Server fixes from Connectathon 32 (#4838)

* NPM test cleanup

* fix imports

* Ongoing cleanup

* Rework memory queue

* Reindex cleanup

* Cleanup

* Clean up

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Test fix

azure-pipelines.yml

@@ -70,8 +70,8 @@ stages:
                   #                  Put to top, but kept in order here
                   #                  -  name: hapi_fhir_jpaserver_test_utilities
                   #                     module: hapi-fhir-jpaserver-test-utilities
-#                  -  name: hapi_fhir_jpaserver_uhnfhirtest
+                  -  name: hapi_fhir_jpaserver_uhnfhirtest
-#                     module: hapi-fhir-jpaserver-uhnfhirtest
+                     module: hapi-fhir-jpaserver-uhnfhirtest
                   -  name: hapi_fhir_server
                      module: hapi-fhir-server
                   -  name: hapi_fhir_server_mdm
@@ -129,8 +129,8 @@ stages:
                      module: hapi-tinder-plugin
                   -  name: hapi_tinder_test
                      module: hapi-tinder-test
-#                  -  name: tests_hapi_fhir_base_test_jaxrsserver_kotlin
+                  -  name: tests_hapi_fhir_base_test_jaxrsserver_kotlin
-#                     module: tests/hapi-fhir-base-test-jaxrsserver-kotlin
+                     module: tests/hapi-fhir-base-test-jaxrsserver-kotlin
                   -  name: tests_hapi_fhir_base_test_mindeps_client
                      module: tests/hapi-fhir-base-test-mindeps-client
                   -  name: tests_hapi_fhir_base_test_mindeps_server

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/DateRangeUtil.java

@@ -29,9 +29,10 @@ 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.
+	 * @param theEndExclusive   an upper bound to apply, or null for unchanged.
 	 * @return a DateRange within the original range, and between theStartInclusive and theEnd
 	 */
 	@Nonnull
@@ -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/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-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-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -961,7 +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);
 				}
@@ -1057,7 +1057,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 						verifyMatchUrlForConditionalCreate(theResource, entity.getCreatedByMatchUrl(), newParams, theRequest);
 					}
 
-					entity.setUpdated(theTransactionDetails.getTransactionDate());
+					if (CURRENTLY_REINDEXING.get(theResource) != Boolean.TRUE) {
+						entity.setUpdated(theTransactionDetails.getTransactionDate());
+					}
 					newParams.populateResourceTableSearchParamsPresentFlags(entity);
 					entity.setIndexStatus(INDEX_STATUS_INDEXED);
 				}
@@ -1151,6 +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

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

@@ -1387,7 +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());
@@ -1397,16 +1397,42 @@ 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) {
@@ -1546,23 +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/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
@@ -128,9 +127,10 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		}
 	}
 
-    public PackageDeleteOutcomeJson uninstall(PackageInstallationSpec theInstallationSpec) {
+	@Override
-        return myPackageCacheManager.uninstallPackage(theInstallationSpec.getName(), theInstallationSpec.getVersion());
+	public PackageDeleteOutcomeJson uninstall(PackageInstallationSpec theInstallationSpec) {
-    }
+		return myPackageCacheManager.uninstallPackage(theInstallationSpec.getName(), theInstallationSpec.getVersion());
+	}
 
 	/**
 	 * Loads and installs an IG from a file on disk or the Simplifier repo using
@@ -152,12 +152,12 @@ 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();
 				});
 				if (exists) {
-						ourLog.info("Package {}#{} is already installed", theInstallationSpec.getName(), theInstallationSpec.getVersion());
+					ourLog.info("Package {}#{} is already installed", theInstallationSpec.getName(), theInstallationSpec.getVersion());
 				}
 
 				NpmPackage npmPackage = myPackageCacheManager.installPackage(theInstallationSpec);
@@ -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-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java

@@ -620,6 +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;

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java

@@ -85,6 +85,7 @@ import org.springframework.data.domain.Slice;
 import org.springframework.util.comparator.ComparableComparator;
 
 import javax.annotation.Nonnull;
+import javax.persistence.Id;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -100,6 +101,7 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.ArgumentMatchers.eq;
@@ -3342,6 +3344,34 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 	}
 
+	/**
+	 * See the class javadoc before changing the counts in this test!
+	 */
+	@Test
+	public void testDeleteResource_WithOutgoingReference() {
+		// Setup
+		createOrganization(withId("A"));
+		IIdType patientId = createPatient(withOrganization(new IdType("Organization/A")), withActiveTrue());
+
+		// Test
+		myCaptureQueriesListener.clear();
+		myPatientDao.delete(patientId, mySrd);
+
+		// Verify
+		assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
+		assertEquals(3, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
+		runInTransaction(()->{
+			ResourceTable version = myResourceTableDao.findById(patientId.getIdPartAsLong()).orElseThrow();
+			assertFalse(version.isParamsTokenPopulated());
+			assertFalse(version.isHasLinks());
+			assertEquals(0, myResourceIndexedSearchParamTokenDao.count());
+			assertEquals(0, myResourceLinkDao.count());
+		});
+
+	}
+
 	/**
 	 * See the class javadoc before changing the counts in this test!
 	 */
@@ -3353,6 +3383,11 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		Observation observation = new Observation().setStatus(Observation.ObservationStatus.FINAL).addCategory(new CodeableConcept().addCoding(new Coding("http://category-type", "12345", null))).setCode(new CodeableConcept().addCoding(new Coding("http://coverage-type", "12345", null)));
 
