrinter withSeparators(Separators separators) {
-					_separators = separators;
-					_objectFieldValueSeparatorWithSpaces = separators.getObjectFieldValueSeparator() + " ";
-					return this;
-				}
-			};
 			prettyPrinter = prettyPrinter.withObjectIndenter(new DefaultIndenter("  ", "\n"));
 
 			myJsonGenerator.setPrettyPrinter(prettyPrinter);

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Operation.java

@@ -118,7 +118,7 @@ public @interface Operation {
 	 * always the right choice), the framework will not attempt to generate a response to
 	 * this method.
 	 * <p>
-	 * This is useful if you want to include an {@link javax.servlet.http.HttpServletResponse}
+	 * This is useful if you want to include an {@link jakarta.servlet.http.HttpServletResponse}
 	 * in your method parameters and create a response yourself directly from your
 	 * <code>@Operation</code> method.
 	 * </p>
@@ -134,7 +134,7 @@ public @interface Operation {
 	 * always the right choice), the framework will not attempt to parse the request body,
 	 * but will instead delegate it to the <code>@Operation</code> method.
 	 * <p>
-	 * This is useful if you want to include an {@link javax.servlet.http.HttpServletRequest}
+	 * This is useful if you want to include an {@link jakarta.servlet.http.HttpServletRequest}
 	 * in your method parameters and parse the request yourself.
 	 * </p>
 	 */

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Read.java

@@ -23,7 +23,10 @@ import ca.uhn.fhir.rest.client.api.IBasicClient;
 import ca.uhn.fhir.rest.client.api.IRestfulClient;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
-import java.lang.annotation.*;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 
 /**
  * RESTful method annotation to be used for the FHIR <a href="http://hl7.org/implement/standards/fhir/http.html#read">read</a> and <a

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Transaction.java

@@ -19,7 +19,10 @@
  */
 package ca.uhn.fhir.rest.annotation;
 
-import java.lang.annotation.*;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 
 /**
  * RESTful method annotation to be used for the FHIR <a href="http://hl7.org/implement/standards/fhir/http.html#transaction">transaction</a> method.

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/TransactionParam.java

@@ -19,7 +19,10 @@
  */
 package ca.uhn.fhir.rest.annotation;
 
-import java.lang.annotation.*;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 import java.util.List;
 
 /**

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Validate.java

@@ -22,7 +22,10 @@ package ca.uhn.fhir.rest.annotation;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
-import java.lang.annotation.*;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 
 /**
  * RESTful method annotation to be used for the FHIR

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

@@ -199,6 +199,8 @@ public class Constants {
 	public static final String PARAM_PRETTY_VALUE_FALSE = "false";
 	public static final String PARAM_PRETTY_VALUE_TRUE = "true";
 	public static final String PARAM_PROFILE = "_profile";
+	public static final String PARAM_PID = "_pid";
+
 	public static final String PARAM_QUERY = "_query";
 	public static final String PARAM_RESPONSE_URL = "response-url"; // Used in messaging
 	public static final String PARAM_REVINCLUDE = "_revinclude";
@@ -218,21 +220,6 @@ public class Constants {
 	public static final String PARAM_TEXT = "_text";
 	public static final String PARAM_VALIDATE = "_validate";
 
-	/**
-	 * $member-match operation
-	 */
-	public static final String PARAM_MEMBER_PATIENT = "MemberPatient";
-
-	public static final String PARAM_MEMBER_IDENTIFIER = "MemberIdentifier";
-
-	public static final String PARAM_OLD_COVERAGE = "OldCoverage";
-	public static final String PARAM_NEW_COVERAGE = "NewCoverage";
-	public static final String PARAM_CONSENT = "Consent";
-	public static final String PARAM_MEMBER_PATIENT_NAME = PARAM_MEMBER_PATIENT + " Name";
-	public static final String PARAM_MEMBER_PATIENT_BIRTHDATE = PARAM_MEMBER_PATIENT + " Birthdate";
-	public static final String PARAM_CONSENT_PATIENT_REFERENCE = PARAM_CONSENT + "'s Patient Reference";
-	public static final String PARAM_CONSENT_PERFORMER_REFERENCE = PARAM_CONSENT + "'s Performer Reference";
-
 	public static final String PARAMQUALIFIER_MISSING = ":missing";
 	public static final String PARAMQUALIFIER_MISSING_FALSE = "false";
 	public static final String PARAMQUALIFIER_MISSING_TRUE = "true";
@@ -331,6 +318,9 @@ public class Constants {
 	 */
 	public static final int UUID_LENGTH = 36;
 
+	public static final String BULK_DATA_ACCESS_IG_URL =
+			"http://hl7.org/fhir/uv/bulkdata/CapabilityStatement/bulk-data";
+
 	/**
 	 * Application configuration key used to enable or disable Hibernate Envers.
 	 */

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

@@ -22,6 +22,8 @@ package ca.uhn.fhir.rest.api;
 import ca.uhn.fhir.context.api.BundleInclusionRule;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -29,8 +31,6 @@ import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.Set;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 /**
  * This interface should be considered experimental and will likely change in future releases of HAPI. Use with caution!

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

@@ -23,10 +23,10 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.rest.annotation.Patch;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import jakarta.annotation.Nonnull;
 
 import java.util.HashMap;
 import java.util.Map;
-import javax.annotation.Nonnull;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;

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

@@ -19,7 +19,7 @@
  */
 package ca.uhn.fhir.rest.api;
 
-import javax.annotation.Nullable;
+import jakarta.annotation.Nullable;
 
 public class PreferHeader {
 

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

@@ -19,8 +19,9 @@
  */
 package ca.uhn.fhir.rest.api;
 
+import jakarta.annotation.Nullable;
+
 import java.util.HashMap;
-import javax.annotation.Nullable;
 
 /**
  * Represents values for "return" value as provided in the the <a href="https://tools.ietf.org/html/rfc7240#section-4.2">HTTP Prefer header</a>.

