Merge branch 'master' of https://github.com/hapifhir/hapi-fhir

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.7.0-SNAPSHOT</version>
+		 <version>6.7.1-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -23,8 +23,6 @@ import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Multimaps;
 import org.apache.commons.lang3.Validate;
-import org.apache.commons.lang3.builder.ToStringBuilder;
-import org.apache.commons.lang3.builder.ToStringStyle;
 
 import javax.annotation.Nonnull;
 import java.util.Collection;
@@ -136,8 +134,14 @@ public class HookParams {
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.SIMPLE_STYLE)
+		StringBuilder b = new StringBuilder();
-			.append("params", myParams)
+		myParams.forEach((key, value) -> {
-			.toString();
+			b.append("  ")
+				.append(key.getSimpleName())
+				.append(": ")
+				.append(value)
+				.append("\n");
+		});
+		return b.toString();
 	}
 }

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

@@ -30,6 +30,8 @@ import ca.uhn.fhir.util.DateUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -355,17 +357,21 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		if (myLowerBound == null || myLowerBound.getValue() == null) {
 			return null;
 		}
-		Date retVal = myLowerBound.getValue();
+		return getLowerBoundAsInstant(myLowerBound);
+	}
 
-		if (myLowerBound.getPrecision().ordinal() <= TemporalPrecisionEnum.DAY.ordinal()) {
+	@Nonnull
+	private static Date getLowerBoundAsInstant(@Nonnull DateParam theLowerBound) {
+		Date retVal = theLowerBound.getValue();
+		if (theLowerBound.getPrecision().ordinal() <= TemporalPrecisionEnum.DAY.ordinal()) {
 			retVal = DateUtils.getLowestInstantFromDate(retVal);
 		}
 
-		if (myLowerBound.getPrefix() != null) {
+		if (theLowerBound.getPrefix() != null) {
-			switch (myLowerBound.getPrefix()) {
+			switch (theLowerBound.getPrefix()) {
 				case GREATERTHAN:
 				case STARTS_AFTER:
-					retVal = myLowerBound.getPrecision().add(retVal, 1);
+					retVal = theLowerBound.getPrecision().add(retVal, 1);
 					break;
 				case EQUAL:
 				case NOT_EQUAL:
@@ -375,7 +381,7 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 				case APPROXIMATE:
 				case LESSTHAN_OR_EQUALS:
 				case ENDS_BEFORE:
-					throw new IllegalStateException(Msg.code(1928) + "Invalid lower bound comparator: " + myLowerBound.getPrefix());
+					throw new IllegalStateException(Msg.code(1928) + "Invalid lower bound comparator: " + theLowerBound.getPrefix());
 			}
 		}
 		return retVal;
@@ -417,14 +423,19 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 			return null;
 		}
 
-		Date retVal = myUpperBound.getValue();
+		return getUpperBoundAsInstant(myUpperBound);
+	}
 
-		if (myUpperBound.getPrecision().ordinal() <= TemporalPrecisionEnum.DAY.ordinal()) {
+	@Nonnull
+	private static Date getUpperBoundAsInstant(@Nonnull DateParam theUpperBound) {
+		Date retVal = theUpperBound.getValue();
+
+		if (theUpperBound.getPrecision().ordinal() <= TemporalPrecisionEnum.DAY.ordinal()) {
 			retVal = DateUtils.getHighestInstantFromDate(retVal);
 		}
 
-		if (myUpperBound.getPrefix() != null) {
+		if (theUpperBound.getPrefix() != null) {
-			switch (myUpperBound.getPrefix()) {
+			switch (theUpperBound.getPrefix()) {
 				case LESSTHAN:
 				case ENDS_BEFORE:
 					retVal = new Date(retVal.getTime() - 1L);
@@ -432,14 +443,14 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 				case EQUAL:
 				case NOT_EQUAL:
 				case LESSTHAN_OR_EQUALS:
-					retVal = myUpperBound.getPrecision().add(retVal, 1);
+					retVal = theUpperBound.getPrecision().add(retVal, 1);
 					retVal = new Date(retVal.getTime() - 1L);
 					break;
 				case GREATERTHAN_OR_EQUALS:
 				case GREATERTHAN:
 				case APPROXIMATE:
 				case STARTS_AFTER:
-					throw new IllegalStateException(Msg.code(1929) + "Invalid upper bound comparator: " + myUpperBound.getPrefix());
+					throw new IllegalStateException(Msg.code(1929) + "Invalid upper bound comparator: " + theUpperBound.getPrefix());
 			}
 		}
 		return retVal;
@@ -626,12 +637,14 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 	 * are the same value. As such, even though the prefixes for the lower and
 	 * upper bounds default to <code>ge</code> and <code>le</code> respectively,
 	 * the resulting prefix is effectively <code>eq</code> where only a single
-	 * date is provided - as required by the FHIR specificiation (i.e. "If no
+	 * date is provided - as required by the FHIR specification (i.e. "If no
 	 * prefix is present, the prefix <code>eq</code> is assumed").
 	 */
 	private void validateAndSet(DateParam lowerBound, DateParam upperBound) {
 		if (hasBound(lowerBound) && hasBound(upperBound)) {
-			if (lowerBound.getValue().getTime() > upperBound.getValue().getTime()) {
+			Date lowerBoundAsInstant = getLowerBoundAsInstant(lowerBound);
+			Date upperBoundAsInstant = getUpperBoundAsInstant(upperBound);
+			if (lowerBoundAsInstant.after(upperBoundAsInstant)) {
 				throw new DataFormatException(Msg.code(1932) + format(
 					"Lower bound of %s is after upper bound of %s",
 					lowerBound.getValueAsString(), upperBound.getValueAsString()));

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

@@ -249,6 +249,22 @@ public class BundleBuilder {
 		return new CreateBuilder(request);
 	}
 
+	/**
+	 * Adds an entry containing a delete (DELETE) request.
+	 * Also sets the Bundle.type value to "transaction" if it is not already set.
+	 * <p>
+	 * Note that the resource is only used to extract its ID and type, and the body of the resource is not included in the entry,
+	 *
+	 * @param theCondition The conditional URL, e.g. "Patient?identifier=foo|bar"
+	 * @since 6.8.0
+	 */
+	public DeleteBuilder addTransactionDeleteConditionalEntry(String theCondition) {
+		Validate.notBlank(theCondition, "theCondition must not be blank");
+
+		setBundleField("type", "transaction");
+		return addDeleteEntry(theCondition);
+	}
+
 	/**
 	 * Adds an entry containing a delete (DELETE) request.
 	 * Also sets the Bundle.type value to "transaction" if it is not already set.

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

@@ -29,6 +29,7 @@ public class DateRangeUtil {
 
 	/**
 	 * Narrow the DateRange to be within theStartInclusive, and theEndExclusive, if provided.
+	 *
 	 * @param theDateRangeParam the initial range, null for unconstrained
 	 * @param theStartInclusive a lower bound to apply, or null for unchanged.
 	 * @param theEndExclusive   an upper bound to apply, or null for unchanged.
@@ -39,16 +40,23 @@ public class DateRangeUtil {
 		if (theStartInclusive == null && theEndExclusive == null) {
 			return theDateRangeParam;
 		}
-		DateRangeParam result = theDateRangeParam==null?new DateRangeParam():new DateRangeParam(theDateRangeParam);
+		DateRangeParam result = theDateRangeParam == null ? new DateRangeParam() : new DateRangeParam(theDateRangeParam);
 
-		if (theStartInclusive != null) {
+		Date startInclusive = theStartInclusive;
+		if (startInclusive != null) {
 			Date inputStart = result.getLowerBoundAsInstant();
-			if (theDateRangeParam == null || inputStart == null || inputStart.before(theStartInclusive)) {
+
-				result.setLowerBoundInclusive(theStartInclusive);
+			Date upperBound = result.getUpperBoundAsInstant();
+			if (upperBound != null && upperBound.before(startInclusive)) {
+				startInclusive = upperBound;
+			}
+
+			if (theDateRangeParam == null || inputStart == null || inputStart.before(startInclusive)) {
+				result.setLowerBoundInclusive(startInclusive);
 			}
 		}
 		if (theEndExclusive != null) {
-			Date inputEnd = result.getUpperBound() == null? null : result.getUpperBound().getValue();
+			Date inputEnd = result.getUpperBound() == null ? null : result.getUpperBound().getValue();
 			if (theDateRangeParam == null || inputEnd == null || inputEnd.after(theEndExclusive)) {
 				result.setUpperBoundExclusive(theEndExclusive);
 			}

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

@@ -28,6 +28,8 @@ public class Logs {
 
 	private static final Logger ourSubscriptionTroubleshootingLog = LoggerFactory.getLogger("ca.cdr.log.subscription_troubleshooting");
 
+	private static final Logger ourSubscriptionTopicLog = LoggerFactory.getLogger("ca.uhn.fhir.log.subscription_topic_troubleshooting");
+
 	public static Logger getBatchTroubleshootingLog() {
 		return ourBatchTroubleshootingLog;
 	}
@@ -39,4 +41,8 @@ public class Logs {
 	public static Logger getSubscriptionTroubleshootingLog() {
 		return ourSubscriptionTroubleshootingLog;
 	}
+
+	public static Logger getSubscriptionTopicLog() {
+		return ourSubscriptionTopicLog;
+	}
 }

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

@@ -129,6 +129,15 @@ public class ParametersUtil {
 		return getParameterPartValue(theCtx, theParameter, theParameterName).map(t -> (IPrimitiveType<?>) t).map(t -> t.getValueAsString()).orElse(null);
 	}
 
+	public static Optional<Integer> getParameterPartValueAsInteger(FhirContext theCtx, IBase theParameter, String theParameterName) {
+		return getParameterPartValue(theCtx, theParameter, theParameterName)
+			.filter(t -> IPrimitiveType.class.isAssignableFrom(t.getClass()))
+			.map(t -> (IPrimitiveType<?>) t)
+			.map(IPrimitiveType::getValue)
+			.filter(t -> Integer.class.isAssignableFrom(t.getClass()))
+			.map(t -> (Integer) t);
+	}
+
 	private static <T> List<T> extractNamedParameters(FhirContext theCtx, IBaseParameters theParameters, String theParameterName, Function<IPrimitiveType<?>, T> theMapper) {
 		List<T> retVal = new ArrayList<>();
 

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

@@ -441,7 +441,10 @@ public final class TerserUtil {
 	private static void replaceField(FhirTerser theTerser, IBaseResource theFrom, IBaseResource theTo, BaseRuntimeChildDefinition childDefinition) {
 		List<IBase> fromValues = childDefinition.getAccessor().getValues(theFrom);
 		List<IBase> toValues = childDefinition.getAccessor().getValues(theTo);
-		if (fromValues != toValues) {
+
+		if (fromValues.isEmpty() && !toValues.isEmpty()) {
+			childDefinition.getMutator().setValue(theTo, null);
+		} else if (fromValues != toValues) {
 			clear(toValues);
 
 			mergeFields(theTerser, theTo, childDefinition, fromValues, toValues);
@@ -529,7 +532,6 @@ public final class TerserUtil {
 	 * Creates a new element taking into consideration elements with choice that are not directly retrievable by element
 	 * name
 	 *
-	 *
 	 * @param theFhirTerser
 	 * @param theChildDefinition  Child to create a new instance for
 	 * @param theFromFieldValue   The base parent field

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

@@ -19,15 +19,16 @@
  */
 package org.hl7.fhir.instance.model.api;
 
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.model.api.IElement;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
 
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.model.api.IElement;
-import ca.uhn.fhir.model.api.Include;
-
 /**
  * For now, this is a simple marker interface indicating that a class is a resource type. 
  * There are two concrete types of implementations of this interrface. The first are
@@ -58,4 +59,10 @@ public interface IBaseResource extends IBase, IElement {
 
 	FhirVersionEnum getStructureFhirVersionEnum();
 
+	/**
+	 * @return <code>true</code> if this resource has been deleted
+	 */
+	default boolean isDeleted() {
+		return ResourceMetadataKeyEnum.DELETED_AT.get(this) != null;
+	}
 }

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

@@ -5,6 +5,7 @@ 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;
 
@@ -59,6 +60,11 @@ class DateRangeUtilTest {
 				new DateParam(theResultStartPrefix, theResultStart), new DateParam(theResultEndPrefix, theResultEnd));
 		}
 
+		static NarrowCase from(String theMessage, DateRangeParam theRange, Date theNarrowStart, Date theNarrowEnd,
+									  DateParam theResultStart, DateParam theResultEnd) {
+			return new NarrowCase(theMessage, theRange, theNarrowStart, theNarrowEnd, theResultStart, theResultEnd);
+		}
+
 		@Override
 		public String toString() {
 			return new ToStringBuilder(this, ToStringStyle.SIMPLE_STYLE)
@@ -89,8 +95,23 @@ class DateRangeUtilTest {
 			// half-open cases
 			NarrowCase.from("end inside open end", new DateRangeParam(dateTwo, null),  null, dateFour, dateTwo, dateFour),
 			NarrowCase.from("start inside open start", new DateRangeParam(null, dateFour),  dateTwo, null, GREATERTHAN_OR_EQUALS, dateTwo, LESSTHAN_OR_EQUALS, dateFour),
-			NarrowCase.from("gt case preserved", new DateRangeParam(new DateParam(GREATERTHAN, dateTwo), null),  null, dateFour, GREATERTHAN, dateTwo, LESSTHAN, dateFour)
+			NarrowCase.from("gt case preserved", new DateRangeParam(new DateParam(GREATERTHAN, dateTwo), null),  null, dateFour, GREATERTHAN, dateTwo, LESSTHAN, dateFour),
 
+			NarrowCase.from("lt date level precision date, narrow from is inside date",
+				new DateRangeParam(new DateParam(LESSTHAN, "2023-05-06")),
+				Date.from(Instant.parse("2023-05-06T10:00:20.512+00:00")),
+				Date.from(Instant.parse("2023-05-10T00:00:00.000+00:00")),
+				new DateParam(GREATERTHAN_OR_EQUALS, Date.from(Instant.parse("2023-05-06T10:00:20.512+00:00"))),
+				new DateParam(LESSTHAN, "2023-05-06")
+			),
+
+			NarrowCase.from("gt date level precision date, narrow to is inside date",
+				new DateRangeParam(new DateParam(GREATERTHAN_OR_EQUALS, "2023-05-06")),
+				Date.from(Instant.parse("2023-05-01T00:00:00.000+00:00")),
+				Date.from(Instant.parse("2023-05-06T10:00:20.512+00:00")),
+				new DateParam(GREATERTHAN_OR_EQUALS, "2023-05-06"),
+				new DateParam(LESSTHAN, Date.from(Instant.parse("2023-05-06T10:00:20.512+00:00")))
+			)
 