 		IIdType idDt = myObservationDao.create(observation, mySrd).getEntity().getIdDt();
+		runInTransaction(()->{
+			assertEquals(4, myResourceIndexedSearchParamTokenDao.count());
+			ResourceTable version = myResourceTableDao.findById(idDt.getIdPartAsLong()).orElseThrow();
+			assertTrue(version.isParamsTokenPopulated());
+		});
 
 		// when
 		myCaptureQueriesListener.clear();
@@ -3360,6 +3395,11 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		// then
 		assertQueryCount(3, 1, 1, 2);
+		runInTransaction(()->{
+			assertEquals(0, myResourceIndexedSearchParamTokenDao.count());
+			ResourceTable version = myResourceTableDao.findById(idDt.getIdPartAsLong()).orElseThrow();
+			assertFalse(version.isParamsTokenPopulated());
+		});
 	}
 
 	private void assertQueryCount(int theExpectedSelectCount, int theExpectedUpdateCount, int theExpectedInsertCount, int theExpectedDeleteCount) {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImplTest.java

@@ -1,132 +0,0 @@
-package ca.uhn.fhir.jpa.packages;
-
-import ca.uhn.fhir.context.FhirContext;
-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.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
-class PackageInstallerSvcImplTest {
-	private final FhirContext myCtx = FhirContext.forR4Cached();
-	private PackageInstallerSvcImpl mySvc;
-
-
-	@BeforeEach
-	public void before() {
-		mySvc = new PackageInstallerSvcImpl();
-		mySvc.setFhirContextForUnitTest(myCtx);
-	}
-
-	@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));
-	}
-}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexStepTest.java

@@ -66,6 +66,7 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		assertEquals(2, outcome.getRecordsProcessed());
 		assertEquals(6, myCaptureQueriesListener.logSelectQueries().size());
 		assertEquals(0, myCaptureQueriesListener.countInsertQueries());
+		myCaptureQueriesListener.logUpdateQueries();
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
 		assertEquals(1, myCaptureQueriesListener.getCommitCount());

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ResourceReindexSvcImplTest.java

@@ -3,12 +3,16 @@ package ca.uhn.fhir.jpa.reindex;
 import ca.uhn.fhir.jpa.api.pid.IResourcePidList;
 import ca.uhn.fhir.jpa.api.pid.TypedResourcePid;
 import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
+import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
+import org.hl7.fhir.r4.model.DateType;
+import org.hl7.fhir.r4.model.InstantType;
 import org.junit.jupiter.api.MethodOrderer;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.TestMethodOrder;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 
@@ -151,5 +155,4 @@ public class ResourceReindexSvcImplTest extends BaseJpaR4Test {
 
 	}
 
-
 }

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

@@ -49,6 +49,7 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
+import ca.uhn.fhir.jpa.search.reindex.IInstanceReindexService;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
@@ -144,6 +145,8 @@ public abstract class BaseJpaR5Test extends BaseJpaTest implements ITestDataBuil
 	@Autowired
 	protected PartitionSettings myPartitionSettings;
 	@Autowired
+	protected IInstanceReindexService myInstanceReindexService;
+	@Autowired
 	protected ITermCodeSystemStorageSvc myTermCodeSystemStorageSvc;
 	@Autowired
 	protected IFhirResourceDao<ClinicalUseDefinition> myClinicalUseDefinitionDao;

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5ReindexTest.java

@@ -0,0 +1,58 @@
+package ca.uhn.fhir.jpa.dao.r5;
+
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r5.model.Enumerations;
+import org.hl7.fhir.r5.model.Parameters;
+import org.hl7.fhir.r5.model.SearchParameter;
+import org.junit.jupiter.api.Test;
+import org.springframework.test.context.ContextConfiguration;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.jupiter.api.Assertions.*;
+
+@ContextConfiguration(classes = TestHSearchAddInConfig.NoFT.class)
+@SuppressWarnings({"Duplicates"})
+public class FhirResourceDaoR5ReindexTest extends BaseJpaR5Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR5ReindexTest.class);
+
+
+	@Test
+	public void testReindexDeletedSearchParameter() {
+
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("foo");
+		sp.addBase(Enumerations.VersionIndependentResourceTypesAll.PATIENT);
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		sp.setExpression("Patient.name");
+		sp.setType(Enumerations.SearchParamType.STRING);
+		IIdType id = mySearchParameterDao.create(sp, mySrd).getId().toUnqualifiedVersionless();
+
+		mySearchParameterDao.delete(id, mySrd);
+
+		runInTransaction(() -> {
+			assertEquals(1, myEntityManager.createNativeQuery("UPDATE HFJ_RESOURCE set sp_uri_present = true").executeUpdate());
+			ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow();
+			assertTrue(table.isParamsUriPopulated());
+			ResourceIndexedSearchParamUri uri = new ResourceIndexedSearchParamUri(new PartitionSettings(), "SearchParameter", "url", "http://foo");
+			uri.setResource(table);
+			uri.calculateHashes();
+			myResourceIndexedSearchParamUriDao.save(uri);
+		});
+
+		Parameters outcome = (Parameters) myInstanceReindexService.reindex(mySrd, id);
+		ourLog.info("Outcome: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
+		assertThat(outcome.getParameter("Narrative").getValueStringType().getValue(), containsString("Reindex completed in"));
+		assertEquals("REMOVE", outcome.getParameter("UriIndexes").getPartFirstRep().getPartFirstRep().getValueCodeType().getValue());
+
+		runInTransaction(() -> {
+			ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow();
+			assertFalse(table.isParamsUriPopulated());
+		});
+	}
+
+}