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

@@ -20,11 +20,11 @@
 package ca.uhn.fhir.rest.api;
 
 import ca.uhn.fhir.util.CoverageIgnore;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.lang3.Validate;
 
 import java.util.HashMap;
 import java.util.Map;
-import javax.annotation.Nonnull;
 
 @CoverageIgnore
 public enum RestOperationTypeEnum {

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

@@ -0,0 +1,103 @@
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2023 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%
+ */
+package ca.uhn.fhir.rest.client.api;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.util.Objects;
+import java.util.StringJoiner;
+
+/**
+ * Used to pass context to {@link Pointcut#CLIENT_RESPONSE}, including a mutable {@link IHttpResponse}
+ */
+public class ClientResponseContext {
+	private final IHttpRequest myHttpRequest;
+	private IHttpResponse myHttpResponse;
+	private final IRestfulClient myRestfulClient;
+	private final FhirContext myFhirContext;
+	private final Class<? extends IBaseResource> myReturnType;
+
+	public ClientResponseContext(
+			IHttpRequest myHttpRequest,
+			IHttpResponse theHttpResponse,
+			IRestfulClient myRestfulClient,
+			FhirContext theFhirContext,
+			Class<? extends IBaseResource> theReturnType) {
+		this.myHttpRequest = myHttpRequest;
+		this.myHttpResponse = theHttpResponse;
+		this.myRestfulClient = myRestfulClient;
+		this.myFhirContext = theFhirContext;
+		this.myReturnType = theReturnType;
+	}
+
+	public IHttpRequest getHttpRequest() {
+		return myHttpRequest;
+	}
+
+	public IHttpResponse getHttpResponse() {
+		return myHttpResponse;
+	}
+
+	public IRestfulClient getRestfulClient() {
+		return myRestfulClient;
+	}
+
+	public FhirContext getFhirContext() {
+		return myFhirContext;
+	}
+
+	public Class<? extends IBaseResource> getReturnType() {
+		return myReturnType;
+	}
+
+	public void setHttpResponse(IHttpResponse theHttpResponse) {
+		this.myHttpResponse = theHttpResponse;
+	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		ClientResponseContext that = (ClientResponseContext) o;
+		return Objects.equals(myHttpRequest, that.myHttpRequest)
+				&& Objects.equals(myHttpResponse, that.myHttpResponse)
+				&& Objects.equals(myRestfulClient, that.myRestfulClient)
+				&& Objects.equals(myFhirContext, that.myFhirContext)
+				&& Objects.equals(myReturnType, that.myReturnType);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(myHttpRequest, myHttpResponse, myRestfulClient, myFhirContext, myReturnType);
+	}
+
+	@Override
+	public String toString() {
+		return new StringJoiner(", ", ClientResponseContext.class.getSimpleName() + "[", "]")
+				.add("myHttpRequest=" + myHttpRequest)
+				.add("myHttpResponse=" + myHttpResponse)
+				.add("myRestfulClient=" + myRestfulClient)
+				.add("myFhirContext=" + myFhirContext)
+				.add("myReturnType=" + myReturnType)
+				.toString();
+	}
+}

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

@@ -24,10 +24,9 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.RequestFormatParamStyleEnum;
 import ca.uhn.fhir.rest.api.SummaryEnum;
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
-import javax.annotation.Nonnull;
-
 public interface IRestfulClient {
 
 	/**

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

@@ -23,7 +23,9 @@ import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
 import org.apache.commons.lang3.ObjectUtils;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java

@@ -27,6 +27,7 @@ import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.DateUtils;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -34,7 +35,6 @@ import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.Objects;
-import javax.annotation.Nonnull;
 
 import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL;
 import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParamPrefixEnum.java

@@ -19,7 +19,9 @@
  */
 package ca.uhn.fhir.rest.param;
 
-import java.util.*;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Comparator/qualifier for values used in REST params, such as {@link DateParam}, {@link NumberParam}, and

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

@@ -19,7 +19,11 @@
  */
 package ca.uhn.fhir.util;
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.ICompositeType;

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

@@ -25,6 +25,8 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.primitive.IdDt;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
@@ -36,8 +38,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.util.Date;
 import java.util.Objects;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 /**
  * This class can be used to build a Bundle resource to be used as a FHIR transaction. Convenience methods provide
@@ -196,11 +196,7 @@ public class BundleBuilder {
 	public UpdateBuilder addTransactionUpdateEntry(IBaseResource theResource) {
 		Validate.notNull(theResource, "theResource must not be null");
 
-		IIdType id = theResource.getIdElement();
+		IIdType id = getIdTypeForUpdate(theResource);
-		if (id.hasIdPart() && !id.hasResourceType()) {
-			String resourceType = myContext.getResourceType(theResource);
-			id = id.withResourceType(resourceType);
-		}
 
 		String requestUrl = id.toUnqualifiedVersionless().getValue();
 		String fullUrl = id.getValue();
@@ -225,13 +221,29 @@ public class BundleBuilder {
 		myEntryRequestUrlChild.getMutator().setValue(request, url);
 
 		// Bundle.entry.request.method
-		IPrimitiveType<?> method = (IPrimitiveType<?>)
+		addRequestMethod(request, theHttpVerb);
-				myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
-		method.setValueAsString(theHttpVerb);
-		myEntryRequestMethodChild.getMutator().setValue(request, method);
 		return url;
 	}
 
+	/**
+	 * Adds an entry containing an update (UPDATE) request without the body of the resource.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 *
+	 * @param theResource The resource to update.
+	 */
+	public void addTransactionUpdateIdOnlyEntry(IBaseResource theResource) {
+		setBundleField("type", "transaction");
+
+		Validate.notNull(theResource, "theResource must not be null");
+
+		IIdType id = getIdTypeForUpdate(theResource);
+		String requestUrl = id.toUnqualifiedVersionless().getValue();
+		String fullUrl = id.getValue();
+		String httpMethod = "PUT";
+
+		addIdOnlyEntry(requestUrl, httpMethod, fullUrl);
+	}
+
 	/**
 	 * Adds an entry containing an create (POST) request.
 	 * Also sets the Bundle.type value to "transaction" if it is not already set.
@@ -247,20 +259,47 @@ public class BundleBuilder {
 		String resourceType = myContext.getResourceType(theResource);
 
 		// Bundle.entry.request.url
-		IPrimitiveType<?> url =
+		addRequestUrl(request, resourceType);
-				(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		url.setValueAsString(resourceType);
-		myEntryRequestUrlChild.getMutator().setValue(request, url);
 
-		// Bundle.entry.request.url
+		// Bundle.entry.request.method
-		IPrimitiveType<?> method = (IPrimitiveType<?>)
+		addRequestMethod(request, "POST");
-				myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
-		method.setValueAsString("POST");
-		myEntryRequestMethodChild.getMutator().setValue(request, method);
 
 		return new CreateBuilder(request);
 	}
 
+	/**
+	 * Adds an entry containing a create (POST) request without the body of the resource.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 *
+	 * @param theResource The resource to create
+	 */
+	public void addTransactionCreateEntryIdOnly(IBaseResource theResource) {
+		setBundleField("type", "transaction");
+
+		String requestUrl = myContext.getResourceType(theResource);
+		String fullUrl = theResource.getIdElement().getValue();
+		String httpMethod = "POST";
+
+		addIdOnlyEntry(requestUrl, httpMethod, fullUrl);
+	}
+
+	private void addIdOnlyEntry(String theRequestUrl, String theHttpMethod, String theFullUrl) {
+		IBase entry = addEntry();
+
+		// Bundle.entry.request
+		IBase request = myEntryRequestDef.newInstance();
+		myEntryRequestChild.getMutator().setValue(entry, request);
+
+		// Bundle.entry.request.url
+		addRequestUrl(request, theRequestUrl);
+
+		// Bundle.entry.request.method
+		addRequestMethod(request, theHttpMethod);
+
+		// Bundle.entry.fullUrl
+		addFullUrl(entry, theFullUrl);
+	}
+
 	/**
 	 * Adds an entry containing a delete (DELETE) request.
 	 * Also sets the Bundle.type value to "transaction" if it is not already set.
@@ -341,20 +380,44 @@ public class BundleBuilder {
 		IBase request = addEntryAndReturnRequest();
 