 		);
 	}

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>6.7.0-SNAPSHOT</version>
+	<version>6.7.1-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>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-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>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -2,8 +2,8 @@ package ca.uhn.fhir.cli;
 
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
-import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
 import ca.uhn.fhir.test.utilities.RestServerR4Helper;
+import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.ParseException;
@@ -29,7 +29,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 class ExampleDataUploaderTest {
 
 	@RegisterExtension
-	public final RestServerR4Helper myRestServerR4Helper = new RestServerR4Helper();
+	public final RestServerR4Helper myRestServerR4Helper = RestServerR4Helper.newWithTransactionLatch();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 
@@ -46,7 +46,8 @@ class ExampleDataUploaderTest {
 
 	@ParameterizedTest
 	@ValueSource(booleans = {true, false})
-	public void testHeaderPassthrough(boolean theIncludeTls) throws ParseException {
+	public void testHeaderPassthrough(boolean theIncludeTls) throws ParseException, InterruptedException {
+		// setup
 		String headerKey = "test-header-key";
 		String headerValue = "test header value";
 
@@ -60,8 +61,11 @@ class ExampleDataUploaderTest {
 		);
 
 		final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
-		testedCommand.run(commandLine);
 
+		// execute
+		myRestServerR4Helper.executeWithLatch(() -> runCommand(commandLine));
+
+		// validate
 		assertNotNull(myCapturingInterceptor.getLastRequest());
 		Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
 		assertFalse(allHeaders.isEmpty());
@@ -78,6 +82,14 @@ class ExampleDataUploaderTest {
 		assertEquals("EX3152", resource.getIdElement().getIdPart());
 	}
 
+	private void runCommand(CommandLine commandLine) {
+		try {
+			testedCommand.run(commandLine);
+		} catch (ParseException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
 	private static class RequestCapturingExampleDataUploader extends ExampleDataUploader {
 		private final CapturingInterceptor myCapturingInterceptor;
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandDstu3Test.java

@@ -43,7 +43,7 @@ public class ExportConceptMapToCsvCommandDstu3Test {
 	}
 
 	@RegisterExtension
-	public final RestServerDstu3Helper myRestServerDstu3Helper = new RestServerDstu3Helper(true);
+	public final RestServerDstu3Helper myRestServerDstu3Helper = RestServerDstu3Helper.newInitialized();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandR4Test.java

@@ -40,7 +40,7 @@ public class ExportConceptMapToCsvCommandR4Test {
 	}
 
 	@RegisterExtension
-	public final RestServerR4Helper myRestServerR4Helper = new RestServerR4Helper(true);
+	public final RestServerR4Helper myRestServerR4Helper = RestServerR4Helper.newInitialized();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandDstu3Test.java

@@ -45,7 +45,7 @@ public class ImportCsvToConceptMapCommandDstu3Test {
 	}
 
 	@RegisterExtension
-	public final RestServerDstu3Helper myRestServerDstu3Helper = new RestServerDstu3Helper(true);
+	public final RestServerDstu3Helper myRestServerDstu3Helper = RestServerDstu3Helper.newInitialized();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java

@@ -50,7 +50,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 
 
 	@RegisterExtension
-	public final RestServerR4Helper myRestServerR4Helper = new RestServerR4Helper(true);
+	public final RestServerR4Helper myRestServerR4Helper = RestServerR4Helper.newInitialized();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 

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

@@ -39,7 +39,7 @@ class ReindexTerminologyCommandTest {
 	private BaseJpaSystemProvider<?, ?> myProvider = spy(new BaseJpaSystemProvider<>() {});
 
 	@RegisterExtension
-	public final RestServerR4Helper myRestServerR4Helper = new RestServerR4Helper(true);
+	public final RestServerR4Helper myRestServerR4Helper = RestServerR4Helper.newInitialized();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 

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

@@ -104,9 +104,9 @@ public class UploadTerminologyCommandTest {
 	}
 
 	@RegisterExtension
-	public final RestServerR4Helper myRestServerR4Helper = new RestServerR4Helper(true);
+	public final RestServerR4Helper myRestServerR4Helper = RestServerR4Helper.newInitialized();
 	@RegisterExtension
-	public final RestServerDstu3Helper myRestServerDstu3Helper = new RestServerDstu3Helper(true);
+	public final RestServerDstu3Helper myRestServerDstu3Helper = RestServerDstu3Helper.newInitialized();
 	@RegisterExtension
 	public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
 

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -1,3 +1,22 @@
+/*-
+ * #%L
+ * HAPI FHIR - Docs
+ * %%
+ * 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.hapi.fhir.docs;
 
 import ca.uhn.fhir.context.FhirContext;

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4697-add-cr-operations.yaml

@@ -1,4 +1,5 @@
 ---
 type: add
 issue: 4697
-title: "Add providers for the operations available in the Clinical Reasoning package."
+title: "Added DSTU3 and R4 support for the FHIR Clinical Reasoning module operations ActivityDefinition/$apply and PlanDefinition/$apply.
+$apply allows for general workflow processing and is used in clinical decision support, prior authorization, quality reporting, and disease surveillance use cases."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4697-add-dtr-operations.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 4697
+title: "Added DSTU3 and R4 support for the DaVinci Documentation Templates and Rules (DTR) Questionnaire/$questionnaire-package operation.
+This operation allows a Questionnaire to be packaged as a Bundle with all the supporting resources that may be required for its use such as ValueSets and Libraries.
+This operation is used in context of prior authorization."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4697-add-package-prepopulate-operations.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 4697
+title: "Added R4 support for Questionnaire/$prepopulate and PlanDefinition/$package operations. These are operations are intended to support extended DaVinci DTR and SDC uses cases."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4697-add-sdc-operations.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 4697
+title: "Added DSTU3 and R4 support for the DaVinci Structured Data Capture (SDC) operations Questionnaire/$populate operation and QuestionnaireResponse/$extract.
+These operations are used in data capture and exchange use cases, and are used by downstream specifications such as DaVinci Documentation Templates and Rules (DTR) for prior authorization."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4814-fix-migrator-on-oracle.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4814
+title: "A recent regression prevented the SQL Migrator from running on Oracle. This has been
+  corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4816-mdm-golden-resource-tag-has-no-version.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 4812
+title: "The tag being added on golden resources does not have a version, might as well add one."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4817-deleted-resource-detection.yaml

@@ -0,0 +1,8 @@
+---
+type: change
+issue: 4817
+title: "Introduce IBaseResource.isDeleted() method and convert code to use it.
+Add subscription_topic_troubleshooting log.
+No longer rely on ResourceGoneException to detect deleted subscription. Instead use the new isDeleted() method.
+Demote unexpected exceptions in HapiTransactionService from error to debug since these exceptions are expected
+e.g. when checking if a resource has been deleted by catching a ResourceGoneException"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4831-fix-transaction-with-delete-and-resurrect.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 4831
+title: "When performing a FHIR transaction containing both a conditional delete as well as a
+  conditional create/update for the same resource, the resource was left in an inconsistent
+  state. This has been corrected. Thanks to Laxman Singh for raising this issue."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4831-optimize-multi-delete.yaml

@@ -0,0 +1,5 @@
+---
+type: perf
+issue: 4831
+title: "Conditional deletes that delete multiple resources at once have been optimized to perform
+   fewer SQL select statements, which should improve performance on large deletes."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4838-delete-expunge-with-lucene-disabled.yaml

@@ -0,0 +1,8 @@
+---
+type: fix
+issue: 4838
+title: "Two failures in the $delete-expunge operation were fixed:
+ <ul>
+ <li>Jobs could fail if hibernate search was loaded but not enabled.</li>
+ <li>Jobs could fail if the criteria included a <code>_lastUpdated=lt[date]</code> clause</li>
+ </ul>"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4838-fix-blocking-queue-in-balp-queue-sink.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 4838
+title: "The BALP AsyncMemoryQueueBackedFhirClientBalpSink incorrectly used a non-blocking method
+   to add events to the blocking queue, resulting in race conditions on a heavily loaded
+   server."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4838-reindex-delete-search-indexes.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 4838
+title: "When performing a resource reindex on a deleted resource, any search index rows will now
+  be deleted. Deleting a resource should generally not leave any such rows behind, but they can
+  be left if the resource is manually deleted using SQL directly against the database and in this
+  case the reindex job will now clean up these unwanted rows."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4838-reindex-deleted-resources-dont-validate.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4838
+title: "When reindexing resources, deleted resources could incorrectly fail validation rules and
+  cause the reindex job to not complete correctly. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4838-reindex-return-status-information.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 4838
+title: "When invoking the instance level `$reindex` and `$reindex-dryrun` operations, the resulting
+   status message and any warnings are now included in the response Parameters object as well as in
+   the generated response HTML narrative."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4842-terser-bug.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 4842
+title: "There was a bug with the TerserUtil, where it would not overwrite non-empty values with empty values from a source resource. This has been corrected. Thanks to @nigtrifork for the fix!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4881-fix-create-bundle-with-index-contained-resources.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 4881
+title: "When _Index Contained References_ is enabled in the JPA server, Bundle resources could not be
+   stored or indexed due to an incompatibility with the default Bundle search parameters. This has been
+   corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/changes.yaml

@@ -0,0 +1,8 @@
+---
+- item:
+    type: "add"
+    title: "The version of a few dependencies have been bumped to the latest versions
+    (dependent HAPI modules listed in brackets):
+    <ul>
+        <li>Hibernate ORM (JPA): 5.6.12.Final -&gt; 5.6.15.Final</li>
+    </ul>"

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -166,7 +166,6 @@ import java.util.stream.Collectors;
 
 import static java.util.Objects.isNull;
 import static java.util.Objects.nonNull;
-import static org.apache.commons.lang3.BooleanUtils.isFalse;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.apache.commons.lang3.StringUtils.left;
@@ -537,20 +536,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 
 	void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
-		String newVersion;
-		long newVersionLong;
 		if (theResourceId == null || theResourceId.getVersionIdPart() == null) {
-			newVersion = "1";
+			theSavedEntity.initializeVersion();
-			newVersionLong = 1;
 		} else {
-			newVersionLong = theResourceId.getVersionIdPartAsLong() + 1;
+			theSavedEntity.markVersionUpdatedInCurrentTransaction();
-			newVersion = Long.toString(newVersionLong);
 		}
 
 		assert theResourceId != null;
+		String newVersion = Long.toString(theSavedEntity.getVersion());
 		IIdType newId = theResourceId.withVersion(newVersion);
 		theResource.getIdElement().setValue(newId.getValue());
-		theSavedEntity.setVersion(newVersionLong);
 	}
 
 	public boolean isLogicalReference(IIdType theId) {
@@ -966,7 +961,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		 * This should be the very first thing..
 		 */
 		if (theResource != null) {
-			if (thePerformIndexing) {
+			if (thePerformIndexing && theDeletedTimestampOrNull == null) {
 				if (!ourValidationDisabledForUnitTest) {
 					validateResourceForStorage((T) theResource, entity);
 				}
@@ -1062,7 +1057,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 						verifyMatchUrlForConditionalCreate(theResource, entity.getCreatedByMatchUrl(), newParams, theRequest);
 					}
 
+					if (CURRENTLY_REINDEXING.get(theResource) != Boolean.TRUE) {
 						entity.setUpdated(theTransactionDetails.getTransactionDate());
+					}
 					newParams.populateResourceTableSearchParamsPresentFlags(entity);
 					entity.setIndexStatus(INDEX_STATUS_INDEXED);
 				}
@@ -1091,9 +1088,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			return entity;
 		}
 
-		if (theUpdateVersion) {
+		if (entity.getId() != null && theUpdateVersion) {
-			long newVersion = entity.getVersion() + 1;
+			entity.markVersionUpdatedInCurrentTransaction();
-			entity.setVersion(newVersion);
 		}
 
 		/*
@@ -1157,6 +1153,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		if (thePerformIndexing) {
 			if (newParams == null) {
 				myExpungeService.deleteAllSearchParams(JpaPid.fromId(entity.getId()));
+				entity.clearAllParamsPopulated();
 			} else {
 
 				// Synchronize search param indexes
@@ -1296,6 +1293,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 	private void createHistoryEntry(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, EncodedResource theChanged) {
 		boolean versionedTags = getStorageSettings().getTagStorageMode() == JpaStorageSettings.TagStorageModeEnum.VERSIONED;
+
 		final ResourceHistoryTable historyEntry = theEntity.toHistory(versionedTags);
 		historyEntry.setEncoding(theChanged.getEncoding());
 		historyEntry.setResource(theChanged.getResourceBinary());
@@ -1412,11 +1410,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		myJpaStorageResourceParser.populateResourceMetadata(entity, false, tagList, version, theResource);
 
 		boolean wasDeleted = false;
-		// NB If this if-else ever gets collapsed, make sure to account for possible null (will happen in mass-ingestion mode)
+		if (theOldResource != null) {
-		if (theOldResource instanceof IResource) {
+			wasDeleted = theOldResource.isDeleted();
-			wasDeleted = ResourceMetadataKeyEnum.DELETED_AT.get((IResource) theOldResource) != null;
-		} else if (theOldResource instanceof IAnyResource) {
-			wasDeleted = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) theOldResource) != null;
 		}
 
 		DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, theResource, theMatchUrl, theOperationType).setCreated(wasDeleted);

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

@@ -35,6 +35,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
 import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
@@ -199,9 +200,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	private TransactionTemplate myTxTemplate;
 	@Autowired
 	private UrlPartitioner myUrlPartitioner;
-
 	@Autowired
 	private ResourceSearchUrlSvc myResourceSearchUrlSvc;
+	@Autowired
+	private IFhirSystemDao<?, ?> mySystemDao;
 
 	public static <T extends IBaseResource> T invokeStoragePreShowResources(IInterceptorBroadcaster theInterceptorBroadcaster, RequestDetails theRequest, T retVal) {
 		if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_PRESHOW_RESOURCES, theInterceptorBroadcaster, theRequest)) {
@@ -263,12 +265,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	 */
 	@Override
 	public DaoMethodOutcome create(final T theResource) {
-		return create(theResource, null, true, new TransactionDetails(), null);
+		return create(theResource, null, true, null, new TransactionDetails());
 	}
 
 	@Override
 	public DaoMethodOutcome create(final T theResource, RequestDetails theRequestDetails) {
-		return create(theResource, null, true, new TransactionDetails(), theRequestDetails);
+		return create(theResource, null, true, theRequestDetails, new TransactionDetails());
 	}
 
 	/**
@@ -281,11 +283,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	@Override
 	public DaoMethodOutcome create(final T theResource, String theIfNoneExist, RequestDetails theRequestDetails) {
-		return create(theResource, theIfNoneExist, true, new TransactionDetails(), theRequestDetails);
+		return create(theResource, theIfNoneExist, true, theRequestDetails, new TransactionDetails());
 	}
 