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/search/reindex/InstanceReindexServiceImplNarrativeR5Test.java

@@ -28,6 +28,7 @@ import org.slf4j.LoggerFactory;
 import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.math.BigDecimal;
+import java.util.Collections;
 import java.util.Date;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -53,7 +54,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myComboTokenNonUnique.add(new ResourceIndexedComboTokenNonUnique(myPartitionSettings, myEntity, "Patient?identifier=123"));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -71,7 +72,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myComboStringUniques.add(new ResourceIndexedComboStringUnique(myEntity, "Patient?identifier=123", new IdType("Parameter/foo")));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -94,7 +95,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.mySearchParamPresentEntities.add(subject);
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -117,7 +118,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myNumberParams.add(new ResourceIndexedSearchParamNumber(myPartitionSettings, "Immunization", "dose", BigDecimal.ONE));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -136,7 +137,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myLinks.add(ResourceLink.forLocalReference("Observation.subject", myEntity, "Patient", 123L, "123", new Date(), 555L));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -156,7 +157,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myLinks.add(ResourceLink.forLogicalReference("Observation.subject", myEntity, "http://foo/base/Patient/456", new Date()));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -177,7 +178,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myLinks.add(ResourceLink.forAbsoluteReference("Observation.subject", myEntity, new IdType("http://foo/base/Patient/123"), new Date()));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -198,7 +199,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myQuantityParams.add(new ResourceIndexedSearchParamQuantity(myPartitionSettings, "Observation", "value-quantity", BigDecimal.valueOf(123), "http://unitsofmeasure.org", "kg"));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -219,7 +220,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myQuantityNormalizedParams.add(new ResourceIndexedSearchParamQuantityNormalized(myPartitionSettings, "Observation", "value-quantity", 123.0, "http://unitsofmeasure.org", "kg"));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -240,7 +241,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myStringParams.add(new ResourceIndexedSearchParamString(myPartitionSettings, myStorageSettings, "Patient", "family", "Simpson", "SIMPSON"));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -260,7 +261,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myTokenParams.add(new ResourceIndexedSearchParamToken(myPartitionSettings, "Observation", "identifier", "http://id-system", "id-value"));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify
@@ -280,7 +281,7 @@ public class InstanceReindexServiceImplNarrativeR5Test {
 		newParams.myUriParams.add(new ResourceIndexedSearchParamUri(myPartitionSettings, "CodeSystem", "uri", "http://some-codesystem"));
 
 		// Test
-		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true);
+		Parameters outcome = mySvc.buildIndexResponse(newParams(), newParams, true, Collections.emptyList());
 		ourLog.info("Output:\n{}", myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 
 		// Verify

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -11,7 +11,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-jpaserver-uhnfhirtest</artifactId>
-	<packaging>war</packaging>
+	<packaging>jar</packaging>
 
 	<name>HAPI FHIR - fhirtest.uhn.ca Deployable WAR</name>
 
@@ -230,26 +230,6 @@
 			</plugins>
 		</pluginManagement>
 		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-war-plugin</artifactId>
-				<configuration>
-					<archive>
-						<manifestEntries>
-							<Build-Time>${maven.build.timestamp}</Build-Time>
-						</manifestEntries>
-					</archive>
-					<overlays>
-						<overlay>
-							<groupId>ca.uhn.hapi.fhir</groupId>
-							<artifactId>hapi-fhir-testpage-overlay</artifactId>
-							<excludes>
-								<exclude>WEB-INF/classes/**/*.class</exclude>
-							</excludes>
-						</overlay>
-					</overlays>
-				</configuration>
-			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-deploy-plugin</artifactId>
@@ -261,4 +241,41 @@
 		<finalName>hapi-fhir-jpaserver</finalName>
 	</build>
 
+	<profiles>
+		<profile>
+			<id>DIST</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-war-plugin</artifactId>
+						<executions>
+							<execution>
+								<goals>
+									<goal>war</goal>
+								</goals>
+							</execution>
+						</executions>
+						<configuration>
+							<archive>
+								<manifestEntries>
+									<Build-Time>${maven.build.timestamp}</Build-Time>
+								</manifestEntries>
+							</archive>
+							<overlays>
+								<overlay>
+									<groupId>ca.uhn.hapi.fhir</groupId>
+									<artifactId>hapi-fhir-testpage-overlay</artifactId>
+									<excludes>
+										<exclude>WEB-INF/classes/**/*.class</exclude>
+									</excludes>
+								</overlay>
+							</overlays>
+						</configuration>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+
 </project>

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

@@ -1,20 +0,0 @@
-package ca.uhn.fhirtest;
-
-import org.springframework.beans.factory.DisposableBean;
-import org.springframework.beans.factory.InitializingBean;
-
-/**
- * Created by mochaholic on 18/02/2015.
- */
-public class MySqlServer implements InitializingBean, DisposableBean {
-    private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MySqlServer.class);
-
-    @Override
-    public void destroy() throws Exception {
-    }
-
-    @Override
-    public void afterPropertiesSet() throws Exception {
-    }
-
-}

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

@@ -333,7 +333,7 @@ public class TestRestfulServer extends RestfulServer {
 	}
 
 	/**
-	 * The public server is deployed to http://fhirtest.uhn.ca and the JEE webserver
+	 * The public server is deployed to <a href="https://hapi.fhir.org">hapi.fhir.org</a> and the JEE webserver
 	 * where this FHIR server is deployed is actually fronted by an Apache HTTPd instance,
 	 * so we use an address strategy to let the server know how it should address itself.
 	 */