 		// Bundle.entry.request.url
-		IPrimitiveType<?> url =
+		addRequestUrl(request, theDeleteUrl);
-				(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		url.setValueAsString(theDeleteUrl);
-		myEntryRequestUrlChild.getMutator().setValue(request, url);
 
 		// Bundle.entry.request.method
-		IPrimitiveType<?> method = (IPrimitiveType<?>)
+		addRequestMethod(request, "DELETE");
-				myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
-		method.setValueAsString("DELETE");
-		myEntryRequestMethodChild.getMutator().setValue(request, method);
 
 		return new DeleteBuilder();
 	}
 
+	private IIdType getIdTypeForUpdate(IBaseResource theResource) {
+		IIdType id = theResource.getIdElement();
+		if (id.hasIdPart() && !id.hasResourceType()) {
+			String resourceType = myContext.getResourceType(theResource);
+			id = id.withResourceType(resourceType);
+		}
+		return id;
+	}
+
+	private void addFullUrl(IBase theEntry, String theFullUrl) {
+		IPrimitiveType<?> fullUrl =
+				(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
+		fullUrl.setValueAsString(theFullUrl);
+		myEntryFullUrlChild.getMutator().setValue(theEntry, fullUrl);
+	}
+
+	private void addRequestUrl(IBase request, String theRequestUrl) {
+		IPrimitiveType<?> url =
+				(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
+		url.setValueAsString(theRequestUrl);
+		myEntryRequestUrlChild.getMutator().setValue(request, url);
+	}
+
+	private void addRequestMethod(IBase theRequest, String theMethod) {
+		IPrimitiveType<?> method = (IPrimitiveType<?>)
+				myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
+		method.setValueAsString(theMethod);
+		myEntryRequestMethodChild.getMutator().setValue(theRequest, method);
+	}
+
 	/**
 	 * Adds an entry for a Collection bundle type
 	 */
@@ -406,10 +469,7 @@ public class BundleBuilder {
 		IBase entry = addEntry();
 
 		// Bundle.entry.fullUrl
-		IPrimitiveType<?> fullUrl =
+		addFullUrl(entry, theFullUrl);
-				(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
-		fullUrl.setValueAsString(theFullUrl);
-		myEntryFullUrlChild.getMutator().setValue(entry, fullUrl);
 
 		// Bundle.entry.resource
 		myEntryResourceChild.getMutator().setValue(entry, theResource);

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

@@ -35,10 +35,12 @@ import ca.uhn.fhir.util.bundle.EntryListAccumulator;
 import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
 import ca.uhn.fhir.util.bundle.SearchBundleEntryParts;
 import com.google.common.collect.Sets;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.slf4j.Logger;
@@ -693,6 +695,25 @@ public class BundleUtil {
 		return bundleEntry;
 	}
 
+	/**
+	 * Get resource from bundle by resource type and reference
+	 * @param theContext   FhirContext
+	 * @param theBundle    IBaseBundle
+	 * @param theReference IBaseReference
+	 * @return IBaseResource if found and null if not found.
+	 */
+	@Nonnull
+	public static IBaseResource getResourceByReferenceAndResourceType(
+			@Nonnull FhirContext theContext, @Nonnull IBaseBundle theBundle, @Nonnull IBaseReference theReference) {
+		return toListOfResources(theContext, theBundle).stream()
+				.filter(theResource -> theReference
+						.getReferenceElement()
+						.getIdPart()
+						.equals(theResource.getIdElement().getIdPart()))
+				.findFirst()
+				.orElse(null);
+	}
+
 	private static class SortLegality {
 		private boolean myIsLegal;
 

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

@@ -24,6 +24,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import com.google.common.base.Charsets;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.BOMInputStream;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -37,7 +38,6 @@ import java.io.Reader;
 import java.nio.charset.StandardCharsets;
 import java.util.function.Function;
 import java.util.zip.GZIPInputStream;
-import javax.annotation.Nonnull;
 
 /**
  * Use this API with caution, it may change!

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.util;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseReference;
@@ -29,7 +30,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.util.Date;
-import javax.annotation.Nonnull;
 
 /**
  * This class can be used to generate <code>Composition</code> resources in

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

@@ -20,10 +20,10 @@
 package ca.uhn.fhir.util;
 
 import ca.uhn.fhir.rest.param.DateRangeParam;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 
 import java.util.Date;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 public class DateRangeUtil {
 

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.util;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.Msg;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -33,7 +34,6 @@ import java.util.List;
 import java.util.Optional;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
 
 /**
  * Utility for modifying with extensions in a FHIR version-independent approach.

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

@@ -42,6 +42,8 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import com.google.common.collect.Lists;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -71,8 +73,6 @@ import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -287,9 +287,33 @@ public class FhirTerser {
 		return retVal;
 	}
 
+	/**
+	 * Extracts all outbound references from a resource
+	 *
+	 * @param theResource the resource to be analyzed
+	 * @return a list of references to other resources
+	 */
 	public List<ResourceReferenceInfo> getAllResourceReferences(final IBaseResource theResource) {
+		return getAllResourceReferencesExcluding(theResource, Lists.newArrayList());
+	}
+
+	/**
+	 * Extracts all outbound references from a resource, excluding any that are located on black-listed parts of the
+	 * resource
+	 *
+	 * @param theResource       the resource to be analyzed
+	 * @param thePathsToExclude a list of dot-delimited paths not to include in the result
+	 * @return a list of references to other resources
+	 */
+	public List<ResourceReferenceInfo> getAllResourceReferencesExcluding(
+			final IBaseResource theResource, List<String> thePathsToExclude) {
 		final ArrayList<ResourceReferenceInfo> retVal = new ArrayList<>();
 		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
+		List<List<String>> tokenizedPathsToExclude = thePathsToExclude.stream()
+				.map(path -> StringUtils.split(path, "."))
+				.map(Lists::newArrayList)
+				.collect(Collectors.toList());
+
 		visit(newMap(), theResource, theResource, null, null, def, new IModelVisitor() {
 			@Override
 			public void acceptElement(
@@ -301,6 +325,10 @@ public class FhirTerser {
 				if (theElement == null || theElement.isEmpty()) {
 					return;
 				}
+
+				if (thePathToElement != null && pathShouldBeExcluded(tokenizedPathsToExclude, thePathToElement)) {
+					return;
+				}
 				if (IBaseReference.class.isAssignableFrom(theElement.getClass())) {
 					retVal.add(new ResourceReferenceInfo(
 							myContext, theOuterResource, thePathToElement, (IBaseReference) theElement));
@@ -310,6 +338,19 @@ public class FhirTerser {
 		return retVal;
 	}
 