 	@Override
-	public DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing, @Nonnull TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
+	public DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing, RequestDetails theRequestDetails, @Nonnull TransactionDetails theTransactionDetails) {
 		RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(theRequestDetails, theResource, getResourceName());
 		return myTransactionService
 			.withRequest(theRequestDetails)
@@ -340,7 +342,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		entity.setResourceType(toResourceName(theResource));
 		entity.setPartitionId(PartitionablePartitionId.toStoragePartition(theRequestPartitionId, myPartitionSettings));
 		entity.setCreatedByMatchUrl(theMatchUrl);
-		entity.setVersion(1);
+		entity.initializeVersion();
 
 		if (isNotBlank(theMatchUrl) && theProcessMatchUrl) {
 			Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest);
@@ -348,19 +350,51 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theMatchUrl, match.size());
 				throw new PreconditionFailedException(Msg.code(958) + msg);
 			} else if (match.size() == 1) {
-				JpaPid pid = match.iterator().next();
 
-				Supplier<LazyDaoMethodOutcome.EntityAndResource> entitySupplier = () -> {
+				/*
-					return myTxTemplate.execute(tx -> {
+				 * Ok, so we've found a single PID that matches the conditional URL.
+				 * That's good, there are two possibilities below.
+				 */
+
+				JpaPid pid = match.iterator().next();
+				if (theTransactionDetails.getDeletedResourceIds().contains(pid)) {
+
+					/*
+					 * If the resource matching the given match URL has already been
+					 * deleted within this transaction. This is a really rare case, since
+					 * it means the client has performed a FHIR transaction with both
+					 * a delete and a create on the same conditional URL. This is rare
+					 * but allowed, and means that it's now ok to create a new one resource
+					 * matching the conditional URL since we'll be deleting any existing
+					 * index rows on the existing resource as a part of this transaction.
+					 * We can also un-resolve the previous match URL in the TransactionDetails
+					 * since we'll resolve it to the new resource ID below
+					 */
+
+					myMatchResourceUrlService.unresolveMatchUrl(theTransactionDetails, getResourceName(), theMatchUrl);
+
+				} else {
+
+					/*
+					 * This is the normal path where the conditional URL matched exactly
+					 * one resource, so we won't be creating anything but instead
+					 * just returning the existing ID. We now have a PID for the matching
+					 * resource, but we haven't loaded anything else (e.g. the forced ID
+					 * or the resource body aren't yet loaded from the DB). We're going to
+					 * return a LazyDaoOutcome with two lazy loaded providers for loading the
+					 * entity and the forced ID since we can avoid these extra SQL loads
+					 * unless we know we're actually going to use them. For example, if
+					 * the client has specified "Prefer: return=minimal" then we won't be
+					 * needing the load the body.
+					 */
+
+					Supplier<LazyDaoMethodOutcome.EntityAndResource> entitySupplier = () -> myTxTemplate.execute(tx -> {
 						ResourceTable foundEntity = myEntityManager.find(ResourceTable.class, pid.getId());
 						IBaseResource resource = myJpaStorageResourceParser.toResource(foundEntity, false);
 						theResource.setId(resource.getIdElement().getValue());
 						return new LazyDaoMethodOutcome.EntityAndResource(foundEntity, resource);
 					});
-				};
+					Supplier<IIdType> idSupplier = () -> myTxTemplate.execute(tx -> {
-
-				Supplier<IIdType> idSupplier = () -> {
-					return myTxTemplate.execute(tx -> {
 						IIdType retVal = myIdHelperService.translatePidIdToForcedId(myFhirContext, myResourceName, pid);
 						if (!retVal.hasVersionIdPart()) {
 							Long version = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getId());
@@ -376,7 +410,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 						}
 						return retVal;
 					});
-				};
 
 					DaoMethodOutcome outcome = toMethodOutcomeLazy(theRequest, pid, entitySupplier, idSupplier).setCreated(false).setNop(true);
 					StorageResponseCodeEnum responseCode = StorageResponseCodeEnum.SUCCESSFUL_CREATE_WITH_CONDITIONAL_MATCH;
@@ -385,6 +418,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 					return outcome;
 				}
 			}
+		}
 
 		String resourceIdBeforeStorage = theResource.getIdElement().getIdPart();
 		boolean resourceHadIdBeforeStorage = isNotBlank(resourceIdBeforeStorage);
@@ -617,12 +651,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			throw new ResourceVersionConflictException(Msg.code(961) + "Trying to delete " + theId + " but this is not the current version");
 		}
 
+		JpaPid persistentId = JpaPid.fromId(entity.getResourceId());
+		theTransactionDetails.addDeletedResourceId(persistentId);
+
 		// Don't delete again if it's already deleted
 		if (isDeleted(entity)) {
 			DaoMethodOutcome outcome = createMethodOutcomeForResourceId(entity.getIdDt().getValue(), MESSAGE_KEY_DELETE_RESOURCE_ALREADY_DELETED, StorageResponseCodeEnum.SUCCESSFUL_DELETE_ALREADY_DELETED);
 
 			// used to exist, so we'll set the persistent id
-			outcome.setPersistentId(JpaPid.fromId(entity.getResourceId()));
+			outcome.setPersistentId(persistentId);
 			outcome.setEntity(entity);
 
 			return outcome;
@@ -681,7 +718,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		return myTransactionService.execute(theRequest, transactionDetails, tx -> {
 			DeleteConflictList deleteConflicts = new DeleteConflictList();
-			DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequest);
+			DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequest, transactionDetails);
 			DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
 			return outcome;
 		});
@@ -692,20 +729,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	 * transaction processors
 	 */
 	@Override
-	public DeleteMethodOutcome deleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequestDetails) {
+	public DeleteMethodOutcome deleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequestDetails, @Nonnull TransactionDetails theTransactionDetails) {
 		validateDeleteEnabled();
-		TransactionDetails transactionDetails = new TransactionDetails();
 
-		return myTransactionService.execute(theRequestDetails, transactionDetails, tx -> doDeleteByUrl(theUrl, deleteConflicts, theRequestDetails));
+		return myTransactionService.execute(theRequestDetails, theTransactionDetails, tx -> doDeleteByUrl(theUrl, deleteConflicts, theTransactionDetails, theRequestDetails));
 	}
 
 	@Nonnull
-	private DeleteMethodOutcome doDeleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequest) {
+	private DeleteMethodOutcome doDeleteByUrl(String theUrl, DeleteConflictList deleteConflicts, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
 		ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(theUrl);
 		SearchParameterMap paramMap = resourceSearch.getSearchParameterMap();
 		paramMap.setLoadSynchronous(true);
 
-		Set<JpaPid> resourceIds = myMatchResourceUrlService.search(paramMap, myResourceType, theRequest, null);
+		Set<JpaPid> resourceIds = myMatchResourceUrlService.search(paramMap, myResourceType, theRequestDetails, null);
 
 		if (resourceIds.size() > 1) {
 			if (!getStorageSettings().isAllowMultipleDelete()) {
@@ -713,7 +749,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 		}
 
-		return deletePidList(theUrl, resourceIds, deleteConflicts, theRequest);
+		return deletePidList(theUrl, resourceIds, deleteConflicts, theRequestDetails, theTransactionDetails);
 	}
 
 	@Override
@@ -733,15 +769,23 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 	}
 
-
 	@Nonnull
 	@Override
-	public <P extends IResourcePersistentId> DeleteMethodOutcome deletePidList(String theUrl, Collection<P> theResourceIds, DeleteConflictList theDeleteConflicts, RequestDetails theRequest) {
+	public <P extends IResourcePersistentId> DeleteMethodOutcome deletePidList(String theUrl, Collection<P> theResourceIds, DeleteConflictList theDeleteConflicts, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
 		StopWatch w = new StopWatch();
 		TransactionDetails transactionDetails = new TransactionDetails();
 		List<ResourceTable> deletedResources = new ArrayList<>();
+
+		List<IResourcePersistentId<?>> resolvedIds = theResourceIds
+			.stream()
+			.map(t -> (IResourcePersistentId<?>) t)
+			.collect(Collectors.toList());
+		mySystemDao.preFetchResources(resolvedIds, false);
+
 		for (P pid : theResourceIds) {
 			JpaPid jpaPid = (JpaPid) pid;
+
+			// This shouldn't actually need to hit the DB because we pre-fetch above
 			ResourceTable entity = myEntityManager.find(ResourceTable.class, jpaPid.getId());
 			deletedResources.add(entity);
 
@@ -750,18 +794,18 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			// Notify IServerOperationInterceptors about pre-action call
 			HookParams hooks = new HookParams()
 				.add(IBaseResource.class, resourceToDelete)
-				.add(RequestDetails.class, theRequest)
+				.add(RequestDetails.class, theRequestDetails)
-				.addIfMatchesType(ServletRequestDetails.class, theRequest)
+				.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
 				.add(TransactionDetails.class, transactionDetails);
-			doCallHooks(transactionDetails, theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hooks);
+			doCallHooks(transactionDetails, theRequestDetails, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hooks);
 
-			myDeleteConflictService.validateOkToDelete(theDeleteConflicts, entity, false, theRequest, transactionDetails);
+			myDeleteConflictService.validateOkToDelete(theDeleteConflicts, entity, false, theRequestDetails, transactionDetails);
 
 			// Perform delete
 
-			preDelete(resourceToDelete, entity, theRequest);
+			preDelete(resourceToDelete, entity, theRequestDetails);
 
-			updateEntityForDelete(theRequest, transactionDetails, entity);
+			updateEntityForDelete(theRequestDetails, transactionDetails, entity);
 			resourceToDelete.setId(entity.getIdDt());
 
 			// Notify JPA interceptors
@@ -770,11 +814,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				public void beforeCommit(boolean readOnly) {
 					HookParams hookParams = new HookParams()
 						.add(IBaseResource.class, resourceToDelete)
-						.add(RequestDetails.class, theRequest)
+						.add(RequestDetails.class, theRequestDetails)
-						.addIfMatchesType(ServletRequestDetails.class, theRequest)
+						.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
 						.add(TransactionDetails.class, transactionDetails)
 						.add(InterceptorInvocationTimingEnum.class, transactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED));
-					doCallHooks(transactionDetails, theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
+					doCallHooks(transactionDetails, theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
 				}
 			});
 		}
@@ -791,6 +835,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		ourLog.debug("Processed delete on {} (matched {} resource(s)) in {}ms", theUrl, deletedResources.size(), w.getMillis());
 
+		theTransactionDetails.addDeletedResourceIds(theResourceIds);
+
 		DeleteMethodOutcome retVal = new DeleteMethodOutcome();
 		retVal.setDeletedEntities(deletedResources);
 		retVal.setOperationOutcome(oo);
@@ -1341,7 +1387,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		if (theReindexParameters.getReindexSearchParameters() == ReindexParameters.ReindexSearchParametersEnum.ALL) {
-			reindexSearchParameters(entity, retVal);
+			reindexSearchParameters(entity, retVal, theTransactionDetails);
 		}
 		if (theReindexParameters.getOptimizeStorage() != ReindexParameters.OptimizeStorageModeEnum.NONE) {
 			reindexOptimizeStorage(entity, theReindexParameters.getOptimizeStorage());
@@ -1351,23 +1397,49 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@SuppressWarnings("unchecked")
-	private void reindexSearchParameters(ResourceTable entity, ReindexOutcome theReindexOutcome) {
+	private void reindexSearchParameters(ResourceTable entity, ReindexOutcome theReindexOutcome, TransactionDetails theTransactionDetails) {
 		try {
 			T resource = (T) myJpaStorageResourceParser.toResource(entity, false);
-			reindex(resource, entity);
+			reindexSearchParameters(resource, entity, theTransactionDetails);
 		} catch (Exception e) {
 			theReindexOutcome.addWarning("Failed to reindex resource " + entity.getIdDt() + ": " + e);
 			myResourceTableDao.updateIndexStatus(entity.getId(), INDEX_STATUS_INDEXING_FAILED);
 		}
 	}
 
+	/**
+	 * @deprecated Use {@link #reindex(IResourcePersistentId, ReindexParameters, RequestDetails, TransactionDetails)}
+	 */
+	@Deprecated
+	@Override
+	public void reindex(T theResource, IBasePersistedResource theEntity) {
+		assert TransactionSynchronizationManager.isActualTransactionActive();
+		ResourceTable entity = (ResourceTable) theEntity;
+		TransactionDetails transactionDetails = new TransactionDetails(entity.getUpdatedDate());
+
+		reindexSearchParameters(theResource, theEntity, transactionDetails);
+	}
+
+	private void reindexSearchParameters(T theResource, IBasePersistedResource theEntity, TransactionDetails transactionDetails) {
+		ourLog.debug("Indexing resource {} - PID {}", theEntity.getIdDt().getValue(), theEntity.getPersistentId());
+		if (theResource != null) {
+			CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
+		}
+
+		ResourceTable resourceTable = updateEntity(null, theResource, theEntity, theEntity.getDeleted(), true, false, transactionDetails, true, false);
+		if (theResource != null) {
+			CURRENTLY_REINDEXING.put(theResource, null);
+		}
+	}
+
+
 	private void reindexOptimizeStorage(ResourceTable entity, ReindexParameters.OptimizeStorageModeEnum theOptimizeStorageMode) {
 		ResourceHistoryTable historyEntity = entity.getCurrentVersionEntity();
 		if (historyEntity != null) {
 			reindexOptimizeStorageHistoryEntity(entity, historyEntity);
 			if (theOptimizeStorageMode == ReindexParameters.OptimizeStorageModeEnum.ALL_VERSIONS) {
 				int pageSize = 100;
-				for (int page = 0; ((long)page * pageSize) < entity.getVersion(); page++) {
+				for (int page = 0; ((long) page * pageSize) < entity.getVersion(); page++) {
 					Slice<ResourceHistoryTable> historyEntities = myResourceHistoryTableDao.findForResourceIdAndReturnEntities(PageRequest.of(page, pageSize), entity.getId(), historyEntity.getVersion());
 					for (ResourceHistoryTable next : historyEntities) {
 						reindexOptimizeStorageHistoryEntity(entity, next);
@@ -1500,23 +1572,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return entity;
 	}
 
-	@Override
-	public void reindex(T theResource, IBasePersistedResource theEntity) {
-		assert TransactionSynchronizationManager.isActualTransactionActive();
-
-		ourLog.debug("Indexing resource {} - PID {}", theEntity.getIdDt().getValue(), theEntity.getPersistentId());
-		if (theResource != null) {
-			CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
-		}
-
-		ResourceTable entity = (ResourceTable) theEntity;
-		TransactionDetails transactionDetails = new TransactionDetails(entity.getUpdatedDate());
-		ResourceTable resourceTable = updateEntity(null, theResource, theEntity, theEntity.getDeleted(), true, false, transactionDetails, true, false);
-		if (theResource != null) {
-			CURRENTLY_REINDEXING.put(theResource, null);
-		}
-	}
-
 	@Transactional
 	@Override
 	public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {

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

@@ -1,3 +1,22 @@
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * 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.jpa.dao;
 
 import ca.uhn.fhir.i18n.Msg;
@@ -7,14 +26,14 @@ import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 
 import java.lang.reflect.Field;
-import java.util.HashMap;
 import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * We are trying to preserve null behaviour despite IBaseCoding using primitive boolean for userSelected.
  */
 public class CodingSpy {
-	final Map<Class, Field> mySpies = new HashMap<>();
+	final Map<Class, Field> mySpies = new ConcurrentHashMap<>();
 
 	/**
 	 * Reach into the Coding and pull out the Boolean instead of the boolean.