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

@@ -5,5 +5,7 @@ import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 public class CommonJpaStorageSettingsConfigurer {
 	public CommonJpaStorageSettingsConfigurer(JpaStorageSettings theStorageSettings) {
 		theStorageSettings.setIndexOnUpliftedRefchains(true);
+		theStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false);
+
 	}
 }

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

@@ -0,0 +1,65 @@
+package ca.uhn.fhirtest.config;
+
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.model.sched.HapiJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.r4.model.DateType;
+import org.quartz.JobExecutionContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.event.ContextRefreshedEvent;
+import org.springframework.context.event.EventListener;
+
+import javax.annotation.PostConstruct;
+import java.util.Date;
+import java.util.List;
+
+public class OldAuditEventPurgeService {
+	private static final Logger ourLog = LoggerFactory.getLogger(OldAuditEventPurgeService.class);
+
+	@Autowired
+	private ISchedulerService mySchedulerSvc;
+	@Autowired
+	private IDeleteExpungeJobSubmitter myDeleteExpungeSubmitter;
+	@Autowired
+	private JpaStorageSettings myStorageSettings;
+
+	@EventListener(ContextRefreshedEvent.class)
+	public void start() {
+		myStorageSettings.setAllowMultipleDelete(true);
+		myStorageSettings.setExpungeEnabled(true);
+		myStorageSettings.setDeleteExpungeEnabled(true);
+
+		ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
+		jobDetail.setId(OldAuditEventPurgeServiceJob.class.getName());
+		jobDetail.setJobClass(OldAuditEventPurgeServiceJob.class);
+		mySchedulerSvc.scheduleLocalJob(DateUtils.MILLIS_PER_DAY, jobDetail);
+	}
+
+	private void doPass() {
+		Date cutoff = DateUtils.addDays(new Date(), -7);
+		String cutoffString = new DateType(cutoff).getValueAsString();
+		String url = "AuditEvent?_lastUpdated=lt" + cutoffString;
+
+		ourLog.info("Submitting an AuditEvent purge job with URL: {}", url);
+
+		myDeleteExpungeSubmitter.submitJob(1000, List.of(url), new SystemRequestDetails());
+	}
+
+	public static class OldAuditEventPurgeServiceJob implements HapiJob {
+
+		@Autowired
+		private OldAuditEventPurgeService mySvc;
+
+		@Override
+		public void execute(JobExecutionContext context) {
+			mySvc.doPass();
+		}
+	}
+
+}

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

@@ -6,34 +6,20 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.config.HapiJpaConfig;
 import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
-import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
-import ca.uhn.fhir.jpa.ips.generator.IIpsGeneratorSvc;
-import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
-import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
-import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.validation.IInstanceValidatorModule;
-import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
-import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
-import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
-import org.hibernate.search.engine.cfg.BackendSettings;
-import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
-import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
 import org.springframework.orm.jpa.JpaTransactionManager;
@@ -167,6 +153,11 @@ public class TestAuditConfig {
 	}
 
 
+	@Bean
+	public OldAuditEventPurgeService oldEventPurgeService() {
+		return new OldAuditEventPurgeService();
+	}
+
 	@Bean
 	public DaoRegistryConfigurer daoRegistryConfigurer() {
 		return new DaoRegistryConfigurer();
@@ -177,7 +168,6 @@ public class TestAuditConfig {
 		@Autowired
 		private DaoRegistry myDaoRegistry;
 
-
 		@PostConstruct
 		public void start() {
 			myDaoRegistry.setSupportedResourceTypes("AuditEvent", "SearchParameter", "Subscription");

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

@@ -261,7 +261,9 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 *
 	 * @param theResource The FHIR resource object corresponding to the entity to reindex
 	 * @param theEntity   The storage entity to reindex
+	 * @deprecated Use {@link #reindex(IResourcePersistentId, ReindexParameters, RequestDetails, TransactionDetails)}
 	 */
+	@Deprecated
 	void reindex(T theResource, IBasePersistedResource theEntity);
 
 	/**

hapi-fhir-storage/src/main/java/ca/uhn/fhir/storage/interceptor/balp/AsyncMemoryQueueBackedFhirClientBalpSink.java

@@ -21,17 +21,21 @@ package ca.uhn.fhir.storage.interceptor.balp;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.util.BundleBuilder;
+import ca.uhn.fhir.util.ThreadPoolUtil;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
-import javax.annotation.PostConstruct;
 import javax.annotation.PreDestroy;
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
-import java.util.concurrent.ArrayBlockingQueue;
-import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicLong;
 
 /**
@@ -41,16 +45,17 @@ import java.util.concurrent.atomic.AtomicLong;
  * events will be converted automatically prior to sending.
  * <p>
  * This sink transmits events asynchronously using an in-memory queue. This means that
- * in the event of a server shutdown data could be lost.
+ * in the event of a server shutdown or unavailability of the target server <b>data could be lost</b>.
  * </p>
  */
 public class AsyncMemoryQueueBackedFhirClientBalpSink extends FhirClientBalpSink implements IBalpAuditEventSink {
 
-	private static final Logger ourLog = LoggerFactory.getLogger(AsyncMemoryQueueBackedFhirClientBalpSink.class);
+	public static final IBaseResource[] EMPTY_RESOURCE_ARRAY = new IBaseResource[0];
-	private final ArrayBlockingQueue<IBaseResource> myQueue;
 	private static final AtomicLong ourNextThreadId = new AtomicLong(0);
-	private boolean myRunning;
+	private static final Logger ourLog = LoggerFactory.getLogger(AsyncMemoryQueueBackedFhirClientBalpSink.class);
-	private TransmitterThread myThread;
+	private final List<IBaseResource> myQueue = new ArrayList<>(100);
+	private final ThreadPoolTaskExecutor myThreadPool;
+	private final Runnable myTransmitterTask = new TransmitterTask();
 