+	private boolean pathShouldBeExcluded(List<List<String>> theTokenizedPathsToExclude, List<String> thePathToElement) {
+		return theTokenizedPathsToExclude.stream().anyMatch(p -> {
+			// Check whether the path to the element starts with the path to be excluded
+			if (p.size() > thePathToElement.size()) {
+				return false;
+			}
+
+			List<String> prefix = thePathToElement.subList(0, p.size());
+
+			return Objects.equals(p, prefix);
+		});
+	}
+
 	private BaseRuntimeChildDefinition getDefinition(
 			BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
 		BaseRuntimeChildDefinition nextDef = theCurrentDef.getChildByNameOrThrowDataFormatException(theSubList.get(0));

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

@@ -27,12 +27,12 @@ import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
+import jakarta.annotation.Nonnull;
 
 import java.io.IOException;
 import java.io.StringWriter;
 import java.io.Writer;
 import java.util.List;
-import javax.annotation.Nonnull;
 
 public class JsonUtil {
 

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

@@ -28,6 +28,9 @@ public class Logs {
 	private static final Logger ourNarrativeGenerationTroubleshootingLog =
 			LoggerFactory.getLogger("ca.uhn.fhir.log.narrative_generation_troubleshooting");
 
+	private static final Logger ourTerminologyTroubleshootingLog =
+			LoggerFactory.getLogger("ca.uhn.fhir.log.terminology_troubleshooting");
+
 	private static final Logger ourSubscriptionTroubleshootingLog =
 			LoggerFactory.getLogger("ca.cdr.log.subscription_troubleshooting");
 
@@ -42,6 +45,10 @@ public class Logs {
 		return ourBatchTroubleshootingLog;
 	}
 
+	public static Logger getTerminologyTroubleshootingLog() {
+		return ourTerminologyTroubleshootingLog;
+	}
+
 	public static Logger getSubscriptionTroubleshootingLog() {
 		return ourSubscriptionTroubleshootingLog;
 	}

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

@@ -28,6 +28,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import jakarta.annotation.Nullable;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
@@ -36,7 +37,6 @@ import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.util.List;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 

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

@@ -27,6 +27,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.primitive.StringDt;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
@@ -45,7 +46,6 @@ import java.util.List;
 import java.util.Optional;
 import java.util.function.Function;
 import java.util.stream.Collectors;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -403,8 +403,15 @@ public class ParametersUtil {
 	public static void addPartDecimal(FhirContext theContext, IBase theParameter, String theName, Double theValue) {
 		IPrimitiveType<BigDecimal> value = (IPrimitiveType<BigDecimal>)
 				theContext.getElementDefinition("decimal").newInstance();
-		value.setValue(theValue == null ? null : BigDecimal.valueOf(theValue));
+		if (theValue == null) {
-
+			value.setValue(null);
+		} else {
+			BigDecimal decimalValue = BigDecimal.valueOf(theValue);
+			if (decimalValue.scale() < 0) {
+				decimalValue = decimalValue.setScale(0);
+			}
+			value.setValue(decimalValue);
+		}
 		addPart(theContext, theParameter, theName, value);
 	}
 

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.util;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.lang3.Validate;
 
 import java.lang.reflect.Constructor;
@@ -39,7 +40,6 @@ import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.concurrent.ConcurrentHashMap;
-import javax.annotation.Nonnull;
 
 public class ReflectionUtil {
 

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

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.i18n.Msg;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -34,7 +35,6 @@ import java.util.List;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
-import javax.annotation.Nullable;
 
 public class SearchParameterUtil {
 

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

@@ -0,0 +1,57 @@
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2023 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%
+ */
+package ca.uhn.fhir.util;
+
+import com.google.common.collect.Iterators;
+import com.google.common.collect.UnmodifiableIterator;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+public class StreamUtil {
+	/** Static util class */
+	private StreamUtil() {}
+
+	/**
+	 * Chunk the stream into Lists of size theChunkSize.
+	 * The last chunk will be smaller unless the stream size is evenly divisible.
+	 * Closes the underlying stream when done.
+	 *
+	 * @param theStream the input stream
+	 * @param theChunkSize the chunk size.
+	 * @return a stream of chunks
+	 */
+	public static <T> Stream<List<T>> partition(Stream<T> theStream, int theChunkSize) {
+		Spliterator<T> spliterator = theStream.spliterator();
+		Iterator<T> iterator = Spliterators.iterator(spliterator);
+		UnmodifiableIterator<List<T>> partition = Iterators.partition(iterator, theChunkSize);
+
+		// we could be fancier here and support parallel, and sizes; but serial-only is fine for now.
+		Spliterator<List<T>> partitionedSpliterator = Spliterators.spliteratorUnknownSize(partition, 0);
+		Stream<List<T>> result = StreamSupport.stream(partitionedSpliterator, false);
+
+		// we lose close() via the Iterator.  Add it back.
+		return result.onClose(theStream::close);
+	}
+}

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

@@ -19,11 +19,12 @@
  */
 package ca.uhn.fhir.util;
 
+import jakarta.annotation.Nonnull;
+
 import java.io.CharArrayWriter;
 import java.nio.charset.StandardCharsets;
 import java.text.Normalizer;
 import java.util.Arrays;
-import javax.annotation.Nonnull;
 
 public class StringUtil {
 

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

@@ -348,7 +348,30 @@ public final class TerserUtil {
 	public static void clearField(FhirContext theFhirContext, IBaseResource theResource, String theFieldName) {
 		BaseRuntimeChildDefinition childDefinition =
 				getBaseRuntimeChildDefinition(theFhirContext, theFieldName, theResource);
-		clear(childDefinition.getAccessor().getValues(theResource));
+		childDefinition.getMutator().setValue(theResource, null);
+	}
+
+	/**
+	 * Clears the specified field on the resource provided by the FHIRPath.  If more than one value matches
+	 * the FHIRPath, all values will be cleared.
+	 *
+	 * @param theFhirContext
+	 * @param theResource
+	 * @param theFhirPath
+	 */
+	public static void clearFieldByFhirPath(FhirContext theFhirContext, IBaseResource theResource, String theFhirPath) {
+
+		if (theFhirPath.contains(".")) {
+			String parentPath = theFhirPath.substring(0, theFhirPath.lastIndexOf("."));
+			String fieldName = theFhirPath.substring(theFhirPath.lastIndexOf(".") + 1);
+			FhirTerser terser = theFhirContext.newTerser();
+			List<IBase> parents = terser.getValues(theResource, parentPath);
+			for (IBase parent : parents) {
+				clearField(theFhirContext, fieldName, parent);
+			}
+		} else {
+			clearField(theFhirContext, theResource, theFhirPath);
+		}
 	}
 