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

@@ -85,6 +85,10 @@ public interface IResourceTableDao extends JpaRepository<ResourceTable, Long>, I
 	@Query("UPDATE ResourceTable t SET t.myIndexStatus = :status WHERE t.myId = :id")
 	void updateIndexStatus(@Param("id") Long theId, @Param("status") Long theIndexStatus);
 
+	@Modifying
+	@Query("UPDATE ResourceTable t SET t.myUpdated = :updated WHERE t.myId = :id")
+	void updateLastUpdated(@Param("id") Long theId, @Param("updated") Date theUpdated);
+
 	@Modifying
 	@Query("DELETE FROM ResourceTable t WHERE t.myId = :pid")
 	void deleteByPid(@Param("pid") Long theId);

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

@@ -39,9 +39,6 @@ import java.util.stream.Collectors;
 
 public class DeleteExpungeSqlBuilder {
 	private static final Logger ourLog = LoggerFactory.getLogger(DeleteExpungeSqlBuilder.class);
-	public static final String PROCESS_NAME = "Delete Expunging";
-	public static final String THREAD_PREFIX = "delete-expunge";
-	
 	private final ResourceTableFKProvider myResourceTableFKProvider;
 	private final JpaStorageSettings myStorageSettings;
 	private final IIdHelperService myIdHelper;

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

@@ -69,7 +69,7 @@ public class DeleteExpungeSvcImpl implements IDeleteExpungeSvc<JpaPid> {
 	 * This method clears the Hibernate Search index for the given resources.
 	 */
 	private void clearHibernateSearchIndex(List<JpaPid> thePersistentIds) {
-		if (myFullTextSearchSvc != null) {
+		if (myFullTextSearchSvc != null && !myFullTextSearchSvc.isDisabled()) {
 			List<Object> objectIds = thePersistentIds.stream().map(JpaPid::getId).collect(Collectors.toList());
 			myFullTextSearchSvc.deleteIndexedDocumentsByTypeAndId(ResourceTable.class, objectIds);
 			ourLog.info("Cleared Hibernate Search indexes.");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java

@@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
+import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
 import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
@@ -58,8 +59,6 @@ import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
@@ -90,7 +89,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 	@Autowired
 	private IHapiPackageCacheManager myPackageCacheManager;
 	@Autowired
-	private PlatformTransactionManager myTxManager;
+	private IHapiTransactionService myTxService;
 	@Autowired
 	private INpmPackageVersionDao myPackageVersionDao;
 	@Autowired
@@ -128,6 +127,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		}
 	}
 
+	@Override
 	public PackageDeleteOutcomeJson uninstall(PackageInstallationSpec theInstallationSpec) {
 		return myPackageCacheManager.uninstallPackage(theInstallationSpec.getName(), theInstallationSpec.getVersion());
 	}
@@ -152,7 +152,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		if (enabled) {
 			try {
 
-				boolean exists = new TransactionTemplate(myTxManager).execute(tx -> {
+				boolean exists = myTxService.withSystemRequest().withRequestPartitionId(RequestPartitionId.defaultPartition()).execute(() -> {
 					Optional<NpmPackageVersionEntity> existing = myPackageVersionDao.findByPackageIdAndVersion(theInstallationSpec.getName(), theInstallationSpec.getVersion());
 					return existing.isPresent();
 				});
@@ -267,8 +267,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 					}
 
 				} catch (IOException e) {
-					throw new ImplementationGuideInstallationException(Msg.code(1287) + String.format(
+					throw new ImplementationGuideInstallationException(Msg.code(1287) + String.format("Cannot resolve dependency %s#%s", id, ver), e);
-						"Cannot resolve dependency %s#%s", id, ver), e);
 				}
 			}
 		}
@@ -278,8 +277,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 	 * Asserts if package FHIR version is compatible with current FHIR version
 	 * by using semantic versioning rules.
 	 */
-	protected void assertFhirVersionsAreCompatible(String fhirVersion, String currentFhirVersion)
+	protected void assertFhirVersionsAreCompatible(String fhirVersion, String currentFhirVersion) throws ImplementationGuideInstallationException {
-		throws ImplementationGuideInstallationException {
 
 		FhirVersionEnum fhirVersionEnum = FhirVersionEnum.forVersionString(fhirVersion);
 		FhirVersionEnum currentFhirVersionEnum = FhirVersionEnum.forVersionString(currentFhirVersion);
@@ -290,9 +288,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 			compatible = true;
 		}
 		if (!compatible) {
-			throw new ImplementationGuideInstallationException(Msg.code(1288) + String.format(
+			throw new ImplementationGuideInstallationException(Msg.code(1288) + String.format("Cannot install implementation guide: FHIR versions mismatch (expected <=%s, package uses %s)", currentFhirVersion, fhirVersion));
-				"Cannot install implementation guide: FHIR versions mismatch (expected <=%s, package uses %s)",
-				currentFhirVersion, fhirVersion));
 		}
 	}
 
@@ -336,26 +332,18 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 					ourLog.info("Skipping update of existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
 				}
 			}
-		}
+		} else {
-		else{
 			ourLog.warn("Failed to upload resource of type {} with ID {} - Error: Resource failed validation", theResource.fhirType(), theResource.getIdElement().getValue());
 		}
 	}
 
 	private IBundleProvider searchResource(IFhirResourceDao theDao, SearchParameterMap theMap) {
-		if (myPartitionSettings.isPartitioningEnabled()) {
+		return theDao.search(theMap, newSystemRequestDetails());
-			SystemRequestDetails requestDetails = newSystemRequestDetails();
-			return theDao.search(theMap, requestDetails);
-		} else {
-			return theDao.search(theMap);
-		}
 	}
 
 	@Nonnull
 	private SystemRequestDetails newSystemRequestDetails() {
-		return
+		return new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition());
-			new SystemRequestDetails()
-				.setRequestPartitionId(RequestPartitionId.defaultPartition());
 	}
 
 	private void createResource(IFhirResourceDao theDao, IBaseResource theResource) {
@@ -400,8 +388,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		}
 
 		if (!isValidResourceStatusForPackageUpload(theResource)) {
-			ourLog.warn("Failed to validate resource of type {} with ID {} - Error: Resource status not accepted value.",
+			ourLog.warn("Failed to validate resource of type {} with ID {} - Error: Resource status not accepted value.", theResource.fhirType(), theResource.getIdElement().getValue());
-				theResource.fhirType(), theResource.getIdElement().getValue());
 			return false;
 		}
 
@@ -458,8 +445,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		try {
 			return validationSupport.generateSnapshot(new ValidationSupportContext(validationSupport), sd, null, null, null);
 		} catch (Exception e) {
-			throw new ImplementationGuideInstallationException(Msg.code(1290) + String.format(
+			throw new ImplementationGuideInstallationException(Msg.code(1290) + String.format("Failure when generating snapshot of StructureDefinition: %s", sd.getIdElement()), e);
-				"Failure when generating snapshot of StructureDefinition: %s", sd.getIdElement()), e);
 		}
 	}
 

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

@@ -26,10 +26,13 @@ import ca.uhn.fhir.interceptor.model.ReadPartitionIdRequestDetails;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
+import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
 import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.*;
 import ca.uhn.fhir.jpa.partition.BaseRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
@@ -40,6 +43,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
 import com.google.common.annotations.VisibleForTesting;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
@@ -59,6 +63,7 @@ import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -132,6 +137,7 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
 	@SuppressWarnings({"unchecked", "rawtypes"})
 	@Nonnull
 	private Parameters reindexInTransaction(RequestDetails theRequestDetails, IIdType theResourceId) {
+		StopWatch sw = new StopWatch();
 		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResourceId.getResourceType());
 		ResourceTable entity = (ResourceTable) dao.readEntity(theResourceId, theRequestDetails);
 		IBaseResource resource = myJpaStorageResourceParser.toResource(entity, false);
@@ -144,16 +150,26 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
 		ResourceIndexedSearchParams existingParamsToPopulate = new ResourceIndexedSearchParams(entity);
 		existingParamsToPopulate.mySearchParamPresentEntities.addAll(entity.getSearchParamPresents());
 
-		dao.reindex(resource, entity);
+		List<String> messages = new ArrayList<>();
+
+		JpaPid pid = JpaPid.fromId(entity.getId());
+		ReindexOutcome outcome = dao.reindex(pid, new ReindexParameters(), theRequestDetails, new TransactionDetails());
+		messages.add("Reindex completed in " + sw);
+
+		for (String next : outcome.getWarnings()) {
+			messages.add("WARNING: " + next);
+		}
 
 		ResourceIndexedSearchParams newParamsToPopulate = new ResourceIndexedSearchParams(entity);
 		newParamsToPopulate.mySearchParamPresentEntities.addAll(entity.getSearchParamPresents());
 
-		return buildIndexResponse(existingParamsToPopulate, newParamsToPopulate, true);
+		return buildIndexResponse(existingParamsToPopulate, newParamsToPopulate, true, messages);
 	}
 
 	@Nonnull
 	private Parameters reindexDryRunInTransaction(RequestDetails theRequestDetails, IIdType theResourceId, RequestPartitionId theRequestPartitionId, TransactionDetails theTransactionDetails, Set<String> theParameters) {
+		StopWatch sw = new StopWatch();
+
 		IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceId.getResourceType());
 		ResourceTable entity = (ResourceTable) dao.readEntity(theResourceId, theRequestDetails);
 		IBaseResource resource = myJpaStorageResourceParser.toResource(entity, false);
@@ -186,7 +202,8 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
 			showAction = false;
 		}
 
-		return buildIndexResponse(existingParamsToPopulate, newParamsToPopulate, showAction);
+		String message = "Reindex dry-run completed in " + sw + ". No changes were committed to any stored data.";
+		return buildIndexResponse(existingParamsToPopulate, newParamsToPopulate, showAction, List.of(message));
 	}
 
 	@Nonnull
@@ -197,12 +214,16 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
 
 	@Nonnull
 	@VisibleForTesting
-	Parameters buildIndexResponse(ResourceIndexedSearchParams theExistingParams, ResourceIndexedSearchParams theNewParams, boolean theShowAction) {
+	Parameters buildIndexResponse(ResourceIndexedSearchParams theExistingParams, ResourceIndexedSearchParams theNewParams, boolean theShowAction, List<String> theMessages) {
 		Parameters parameters = new Parameters();
 
 		Parameters.ParametersParameterComponent narrativeParameter = parameters.addParameter();
 		narrativeParameter.setName("Narrative");
 
+		for (String next : theMessages) {
+			parameters.addParameter("Message", new StringType(next));
+		}
+
 		// Normal indexes
 		addParamsNonMissing(parameters, "CoordinateIndexes", "Coords", theExistingParams.myCoordsParams, theNewParams.myCoordsParams, new CoordsParamPopulator(), theShowAction);
 		addParamsNonMissing(parameters, "DateIndexes", "Date", theExistingParams.myDateParams, theNewParams.myDateParams, new DateParamPopulator(), theShowAction);

hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/search/reindex/reindex-outcome.html

@@ -1,5 +1,15 @@
 <div xmlns:th="http://www.thymeleaf.org">
 
+   <!--/* Messages */-->
+   <div th:if="${resource.hasParameter('Message')}" id="Messages">
+      <h1>Outcome</h1>
+      <ul>
+         <li th:each="part : ${resource.getParameters('Message')}">
+            [[${part.getValue().getValue()}]]
+         </li>
+      </ul>
+   </div>
+
    <!--/* Number Indexes */-->
    <div th:if="${resource.hasParameter('NumberIndexes')}" id="NumberIndexes">
       <h1>Number Indexes</h1>

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImplTest.java

@@ -1,12 +1,263 @@
 package ca.uhn.fhir.jpa.packages;
 
-import org.elasticsearch.common.inject.Inject;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
+import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
+import ca.uhn.fhir.jpa.dao.tx.NonTransactionalHapiTransactionService;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistryController;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.Communication;
+import org.hl7.fhir.r4.model.DocumentReference;
+import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r4.model.SearchParameter;
+import org.hl7.fhir.r4.model.Subscription;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.PackageGenerator;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.Spy;
+import org.mockito.junit.jupiter.MockitoExtension;
 
+import javax.annotation.Nonnull;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+import java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.verifyNoInteractions;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
 public class PackageInstallerSvcImplTest {
 