 	/**
 	 * Sets the FhirContext to use when initiating outgoing connections
@@ -66,6 +71,7 @@ public class AsyncMemoryQueueBackedFhirClientBalpSink extends FhirClientBalpSink
 		this(theFhirContext, theTargetBaseUrl, null);
 	}
 
+
 	/**
 	 * Sets the FhirContext to use when initiating outgoing connections
 	 *
@@ -82,7 +88,6 @@ public class AsyncMemoryQueueBackedFhirClientBalpSink extends FhirClientBalpSink
 		this(createClient(theFhirContext, theTargetBaseUrl, theClientInterceptors));
 	}
 
-
 	/**
 	 * Constructor
 	 *
@@ -90,76 +95,61 @@ public class AsyncMemoryQueueBackedFhirClientBalpSink extends FhirClientBalpSink
 	 */
 	public AsyncMemoryQueueBackedFhirClientBalpSink(IGenericClient theClient) {
 		super(theClient);
-		myQueue = new ArrayBlockingQueue<>(100);
+		myThreadPool = ThreadPoolUtil.newThreadPool(1, 1, "BalpClientSink-" + ourNextThreadId.getAndIncrement() + "-", 100);
 	}
 
 	@Override
 	protected void recordAuditEvent(IBaseResource theAuditEvent) {
-		myQueue.add(theAuditEvent);
+		synchronized (myQueue) {
-	}
+			myQueue.add(theAuditEvent);
-
-	@PostConstruct
-	public void start() {
-		if (!myRunning) {
-			myRunning = true;
-			myThread = new TransmitterThread();
-			myThread.start();
 		}
+		myThreadPool.submit(myTransmitterTask);
 	}
 
 	@PreDestroy
 	public void stop() {
-		if (myRunning) {
+		myThreadPool.shutdown();
-			myRunning = false;
-			myThread.interrupt();
-		}
 	}
 
-	public boolean isRunning() {
+	private class TransmitterTask implements Runnable {
-		return myThread != null && myThread.isRunning();
-	}
-
-	private class TransmitterThread extends Thread {
-
-		private boolean myThreadRunning;
-
-		public TransmitterThread() {
-			setName("BalpClientSink-" + ourNextThreadId.getAndIncrement());
-		}
 
 		@Override
 		public void run() {
-			ourLog.info("Starting BALP Client Sink Transmitter");
+			IBaseResource[] queue;
-			myThreadRunning = true;
+			synchronized (myQueue) {
-			while (myRunning) {
+				if (myQueue.isEmpty()) {
-				IBaseResource next = null;
+					queue = EMPTY_RESOURCE_ARRAY;
-				try {
+				} else {
-					next = myQueue.poll(10, TimeUnit.SECONDS);
+					queue = myQueue.toArray(EMPTY_RESOURCE_ARRAY);
-				} catch (InterruptedException e) {
+					myQueue.clear();
-					Thread.currentThread().interrupt();
 				}
-
-				// TODO: Currently we transmit events one by one, but a nice optimization
-				// would be to batch them into FHIR transaction Bundles. If we do this, we
-				// would get better performance, but we'd also want to have some retry
-				// logic that submits events individually if a transaction fails.
-
-				if (next != null) {
-					try {
-						transmitEventToClient(next);
-					} catch (Exception e) {
-						ourLog.warn("Failed to transmit AuditEvent to sink: {}", e.toString());
-						myQueue.add(next);
-					}
-				}
-
 			}
-			ourLog.info("Stopping BALP Client Sink Transmitter");
-			myThreadRunning = false;
-		}
 
-		public boolean isRunning() {
+			if (queue.length == 0) {
-			return myThreadRunning;
+				return;
+			}
+
+			BundleBuilder bundleBuilder = new BundleBuilder(myClient.getFhirContext());
+			for (IBaseResource next : queue) {
+				bundleBuilder.addTransactionCreateEntry(next);
+			}
+
+			IBaseBundle transactionBundle = bundleBuilder.getBundle();
+			try {
+				myClient.transaction().withBundle(transactionBundle).execute();
+				return;
+			} catch (BaseServerResponseException e) {
+				ourLog.error("Failed to transmit AuditEvent items to target. Will re-attempt {} failed events once. Error: {}", queue.length, e.toString());
+			}
+
+			// Retry once then give up
+			for (IBaseResource next : queue) {
+				try {
+					myClient.create().resource(next).execute();
+				} catch (BaseServerResponseException e) {
+					ourLog.error("Second failure uploading AuditEvent. Error: {}", e.toString());
+				}
+			}
 		}
 	}
 

hapi-fhir-storage/src/main/java/ca/uhn/fhir/storage/interceptor/balp/FhirClientBalpSink.java

@@ -32,7 +32,7 @@ import java.util.List;
 
 public class FhirClientBalpSink implements IBalpAuditEventSink {
 
-	private final IGenericClient myClient;
+	protected final IGenericClient myClient;
 	private final VersionCanonicalizer myVersionCanonicalizer;
 
 	/**

hapi-fhir-storage/src/test/java/ca/uhn/fhir/storage/interceptor/balp/AsyncMemoryQueueBackedFhirClientBalpSinkTest.java