 	/**
@@ -362,7 +385,16 @@ public final class TerserUtil {
 		BaseRuntimeElementDefinition definition = theFhirContext.getElementDefinition(theBase.getClass());
 		BaseRuntimeChildDefinition childDefinition = definition.getChildByName(theFieldName);
 		Validate.notNull(childDefinition);
-		clear(childDefinition.getAccessor().getValues(theBase));
+		BaseRuntimeChildDefinition.IAccessor accessor = childDefinition.getAccessor();
+		clear(accessor.getValues(theBase));
+		List<IBase> newValue = accessor.getValues(theBase);
+
+		if (newValue != null && !newValue.isEmpty()) {
+			// Our clear failed, probably because it was an immutable SingletonList returned by a FieldPlainAccessor
+			// that cannot be cleared.
+			// Let's just null it out instead.
+			childDefinition.getMutator().setValue(theBase, null);
+		}
 	}
 
 	/**

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

@@ -28,6 +28,8 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import com.google.common.escape.Escaper;
 import com.google.common.net.PercentEscaper;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.utils.URLEncodedUtils;
@@ -50,8 +52,6 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.StringTokenizer;
 import java.util.stream.Collectors;
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
 import static org.apache.commons.lang3.StringUtils.defaultString;

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

@@ -123,8 +123,15 @@ public enum VersionEnum {
 	V6_8_0,
 	V6_8_1,
 	V6_8_2,
+	V6_8_3,
+	V6_8_4,
+	V6_8_5,
 	V6_9_0,
 
+	V6_10_0,
+	V6_10_1,
+	V6_11_0,
+
 	V7_0_0;
 
 	public static VersionEnum latestVersion() {

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

@@ -24,7 +24,8 @@ import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.riot.Lang;
 import org.apache.jena.riot.RDFDataMgr;
 
-import java.io.*;
+import java.io.Reader;
+import java.io.Writer;
 
 public class RDFUtil {
 

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

@@ -21,9 +21,9 @@ package ca.uhn.fhir.validation;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.EncodingEnum;
+import jakarta.annotation.Nonnull;
 
 import java.util.List;
-import javax.annotation.Nonnull;
 
 public interface IValidationContext<T> {
 

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

@@ -26,11 +26,11 @@ import ca.uhn.fhir.parser.LenientErrorHandler;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.ObjectUtil;
+import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import java.util.ArrayList;
 import java.util.List;
-import javax.annotation.Nonnull;
 
 import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
 

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

@@ -37,8 +37,8 @@ import com.helger.commons.io.resource.ClassPathResource;
 import com.helger.commons.io.resource.IReadableResource;
 import com.helger.schematron.ISchematronResource;
 import com.helger.schematron.SchematronHelper;
+import com.helger.schematron.sch.SchematronResourceSCH;
 import com.helger.schematron.svrl.jaxb.SchematronOutputType;
-import com.helger.schematron.xslt.SchematronResourceSCH;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
@@ -90,7 +90,12 @@ public class SchematronBaseValidator implements IValidatorModule {
 		}
 		StreamSource source = new StreamSource(new StringReader(resourceAsString));
 
-		SchematronOutputType results = SchematronHelper.applySchematron(sch, source);
+		SchematronOutputType results;
+		try {
+			results = sch.applySchematronValidationToSVRL(source);
+		} catch (Exception e) {
+			throw new InternalErrorException(Msg.code(2433) + e.getMessage(), e);
+		}
 		if (results == null) {
 			return;
 		}

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

@@ -19,7 +19,7 @@
  */
 package org.hl7.fhir.instance.model.api;
 
-import javax.annotation.Nullable;
+import jakarta.annotation.Nullable;
 
 public interface IPrimitiveType<T> extends IBaseDatatype {
 

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

@@ -206,10 +206,3 @@ ca.uhn.fhir.jpa.provider.DiffProvider.cantDiffDifferentTypes=Unable to diff two
 
 ca.uhn.fhir.jpa.interceptor.validation.RuleRequireProfileDeclaration.noMatchingProfile=Resource of type "{0}" does not declare conformance to profile from: {1} 
 ca.uhn.fhir.jpa.interceptor.validation.RuleRequireProfileDeclaration.illegalProfile=Resource of type "{0}" must not declare conformance to profile: {1}
-
-operation.member.match.error.coverage.not.found=Could not find coverage for member based on coverage id or coverage identifier.
-operation.member.match.error.beneficiary.not.found=Could not find beneficiary for coverage.
-operation.member.match.error.missing.parameter=Parameter "{0}" is required.
-operation.member.match.error.beneficiary.without.identifier=Coverage beneficiary does not have an identifier.
-operation.member.match.error.patient.not.found=Could not find matching patient for coverage.
-operation.member.match.error.consent.release.data.mismatch=Consent policy does not match the data release segmentation capabilities.

hapi-fhir-base/src/test/java/ca/uhn/fhir/i18n/HapiLocalizerTest.java

@@ -1,12 +1,14 @@
 package ca.uhn.fhir.i18n;
 
-import static org.hamcrest.Matchers.*;
+import org.junit.jupiter.api.Test;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.hamcrest.MatcherAssert.assertThat;
 
 import java.util.Set;
 
-import org.junit.jupiter.api.Test;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.matchesPattern;
+import static org.hamcrest.Matchers.not;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class HapiLocalizerTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnumTest.java

@@ -2,7 +2,8 @@ package ca.uhn.fhir.model.api;
 
 import org.junit.jupiter.api.Test;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
 
 public class ResourceMetadataKeyEnumTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/TagTest.java

@@ -5,7 +5,10 @@ import org.junit.jupiter.api.Test;
 import java.net.URI;
 import java.net.URISyntaxException;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class TagTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/CacheControlDirectiveTest.java

@@ -5,7 +5,9 @@ import org.junit.jupiter.api.Test;
 import java.util.Arrays;
 import java.util.List;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class CacheControlDirectiveTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/EncodingEnumTest.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.api;
 
 import org.junit.jupiter.api.Test;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class EncodingEnumTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/MethodOutcomeTest.java

