Convert Reindex into Batch2 Job (#3458)

* Start working on reindex job

* Updates

* Ongoing work

* Ongoing work

* Work on reindex

* Reindex work

* Add logging

* Fix typo

* Test fix

* Test fix

* Address fixme

* Liocense header

* Resolve fixme

* Add logging

* Update logs

* Address review comments

* License header

* Test fixes

* Test fix

* Test fixes

* Test fix

* Version bump

* Version bump

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.0.0-PRE6-SNAPSHOT</version>
+		 <version>6.0.0-PRE8-SNAPSHOT</version>
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/BatchConstants.java

@@ -42,14 +42,6 @@ public final class BatchConstants {
 	 * Delete Expunge
 	 */
 	public static final String DELETE_EXPUNGE_JOB_NAME = "deleteExpungeJob";
-	/**
-	 * Reindex
-	 */
-	public static final String REINDEX_JOB_NAME = "reindexJob";
-	/**
-	 * Reindex Everything
-	 */
-	public static final String REINDEX_EVERYTHING_JOB_NAME = "reindexEverythingJob";
 	/**
 	 * MDM Clear
 	 */

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>6.0.0-PRE6-SNAPSHOT</version>
+    <version>6.0.0-PRE8-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
     

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java

@@ -27,8 +27,6 @@ import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
 import ca.uhn.fhir.jpa.bulk.imprt.job.BulkImportJobConfig;
 import ca.uhn.fhir.jpa.config.BatchJobRegisterer;
 import ca.uhn.fhir.jpa.delete.job.DeleteExpungeJobConfig;
-import ca.uhn.fhir.jpa.reindex.job.ReindexEverythingJobConfig;
-import ca.uhn.fhir.jpa.reindex.job.ReindexJobConfig;
 import ca.uhn.fhir.jpa.term.job.TermCodeSystemDeleteJobConfig;
 import ca.uhn.fhir.jpa.term.job.TermCodeSystemVersionDeleteJobConfig;
 import org.springframework.batch.core.configuration.JobRegistry;
@@ -48,8 +46,6 @@ import org.springframework.context.annotation.Import;
 	BulkExportJobConfig.class,
 	BulkImportJobConfig.class,
 	DeleteExpungeJobConfig.class,
-	ReindexJobConfig.class,
-	ReindexEverythingJobConfig.class,
 	MdmClearJobConfig.class,
 	TermCodeSystemDeleteJobConfig.class,
 	TermCodeSystemVersionDeleteJobConfig.class

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/CommonBatchJobConfig.java

@@ -27,9 +27,7 @@ import ca.uhn.fhir.jpa.batch.processor.GoldenResourceAnnotatingProcessor;
 import ca.uhn.fhir.jpa.batch.processor.PidToIBaseResourceProcessor;
 import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
 import ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter;
-import ca.uhn.fhir.jpa.reindex.job.ReindexWriter;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
-import org.springframework.batch.core.JobParametersValidator;
 import org.springframework.batch.core.configuration.annotation.StepScope;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -73,10 +71,4 @@ public class CommonBatchJobConfig {
 		return new GoldenResourceAnnotatingProcessor();
 	}
 
-	@Bean
-	@StepScope
-	public ReindexWriter reindexWriter() {
-		return new ReindexWriter();
-	}
-
 }

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

@@ -174,6 +174,11 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 		myWorkChunkRepository.updateChunkStatusAndClearDataForEndSuccess(theChunkId, new Date(), theRecordsProcessed, StatusEnum.COMPLETED);
 	}
 
+	@Override
+	public void incrementWorkChunkErrorCount(String theChunkId, int theIncrementBy) {
+		myWorkChunkRepository.incrementWorkChunkErrorCount(theChunkId, theIncrementBy);
+	}
+
 	@Override
 	public List<WorkChunk> fetchWorkChunksWithoutData(String theInstanceId, int thePageSize, int thePageIndex) {
 		List<Batch2WorkChunkEntity> chunks = myWorkChunkRepository.fetchChunks(PageRequest.of(thePageIndex, thePageSize), theInstanceId);