@@ -5,12 +5,15 @@ import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
 import ca.uhn.fhir.interceptor.api.IPointcut;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.rest.annotation.Transaction;
+import ca.uhn.fhir.rest.annotation.TransactionParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.storage.interceptor.balp.AsyncMemoryQueueBackedFhirClientBalpSink;
 import ca.uhn.fhir.test.utilities.server.HashMapResourceProviderExtension;
 import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
 import org.hl7.fhir.dstu3.model.AuditEvent;
-import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.RegisterExtension;
@@ -23,26 +26,48 @@ import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.lessThan;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class AsyncMemoryQueueBackedFhirClientBalpSinkTest {
 
 	@RegisterExtension
 	@Order(0)
-	private RestfulServerExtension myServer = new RestfulServerExtension(FhirVersionEnum.DSTU3);
+	private RestfulServerExtension myServer = new RestfulServerExtension(FhirVersionEnum.DSTU3)
+		.withServer(t->t.registerProvider(new MySystemProvider()));
 	@RegisterExtension
 	@Order(1)
 	private HashMapResourceProviderExtension<AuditEvent> myAuditEventProvider = new HashMapResourceProviderExtension<>(myServer, AuditEvent.class);
 
+
+	@Test
+	public void testStressTest() {
+		AsyncMemoryQueueBackedFhirClientBalpSink sink = new AsyncMemoryQueueBackedFhirClientBalpSink(myServer.getFhirContext(), myServer.getBaseUrl());
+		try {
+			for (int i = 0; i < 10; i++) {
+				for (int j = 0; j < 100; j++) {
+					AuditEvent auditEvent = new AuditEvent();
+					auditEvent.setAction(AuditEvent.AuditEventAction.C);
+					sink.recordAuditEvent(auditEvent);
+				}
+			}
+
+			await().until(() -> myAuditEventProvider.getStoredResources().size(), equalTo(1000));
+
+		} finally {
+			sink.stop();
+		}
+	}
+
+
 	@Test
 	public void recordAuditEvent() {
 		// Setup
 		AsyncMemoryQueueBackedFhirClientBalpSink sink = new AsyncMemoryQueueBackedFhirClientBalpSink(myServer.getFhirContext(), myServer.getBaseUrl());
-		sink.start();
 		try {
 			org.hl7.fhir.r4.model.AuditEvent auditEvent1 = new org.hl7.fhir.r4.model.AuditEvent();
-			auditEvent1.addEntity().setWhat(new Reference("Patient/123"));
+			auditEvent1.addEntity().setWhat(new org.hl7.fhir.r4.model.Reference("Patient/123"));
 			org.hl7.fhir.r4.model.AuditEvent auditEvent2 = new org.hl7.fhir.r4.model.AuditEvent();
-			auditEvent2.addEntity().setWhat(new Reference("Patient/456"));
+			auditEvent2.addEntity().setWhat(new org.hl7.fhir.r4.model.Reference("Patient/456"));
 
 			// Test
 			sink.recordAuditEvent(auditEvent1);
@@ -58,7 +83,6 @@ public class AsyncMemoryQueueBackedFhirClientBalpSinkTest {
 			assertThat(whats, containsInAnyOrder("Patient/123", "Patient/456"));
 		} finally {
 			sink.stop();
-			await().until(sink::isRunning, equalTo(false));
 		}
 	}
 
@@ -66,18 +90,17 @@ public class AsyncMemoryQueueBackedFhirClientBalpSinkTest {
 	public void recordAuditEvent_AutoRetry() {
 		// Setup
 		AsyncMemoryQueueBackedFhirClientBalpSink sink = new AsyncMemoryQueueBackedFhirClientBalpSink(myServer.getFhirContext(), myServer.getBaseUrl());
-		sink.start();
 		try {
 			org.hl7.fhir.r4.model.AuditEvent auditEvent1 = new org.hl7.fhir.r4.model.AuditEvent();
-			auditEvent1.addEntity().setWhat(new Reference("Patient/123"));
+			auditEvent1.addEntity().setWhat(new org.hl7.fhir.r4.model.Reference("Patient/123"));
 			org.hl7.fhir.r4.model.AuditEvent auditEvent2 = new org.hl7.fhir.r4.model.AuditEvent();
-			auditEvent2.addEntity().setWhat(new Reference("Patient/456"));
+			auditEvent2.addEntity().setWhat(new org.hl7.fhir.r4.model.Reference("Patient/456"));
 
-			AtomicInteger counter = new AtomicInteger(10);
+			AtomicInteger counter = new AtomicInteger(1);
 			myServer.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED, new IAnonymousInterceptor() {
 				@Override
 				public void invoke(IPointcut thePointcut, HookParams theArgs) {
-					if (counter.decrementAndGet() > 0) {
+					if (counter.getAndDecrement() > 0) {
 						throw new InternalErrorException("Intentional error for unit test");
 					}
 				}
@@ -98,9 +121,30 @@ public class AsyncMemoryQueueBackedFhirClientBalpSinkTest {
 			assertThat(whats.toString(), whats, containsInAnyOrder("Patient/123", "Patient/456"));
 		} finally {
 			sink.stop();
-			await().until(sink::isRunning, equalTo(false));
 		}
 	}
 