+	public static final String PACKAGE_VERSION = "1.0";
+	public static final String PACKAGE_ID_1 = "package1";
+
+	@Mock
+	private INpmPackageVersionDao myPackageVersionDao;
+	@Mock
+	private IHapiPackageCacheManager myPackageCacheManager;
+	@Mock
+	private ISearchParamRegistryController mySearchParamRegistryController;
+	@Mock
+	private DaoRegistry myDaoRegistry;
+	@Mock
+	private IFhirResourceDao<CodeSystem> myCodeSystemDao;
+	@Spy
+	private FhirContext myCtx = FhirContext.forR4Cached();
+	@Spy
+	private IHapiTransactionService myTxService = new NonTransactionalHapiTransactionService();
+	@Spy
+	private PackageResourceParsingSvc myPackageResourceParsingSvc = new PackageResourceParsingSvc(myCtx);
+	@Spy
+	private PartitionSettings myPartitionSettings = new PartitionSettings();
+	@InjectMocks
+	private PackageInstallerSvcImpl mySvc;
+
 	@Test
 	public void testPackageCompatibility() {
-		new PackageInstallerSvcImpl().assertFhirVersionsAreCompatible("R4", "R4B");
+		mySvc.assertFhirVersionsAreCompatible("R4", "R4B");
 	}
+
+	@Test
+	public void testValidForUpload_SearchParameterWithMetaParam() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("_id");
+		assertFalse(mySvc.validForUpload(sp));
+	}
+
+	@Test
+	public void testValidForUpload_SearchParameterWithNoBase() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("name");
+		sp.setExpression("Patient.name");
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		assertFalse(mySvc.validForUpload(sp));
+	}
+
+	@Test
+	public void testValidForUpload_SearchParameterWithNoExpression() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("name");
+		sp.addBase("Patient");
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		assertFalse(mySvc.validForUpload(sp));
+	}
+
+
+	@Test
+	public void testValidForUpload_GoodSearchParameter() {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("name");
+		sp.addBase("Patient");
+		sp.setExpression("Patient.name");
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		assertTrue(mySvc.validForUpload(sp));
+	}
+
+	@Test
+	public void testValidForUpload_RequestedSubscription() {
+		Subscription.SubscriptionChannelComponent subscriptionChannelComponent =
+			new Subscription.SubscriptionChannelComponent()
+				.setType(Subscription.SubscriptionChannelType.RESTHOOK)
+				.setEndpoint("https://tinyurl.com/2p95e27r");
+		Subscription subscription = new Subscription();
+		subscription.setCriteria("Patient?name=smith");
+		subscription.setChannel(subscriptionChannelComponent);
+		subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
+		assertTrue(mySvc.validForUpload(subscription));
+	}
+
+	@Test
+	public void testValidForUpload_ErrorSubscription() {
+		Subscription.SubscriptionChannelComponent subscriptionChannelComponent =
+			new Subscription.SubscriptionChannelComponent()
+				.setType(Subscription.SubscriptionChannelType.RESTHOOK)
+				.setEndpoint("https://tinyurl.com/2p95e27r");
+		Subscription subscription = new Subscription();
+		subscription.setCriteria("Patient?name=smith");
+		subscription.setChannel(subscriptionChannelComponent);
+		subscription.setStatus(Subscription.SubscriptionStatus.ERROR);
+		assertFalse(mySvc.validForUpload(subscription));
+	}
+
+	@Test
+	public void testValidForUpload_ActiveSubscription() {
+		Subscription.SubscriptionChannelComponent subscriptionChannelComponent =
+			new Subscription.SubscriptionChannelComponent()
+				.setType(Subscription.SubscriptionChannelType.RESTHOOK)
+				.setEndpoint("https://tinyurl.com/2p95e27r");
+		Subscription subscription = new Subscription();
+		subscription.setCriteria("Patient?name=smith");
+		subscription.setChannel(subscriptionChannelComponent);
+		subscription.setStatus(Subscription.SubscriptionStatus.ACTIVE);
+		assertFalse(mySvc.validForUpload(subscription));
+	}
+
+	@Test
+	public void testValidForUpload_DocumentRefStatusValuePresent() {
+		DocumentReference documentReference = new DocumentReference();
+		documentReference.setStatus(Enumerations.DocumentReferenceStatus.ENTEREDINERROR);
+		assertTrue(mySvc.validForUpload(documentReference));
+	}
+
+	@Test
+	public void testValidForUpload_DocumentRefStatusValueNull() {
+		DocumentReference documentReference = new DocumentReference();
+		documentReference.setStatus(Enumerations.DocumentReferenceStatus.NULL);
+		assertFalse(mySvc.validForUpload(documentReference));
+		documentReference.setStatus(null);
+		assertFalse(mySvc.validForUpload(documentReference));
+	}
+
+	@Test
+	public void testValidForUpload_CommunicationStatusValuePresent() {
+		Communication communication = new Communication();
+		communication.setStatus(Communication.CommunicationStatus.NOTDONE);
+		assertTrue(mySvc.validForUpload(communication));
+	}
+
+	@Test
+	public void testValidForUpload_CommunicationStatusValueNull() {
+		Communication communication = new Communication();
+		communication.setStatus(Communication.CommunicationStatus.NULL);
+		assertFalse(mySvc.validForUpload(communication));
+		communication.setStatus(null);
+		assertFalse(mySvc.validForUpload(communication));
+	}
+
+	@Test
+	public void testDontTryToInstallDuplicateCodeSystem_CodeSystemAlreadyExistsWithDifferentId() throws IOException {
+		// Setup
+
+		// The CodeSystem that is already saved in the repository
+		CodeSystem existingCs = new CodeSystem();
+		existingCs.setId("CodeSystem/existingcs");
+		existingCs.setUrl("http://my-code-system");
+		existingCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+
+		// A new code system in a package we're installing that has the
+		// same URL as the previously saved one, but a different ID.
+		CodeSystem cs = new CodeSystem();
+		cs.setId("CodeSystem/mycs");
+		cs.setUrl("http://my-code-system");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+
+		NpmPackage pkg = createPackage(cs, PACKAGE_ID_1);
+
+		when(myPackageVersionDao.findByPackageIdAndVersion(any(), any())).thenReturn(Optional.empty());
+		when(myPackageCacheManager.installPackage(any())).thenReturn(pkg);
+		when(myDaoRegistry.getResourceDao(CodeSystem.class)).thenReturn(myCodeSystemDao);
+		when(myCodeSystemDao.search(any(), any())).thenReturn(new SimpleBundleProvider(existingCs));
+		when(myCodeSystemDao.update(any(),any(RequestDetails.class))).thenReturn(new DaoMethodOutcome());
+
+		PackageInstallationSpec spec = new PackageInstallationSpec();
+		spec.setName(PACKAGE_ID_1);
+		spec.setVersion(PACKAGE_VERSION);
+		spec.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		spec.setPackageContents(packageToBytes(pkg));
+
+		// Test
+		mySvc.install(spec);
+
+		// Verify
+		verify(myCodeSystemDao, times(1)).search(mySearchParameterMapCaptor.capture(), any());
+		SearchParameterMap map = mySearchParameterMapCaptor.getValue();
+		assertEquals("?url=http%3A%2F%2Fmy-code-system", map.toNormalizedQueryString(myCtx));
+
+		verify(myCodeSystemDao, times(1)).update(myCodeSystemCaptor.capture(), any(RequestDetails.class));
+		CodeSystem codeSystem = myCodeSystemCaptor.getValue();
+		assertEquals("existingcs", codeSystem.getIdPart());
+	}
+
+	@Nonnull
+	private static byte[] packageToBytes(NpmPackage pkg) throws IOException {
+		ByteArrayOutputStream stream = new ByteArrayOutputStream();
+		pkg.save(stream);
+		byte[] bytes = stream.toByteArray();
+		return bytes;
+	}
+
+	@Captor
+	private ArgumentCaptor<SearchParameterMap> mySearchParameterMapCaptor;
+	@Captor
+	private ArgumentCaptor<CodeSystem> myCodeSystemCaptor;
+
+	@Nonnull
+	private NpmPackage createPackage(CodeSystem cs, String packageId) throws IOException {
+		PackageGenerator manifestGenerator = new PackageGenerator();
+		manifestGenerator.name(packageId);
+		manifestGenerator.version(PACKAGE_VERSION);
+		manifestGenerator.description("a package");
+		manifestGenerator.fhirVersions(List.of(FhirVersionEnum.R4.getFhirVersionString()));
+
+		NpmPackage pkg = NpmPackage.empty(manifestGenerator);
+
+		String csString = myCtx.newJsonParser().encodeResourceToString(cs);
+		pkg.addFile("package", "cs.json", csString.getBytes(StandardCharsets.UTF_8), "CodeSystem");
+
+		return pkg;
+	}
+
+
 }

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/PersistObservationIndexedSearchParamLastNR4IT.java

@@ -127,7 +127,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
 		ResourceTable entity = new ResourceTable();
 		entity.setId(55L);
 		entity.setResourceType("Observation");
-		entity.setVersion(0L);
+		entity.setVersionForUnitTest(0L);
 
 		testObservationPersist.deleteObservationIndex(entity);
 		elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);

hapi-fhir-jpaserver-ips/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/BaseMdmHelper.java

@@ -20,6 +20,7 @@ import org.mockito.MockitoAnnotations;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.servlet.http.HttpServletRequest;
+import java.util.function.Supplier;
 
 import static org.awaitility.Awaitility.await;
 import static org.mockito.Mockito.when;
@@ -108,4 +109,19 @@ public abstract class BaseMdmHelper implements BeforeEachCallback, AfterEachCall
 	public PointcutLatch getAfterMdmLatch() {
 		return myAfterMdmLatch;
 	}
+
+	/**
+	 * Expect 1 call to the MDM_AFTER_PERSISTED_RESOURCE_CHECKED pointcut when calling theSupplier.  Wait until
+	 * the mdm message arrives and this pointcut is called before returning the result of theSupplier.
+	 * @param theSupplier
+	 * @return
+	 * @param <T>
+	 * @throws InterruptedException
+	 */
+	public <T> T executeWithLatch(Supplier<T> theSupplier) throws InterruptedException {
+		myAfterMdmLatch.setExpectedCount(1);
+		T retval = theSupplier.get();
+		myAfterMdmLatch.awaitExpected();
+		return retval;
+	}
 }

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/MdmHelperR4.java

@@ -1,15 +1,20 @@
 package ca.uhn.fhir.jpa.mdm.helper;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.mdm.api.MdmLinkEvent;
 import ca.uhn.fhir.rest.server.TransactionLogMessages;
+import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
+import ca.uhn.test.concurrency.PointcutLatch;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Patient;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
+import java.util.List;
 
 import static ca.uhn.fhir.mdm.api.MdmConstants.CODE_GOLDEN_RECORD;
 import static ca.uhn.fhir.mdm.api.MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS;
@@ -27,8 +32,8 @@ public class MdmHelperR4 extends BaseMdmHelper {
 	public OutcomeAndLogMessageWrapper createWithLatch(IBaseResource theBaseResource, boolean isExternalHttpRequest) throws InterruptedException {
 		myAfterMdmLatch.setExpectedCount(1);
 		DaoMethodOutcome daoMethodOutcome = doCreateResource(theBaseResource, isExternalHttpRequest);
-		myAfterMdmLatch.awaitExpected();
+		List<HookParams> hookParams = myAfterMdmLatch.awaitExpected();
-		return new OutcomeAndLogMessageWrapper(daoMethodOutcome, myAfterMdmLatch.getLatchInvocationParameterOfType(TransactionLogMessages.class));
+		return new OutcomeAndLogMessageWrapper(daoMethodOutcome, hookParams);
 	}
 
 	public OutcomeAndLogMessageWrapper updateWithLatch(IBaseResource theIBaseResource) throws InterruptedException {
@@ -38,8 +43,8 @@ public class MdmHelperR4 extends BaseMdmHelper {
 	public OutcomeAndLogMessageWrapper updateWithLatch(IBaseResource theIBaseResource, boolean isExternalHttpRequest) throws InterruptedException {
 		myAfterMdmLatch.setExpectedCount(1);
 		DaoMethodOutcome daoMethodOutcome = doUpdateResource(theIBaseResource, isExternalHttpRequest);
-		myAfterMdmLatch.awaitExpected();
+		List<HookParams> hookParams = myAfterMdmLatch.awaitExpected();
-		return new OutcomeAndLogMessageWrapper(daoMethodOutcome, myAfterMdmLatch.getLatchInvocationParameterOfType(TransactionLogMessages.class));
+		return new OutcomeAndLogMessageWrapper(daoMethodOutcome, hookParams);
 	}
 
 	public DaoMethodOutcome doCreateResource(IBaseResource theResource, boolean isExternalHttpRequest) {
@@ -68,12 +73,12 @@ public class MdmHelperR4 extends BaseMdmHelper {
 	 * by the MDM module.
 	 */
 	public class OutcomeAndLogMessageWrapper {
-		DaoMethodOutcome myDaoMethodOutcome;
+		private final DaoMethodOutcome myDaoMethodOutcome;
-		TransactionLogMessages myLogMessages;
+		private final List<HookParams> myHookParams;
 
-		private OutcomeAndLogMessageWrapper(DaoMethodOutcome theDaoMethodOutcome, TransactionLogMessages theTransactionLogMessages) {
+		public OutcomeAndLogMessageWrapper(DaoMethodOutcome theDaoMethodOutcome, List<HookParams> theHookParams) {
 			myDaoMethodOutcome = theDaoMethodOutcome;
-			myLogMessages = theTransactionLogMessages;
+			myHookParams = theHookParams;
 		}
 
 		public DaoMethodOutcome getDaoMethodOutcome() {
@@ -81,7 +86,19 @@ public class MdmHelperR4 extends BaseMdmHelper {
 		}
 
 		public TransactionLogMessages getLogMessages() {
-			return myLogMessages;
+			return PointcutLatch.getInvocationParameterOfType(myHookParams, TransactionLogMessages.class);
+		}
+
+		public List<HookParams> getHookParams() {
+			return myHookParams;
+		}
+
+		public MdmLinkEvent getMdmLinkEvent() {
+			return PointcutLatch.getInvocationParameterOfType(myHookParams, MdmLinkEvent.class);
+		}
+
+		public ResourceOperationMessage getResourceOperationMessage() {
+			return PointcutLatch.getInvocationParameterOfType(myHookParams, ResourceOperationMessage.class);
 		}
 	}
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java

@@ -58,9 +58,9 @@ public class MdmEventIT extends BaseMdmR4Test {
 		addExternalEID(patient2, "eid-11");
 		addExternalEID(patient2, "eid-22");
 
-		myMdmHelper.updateWithLatch(patient2);
+		MdmHelperR4.OutcomeAndLogMessageWrapper outcome = myMdmHelper.updateWithLatch(patient2);
 
-		MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
+		MdmLinkEvent linkChangeEvent = outcome.getMdmLinkEvent();
 		assertNotNull(linkChangeEvent);
 
 		ourLog.info("Got event: {}", linkChangeEvent);
@@ -84,15 +84,15 @@ public class MdmEventIT extends BaseMdmR4Test {
 	@Test
 	public void testCreateLinkChangeEvent() throws InterruptedException {
 		Practitioner pr = buildPractitionerWithNameAndId("Young", "AC-DC");
-		myMdmHelper.createWithLatch(pr);
+		MdmHelperR4.OutcomeAndLogMessageWrapper outcome = myMdmHelper.createWithLatch(pr);
 
-		ResourceOperationMessage resourceOperationMessage = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(ResourceOperationMessage.class);
+		ResourceOperationMessage resourceOperationMessage = outcome.getResourceOperationMessage();
 		assertNotNull(resourceOperationMessage);
 		assertEquals(pr.getIdElement().toUnqualifiedVersionless().getValue(), resourceOperationMessage.getId());
 
 		MdmLink link = getLinkByTargetId(pr);
 
-		MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
+		MdmLinkEvent linkChangeEvent = outcome.getMdmLinkEvent();
 		assertNotNull(linkChangeEvent);
 
 		assertEquals(1, linkChangeEvent.getMdmLinks().size());
@@ -110,9 +110,9 @@ public class MdmEventIT extends BaseMdmR4Test {
 	@Test
 	public void testUpdateLinkChangeEvent() throws InterruptedException {
 		Patient patient1 = addExternalEID(buildJanePatient(), "eid-1");
-		myMdmHelper.createWithLatch(patient1);
+		MdmHelperR4.OutcomeAndLogMessageWrapper outcome = myMdmHelper.createWithLatch(patient1);
 
-		MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
+		MdmLinkEvent linkChangeEvent = outcome.getMdmLinkEvent();
 		assertNotNull(linkChangeEvent);
 		assertEquals(1, linkChangeEvent.getMdmLinks().size());
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSearchExpandingInterceptorIT.java

@@ -257,12 +257,11 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
 	}
 
 	@Test
-	public void testReferenceExpansionQuietlyFailsOnMissingMdmMatches() {
+	public void testReferenceExpansionQuietlyFailsOnMissingMdmMatches() throws InterruptedException {
 		myStorageSettings.setAllowMdmExpansion(true);
 		Patient patient = buildJanePatient();
 		patient.getMeta().addTag(MdmConstants.SYSTEM_MDM_MANAGED, MdmConstants.CODE_NO_MDM_MANAGED, "Don't MDM on me!");
-		DaoMethodOutcome daoMethodOutcome = myMdmHelper.doCreateResource(patient, true);
+		String id = myMdmHelper.executeWithLatch(() -> myMdmHelper.doCreateResource(patient, true)).getId().getIdPart();
-		String id = daoMethodOutcome.getId().getIdPart();
 		createObservationWithSubject(id);
 
 		//Even though the user has NO mdm links, that should not cause a request failure.