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

@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
+import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
 import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.config.BatchConstants;
@@ -84,7 +85,7 @@ import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
 import ca.uhn.fhir.jpa.provider.r4.MemberMatcherR4Helper;
-import ca.uhn.fhir.jpa.reindex.ReindexJobSubmitterImpl;
+import ca.uhn.fhir.jpa.reindex.ResourceReindexSvcImpl;
 import ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory;
 import ca.uhn.fhir.jpa.sched.HapiSchedulerServiceImpl;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
@@ -137,12 +138,10 @@ import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
-import ca.uhn.fhir.rest.api.server.storage.IReindexJobSubmitter;
 import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
-import ca.uhn.fhir.rest.server.provider.ReindexProvider;
 import ca.uhn.fhir.util.ThreadPoolUtil;
 import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -463,24 +462,12 @@ public class JpaConfig {
 		return new PartitionedUrlValidator();
 	}
 
-	@Bean
-	@Lazy
-	public IReindexJobSubmitter myReindexJobSubmitter() {
-		return new ReindexJobSubmitterImpl();
-	}
-
 	@Bean
 	@Lazy
 	public DeleteExpungeProvider deleteExpungeProvider(FhirContext theFhirContext, IDeleteExpungeJobSubmitter theDeleteExpungeJobSubmitter) {
 		return new DeleteExpungeProvider(theFhirContext, theDeleteExpungeJobSubmitter);
 	}
 
-	@Bean
-	@Lazy
-	public ReindexProvider reindexProvider(FhirContext theFhirContext, IReindexJobSubmitter theReindexJobSubmitter) {
-		return new ReindexProvider(theFhirContext, theReindexJobSubmitter);
-	}
-
 	@Bean
 	@Lazy
 	public IBulkDataImportSvc bulkDataImportSvc() {
@@ -517,6 +504,10 @@ public class JpaConfig {
 		return new ResourceVersionSvcDaoImpl();
 	}
 
+	@Bean
+	public IResourceReindexSvc resourceReindexSvc() {
+		return new ResourceReindexSvcImpl();
+	}
 
 	/* **************************************************************** *
 	 * Prototype Beans Below                                            *

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

@@ -1139,7 +1139,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			} catch (Exception e) {
 				StringBuilder b = new StringBuilder();
 				b.append("Failed to parse database resource[");
-				b.append(resourceType);
+				b.append(myFhirContext.getResourceType(resourceType));
 				b.append("/");
 				b.append(theEntity.getIdDt().getIdPart());
 				b.append(" (pid ");

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

@@ -59,11 +59,11 @@ import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.dstu2.resource.ListResource;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -86,6 +86,7 @@ import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.rest.server.IPagingProvider;
 import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
 import ca.uhn.fhir.rest.server.RestfulServerUtils;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@@ -333,10 +334,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		if (resourceHadIdBeforeStorage) {
 			if (resourceIdWasServerAssigned) {
 				boolean createForPureNumericIds = true;
-				createForcedIdIfNeeded(entity, resourceIdBeforeStorage, createForPureNumericIds, persistentId, theRequestPartitionId);
+				createForcedIdIfNeeded(entity, resourceIdBeforeStorage, createForPureNumericIds);
 			} else {
 				boolean createForPureNumericIds = getConfig().getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC;
-				createForcedIdIfNeeded(entity, resourceIdBeforeStorage, createForPureNumericIds, persistentId, theRequestPartitionId);
+				createForcedIdIfNeeded(entity, resourceIdBeforeStorage, createForPureNumericIds);
 			}
 		} else {
 			switch (getConfig().getResourceClientIdStrategy()) {
@@ -345,7 +346,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 					break;
 				case ANY:
 					boolean createForPureNumericIds = true;
-					createForcedIdIfNeeded(updatedEntity, theResource.getIdElement().getIdPart(), createForPureNumericIds, persistentId, theRequestPartitionId);
+					createForcedIdIfNeeded(updatedEntity, theResource.getIdElement().getIdPart(), createForPureNumericIds);
 					// for client ID mode ANY, we will always have a forced ID. If we ever
 					// stop populating the transient forced ID be warned that we use it
 					// (and expect it to be set correctly) farther below.
@@ -399,7 +400,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return outcome;
 	}
 