 
+	public class MySystemProvider {
+
+		@Transaction
+		public Bundle transaction(@TransactionParam Bundle theInput, RequestDetails theRequestDetails) {
+			Bundle retVal = new Bundle();
+			retVal.setType(Bundle.BundleType.TRANSACTIONRESPONSE);
+
+			for (Bundle.BundleEntryComponent next : theInput.getEntry()) {
+				assertEquals(Bundle.HTTPVerb.POST, next.getRequest().getMethod());
+				assertEquals("AuditEvent", next.getRequest().getUrl());
+				AuditEvent resource = (AuditEvent) next.getResource();
+				IIdType outcome = myAuditEventProvider.create(resource, theRequestDetails).getId();
+
+				Bundle.BundleEntryComponent respEntry = retVal.addEntry();
+				respEntry.getResponse().setStatus("201 Created");
+				respEntry.getResponse().setLocation(outcome.getValue());
+			}
+
+			return retVal;
+		}
+
+	}
 }

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamR4Test.java

@@ -21,6 +21,7 @@ import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.apache.jena.base.Sys;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
@@ -59,7 +60,7 @@ public class DateRangeParamR4Test {
 	private static final SimpleDateFormat ourFmtUpperForTime;
 	private static final Logger ourLog = LoggerFactory.getLogger(DateRangeParamR4Test.class);
 	private static CloseableHttpClient ourClient;
-	private static FhirContext ourCtx = FhirContext.forR4();
+	private static FhirContext ourCtx = FhirContext.forR4Cached();
 	private static DateRangeParam ourLastDateRange;
 	private static int ourPort;
 	private static Server ourServer;
@@ -315,8 +316,8 @@ public class DateRangeParamR4Test {
 	@Test
 	public void testSetBoundsWithDatesExclusive() {
 		DateRangeParam range = new DateRangeParam();
-		range.setLowerBoundExclusive(new Date());
+		range.setLowerBoundExclusive(new Date(System.currentTimeMillis()));
-		range.setUpperBoundExclusive(new Date());
+		range.setUpperBoundExclusive(new Date(System.currentTimeMillis() + 1000));
 
 		assertEquals(ParamPrefixEnum.GREATERTHAN, range.getLowerBound().getPrefix());
 		assertEquals(ParamPrefixEnum.LESSTHAN, range.getUpperBound().getPrefix());

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SearchR4Test.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.annotation.IncludeParam;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
 import ca.uhn.fhir.rest.annotation.Search;
@@ -77,6 +78,7 @@ public class SearchR4Test {
 		ourLastMethod = null;
 		ourIdentifiers = null;
 		myPort = myRestfulServerExtension.getPort();
+		myCtx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 	}
 
 	private Bundle executeSearchAndValidateHasLinkNext(HttpGet httpGet, EncodingEnum theExpectEncoding) throws IOException {
@@ -139,13 +141,13 @@ public class SearchR4Test {
 		String linkSelf;
 
 		// Initial search
-		httpGet = new HttpGet("http://localhost:" + myPort + "/Patient?identifier=foo%7Cbar&_elements=name&_elements:exclude=birthDate,active");
+		httpGet = new HttpGet("http://localhost:" + myPort + "/Patient?identifier=foo%7Cbar&_elements=identifier,name&_elements:exclude=birthDate,active");
 		bundle = executeSearchAndValidateHasLinkNext(httpGet, EncodingEnum.JSON);
 		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkSelf = bundle.getLink(Constants.LINK_SELF).getUrl();
-		assertThat(linkSelf, containsString("_elements=name"));
+		assertThat(linkSelf, containsString("_elements=identifier%2Cname"));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=identifier,name"));
 
 		ourLog.info(toJson(bundle));
 
@@ -154,7 +156,7 @@ public class SearchR4Test {
 		bundle = executeSearchAndValidateHasLinkNext(httpGet, EncodingEnum.JSON);
 		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=identifier,name"));
 		assertThat(linkNext, containsString("_elements:exclude=active,birthDate"));
 
 		// Fetch the next page
@@ -162,7 +164,7 @@ public class SearchR4Test {
 		bundle = executeSearchAndValidateHasLinkNext(httpGet, EncodingEnum.JSON);
 		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=identifier,name"));
 		assertThat(linkNext, containsString("_elements:exclude=active,birthDate"));
 
 		// Fetch the next page
@@ -170,7 +172,7 @@ public class SearchR4Test {
 		bundle = executeSearchAndValidateHasLinkNext(httpGet, EncodingEnum.JSON);
 		assertThat(toJson(bundle), not(containsString("\"active\"")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_elements=name"));
+		assertThat(linkNext, containsString("_elements=identifier,name"));
 		assertThat(linkNext, containsString("_elements:exclude=active,birthDate"));
 
 	}
@@ -519,6 +521,7 @@ public class SearchR4Test {
 				patient.getIdElement().setValue("Patient/" + i + "/_history/222");
 				ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(patient, BundleEntrySearchModeEnum.INCLUDE);
 				patient.addName(new HumanName().setFamily("FAMILY"));
+				patient.addIdentifier().setSystem("http://foo").setValue("bar");
 				patient.setActive(true);
 				retVal.add(patient);
 			}

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

@@ -5,6 +5,7 @@ import ca.uhn.fhir.context.api.BundleInclusionRule;
 import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.annotation.GraphQL;
 import ca.uhn.fhir.rest.annotation.GraphQLQueryUrl;
 import ca.uhn.fhir.rest.annotation.IdParam;
@@ -105,6 +106,7 @@ public class ResponseHighlightingInterceptorTest {
 		ourInterceptor.setShowRequestHeaders(defaults.isShowRequestHeaders());
 		ourInterceptor.setShowResponseHeaders(defaults.isShowResponseHeaders());
 		ourInterceptor.setShowNarrative(defaults.isShowNarrative());
+		ourCtx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 	}
 