@@ -7,7 +7,8 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Optional;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 class MethodOutcomeTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/DateParamTest.java

@@ -17,7 +17,9 @@ import static java.util.concurrent.TimeUnit.SECONDS;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.endsWith;
 import static org.hamcrest.Matchers.startsWith;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class DateParamTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DateParamTest.class);

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/QualifierDetailsTest.java

@@ -3,7 +3,8 @@ package ca.uhn.fhir.rest.param;
 import com.google.common.collect.Sets;
 import org.junit.jupiter.api.Test;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class QualifierDetailsTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/StringParamTest.java

@@ -1,14 +1,11 @@
 package ca.uhn.fhir.rest.param;
 
-import static ca.uhn.fhir.rest.api.Constants.PARAMQUALIFIER_STRING_TEXT;
-import static org.junit.jupiter.api.Assertions.*;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
 import ch.qos.logback.classic.spi.ILoggingEvent;
 import ch.qos.logback.core.read.ListAppender;
-import org.apache.commons.lang3.StringUtils;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Nested;
@@ -18,12 +15,17 @@ import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
-import ch.qos.logback.classic.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.List;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.rest.api.Constants.PARAMQUALIFIER_STRING_TEXT;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
 @ExtendWith(MockitoExtension.class)
 public class StringParamTest {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/exceptions/BaseServerResponseExceptionTest.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.server.exceptions;
 
 import org.junit.jupiter.api.Test;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class BaseServerResponseExceptionTest {
 

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

@@ -5,7 +5,6 @@ import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
-import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
 
@@ -19,7 +18,9 @@ import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS;
 import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN;
 import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN_OR_EQUALS;
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.notNullValue;
+import static org.hamcrest.Matchers.nullValue;
 
 class DateRangeUtilTest {
 

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

@@ -5,7 +5,11 @@ import org.slf4j.Logger;
 import org.slf4j.event.Level;
 
 import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.any;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.verifyNoMoreInteractions;
 
 public class LogUtilTest {
 

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

@@ -1,15 +1,17 @@
 package ca.uhn.fhir.util;
 
-import static org.junit.jupiter.api.Assertions.*;
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.i18n.Msg;
+import org.junit.jupiter.api.Test;
 
 import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.List;
 
-import ca.uhn.fhir.i18n.Msg;
+import static org.junit.jupiter.api.Assertions.assertEquals;
-import org.junit.jupiter.api.Test;
+import static org.junit.jupiter.api.Assertions.assertFalse;
-
+import static org.junit.jupiter.api.Assertions.assertTrue;
-import ca.uhn.fhir.context.ConfigurationException;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class ReflectionUtilTest {
 

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

@@ -0,0 +1,65 @@
+package ca.uhn.fhir.util;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
+
+class StreamUtilTest {
+
+	@ParameterizedTest
+	@MethodSource("streamPartitionTestCases")
+	void testStreamPartitionBy4(String theCase, List<Integer> theInput, List<List<Integer>> theOutput) {
+		List<List<Integer>> result = StreamUtil.partition(theInput.stream(), 4).toList();
+
+		assertEquals(theOutput, result, theCase);
+	}
+
+	static Object[][] streamPartitionTestCases() {
+		return new Object[][]{
+			{
+				"empty list produces empty stream",
+				List.of(),
+				List.of()
+			},
+			{
+				"short list produces single chunk",
+				List.of(1, 2, 3),
+				List.of(List.of(1, 2, 3))
+			},
+			{
+				"longer list produces several chunks",
+				List.of(1, 2, 3, 1, 2, 3, 1, 2, 3),
+				List.of(List.of(1, 2, 3, 1), List.of(2, 3, 1, 2), List.of(3))
+			},
+			{
+				"even size produces even chunks",
+				List.of(1, 2, 3,4,5,6,7,8),
+				List.of(List.of(1, 2, 3,4), List.of(5,6,7,8))
+			},
+		};
+	}
+
+	@Test
+	void testStreamPartitionClosesOriginalStream() {
+	    // given
+		AtomicBoolean closed = new AtomicBoolean(false);
+		Stream<Integer> baseStream = Stream.of(1, 2, 3).onClose(()->closed.set(true));
+
+		// when
+		StreamUtil.partition(baseStream, 2).close();
+
+		// then
+	    assertThat("partition closed underlying stream", closed.get());
+	}
+
+
+}

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

@@ -8,7 +8,7 @@ import org.mockito.Captor;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 
-import javax.annotation.Nonnull;
+import jakarta.annotation.Nonnull;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.verify;

hapi-fhir-base/src/test/java/ca/uhn/fhir/validation/ResultSeverityEnumTest.java

@@ -1,9 +1,9 @@
 package ca.uhn.fhir.validation;
 
-import static org.junit.jupiter.api.Assertions.*;
-
 import org.junit.jupiter.api.Test;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 public class ResultSeverityEnumTest {
 
 	@Test

hapi-fhir-bom/pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>6.9.7-SNAPSHOT</version>
+	<version>6.11.7-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
@@ -12,7 +12,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.7-SNAPSHOT</version>
+		<version>6.11.7-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>6.9.7-SNAPSHOT</version>
+		<version>6.11.7-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>
@@ -42,7 +42,6 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-checkstyle-plugin</artifactId>
-					<version>3.2.0</version>
 					<dependencies>
 						<dependency>
 							<groupId>com.puppycrawl.tools</groupId>
@@ -109,7 +108,6 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-checkstyle-plugin</artifactId>
-						<version>${maven_checkstyle_version}</version>
 						<configuration>
 							<excludes>**/osgi/**/*, **/.mvn/**/*, **/.mvn_/**/*</excludes>
 							<sourceDirectories>