-	private void createForcedIdIfNeeded(ResourceTable theEntity, String theResourceId, boolean theCreateForPureNumericIds, ResourcePersistentId thePersistentId, RequestPartitionId theRequestPartitionId) {
+	private void createForcedIdIfNeeded(ResourceTable theEntity, String theResourceId, boolean theCreateForPureNumericIds) {
 		if (isNotBlank(theResourceId) && theEntity.getForcedId() == null) {
 			if (theCreateForPureNumericIds || !IdHelperService.isValidPid(theResourceId)) {
 				ForcedId forcedId = new ForcedId();
@@ -1288,6 +1289,25 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return Long.toString(readEntity(theReferenceElement.toVersionless(), null).getVersion());
 	}
 
+	@SuppressWarnings("unchecked")
+	@Override
+	public void reindex(ResourcePersistentId theResourcePersistentId, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
+		Optional<ResourceTable> entityOpt = myResourceTableDao.findById(theResourcePersistentId.getIdAsLong());
+		if (!entityOpt.isPresent()) {
+			ourLog.warn("Unable to find entity with PID: {}", theResourcePersistentId.getId());
+			return;
+		}
+
+		ResourceTable entity = entityOpt.get();
+		try {
+			T resource = (T) toResource(entity, false);
+			reindex(resource, entity);
+		} catch (BaseServerResponseException | DataFormatException e) {
+			myResourceTableDao.updateIndexStatus(entity.getId(), INDEX_STATUS_INDEXING_FAILED);
+			throw e;
+		}
+	}
+
 	@Override
 	@Transactional
 	public BaseHasResource readEntity(IIdType theId, boolean theCheckForForcedId, RequestDetails theRequest) {
@@ -1569,7 +1589,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
-	public Set<ResourcePersistentId> searchForIds(SearchParameterMap theParams, RequestDetails theRequest, @Nullable IBaseResource theConditionalOperationTargetOrNull) {
+	public List<ResourcePersistentId> searchForIds(SearchParameterMap theParams, RequestDetails theRequest, @Nullable IBaseResource theConditionalOperationTargetOrNull) {
 		TransactionDetails transactionDetails = new TransactionDetails();
 
 		return myTransactionService.execute(theRequest, transactionDetails, tx -> {
@@ -1582,7 +1602,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			ISearchBuilder builder = mySearchBuilderFactory.newSearchBuilder(this, getResourceName(), getResourceType());
 
-			HashSet<ResourcePersistentId> retVal = new HashSet<>();
+			List<ResourcePersistentId> ids = new ArrayList<>();
 
 			String uuid = UUID.randomUUID().toString();
 			RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(theRequest, getResourceName(), theParams, theConditionalOperationTargetOrNull);
@@ -1590,13 +1610,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
 			try (IResultIterator iter = builder.createQuery(theParams, searchRuntimeDetails, theRequest, requestPartitionId)) {
 				while (iter.hasNext()) {
-					retVal.add(iter.next());
+					ids.add(iter.next());
 				}
 			} catch (IOException e) {
 				ourLog.error("IO failure during database access", e);
 			}
 
-			return retVal;
+			return ids;
 		});
 	}
 
@@ -1929,10 +1949,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		myIdHelperService = theIdHelperService;
 	}
 
-	private static ResourceIndexedSearchParams toResourceIndexedSearchParams(ResourceTable theEntity) {
-		return new ResourceIndexedSearchParams(theEntity);
-	}
-
 	private static class IdChecker implements IValidatorModule {
 
 		private final ValidationModeEnum myMode;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java

@@ -180,7 +180,7 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		}
 
 		List<IIdType> valueSetIds;
-		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(ValueSet.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		List<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(ValueSet.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		valueSetIds = new ArrayList<>();
 		for (ResourcePersistentId next : ids) {
 			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "ValueSet", next);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java

@@ -51,4 +51,8 @@ public interface IBatch2WorkChunkRepository extends JpaRepository<Batch2WorkChun
 	@Modifying
 	@Query("DELETE FROM Batch2WorkChunkEntity e WHERE e.myInstanceId = :instanceId")
 	void deleteAllForInstance(@Param("instanceId") String theInstanceId);
+
+	@Modifying
+	@Query("UPDATE Batch2WorkChunkEntity e SET e.myErrorCount = e.myErrorCount + :by WHERE e.myId = :id")
+	void incrementWorkChunkErrorCount(@Param("id") String theChunkId, @Param("by") int theIncrementBy);
 }