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

@@ -32,7 +32,7 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
 	@Autowired
 	private IMdmSubmitSvc myMdmSubmitSvc;
 	@Autowired
-	private MdmSettings myMdmSettings;
+	protected MdmSettings myMdmSettings;
 	@Autowired
 	private MdmControllerHelper myMdmHelper;
 	@Autowired

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderCreateLinkR4Test.java

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.mdm.provider;
 
-import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.entity.PartitionEntity;
 import ca.uhn.fhir.mdm.api.MdmConstants;
@@ -73,6 +73,7 @@ public class MdmProviderCreateLinkR4Test extends BaseLinkR4Test {
 	@Test
 	public void testCreateLinkWithMatchResultOnDifferentPartitions() {
 		myPartitionSettings.setPartitioningEnabled(true);
+		myMdmSettings.setSearchAllPartitionForMatch(false);
 		myPartitionLookupSvc.createPartition(new PartitionEntity().setId(1).setName(PARTITION_1), null);
 		myPartitionLookupSvc.createPartition(new PartitionEntity().setId(2).setName(PARTITION_2), null);
 		assertLinkCount(1);

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderMergeGoldenResourcesR4Test.java

@@ -148,6 +148,7 @@ public class MdmProviderMergeGoldenResourcesR4Test extends BaseProviderR4Test {
 	@Test
 	public void testMergeOnDifferentPartitions() {
 		myPartitionSettings.setPartitioningEnabled(true);
+		myMdmSettings.setSearchAllPartitionForMatch(false);
 		myPartitionLookupSvc.createPartition(new PartitionEntity().setId(1).setName(PARTITION_1), null);
 		RequestPartitionId requestPartitionId1 = RequestPartitionId.fromPartitionId(1);
 		myPartitionLookupSvc.createPartition(new PartitionEntity().setId(2).setName(PARTITION_2), null);

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -153,10 +153,6 @@ public abstract class BaseHasResource extends BasePartitionable implements IBase
 		myUpdated = theUpdated;
 	}
 
-	public void setUpdated(InstantDt theUpdated) {
-		myUpdated = theUpdated.getValue();
-	}
-
 	@Override
 	public abstract long getVersion();
 

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

@@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.model.search.ResourceTableRoutingBinder;
 import ca.uhn.fhir.jpa.model.search.SearchParamTextPropertyBinder;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.Constants;
+import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.Session;
@@ -59,6 +60,7 @@ import javax.persistence.Index;
 import javax.persistence.NamedEntityGraph;
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
+import javax.persistence.PostPersist;
 import javax.persistence.PrePersist;
 import javax.persistence.PreUpdate;
 import javax.persistence.Table;
@@ -67,12 +69,13 @@ import javax.persistence.Version;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-@Indexed(routingBinder= @RoutingBinderRef(type = ResourceTableRoutingBinder.class))
+@Indexed(routingBinder = @RoutingBinderRef(type = ResourceTableRoutingBinder.class))
 @Entity
 @Table(name = ResourceTable.HFJ_RESOURCE, uniqueConstraints = {}, indexes = {
 	// Do not reuse previously used index name: IDX_INDEXSTATUS, IDX_RES_TYPE
@@ -83,23 +86,22 @@ import java.util.stream.Collectors;
 @NamedEntityGraph(name = "Resource.noJoins")
 public class ResourceTable extends BaseHasResource implements Serializable, IBasePersistedResource<JpaPid> {
 	public static final int RESTYPE_LEN = 40;
-	private static final int MAX_LANGUAGE_LENGTH = 20;
-	private static final long serialVersionUID = 1L;
 	public static final String HFJ_RESOURCE = "HFJ_RESOURCE";
 	public static final String RES_TYPE = "RES_TYPE";
-
+	private static final int MAX_LANGUAGE_LENGTH = 20;
+	private static final long serialVersionUID = 1L;
 	/**
 	 * Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
 	 * Note the extra config needed in HS6 for indexing transient props:
 	 * https://docs.jboss.org/hibernate/search/6.0/migration/html_single/#indexed-transient-requires-configuration
-	 *
+	 * <p>
 	 * Note that we depend on `myVersion` updated for this field to be indexed.
 	 */
 	@Transient
 	@FullTextField(name = "myContentText", searchable = Searchable.YES, projectable = Projectable.YES, analyzer = "standardAnalyzer")
-	@FullTextField(name = "myContentTextEdgeNGram", searchable= Searchable.YES, projectable= Projectable.NO, analyzer =  "autocompleteEdgeAnalyzer")
+	@FullTextField(name = "myContentTextEdgeNGram", searchable = Searchable.YES, projectable = Projectable.NO, analyzer = "autocompleteEdgeAnalyzer")
-	@FullTextField(name = "myContentTextNGram", searchable= Searchable.YES, projectable= Projectable.NO, analyzer =  "autocompleteNGramAnalyzer")
+	@FullTextField(name = "myContentTextNGram", searchable = Searchable.YES, projectable = Projectable.NO, analyzer = "autocompleteNGramAnalyzer")
-	@FullTextField(name = "myContentTextPhonetic", searchable= Searchable.YES, projectable= Projectable.NO, analyzer =  "autocompletePhoneticAnalyzer")
+	@FullTextField(name = "myContentTextPhonetic", searchable = Searchable.YES, projectable = Projectable.NO, analyzer = "autocompletePhoneticAnalyzer")
 	@OptimisticLock(excluded = true)
 	@IndexingDependency(derivedFrom = @ObjectPath(@PropertyValue(propertyName = "myVersion")))
 	private String myContentText;
@@ -133,9 +135,9 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	 */
 	@Transient()
 	@FullTextField(name = "myNarrativeText", searchable = Searchable.YES, projectable = Projectable.YES, analyzer = "standardAnalyzer")
-	@FullTextField(name = "myNarrativeTextEdgeNGram", searchable= Searchable.YES, projectable= Projectable.NO, analyzer =  "autocompleteEdgeAnalyzer")
+	@FullTextField(name = "myNarrativeTextEdgeNGram", searchable = Searchable.YES, projectable = Projectable.NO, analyzer = "autocompleteEdgeAnalyzer")
-	@FullTextField(name = "myNarrativeTextNGram", searchable= Searchable.YES, projectable= Projectable.NO, analyzer =  "autocompleteNGramAnalyzer")
+	@FullTextField(name = "myNarrativeTextNGram", searchable = Searchable.YES, projectable = Projectable.NO, analyzer = "autocompleteNGramAnalyzer")
-	@FullTextField(name = "myNarrativeTextPhonetic", searchable= Searchable.YES, projectable= Projectable.NO, analyzer =  "autocompletePhoneticAnalyzer")
+	@FullTextField(name = "myNarrativeTextPhonetic", searchable = Searchable.YES, projectable = Projectable.NO, analyzer = "autocompletePhoneticAnalyzer")
 	@OptimisticLock(excluded = true)
 	@IndexingDependency(derivedFrom = @ObjectPath(@PropertyValue(propertyName = "myVersion")))
 	private String myNarrativeText;
@@ -278,18 +280,17 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	@Transient
 	private transient boolean myUnchangedInCurrentOperation;
 
-
 	/**
 	 * The id of the Resource.
 	 * Will contain either the client-assigned id, or the sequence value.
 	 * Will be null during insert time until the first read.
-	 *
 	 */
-	@Column(name= "FHIR_ID",
+	@Column(name = "FHIR_ID",
 		// [A-Za-z0-9\-\.]{1,64} - https://www.hl7.org/fhir/datatypes.html#id
 		length = 64,
 		// we never update this after insert, and the Generator will otherwise "dirty" the object.
 		updatable = false)
+
 	// inject the pk for server-assigned sequence ids.
 	@GeneratorType(when = GenerationTime.INSERT, type = FhirIdGenerator.class)
 	// Make sure the generator doesn't bump the history version.
@@ -305,30 +306,21 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	@Column(name = "SEARCH_URL_PRESENT", nullable = true)
 	private Boolean mySearchUrlPresent = false;
 
-	/**
-	 * Populate myFhirId with server-assigned sequence id when no client-id provided.
-	 * We eat this complexity during insert to simplify query time with a uniform column.
-	 * Server-assigned sequence ids aren't available until just before insertion.
-	 * Hibernate calls insert Generators after the pk has been assigned, so we can use myId safely here.
-	 */
-	public static final class FhirIdGenerator implements ValueGenerator<String> {
-		@Override
-		public String generateValue(Session session, Object owner) {
-			ResourceTable that = (ResourceTable) owner;
-			return that.myFhirId != null ? that.myFhirId : that.myId.toString();
-		}
-	}
-
 	@Version
 	@Column(name = "RES_VER")
 	private long myVersion;
-
 	@OneToMany(mappedBy = "myResourceTable", fetch = FetchType.LAZY)
 	private Collection<ResourceHistoryProvenanceEntity> myProvenance;
 
 	@Transient
 	private transient ResourceHistoryTable myCurrentVersionEntity;
 
+	@Transient
+	private transient ResourceHistoryTable myNewVersionEntity;
+
+	@Transient
+	private transient boolean myVersionUpdatedInCurrentTransaction;
+
 	@OneToOne(optional = true, fetch = FetchType.EAGER, cascade = {}, orphanRemoval = false, mappedBy = "myResource")
 	@OptimisticLock(excluded = true)
 	private ForcedId myForcedId;
@@ -343,6 +335,39 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		super();
 	}
 
+	/**
+	 * Setting this flag is an indication that we're making changes and the version number will
+	 * be incremented in the current transaction. When this is set, calls to {@link #getVersion()}
+	 * will be incremented by one.
+	 * This flag is cleared in {@link #postPersist()} since at that time the new version number
+	 * should be reflected.
+	 */
+	public void markVersionUpdatedInCurrentTransaction() {
+		if (!myVersionUpdatedInCurrentTransaction) {
+			/*
+			 * Note that modifying this number doesn't actually directly affect what
+			 * gets stored in the database since this is a @Version field and the
+			 * value is therefore managed by Hibernate. So in other words, if the
+			 * row in the database is updated, it doesn't matter what we set
+			 * this field to, hibernate will increment it by one. However, we still
+			 * increment it for two reasons:
+			 * 1. The value gets used for the version attribute in the ResourceHistoryTable
+			 *    entity we create for each new version.
+			 * 2. For updates to existing resources, there may actually not be any other
+			 *    changes to this entity so incrementing this is a signal to
+			 *    Hibernate that something changed and we need to force an entity
+			 *    update.
+			 */
+			myVersion++;
+			this.myVersionUpdatedInCurrentTransaction = true;
+		}
+	}
+
+	@PostPersist
+	public void postPersist() {
+		myVersionUpdatedInCurrentTransaction = false;
+	}
+
 	@Override
 	public ResourceTag addTag(TagDefinition theTag) {
 		for (ResourceTag next : getTags()) {
@@ -355,7 +380,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		return tag;
 	}
 
-
 	public String getHashSha256() {
 		return myHashSha256;
 	}
@@ -558,6 +582,26 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		return myVersion;
 	}
 
+	/**
+	 * Sets the version on this entity to {@literal 1}. This should only be called
+	 * on resources that are not yet persisted. After that time the version number
+	 * is managed by hibernate.
+	 */
+	public void initializeVersion() {
+		assert myId == null;
+		myVersion = 1;
+	}
+
+	/**
+	 * Don't call this in any JPA environments, the version will be ignored
+	 * since this field is managed by hibernate
+	 */
+	@VisibleForTesting
+	public void setVersionForUnitTest(long theVersion) {
+		myVersion = theVersion;
+	}
+
+
 	@Override
 	public boolean isDeleted() {
 		return getDeleted() != null;
@@ -568,10 +612,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		setDeleted(null);
 	}
 
-	public void setVersion(long theVersion) {
-		myVersion = theVersion;
-	}
-
 	public boolean isHasLinks() {
 		return myHasLinks;
 	}
@@ -580,6 +620,23 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		myHasLinks = theHasLinks;
 	}
 
+	/**
+	 * Clears all the index population flags, e.g. {@link #isParamsStringPopulated()}
+	 *
+	 * @since 6.8.0
+	 */
+	public void clearAllParamsPopulated() {
+		myParamsTokenPopulated = false;
+		myParamsCoordsPopulated = false;
+		myParamsDatePopulated = false;
+		myParamsNumberPopulated = false;
+		myParamsStringPopulated = false;
+		myParamsQuantityPopulated = false;
+		myParamsQuantityNormalizedPopulated = false;
+		myParamsUriPopulated = false;
+		myHasLinks = false;
+	}
+
 	public boolean isParamsComboStringUniquePresent() {
 		if (myParamsComboStringUniquePresent == null) {
 			return false;
@@ -689,14 +746,14 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		myUnchangedInCurrentOperation = theUnchangedInCurrentOperation;
 	}
 
-	public void setContentText(String theContentText) {
-		myContentText = theContentText;
-	}
-
 	public String getContentText() {
 		return myContentText;
 	}
 
+	public void setContentText(String theContentText) {
+		myContentText = theContentText;
+	}
+
 	public void setNarrativeText(String theNarrativeText) {
 		myNarrativeText = theNarrativeText;
 	}
@@ -709,12 +766,27 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		mySearchUrlPresent = theSearchUrlPresent;
 	}
 