hapi-fhir-checkstyle/src/checkstyle/hapi-base-checkstyle.xml

@@ -18,15 +18,32 @@
 			<property name="format" value="(?i)FIXME"/>
 		</module>
 
+		<!-- Ban star imports - TODO: enable this -->
+		<!--
+		<module name="RegexpSinglelineJava">
+			<property name="format" value="^import .*\*;"/>
+		</module>
+		-->
+
 		<module name="RegexpSinglelineJava">
 			<property name="format" value="System\.out\.println"/>
 			<property name="ignoreComments" value="true"/>
 		</module>
 		<module name="RegexpSinglelineJava">
 			<property name="format" value="org\.jetbrains\.annotations\.NotNull"/>
+			<property name="message" value="Incorrect &quot;org.jetbrains.annotation.NotNull&quot; annotation used: The &quot;jakarta.annotation.Nonnull&quot; annotation should be used for non-null values"/>
 		</module>
 		<module name="RegexpSinglelineJava">
 			<property name="format" value="org\.jetbrains\.annotations\.Nullable"/>
+			<property name="message" value="Incorrect &quot;org.jetbrains.annotation.Nullable&quot; annotation used: The &quot;jakarta.annotation.Nullable&quot; annotation should be used for nullable values"/>
+		</module>
+		<module name="RegexpSinglelineJava">
+			<property name="format" value="javax\.annotation\.Nonnull"/>
+			<property name="message" value="Incorrect &quot;javax.annotation.Nonnull&quot; used: &quot;jakarta.annotation.Nonnull&quot; should be used for non-null values"/>
+		</module>
+		<module name="RegexpSinglelineJava">
+			<property name="format" value="javax\.annotation\.Nullable"/>
+			<property name="message" value="Incorrect &quot;javax.annotation.Nullable&quot; used: &quot;jakarta.annotation.Nonnull&quot; should be used for nullable values"/>
 		</module>
 		<!-- Should always use the Spring transactional interface, per: https://stackoverflow.com/questions/26387399/javax-transaction-transactional-vs-org-springframework-transaction-annotation-tr -->
 		<module name="RegexpSinglelineJava">

hapi-fhir-checkstyle/src/main/java/ca/uhn/fhir/checks/HapiErrorCodeCheck.java

@@ -73,7 +73,11 @@ public final class HapiErrorCodeCheck extends AbstractCheck {
 				} else {
 					String location = getFilePath() + ":" + instantiation.getLineNo() + ":"
 							+ instantiation.getColumnNo() + "(" + code + ")";
-					ourCache.put(code, location);
+					// Ignore errors thrown in test for duplicates, as some fake implementations are throwing the same
+					// codes for test purpsoes.
+					if (!location.contains("/test/")) {
+						ourCache.put(code, location);
+					}
 				}
 			} else {
 				log(theAst.getLineNo(), "Called Msg.code() with a non-integer argument");

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>6.9.7-SNAPSHOT</version>
+		<version>6.11.7-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
@@ -152,38 +152,25 @@
 			<artifactId>spring-web</artifactId>
 		</dependency>
 
+		<!-- Web Server -->
 		<dependency>
-			<groupId>org.eclipse.jetty</groupId>
+			<groupId>org.eclipse.jetty.ee10.websocket</groupId>
-			<artifactId>jetty-servlets</artifactId>
+			<artifactId>jetty-ee10-websocket-jakarta-client</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.eclipse.jetty</groupId>
+			<groupId>jakarta.websocket</groupId>
-			<artifactId>jetty-servlet</artifactId>
+			<artifactId>jakarta.websocket-client-api</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-server</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.eclipse.jetty</groupId>
+			<groupId>org.eclipse.jetty.ee10</groupId>
-			<artifactId>jetty-util</artifactId>
+			<artifactId>jetty-ee10-servlet</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.eclipse.jetty</groupId>
-			<artifactId>jetty-webapp</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.eclipse.jetty.websocket</groupId>
-			<artifactId>websocket-jetty-api</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.eclipse.jetty.websocket</groupId>
-			<artifactId>websocket-core-client</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.eclipse.jetty.websocket</groupId>
-			<artifactId>websocket-jetty-client</artifactId>
 		</dependency>
+
+
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>jcl-over-slf4j</artifactId>
@@ -195,39 +182,17 @@
 		</dependency>
 		<dependency>
 			<groupId>org.thymeleaf</groupId>
-			<artifactId>thymeleaf-spring5</artifactId>
+			<artifactId>thymeleaf-spring6</artifactId>
 		</dependency>
 
 		<!-- Dependencies for Schematron -->
 		<dependency>
-			<groupId>com.helger</groupId>
+			<groupId>com.helger.schematron</groupId>
-			<artifactId>ph-schematron</artifactId>
+			<artifactId>ph-schematron-api</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>org.glassfish.jaxb</groupId>
-					<artifactId>jaxb-runtime</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.glassfish.jaxb</groupId>
-					<artifactId>jaxb-core</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>com.sun.istack</groupId>
-					<artifactId>istack-commons-runtime</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.helger</groupId>
+			<groupId>com.helger.schematron</groupId>
-			<artifactId>ph-commons</artifactId>
+			<artifactId>ph-schematron-xslt</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>javax.xml.bind</groupId>
-			<artifactId>jaxb-api</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.glassfish.jaxb</groupId>
-			<artifactId>jaxb-runtime</artifactId>
 		</dependency>
 
 
@@ -257,11 +222,30 @@
 			<artifactId>spring-test</artifactId>
 			<scope>test</scope>
 		</dependency>
-
+		<dependency>
+			<groupId>org.simplejavamail</groupId>
+			<artifactId>simple-java-mail</artifactId>
+			<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
+			<exclusions>
+				<exclusion>
+					<groupId>com.sun.activation</groupId>
+					<artifactId>jakarta.activation</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
 	</dependencies>
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<parallel>none</parallel>
+					<reuseForks>false</reuseForks>
+					<forkCount>1</forkCount>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -34,6 +34,7 @@ import com.google.common.base.Charsets;
 import com.google.common.collect.Sets;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParser;
+import jakarta.annotation.Nullable;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionGroup;
@@ -75,7 +76,6 @@ import java.util.Optional;
 import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
-import javax.annotation.Nullable;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BulkImportCommand.java

@@ -31,6 +31,7 @@ import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.ParametersUtil;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
@@ -40,11 +41,12 @@ import org.apache.commons.io.file.PathUtils;
 import org.apache.commons.io.filefilter.FileFileFilter;
 import org.apache.commons.io.filefilter.IOFileFilter;
 import org.apache.commons.io.filefilter.SuffixFileFilter;
+import org.apache.commons.lang3.time.DateUtils;
+import org.eclipse.jetty.ee10.servlet.ServletContextHandler;
+import org.eclipse.jetty.ee10.servlet.ServletHolder;
 import org.eclipse.jetty.server.Connector;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.server.ServerConnector;
-import org.eclipse.jetty.servlet.ServletContextHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -67,7 +69,6 @@ import java.util.List;
 import java.util.Locale;
 import java.util.concurrent.ExecutionException;
 import java.util.zip.GZIPInputStream;
-import javax.annotation.Nonnull;
 
 public class BulkImportCommand extends BaseCommand {
 
@@ -234,7 +235,12 @@ public class BulkImportCommand extends BaseCommand {
 
 	private List<String> startServer(int thePort, List<File> files) {
 		List<String> indexes = new ArrayList<>();
-		myServer = new Server(thePort);
+
+		myServer = new Server();
+		ServerConnector connector = new ServerConnector(myServer);
+		connector.setIdleTimeout(DateUtils.MILLIS_PER_MINUTE);
+		connector.setPort(myPort);
+		myServer.setConnectors(new Connector[] {connector});
 
 		myServlet = new BulkImportFileServlet();
 		for (File t : files) {

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu2.java

@@ -36,6 +36,11 @@ public class LoadingValidationSupportDstu2 implements IValidationSupport {
 	private static final org.slf4j.Logger ourLog =
 			org.slf4j.LoggerFactory.getLogger(LoadingValidationSupportDstu2.class);
 