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

@@ -57,6 +57,24 @@ public interface IResourceTableDao extends JpaRepository<ResourceTable, Long>, I
 	@Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high ORDER BY t.myUpdated ASC")
 	Slice<Long> findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh);
 
+	/**
+	 * @return List of arrays containing [PID, resourceType, lastUpdated]
+	 */
+	@Query("SELECT t.myId, t.myResourceType, t.myUpdated FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high ORDER BY t.myUpdated ASC")
+	Slice<Object[]> findIdsTypesAndUpdateTimesOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh);
+
+	/**
+	 * @return List of arrays containing [PID, resourceType, lastUpdated]
+	 */
+	@Query("SELECT t.myId, t.myResourceType, t.myUpdated FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high AND t.myPartitionIdValue IN (:partition_ids) ORDER BY t.myUpdated ASC")
+	Slice<Object[]> findIdsTypesAndUpdateTimesOfResourcesWithinUpdatedRangeOrderedFromOldestForPartitionIds(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh, @Param("partition_ids") List<Integer> theRequestPartitionIds);
+
+	/**
+	 * @return List of arrays containing [PID, resourceType, lastUpdated]
+	 */
+	@Query("SELECT t.myId, t.myResourceType, t.myUpdated FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high ORDER BY t.myUpdated ASC")
+	Slice<Object[]> findIdsTypesAndUpdateTimesOfResourcesWithinUpdatedRangeOrderedFromOldestForDefaultPartition(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh);
+
 	// TODO in the future, consider sorting by pid as well so batch jobs process in the same order across restarts
 	@Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high AND t.myPartitionIdValue = :partition_id ORDER BY t.myUpdated ASC")
 	Slice<Long> findIdsOfPartitionedResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh, @Param("partition_id") Integer theRequestPartitionId);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -76,7 +76,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
-		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		List<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		List<IIdType> valueSetIds = new ArrayList<>();
 		for (ResourcePersistentId next : ids) {
 			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java

@@ -74,7 +74,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
 		List<IIdType> valueSetIds;
-		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		List<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		valueSetIds = new ArrayList<>();
 		for (ResourcePersistentId next : ids) {
 			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java

@@ -75,7 +75,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
 		List<IIdType> valueSetIds;
-		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(org.hl7.fhir.r4.model.CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		List<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(org.hl7.fhir.r4.model.CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		valueSetIds = new ArrayList<>();
 		for (ResourcePersistentId next : ids) {
 			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);

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

@@ -272,6 +272,11 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 
 		replaceNumericSPIndices(version);
 		replaceQuantitySPIndices(version);
+        
+        // Drop Index on HFJ_RESOURCE.INDEX_STATUS
+        version
+        .onTable("HFJ_RESOURCE")
+        .dropIndex("20220314.1", "IDX_INDEXSTATUS");
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.provider;
  * #L%
  */
 
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.rest.annotation.Operation;
@@ -45,7 +46,7 @@ public abstract class BaseJpaSystemProviderDstu2Plus<T, MT> extends BaseJpaSyste
 	})
 	/**
 	 * @deprecated
-	 * @see ca.uhn.fhir.rest.server.provider.ReindexProvider#Reindex(List, IPrimitiveType, RequestDetails)
+	 * @see ReindexProvider#Reindex(List, IPrimitiveType, RequestDetails)
 	 */
 	@Deprecated
 	public IBaseResource markAllResourcesForReindexing(
@@ -72,7 +73,7 @@ public abstract class BaseJpaSystemProviderDstu2Plus<T, MT> extends BaseJpaSyste
 	})
 	/**
 	 * @deprecated
-	 * @see ca.uhn.fhir.rest.server.provider.ReindexProvider#Reindex(List, IPrimitiveType, RequestDetails)
+	 * @see ReindexProvider#Reindex(List, IPrimitiveType, RequestDetails)
 	 */
 	@Deprecated
 	public IBaseResource performReindexingPass() {