 	/**
@@ -310,7 +312,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_JSON_NEW + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test
@@ -323,7 +325,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_JSON + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test
@@ -336,7 +338,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_JSON + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test
@@ -349,7 +351,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_XML_NEW + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test
@@ -362,7 +364,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_XML + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test
@@ -375,7 +377,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_XML + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test
@@ -390,9 +392,8 @@ public class ResponseHighlightingInterceptorTest {
 
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals("text/html;charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, containsString("html"));
+		assertThat(responseContent, containsString("<html"));
 		assertThat(responseContent, containsString(">{<"));
-		assertThat(responseContent, not(containsString("&lt;")));
 		assertThat(responseContent, containsString(Constants.HEADER_REQUEST_ID));
 
 	}
@@ -410,7 +411,7 @@ public class ResponseHighlightingInterceptorTest {
 
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals("text/html;charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, containsString("html"));
+		assertThat(responseContent, containsString("<html"));
 		assertThat(responseContent, containsString("<span class='hlQuot'>&quot;urn:hapitest:mrns&quot;</span>"));
 		assertThat(responseContent, containsString(Constants.HEADER_REQUEST_ID));
 
@@ -426,9 +427,8 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals("text/html;charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, containsString("html"));
+		assertThat(responseContent, containsString("<html"));
 		assertThat(responseContent, containsString(">{<"));
-		assertThat(responseContent, not(containsString("&lt;")));
 
 		ourLog.info(responseContent);
 	}
@@ -443,7 +443,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals("text/html;charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, containsString("html"));
+		assertThat(responseContent, containsString("<html"));
 		assertThat(responseContent, not(containsString(">{<")));
 		assertThat(responseContent, containsString("&lt;"));
 	}
@@ -458,7 +458,7 @@ public class ResponseHighlightingInterceptorTest {
 		status.close();
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		assertEquals(Constants.CT_FHIR_JSON_NEW + ";charset=utf-8", status.getFirstHeader("content-type").getValue().replace(" ", "").toLowerCase());
-		assertThat(responseContent, not(containsString("html")));
+		assertThat(responseContent, not(containsString("<html")));
 	}
 
 	@Test

pom.xml

@@ -112,12 +112,12 @@
 		<module>hapi-fhir-jpaserver-ips</module>
 		<module>hapi-fhir-jpaserver-mdm</module>
 		<module>hapi-fhir-testpage-overlay</module>
-<!--		<module>hapi-fhir-jpaserver-uhnfhirtest</module>-->
+		<module>hapi-fhir-jpaserver-uhnfhirtest</module>
 		<module>hapi-fhir-client-okhttp</module>
 		<module>hapi-fhir-android</module>
 		<module>hapi-fhir-cli</module>
 		<module>hapi-fhir-dist</module>
-<!--		<module>tests/hapi-fhir-base-test-jaxrsserver-kotlin</module>-->
+		<module>tests/hapi-fhir-base-test-jaxrsserver-kotlin</module>
 		<module>tests/hapi-fhir-base-test-mindeps-client</module>
 		<module>tests/hapi-fhir-base-test-mindeps-server</module>
 		<module>hapi-fhir-spring-boot</module>

tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml

@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<!-- Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management. You do not need to use this in your own projects, so the "parent" tag and it's contents below may be removed
@@ -12,7 +13,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-base-test-jaxrsserver-kotlin</artifactId>
-	<packaging>war</packaging>
+	<packaging>jar</packaging>
 
 	<name>HAPI FHIR JAX-RS Server Kotlin test</name>
 
@@ -80,12 +81,12 @@
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>
 		</dependency>
-	  <dependency>
+		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-test-utilities</artifactId>
 			<version>${project.version}</version>
 			<scope>test</scope>
-	  </dependency>
+		</dependency>
 		<dependency>
 			<groupId>org.jetbrains.kotlin</groupId>
 			<artifactId>kotlin-maven-allopen</artifactId>
@@ -132,7 +133,9 @@
 				<executions>
 					<execution>
 						<id>compile</id>
-						<goals> <goal>compile</goal> </goals>
+						<goals>
+							<goal>compile</goal>
+						</goals>
 						<configuration>
 							<sourceDirs>
 								<sourceDir>${project.basedir}/src/main/kotlin</sourceDir>
@@ -142,7 +145,9 @@
 					</execution>
 					<execution>
 						<id>test-compile</id>
-						<goals> <goal>test-compile</goal> </goals>
+						<goals>
+							<goal>test-compile</goal>
+						</goals>
 						<configuration>
 							<sourceDirs>
 								<sourceDir>${project.basedir}/src/test/kotlin</sourceDir>
@@ -155,6 +160,43 @@
 		</plugins>
 	</build>
 
+	<profiles>
+		<profile>
+			<id>DIST</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-war-plugin</artifactId>
+						<executions>
+							<execution>
+								<goals>
+									<goal>war</goal>
+								</goals>
+							</execution>
+						</executions>
+						<configuration>
+							<archive>
+								<manifestEntries>
+									<Build-Time>${maven.build.timestamp}</Build-Time>
+								</manifestEntries>
+							</archive>
+							<overlays>
+								<overlay>
+									<groupId>ca.uhn.hapi.fhir</groupId>
+									<artifactId>hapi-fhir-testpage-overlay</artifactId>
+									<excludes>
+										<exclude>WEB-INF/classes/**/*.class</exclude>
+									</excludes>
+								</overlay>
+							</overlays>
+						</configuration>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+
 	<properties>
 		<!--<kotlin.compiler.incremental>true</kotlin.compiler.incremental>-->
 		<kotlin.version>1.6.21</kotlin.version>