+	@Override
+	public String getName() {
+		return "Dstu2 CLI Loading Validation Support";
+	}
+
 	@Override
 	public <T extends IBaseResource> T fetchResource(Class<T> theClass, String theUri) {
 		String resName = myCtx.getResourceType(theClass);

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu3.java

@@ -35,6 +35,11 @@ public class LoadingValidationSupportDstu3 implements IValidationSupport {
 	private static final org.slf4j.Logger ourLog =
 			org.slf4j.LoggerFactory.getLogger(LoadingValidationSupportDstu3.class);
 
+	@Override
+	public String getName() {
+		return "Dstu3 CLI Loading Validation Support";
+	}
+
 	@Override
 	public <T extends IBaseResource> T fetchResource(Class<T> theClass, String theUri) {
 		String resName = myCtx.getResourceType(theClass);

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ReindexTerminologyCommand.java

@@ -24,7 +24,7 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.util.ParametersUtil;
-import joptsimple.internal.Strings;
+import jakarta.annotation.Nonnull;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.ParseException;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
@@ -32,7 +32,6 @@ import org.hl7.fhir.r4.model.Parameters;
 
 import java.util.List;
 import java.util.Optional;
-import javax.annotation.Nonnull;
 
 import static ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider.RESP_PARAM_SUCCESS;
 
@@ -111,7 +110,7 @@ public class ReindexTerminologyCommand extends BaseRequestGeneratingCommand {
 	@Nonnull
 	private String getResponseMessage(IBaseParameters response) {
 		List<String> message = ParametersUtil.getNamedParameterValuesAsString(myFhirCtx, response, "message");
-		return Strings.join(message, NL);
+		return String.join(NL, message);
 	}
 
 	public static final String NL = System.getProperty("line.separator");

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/WebsocketSubscribeCommand.java

@@ -21,19 +21,17 @@ package ca.uhn.fhir.cli;
 
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.model.primitive.IdDt;
+import jakarta.websocket.ClientEndpoint;
+import jakarta.websocket.ContainerProvider;
+import jakarta.websocket.OnClose;
+import jakarta.websocket.OnError;
+import jakarta.websocket.OnMessage;
+import jakarta.websocket.OnOpen;
+import jakarta.websocket.Session;
+import jakarta.websocket.WebSocketContainer;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.eclipse.jetty.websocket.api.Frame;
-import org.eclipse.jetty.websocket.api.Session;
-import org.eclipse.jetty.websocket.api.annotations.OnWebSocketClose;
-import org.eclipse.jetty.websocket.api.annotations.OnWebSocketConnect;
-import org.eclipse.jetty.websocket.api.annotations.OnWebSocketError;
-import org.eclipse.jetty.websocket.api.annotations.OnWebSocketFrame;
-import org.eclipse.jetty.websocket.api.annotations.OnWebSocketMessage;
-import org.eclipse.jetty.websocket.api.annotations.WebSocket;
-import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
-import org.eclipse.jetty.websocket.client.WebSocketClient;
 
 import java.net.URI;
 
@@ -46,6 +44,7 @@ public class WebsocketSubscribeCommand extends BaseCommand {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(WebsocketSubscribeCommand.class);
 
 	private boolean myQuit;
+	private Session mySession;
 
 	@Override
 	public String getCommandDescription() {
@@ -75,14 +74,13 @@ public class WebsocketSubscribeCommand extends BaseCommand {
 
 		IdDt subsId = new IdDt(theCommandLine.getOptionValue("i"));
 
-		WebSocketClient client = new WebSocketClient();
 		SimpleEchoSocket socket = new SimpleEchoSocket(subsId.getIdPart());
 		try {
-			client.start();
 			URI echoUri = new URI(target);
-			ClientUpgradeRequest request = new ClientUpgradeRequest();
 			ourLog.info("Connecting to : {}", echoUri);
-			client.connect(socket, echoUri, request);
+
+			WebSocketContainer container = ContainerProvider.getWebSocketContainer();
+			mySession = container.connectToServer(socket, echoUri);
 
 			while (!myQuit) {
 				Thread.sleep(500L);
@@ -93,7 +91,9 @@ public class WebsocketSubscribeCommand extends BaseCommand {
 			throw new CommandFailureException(Msg.code(1537) + e);
 		} finally {
 			try {
-				client.stop();
+				if (mySession != null) {
+					mySession.close();
+				}
 			} catch (Exception e) {
 				ourLog.error("Failure", e);
 			}
@@ -103,7 +103,7 @@ public class WebsocketSubscribeCommand extends BaseCommand {
 	/**
 	 * Basic Echo Client Socket
 	 */
-	@WebSocket(maxTextMessageSize = 64 * 1024)
+	@ClientEndpoint
 	public class SimpleEchoSocket {
 
 		private String mySubsId;
@@ -115,37 +115,32 @@ public class WebsocketSubscribeCommand extends BaseCommand {
 			mySubsId = theSubsId;
 		}
 
-		@OnWebSocketClose
+		@OnClose
 		public void onClose(int statusCode, String reason) {
 			ourLog.info("Received CLOSE status={} reason={}", statusCode, reason);
 		}
 
-		@OnWebSocketConnect
+		@OnOpen
 		public void onConnect(Session theSession) {
 			ourLog.info("Successfully connected");
 			this.session = theSession;
 			try {
 				String sending = "bind " + mySubsId;
 				LOG_SEND.info("{}", sending);
-				theSession.getRemote().sendString(sending);
+				theSession.getBasicRemote().sendText(sending);
 			} catch (Throwable t) {
 				ourLog.error("Failure", t);
 				myQuit = true;
 			}
 		}
 
-		@OnWebSocketError
+		@OnError
 		public void onError(Throwable theError) {
 			ourLog.error("Websocket error: ", theError);
 			myQuit = true;
 		}
 
-		@OnWebSocketFrame
+		@OnMessage
-		public void onFrame(Frame theFrame) {
-			ourLog.debug("Websocket frame: {}", theFrame);
-		}
-
-		@OnWebSocketMessage
 		public void onMessage(String theMsg) {
 			LOG_RECV.info("{}", theMsg);
 		}