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

@@ -1,108 +0,0 @@
-package ca.uhn.fhir.jpa.reindex;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.i18n.Msg;
-import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
-import ca.uhn.fhir.jpa.batch.config.BatchConstants;
-import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
-import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
-import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
-import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.IReindexJobSubmitter;
-import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
-import ca.uhn.fhir.rest.server.provider.ProviderConstants;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
-import org.springframework.batch.core.Job;
-import org.springframework.batch.core.JobExecution;
-import org.springframework.batch.core.JobParameters;
-import org.springframework.batch.core.JobParametersInvalidException;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-
-import javax.transaction.Transactional;
-import java.util.List;
-
-public class ReindexJobSubmitterImpl implements IReindexJobSubmitter {
-	@Autowired
-	PartitionedUrlValidator myPartitionedUrlValidator;
-	@Autowired
-	DaoConfig myDaoConfig;
-	@Autowired
-	private ISearchParamRegistry mySearchParamRegistry;
-	@Autowired
-	private IBatchJobSubmitter myBatchJobSubmitter;
-	@Autowired
-	@Qualifier(BatchConstants.REINDEX_JOB_NAME)
-	private Job myReindexJob;
-	@Autowired
-	@Qualifier(BatchConstants.REINDEX_EVERYTHING_JOB_NAME)
-	private Job myReindexEverythingJob;
-
-	@Override
-	@Transactional(Transactional.TxType.NEVER)
-	public JobExecution submitJob(Integer theBatchSize, List<String> theUrlsToReindex, RequestDetails theRequest) throws JobParametersInvalidException {
-		if (theBatchSize == null) {
-			theBatchSize = myDaoConfig.getReindexBatchSize();
-		}
-		RequestListJson requestListJson = myPartitionedUrlValidator.buildRequestListJson(theRequest, theUrlsToReindex);
-		if (!myDaoConfig.isReindexEnabled()) {
-			throw new ForbiddenOperationException(Msg.code(1273) + "Reindexing is disabled on this server.");
-		}
-
-		/*
-		 * On the first time we run a particular reindex job, let's make sure we
-		 * have the latest search parameters loaded. A common reason to
-		 * be reindexing is that the search parameters have changed in some way, so
-		 * this makes sure we're on the latest versions
-		 */
-		mySearchParamRegistry.forceRefresh();
-
-		JobParameters jobParameters = ReverseCronologicalBatchResourcePidReader.buildJobParameters(ProviderConstants.OPERATION_REINDEX, theBatchSize, requestListJson);
-		return myBatchJobSubmitter.runJob(myReindexJob, jobParameters);
-	}
-
-	@Override
-	@Transactional(Transactional.TxType.NEVER)
-	public JobExecution submitEverythingJob(Integer theBatchSize, RequestDetails theRequest) throws JobParametersInvalidException {
-		if (theBatchSize == null) {
-			theBatchSize = myDaoConfig.getReindexBatchSize();
-		}
-		RequestPartitionId requestPartitionId = myPartitionedUrlValidator.requestPartitionIdFromRequest(theRequest);
-		if (!myDaoConfig.isReindexEnabled()) {
-			throw new ForbiddenOperationException(Msg.code(1274) + "Reindexing is disabled on this server.");
-		}
-
-		/*
-		 * On the first time we run a particular reindex job, let's make sure we
-		 * have the latest search parameters loaded. A common reason to
-		 * be reindexing is that the search parameters have changed in some way, so
-		 * this makes sure we're on the latest versions
-		 */
-		mySearchParamRegistry.forceRefresh();
-
-		JobParameters jobParameters = CronologicalBatchAllResourcePidReader.buildJobParameters(theBatchSize, requestPartitionId);
-		return myBatchJobSubmitter.runJob(myReindexEverythingJob, jobParameters);
-	}
-}