+	/**
+	 * This method creates a new history entity, or might reuse the current one if we've
+	 * already created one in the current transaction. This is because we can only increment
+	 * the version once in a DB transaction (since hibernate manages that number) so creating
+	 * multiple {@link ResourceHistoryTable} entities will result in a constraint error.
+	 */
 	public ResourceHistoryTable toHistory(boolean theCreateVersionTags) {
-		ResourceHistoryTable retVal = new ResourceHistoryTable();
+		boolean createVersionTags = theCreateVersionTags;
+
+		ResourceHistoryTable retVal = myNewVersionEntity;
+		if (retVal == null) {
+			retVal = new ResourceHistoryTable();
+			myNewVersionEntity = retVal;
+		} else {
+			// Tags should already be set
+			createVersionTags = false;
+		}
 
 		retVal.setResourceId(myId);
 		retVal.setResourceType(myResourceType);
-		retVal.setVersion(myVersion);
+		retVal.setVersion(getVersion());
 		retVal.setTransientForcedId(getTransientForcedId());
 
 		retVal.setPublished(getPublishedDate());
@@ -725,10 +797,8 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		retVal.setForcedId(getForcedId());
 		retVal.setPartitionId(getPartitionId());
 
-		retVal.getTags().clear();
-
 		retVal.setHasTags(isHasTags());
-		if (isHasTags() && theCreateVersionTags) {
+		if (isHasTags() && createVersionTags) {
 			for (ResourceTag next : getTags()) {
 				retVal.addTag(next);
 			}
@@ -772,16 +842,16 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	 * This is a convenience to avoid loading the version a second time within a single transaction. It is
 	 * not persisted.
 	 */
-	public void setCurrentVersionEntity(ResourceHistoryTable theCurrentVersionEntity) {
+	public ResourceHistoryTable getCurrentVersionEntity() {
-		myCurrentVersionEntity = theCurrentVersionEntity;
+		return myCurrentVersionEntity;
 	}
 
 	/**
 	 * This is a convenience to avoid loading the version a second time within a single transaction. It is
 	 * not persisted.
 	 */
-	public ResourceHistoryTable getCurrentVersionEntity() {
+	public void setCurrentVersionEntity(ResourceHistoryTable theCurrentVersionEntity) {
-		return myCurrentVersionEntity;
+		myCurrentVersionEntity = theCurrentVersionEntity;
 	}
 
 	@Override
@@ -799,8 +869,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		myForcedId = theForcedId;
 	}
 
-
-
 	@Override
 	public IdDt getIdDt() {
 		IdDt retVal = new IdDt();
@@ -808,7 +876,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		return retVal;
 	}
 
-
 	public IIdType getIdType(FhirContext theContext) {
 		IIdType retVal = theContext.getVersion().newIdType();
 		populateId(retVal);
@@ -830,14 +897,14 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		}
 	}
 
-	public void setCreatedByMatchUrl(String theCreatedByMatchUrl) {
-		myCreatedByMatchUrl = theCreatedByMatchUrl;
-	}
-
 	public String getCreatedByMatchUrl() {
 		return myCreatedByMatchUrl;
 	}
 
+	public void setCreatedByMatchUrl(String theCreatedByMatchUrl) {
+		myCreatedByMatchUrl = theCreatedByMatchUrl;
+	}
+
 	public void setLuceneIndexData(ExtendedHSearchIndexData theLuceneIndexData) {
 		myLuceneIndexData = theLuceneIndexData;
 	}
@@ -862,4 +929,18 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	public void setFhirId(String theFhirId) {
 		myFhirId = theFhirId;
 	}
+
+	/**
+	 * Populate myFhirId with server-assigned sequence id when no client-id provided.
+	 * We eat this complexity during insert to simplify query time with a uniform column.
+	 * Server-assigned sequence ids aren't available until just before insertion.
+	 * Hibernate calls insert Generators after the pk has been assigned, so we can use myId safely here.
+	 */
+	public static final class FhirIdGenerator implements ValueGenerator<String> {
+		@Override
+		public String generateValue(Session session, Object owner) {
+			ResourceTable that = (ResourceTable) owner;
+			return that.myFhirId != null ? that.myFhirId : that.myId.toString();
+		}
+	}
 }

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -224,6 +224,9 @@ public class SearchParamExtractorService {
 
 			@Override
 			public IBaseResource fetchResourceAtPath(@Nonnull PathAndRef thePathAndRef) {
+				if (thePathAndRef.getRef() == null) {
+					return null;
+				}
 				return findContainedResource(containedResources, thePathAndRef.getRef());
 			}
 		};

hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParamRegistryImplTest.java

@@ -94,7 +94,7 @@ public class SearchParamRegistryImplTest {
 		ResourceTable searchParamEntity = new ResourceTable();
 		searchParamEntity.setResourceType("SearchParameter");
 		searchParamEntity.setId(theId);
-		searchParamEntity.setVersion(theVersion);
+		searchParamEntity.setVersionForUnitTest(theVersion);
 		return searchParamEntity;
 	}
 
@@ -199,7 +199,7 @@ public class SearchParamRegistryImplTest {
 
 		// Update the resource without changing anything that would affect our cache
 		ResourceTable lastEntity = newEntities.get(newEntities.size() - 1);
-		lastEntity.setVersion(2);
+		lastEntity.setVersionForUnitTest(2);
 		resetMock(Enumerations.PublicationStatus.ACTIVE, newEntities);
 		mySearchParamRegistry.requestRefresh();
 		assertResult(mySearchParamRegistry.refreshCacheIfNecessary(), 0, 1, 0);

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/channel/subscription/SubscriptionChannelCache.java

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.jpa.subscription.channel.subscription;
 
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
+import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -60,6 +61,7 @@ class SubscriptionChannelCache {
 		return myCache.containsKey(theChannelName);
 	}
 
+	@VisibleForTesting
 	void logForUnitTest() {
 		for (String key : myCache.keySet()) {
 			ourLog.info("SubscriptionChannelCache: {}", key);

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/channel/subscription/SubscriptionChannelRegistry.java

@@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.subscription.channel.models.ReceivingChannelParameters;
 import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.subscription.model.ChannelRetryConfiguration;
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.MultimapBuilder;
 import org.slf4j.Logger;
@@ -147,4 +148,9 @@ public class SubscriptionChannelRegistry {
 	public synchronized int size() {
 		return myDeliveryReceiverChannels.size();
 	}
+
+	@VisibleForTesting
+	public void logForUnitTest() {
+		myDeliveryReceiverChannels.logForUnitTest();
+	}
 }

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

@@ -29,7 +29,6 @@ import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
@@ -93,17 +92,15 @@ public class SubscriptionRegisteringSubscriber implements MessageHandler {
 		// - in order to store partition id in the userdata of the resource for partitioned subscriptions
 		// - in case we're processing out of order and a create-then-delete has been processed backwards (or vice versa)
 
-		IBaseResource payloadResource;
 		IIdType payloadId = payload.getPayloadId(myFhirContext).toUnqualifiedVersionless();
-		try {
 		IFhirResourceDao<?> subscriptionDao = myDaoRegistry.getResourceDao("Subscription");
 		RequestDetails systemRequestDetails = getPartitionAwareRequestDetails(payload);
-			payloadResource = subscriptionDao.read(payloadId, systemRequestDetails);
+		IBaseResource payloadResource = subscriptionDao.read(payloadId, systemRequestDetails, true);
 		if (payloadResource == null) {
 			// Only for unit test
 			payloadResource = payload.getPayload(myFhirContext);
 		}
-		} catch (ResourceGoneException e) {
+		if (payloadResource.isDeleted()) {
 			mySubscriptionRegistry.unregisterSubscriptionIfRegistered(payloadId.getIdPart());
 			return;
 		}

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicCanonicalizer.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.topic;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.Msg;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
 
@@ -31,11 +32,10 @@ public final class SubscriptionTopicCanonicalizer {
 	}
 
 	// WIP STR5 use elsewhere
-	public static SubscriptionTopic canonicalize(FhirContext theFhirContext, IBaseResource theSubscriptionTopic) {
+	public static SubscriptionTopic canonicalizeTopic(FhirContext theFhirContext, IBaseResource theSubscriptionTopic) {
 		switch (theFhirContext.getVersion().getVersion()) {
 			case R4B:
-				String encoded = theFhirContext.newJsonParser().encodeResourceToString(theSubscriptionTopic);
+			return (SubscriptionTopic) VersionConvertorFactory_43_50.convertResource((org.hl7.fhir.r4b.model.SubscriptionTopic) theSubscriptionTopic);
-				return ourFhirContextR5.newJsonParser().parseResource(SubscriptionTopic.class, encoded);
 			case R5:
 				return (SubscriptionTopic) theSubscriptionTopic;
 			default:

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicLoader.java

@@ -26,11 +26,11 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionConstants;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.util.Logs;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.Enumerations;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -40,7 +40,7 @@ import java.util.Set;
 
 
 public class SubscriptionTopicLoader extends BaseResourceCacheSynchronizer {
-	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionTopicLoader.class);
+	private static final Logger ourLog = Logs.getSubscriptionTopicLog();
 
 	@Autowired
 	private FhirContext myFhirContext;
@@ -107,10 +107,7 @@ public class SubscriptionTopicLoader extends BaseResourceCacheSynchronizer {
 		if (theResource instanceof SubscriptionTopic) {
 			return (SubscriptionTopic) theResource;
 		} else if (theResource instanceof org.hl7.fhir.r4b.model.SubscriptionTopic) {
-			return myFhirContext.newJsonParser().parseResource(SubscriptionTopic.class, FhirContext.forR4BCached().newJsonParser().encodeResourceToString(theResource));
+			return SubscriptionTopicCanonicalizer.canonicalizeTopic(myFhirContext, theResource);
-			// WIP STR5 VersionConvertorFactory_43_50 when it supports SubscriptionTopic
-			// track here: https://github.com/hapifhir/org.hl7.fhir.core/issues/1212
-//			return (SubscriptionTopic) VersionConvertorFactory_43_50.convertResource((org.hl7.fhir.r4b.model.SubscriptionTopic) theResource);
 		} else {
 			throw new IllegalArgumentException(Msg.code(2332) + "Only R4B and R5 SubscriptionTopic is currently supported.  Found " + theResource.getClass());
 		}

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicMatchingSubscriber.java

@@ -29,11 +29,11 @@ import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
+import ca.uhn.fhir.util.Logs;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.messaging.Message;
 import org.springframework.messaging.MessageHandler;
@@ -45,7 +45,7 @@ import java.util.List;
 import java.util.UUID;
 
 public class SubscriptionTopicMatchingSubscriber implements MessageHandler {
-	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionTopicMatchingSubscriber.class);
+	private static final Logger ourLog = Logs.getSubscriptionTopicLog();
 
 	private final FhirContext myFhirContext;
 	@Autowired

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicPayloadBuilder.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
 import ca.uhn.fhir.util.BundleBuilder;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.Bundle;
@@ -55,11 +56,7 @@ public class SubscriptionTopicPayloadBuilder {
 
 		if (fhirVersion == FhirVersionEnum.R4B) {
 			bundleBuilder.setType(Bundle.BundleType.HISTORY.toCode());
-			String serializedSubscriptionStatus = FhirContext.forR5Cached().newJsonParser().encodeResourceToString(subscriptionStatus);
+			subscriptionStatus = VersionConvertorFactory_43_50.convertResource((org.hl7.fhir.r5.model.SubscriptionStatus) subscriptionStatus);
-			subscriptionStatus = myFhirContext.newJsonParser().parseResource(org.hl7.fhir.r4b.model.SubscriptionStatus.class, serializedSubscriptionStatus);
-			// WIP STR5 VersionConvertorFactory_43_50 when it supports SubscriptionStatus
-			// track here: https://github.com/hapifhir/org.hl7.fhir.core/issues/1212
-//			subscriptionStatus = (SubscriptionStatus) VersionConvertorFactory_43_50.convertResource((org.hl7.fhir.r4b.model.SubscriptionStatus) subscriptionStatus);
 		} else if (fhirVersion == FhirVersionEnum.R5) {
 			bundleBuilder.setType(Bundle.BundleType.SUBSCRIPTIONNOTIFICATION.toCode());
 		} else {

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicRegisteringSubscriber.java

@@ -28,12 +28,12 @@ import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.util.Logs;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r5.model.Enumerations;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.messaging.Message;
 import org.springframework.messaging.MessageHandler;
@@ -48,7 +48,8 @@ import javax.annotation.Nonnull;
  * Also validates criteria.  If invalid, rejects the subscription without persisting the subscription.
  */
 public class SubscriptionTopicRegisteringSubscriber implements MessageHandler {
-	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionTopicRegisteringSubscriber.class);
+	private static final Logger ourLog = Logs.getSubscriptionTopicLog();
+
 	@Autowired
 	private FhirContext myFhirContext;
 	@Autowired
@@ -106,7 +107,7 @@ public class SubscriptionTopicRegisteringSubscriber implements MessageHandler {
 			return;
 		}
 
-		SubscriptionTopic subscriptionTopic = SubscriptionTopicCanonicalizer.canonicalize(myFhirContext, payloadResource);
+		SubscriptionTopic subscriptionTopic = SubscriptionTopicCanonicalizer.canonicalizeTopic(myFhirContext, payloadResource);
 		if (subscriptionTopic.getStatus() == Enumerations.PublicationStatus.ACTIVE) {
 			mySubscriptionTopicRegistry.register(subscriptionTopic);
 		} else {

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicValidatingInterceptor.java

@@ -30,14 +30,15 @@ import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.Logs;
 import com.google.common.annotations.VisibleForTesting;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 public class SubscriptionTopicValidatingInterceptor {
-	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionTopicValidatingInterceptor.class);
+	private static final Logger ourLog = Logs.getSubscriptionTopicLog();
+
 	private final FhirContext myFhirContext;
 	private final SubscriptionQueryValidator mySubscriptionQueryValidator;
 
@@ -69,7 +70,7 @@ public class SubscriptionTopicValidatingInterceptor {
 			return;
 		}
 
-		SubscriptionTopic subscriptionTopic = SubscriptionTopicCanonicalizer.canonicalize(myFhirContext, theSubscription);
+		SubscriptionTopic subscriptionTopic = SubscriptionTopicCanonicalizer.canonicalizeTopic(myFhirContext, theSubscription);
 
 		boolean finished = false;
 		if (subscriptionTopic.getStatus() == null) {

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTriggerMatcher.java

@@ -24,17 +24,18 @@ import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryMatchResult;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.server.messaging.BaseResourceMessage;
+import ca.uhn.fhir.util.Logs;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r5.model.Enumeration;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import java.util.List;
 
 public class SubscriptionTriggerMatcher {
-	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionTriggerMatcher.class);
+	private static final Logger ourLog = Logs.getSubscriptionTopicLog();
+
 	private final SubscriptionTopicSupport mySubscriptionTopicSupport;
 	private final BaseResourceMessage.OperationTypeEnum myOperation;
 	private final SubscriptionTopic.SubscriptionTopicResourceTriggerComponent myTrigger;

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionRegisteringSubscriberTest.java