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

@@ -0,0 +1,141 @@
+package ca.uhn.fhir.jpa.reindex;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+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.svc.IResourceReindexSvc;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
+import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.SortOrderEnum;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Slice;
+import org.springframework.transaction.annotation.Transactional;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class ResourceReindexSvcImpl implements IResourceReindexSvc {
+
+	@Autowired
+	private IResourceTableDao myResourceTableDao;
+
+	@Autowired
+	private MatchUrlService myMatchUrlService;
+
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
+	@Autowired
+	private FhirContext myFhirContext;
+
+	@Override
+	public boolean isAllResourceTypeSupported() {
+		return true;
+	}
+
+	@Override
+	@Transactional
+	public IdChunk fetchResourceIdsPage(Date theStart, Date theEnd, @Nullable RequestPartitionId theRequestPartitionId, @Nullable String theUrl) {
+
+		int pageSize = 20000;
+		if (theUrl == null) {
+			return fetchResourceIdsPageNoUrl(theStart, theEnd, pageSize, theRequestPartitionId);
+		} else {
+			return fetchResourceIdsPageWithUrl(theStart, theEnd, pageSize, theUrl, theRequestPartitionId);
+		}
+	}
+
+	private IdChunk fetchResourceIdsPageWithUrl(Date theStart, Date theEnd, int thePageSize, String theUrl, RequestPartitionId theRequestPartitionId) {
+
+		String resourceType = theUrl.substring(0, theUrl.indexOf('?'));
+		RuntimeResourceDefinition def = myFhirContext.getResourceDefinition(resourceType);
+
+		SearchParameterMap searchParamMap = myMatchUrlService.translateMatchUrl(theUrl, def);
+		searchParamMap.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
+		searchParamMap.setLastUpdated(new DateRangeParam(theStart, theEnd));
+		searchParamMap.setCount(thePageSize);
+
+		IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
+		SystemRequestDetails request = new SystemRequestDetails();
+		request.setRequestPartitionId(theRequestPartitionId);
+		List<ResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
+
+		// just a list of the same size where every element is the same resource type
+		List<String> resourceTypes = ids
+			.stream()
+			.map(t -> resourceType)
+			.collect(Collectors.toList());
+
+		Date lastDate = null;
+		if (ids.size() > 0) {
+			lastDate = dao.readByPid(ids.get(ids.size() - 1)).getMeta().getLastUpdated();
+		}
+
+		return new IdChunk(ids, resourceTypes, lastDate);
+	}
+
+	@Nonnull
+	private IdChunk fetchResourceIdsPageNoUrl(Date theStart, Date theEnd, int thePagesize, RequestPartitionId theRequestPartitionId) {
+		Pageable page = Pageable.ofSize(thePagesize);
+		Slice<Object[]> slice;
+		if (theRequestPartitionId == null || theRequestPartitionId.isAllPartitions()) {
+			slice = myResourceTableDao.findIdsTypesAndUpdateTimesOfResourcesWithinUpdatedRangeOrderedFromOldest(page, theStart, theEnd);
+		} else if (theRequestPartitionId.isDefaultPartition()) {
+			slice = myResourceTableDao.findIdsTypesAndUpdateTimesOfResourcesWithinUpdatedRangeOrderedFromOldestForDefaultPartition(page, theStart, theEnd);
+		} else {
+			slice = myResourceTableDao.findIdsTypesAndUpdateTimesOfResourcesWithinUpdatedRangeOrderedFromOldestForPartitionIds(page, theStart, theEnd, theRequestPartitionId.getPartitionIds());
+		}
+
+		List<Object[]> content = slice.getContent();
+		if (content.isEmpty()) {
+			return new IdChunk(Collections.emptyList(), Collections.emptyList(), null);
+		}
+
+		List<ResourcePersistentId> ids = content
+			.stream()
+			.map(t -> new ResourcePersistentId(t[0]))
+			.collect(Collectors.toList());
+
+		List<String> types = content
+			.stream()
+			.map(t -> (String) t[1])
+			.collect(Collectors.toList());
+
+		Date lastDate = (Date) content.get(content.size() - 1)[2];
+
+		return new IdChunk(ids, types, lastDate);
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexEverythingJobConfig.java

@@ -1,90 +0,0 @@
-package ca.uhn.fhir.jpa.reindex.job;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
-import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
-import org.springframework.batch.core.Job;
-import org.springframework.batch.core.Step;
-import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
-import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
-import org.springframework.batch.core.configuration.annotation.StepScope;
-import org.springframework.batch.core.listener.ExecutionContextPromotionListener;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Lazy;
-
-import java.util.List;
-
-import static ca.uhn.fhir.jpa.batch.config.BatchConstants.REINDEX_EVERYTHING_JOB_NAME;
-
-/**
- * Spring batch Job configuration file. Contains all necessary plumbing to run a
- * Reindex job.
- */
-@Configuration
-public class ReindexEverythingJobConfig {
-	public static final String REINDEX_EVERYTHING_STEP_NAME = "reindex-everything-step";
-
-	@Autowired
-	private StepBuilderFactory myStepBuilderFactory;
-	@Autowired
-	private JobBuilderFactory myJobBuilderFactory;
-	@Autowired
-	private ReindexWriter myReindexWriter;
-	@Autowired
-	private PidReaderCounterListener myPidCountRecorderListener;
-
-	@Bean(name = REINDEX_EVERYTHING_JOB_NAME)
-	@Lazy
-	public Job reindexJob() {
-		return myJobBuilderFactory.get(REINDEX_EVERYTHING_JOB_NAME)
-			.start(reindexEverythingStep())
-			.build();
-	}
-
-	@Bean
-	public Step reindexEverythingStep() {
-		return myStepBuilderFactory.get(REINDEX_EVERYTHING_STEP_NAME)
-			.<List<Long>, List<Long>>chunk(1)
-			.reader(cronologicalBatchAllResourcePidReader())
-			.writer(myReindexWriter)
-			.listener(myPidCountRecorderListener)
-			.listener(reindexEverythingPromotionListener())
-			.build();
-	}
-
-	@Bean
-	@StepScope
-	public CronologicalBatchAllResourcePidReader cronologicalBatchAllResourcePidReader() {
-		return new CronologicalBatchAllResourcePidReader();
-	}
-
-	@Bean
-	public ExecutionContextPromotionListener reindexEverythingPromotionListener() {
-		ExecutionContextPromotionListener listener = new ExecutionContextPromotionListener();
-
-		listener.setKeys(new String[]{PidReaderCounterListener.RESOURCE_TOTAL_PROCESSED});
-
-		return listener;
-	}
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexJobConfig.java

@@ -1,92 +0,0 @@
-package ca.uhn.fhir.jpa.reindex.job;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
-import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
-import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
-import org.springframework.batch.core.Job;
-import org.springframework.batch.core.Step;
-import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
-import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
-import org.springframework.batch.core.listener.ExecutionContextPromotionListener;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Lazy;
-
-import java.util.List;
-
-import static ca.uhn.fhir.jpa.batch.config.BatchConstants.REINDEX_JOB_NAME;
-
-/**
- * Spring batch Job configuration file. Contains all necessary plumbing to run a
- * Reindex job.
- */
-@Configuration
-public class ReindexJobConfig {
-	public static final String REINDEX_URL_LIST_STEP_NAME = "reindex-url-list-step";
-
-	@Autowired
-	private StepBuilderFactory myStepBuilderFactory;
-	@Autowired
-	private JobBuilderFactory myJobBuilderFactory;
-	@Autowired
-	private ReindexWriter myReindexWriter;
-
-	@Autowired
-	private MultiUrlJobParameterValidator myMultiUrlProcessorParameterValidator;
-
-	@Autowired
-	private PidReaderCounterListener myPidCountRecorderListener;
-
-	@Autowired
-	private ReverseCronologicalBatchResourcePidReader myReverseCronologicalBatchResourcePidReader;
-
-	@Bean(name = REINDEX_JOB_NAME)
-	@Lazy
-	public Job reindexJob() {
-		return myJobBuilderFactory.get(REINDEX_JOB_NAME)
-			.validator(myMultiUrlProcessorParameterValidator)
-			.start(reindexUrlListStep())
-			.build();
-	}
-
-	@Bean
-	public Step reindexUrlListStep() {
-		return myStepBuilderFactory.get(REINDEX_URL_LIST_STEP_NAME)
-			.<List<Long>, List<Long>>chunk(1)
-			.reader(myReverseCronologicalBatchResourcePidReader)
-			.writer(myReindexWriter)
-			.listener(myPidCountRecorderListener)
-			.listener(reindexPromotionListener())
-			.build();
-	}
-
-	@Bean
-	public ExecutionContextPromotionListener reindexPromotionListener() {
-		ExecutionContextPromotionListener listener = new ExecutionContextPromotionListener();
-
-		listener.setKeys(new String[]{PidReaderCounterListener.RESOURCE_TOTAL_PROCESSED});
-
-		return listener;
-	}
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexWriter.java