@@ -4,17 +4,19 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
-import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.server.messaging.BaseResourceMessage;
 import ca.uhn.fhir.rest.server.messaging.json.ResourceOperationJsonMessage;
+import org.hl7.fhir.r4.model.InstantType;
 import org.hl7.fhir.r4.model.Subscription;
 import org.hl7.fhir.r4.model.codesystems.SubscriptionStatus;
+import org.jetbrains.annotations.NotNull;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -34,6 +36,7 @@ import java.util.List;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.never;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
@@ -46,8 +49,8 @@ public class SubscriptionRegisteringSubscriberTest {
 	private FhirContext myFhirContext = FhirContext.forR4Cached();
 	@Mock
 	private SubscriptionRegistry mySubscriptionRegistry;
-	@Mock
+	@Spy
-	private SubscriptionCanonicalizer mySubscriptionCanonicalizer;
+	private SubscriptionCanonicalizer mySubscriptionCanonicalizer = new SubscriptionCanonicalizer(myFhirContext);
 	@Mock
 	private DaoRegistry myDaoRegistry;
 	@Mock
@@ -61,8 +64,15 @@ public class SubscriptionRegisteringSubscriberTest {
 
 	@BeforeEach
 	public void beforeEach() {
-		mySubscription = new Subscription();
+		mySubscription = buildSubscription();
-		mySubscription.setId("Subscription/testrest");
+	}
+
+	@NotNull
+	private static Subscription buildSubscription() {
+		Subscription subscription = new Subscription();
+		subscription.setId("Subscription/testrest");
+		subscription.setStatus(Subscription.SubscriptionStatus.ACTIVE);
+		return subscription;
 	}
 
 	@Test
@@ -79,7 +89,9 @@ public class SubscriptionRegisteringSubscriberTest {
 		ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(resourceModifiedMessage);
 
 		when(myDaoRegistry.getResourceDao("Subscription")).thenReturn(mySubscriptionDao);
-		when(mySubscriptionDao.read(any(), any())).thenThrow(ResourceGoneException.class);
+		Subscription deletedSubscription = buildSubscription();
+		ResourceMetadataKeyEnum.DELETED_AT.put(deletedSubscription, InstantType.withCurrentTime());
+		when(mySubscriptionDao.read(any(), any(), eq(true))).thenReturn(deletedSubscription);
 
 		mySubscriptionRegisteringSubscriber.handleMessage(message);
 		verify(mySubscriptionRegistry, times(1)).unregisterSubscriptionIfRegistered(any());
@@ -92,7 +104,7 @@ public class SubscriptionRegisteringSubscriberTest {
 		ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(resourceModifiedMessage);
 
 		when(myDaoRegistry.getResourceDao("Subscription")).thenReturn(mySubscriptionDao);
-		when(mySubscriptionDao.read(any(), any())).thenReturn(mySubscription);
+		when(mySubscriptionDao.read(any(), any(), eq(true))).thenReturn(mySubscription);
 		when(mySubscriptionCanonicalizer.getSubscriptionStatus(mySubscription)).thenReturn(SubscriptionStatus.ACTIVE.toCode());
 
 		mySubscriptionRegisteringSubscriber.handleMessage(message);
@@ -106,7 +118,7 @@ public class SubscriptionRegisteringSubscriberTest {
 		ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(resourceModifiedMessage);
 
 		when(myDaoRegistry.getResourceDao("Subscription")).thenReturn(mySubscriptionDao);
-		when(mySubscriptionDao.read(any(), any())).thenReturn(mySubscription);
+		when(mySubscriptionDao.read(any(), any(), eq(true))).thenReturn(mySubscription);
 		when(mySubscriptionCanonicalizer.getSubscriptionStatus(mySubscription)).thenReturn(SubscriptionStatus.ERROR.toCode());
 
 		mySubscriptionRegisteringSubscriber.handleMessage(message);
@@ -126,7 +138,7 @@ public class SubscriptionRegisteringSubscriberTest {
 		ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(resourceModifiedMessage);
 
 		when(myDaoRegistry.getResourceDao("Subscription")).thenReturn(mySubscriptionDao);
-		when(mySubscriptionDao.read(any(), requestDetailsCaptor.capture())).thenReturn(mySubscription);
+		when(mySubscriptionDao.read(any(), requestDetailsCaptor.capture(), eq(true))).thenReturn(mySubscription);
 		when(mySubscriptionCanonicalizer.getSubscriptionStatus(mySubscription)).thenReturn(SubscriptionStatus.ACTIVE.toCode());
 
 		mySubscriptionRegisteringSubscriber.handleMessage(message);
@@ -147,7 +159,7 @@ public class SubscriptionRegisteringSubscriberTest {
 		ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(resourceModifiedMessage);
 
 		when(myDaoRegistry.getResourceDao("Subscription")).thenReturn(mySubscriptionDao);
-		when(mySubscriptionDao.read(any(), requestDetailsCaptor.capture())).thenReturn(mySubscription);
+		when(mySubscriptionDao.read(any(), requestDetailsCaptor.capture(), eq(true))).thenReturn(mySubscription);
 		when(mySubscriptionCanonicalizer.getSubscriptionStatus(mySubscription)).thenReturn(SubscriptionStatus.ACTIVE.toCode());
 
 		mySubscriptionRegisteringSubscriber.handleMessage(message);

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/BaseSubscriptionTest.java

@@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.subscription.channel.subscription.IChannelNamer;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelFactory;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.module.config.MockFhirClientSearchParamProvider;
+import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.system.HapiSystemProperties;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -35,6 +36,7 @@ import static org.mockito.Mockito.mock;
 	BaseSubscriptionTest.MyConfig.class
 })
 public abstract class BaseSubscriptionTest {
+	private static final SubscriptionDebugLogInterceptor ourSubscriptionDebugLogInterceptor = new SubscriptionDebugLogInterceptor();
 
 	static {
 		HapiSystemProperties.enableUnitTestMode();
@@ -52,11 +54,13 @@ public abstract class BaseSubscriptionTest {
 	@BeforeEach
 	public void before() {
 		mySearchParamRegistry.handleInit(Collections.emptyList());
+		myInterceptorRegistry.registerInterceptor(ourSubscriptionDebugLogInterceptor);
 	}
 
 	@AfterEach
 	public void afterClearAnonymousLambdas() {
 		myInterceptorRegistry.unregisterAllInterceptors();
+		myInterceptorRegistry.unregisterInterceptor(ourSubscriptionDebugLogInterceptor);
 	}
 
 	public void initSearchParamRegistry(IBaseResource theReadResource) {
@@ -68,7 +72,7 @@ public abstract class BaseSubscriptionTest {
 	public static class MyConfig {
 
 		@Bean
-		public JpaStorageSettings storageSettings() {
+		public JpaStorageSettings jpaStorageSettings() {
 			return new JpaStorageSettings();
 		}
 

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/config/TestSubscriptionConfig.java

@@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.subscription.module.config;
 import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
 import ca.uhn.fhir.jpa.cache.ResourceVersionMap;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
-import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.InMemorySubscriptionMatcher;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import org.springframework.context.annotation.Bean;
@@ -25,11 +24,6 @@ public class TestSubscriptionConfig {
 		return new PartitionSettings();
 	}
 
-	@Bean
-	public StorageSettings storageSettings() {
-		return new StorageSettings();
-	}
-
 	@Bean
 	public IGenericClient fhirClient() {
 		return mock(IGenericClient.class);

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/standalone/BaseBlockingQueueSubscribableChannelDstu3Test.java

@@ -11,7 +11,6 @@ import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.channel.api.ChannelConsumerSettings;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.ISubscriptionDeliveryChannelNamer;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelFactory;
-import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionLoader;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
@@ -100,8 +99,6 @@ public abstract class BaseBlockingQueueSubscribableChannelDstu3Test extends Base
 	@Autowired
 	IInterceptorService myInterceptorRegistry;
 	@Autowired
-	private SubscriptionLoader mySubscriptionLoader;
-	@Autowired
 	private ISubscriptionDeliveryChannelNamer mySubscriptionDeliveryChannelNamer;
 
 	@BeforeEach
@@ -131,6 +128,8 @@ public abstract class BaseBlockingQueueSubscribableChannelDstu3Test extends Base
 		mySubscriptionMatchingPost.clear();
 		mySubscriptionActivatedPost.clear();
 		ourObservationListener.clear();
+		mySubscriptionResourceMatched.clear();
+		mySubscriptionResourceNotMatched.clear();
 		super.clearRegistry();
 	}
 
@@ -148,9 +147,11 @@ public abstract class BaseBlockingQueueSubscribableChannelDstu3Test extends Base
 	}
 
 	protected Subscription sendSubscription(Subscription theSubscription, RequestPartitionId theRequestPartitionId, Boolean mockDao) throws InterruptedException {
+		mySubscriptionResourceNotMatched.setExpectedCount(1);
 		mySubscriptionActivatedPost.setExpectedCount(1);
 		Subscription retVal = sendResource(theSubscription, theRequestPartitionId);
 		mySubscriptionActivatedPost.awaitExpected();
+		mySubscriptionResourceNotMatched.awaitExpected();
 		return retVal;
 	}
 

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

@@ -35,7 +35,9 @@ public class SubscriptionCheckingSubscriberTest extends BaseBlockingQueueSubscri
 		assertEquals(2, mySubscriptionRegistry.size());
 
 		ourObservationListener.setExpectedCount(1);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(1, ourContentTypes.size());
@@ -58,7 +60,9 @@ public class SubscriptionCheckingSubscriberTest extends BaseBlockingQueueSubscri
 		assertEquals(2, mySubscriptionRegistry.size());
 
 		ourObservationListener.setExpectedCount(1);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(1, ourContentTypes.size());
@@ -82,7 +86,9 @@ public class SubscriptionCheckingSubscriberTest extends BaseBlockingQueueSubscri
 
 		mySubscriptionAfterDelivery.setExpectedCount(1);
 		ourObservationListener.setExpectedCount(0);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.clear();
 		mySubscriptionAfterDelivery.awaitExpected();
 
@@ -120,7 +126,9 @@ public class SubscriptionCheckingSubscriberTest extends BaseBlockingQueueSubscri
 
 		observation.setStatus(Observation.ObservationStatus.FINAL);
 
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendResource(observation);
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(1, ourContentTypes.size());

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

@@ -76,7 +76,9 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		assertEquals(2, mySubscriptionRegistry.size());
 
 		ourObservationListener.setExpectedCount(1);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(1, ourContentTypes.size());
@@ -99,7 +101,9 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		assertEquals(2, mySubscriptionRegistry.size());
 
 		ourObservationListener.setExpectedCount(1);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(1, ourContentTypes.size());
@@ -117,7 +121,9 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 
 		assertEquals(1, mySubscriptionRegistry.size());
 		ourObservationListener.setExpectedCount(1);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendResource(observation);
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(1, ourContentTypes.size());
@@ -141,7 +147,9 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 
 		mySubscriptionAfterDelivery.setExpectedCount(1);
 		ourObservationListener.setExpectedCount(0);
+		mySubscriptionResourceMatched.setExpectedCount(1);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.clear();
 		mySubscriptionAfterDelivery.awaitExpected();
 
@@ -168,7 +176,9 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		assertEquals(3, mySubscriptionRegistry.size());
 
 		ourObservationListener.setExpectedCount(2);
+		mySubscriptionResourceMatched.setExpectedCount(2);
 		sendObservation(code, "SNOMED-CT");
+		mySubscriptionResourceMatched.awaitExpected();
 		ourObservationListener.awaitExpected();
 
 		assertEquals(2, ourContentTypes.size());
@@ -401,7 +411,7 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		Subscription modifiedSubscription = subscription.copy();
 		// the original partition info was the request info, but we need the actual storage partition.
 		modifiedSubscription.setUserData(Constants.RESOURCE_PARTITION_ID, theRequestPartitionId);
-		when(myMockSubscriptionDao.read(eq(subscription.getIdElement()), any())).thenReturn(modifiedSubscription);
+		when(myMockSubscriptionDao.read(eq(subscription.getIdElement()), any(), eq(true))).thenReturn(modifiedSubscription);
 	}
 
 	@Nested

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicCanonicalizerTest.java

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.jpa.topic;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.r4b.model.Enumerations;
+import org.hl7.fhir.r4b.model.SubscriptionTopic;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+class SubscriptionTopicCanonicalizerTest {
+	@Test
+	public void testCanonicalizeTopic() {
+		SubscriptionTopic topic = new SubscriptionTopic();
+		topic.setId("123");
+		topic.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		org.hl7.fhir.r5.model.SubscriptionTopic canonicalized = SubscriptionTopicCanonicalizer.canonicalizeTopic(FhirContext.forR4BCached(), topic);
+		assertEquals("123", canonicalized.getId());
+		assertEquals(org.hl7.fhir.r5.model.Enumerations.PublicationStatus.ACTIVE, canonicalized.getStatus());
+	}
+}

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -104,7 +104,6 @@ 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.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
@@ -693,7 +692,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		IBundleProvider history = myPatientDao.history(null, null, null, mySrd);
 		assertEquals(4 + initialHistory, history.sizeOrThrowNpe());
 		List<IBaseResource> resources = history.getResources(0, 4);
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) resources.get(0)));
+		assertTrue(resources.get(0).isDeleted());
 
 		try {
 			myPatientDao.delete(id2, mySrd);
@@ -796,10 +795,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		IBundleProvider history = myPatientDao.history(id, null, null, null, mySrd);
 		assertEquals(2, history.size().intValue());
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)));
+		assertTrue(history.getResources(0, 1).get(0).isDeleted());
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)).getValue());
+		assertFalse(history.getResources(1, 2).get(0).isDeleted());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 2).get(0)));
-
 	}
 
 	@Test
@@ -1206,13 +1203,13 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertEquals(id.withVersion("2"), entries.get(1).getIdElement());
 		assertEquals(id.withVersion("1"), entries.get(2).getIdElement());
 
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) entries.get(0)));
+		assertFalse(entries.get(0).isDeleted());
 		assertEquals(BundleEntryTransactionMethodEnum.PUT, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get((IResource) entries.get(0)));
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) entries.get(1)));
+		assertTrue(entries.get(1).isDeleted());
 		assertEquals(BundleEntryTransactionMethodEnum.DELETE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get((IResource) entries.get(1)));
 
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) entries.get(2)));
+		assertFalse(entries.get(2).isDeleted());
 		assertEquals(BundleEntryTransactionMethodEnum.POST, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get((IResource) entries.get(2)));
 	}
 

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -5,7 +5,6 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
@@ -63,6 +62,7 @@ import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.jupiter.api.Assertions.assertArrayEquals;
 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.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
@@ -739,10 +739,8 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		IBundleProvider history = myPatientDao.history(id, null, null, null, mySrd);
 		assertEquals(2, history.size().intValue());
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)));
+		assertTrue(history.getResources(0, 1).get(0).isDeleted());
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)).getValue());
+		assertFalse(history.getResources(1, 2).get(0).isDeleted());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 2).get(0)));
-
 	}
 
 	@Test

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.7.0-SNAPSHOT</version>
+		<version>6.7.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>