@@ -1,67 +0,0 @@
-package ca.uhn.fhir.jpa.reindex.job;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.dao.expunge.PartitionRunner;
-import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.batch.item.ItemWriter;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.SliceImpl;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.support.TransactionTemplate;
-
-import java.util.List;
-
-/**
- * Reindex the provided list of pids of resources
- */
-
-public class ReindexWriter implements ItemWriter<List<Long>> {
-	private static final Logger ourLog = LoggerFactory.getLogger(ReindexWriter.class);
-
-	public static final String PROCESS_NAME = "Reindexing";
-	public static final String THREAD_PREFIX = "reindex";
-
-	@Autowired
-	ResourceReindexer myResourceReindexer;
-	@Autowired
-	DaoConfig myDaoConfig;
-	@Autowired
-	protected PlatformTransactionManager myTxManager;
-
-	@Override
-	public void write(List<? extends List<Long>> thePidLists) throws Exception {
-		PartitionRunner partitionRunner = new PartitionRunner(PROCESS_NAME, THREAD_PREFIX, myDaoConfig.getReindexBatchSize(), myDaoConfig.getReindexThreadCount());
-
-		// Note that since our chunk size is 1, there will always be exactly one list
-		for (List<Long> pidList : thePidLists) {
-			partitionRunner.runInPartitionedThreads(new SliceImpl<>(pidList), pids -> reindexPids(pids));
-		}
-	}
-
-	private void reindexPids(List<Long> pidList) {
-		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
-		txTemplate.executeWithoutResult(t -> pidList.forEach(pid -> myResourceReindexer.readAndReindexResourceByPid(pid)));
-	}
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/ReindexController.java

@@ -1,19 +0,0 @@
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/ReindexFailureException.java

@@ -1,36 +0,0 @@
-package ca.uhn.fhir.jpa.util;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-public class ReindexFailureException extends RuntimeException {
-	private static final long serialVersionUID = 1L;
-	
-	private Long myResourceId;
-
-	public ReindexFailureException(Long theResourceId) {
-		myResourceId = theResourceId;
-	}
-
-	public Long getResourceId() {
-		return myResourceId;
-	}
-
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplTest.java

@@ -260,6 +260,27 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testIncrementWorkChunkErrorCount() {
+		// Setup
+
+		JobInstance instance = createInstance();
+		String instanceId = mySvc.storeNewInstance(instance);
+		String chunkId = mySvc.storeWorkChunk("definition-chunkId", 1, "step-chunkId", instanceId, 1, null);
+		assertNotNull(chunkId);
+
+		// Execute
+
+		mySvc.incrementWorkChunkErrorCount(chunkId, 2);
+		mySvc.incrementWorkChunkErrorCount(chunkId, 3);
+
+		// Verify
+
+		List<WorkChunk> chunks = mySvc.fetchWorkChunksWithoutData(instanceId, 100, 0);
+		assertEquals(1, chunks.size());
+		assertEquals(5, chunks.get(0).getErrorCount());
+	}
+
 	@Test
 	public void testMarkChunkAsCompleted_Error() {
 		JobInstance instance = createInstance();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/BulkImportR4Test.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.bulk.imprt2;
 
 import ca.uhn.fhir.batch2.api.IJobCleanerService;
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
-import ca.uhn.fhir.batch2.jobs.imprt.BulkImport2AppCtx;
+import ca.uhn.fhir.batch2.jobs.imprt.BulkImportAppCtx;
 import ca.uhn.fhir.batch2.jobs.imprt.BulkImportFileServlet;
 import ca.uhn.fhir.batch2.jobs.imprt.BulkImportJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstance;
@@ -87,7 +87,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		}
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(parameters);
 
 		// Execute
@@ -134,7 +134,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		}
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(parameters);
 
 		IAnonymousInterceptor anonymousInterceptor = (thePointcut, theArgs) -> {
@@ -212,7 +212,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		}
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(parameters);
 
 		// Execute
@@ -249,7 +249,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		parameters.addNdJsonUrl(url);
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(parameters);
 
 		IAnonymousInterceptor anonymousInterceptor = (thePointcut, theArgs) -> {
@@ -294,7 +294,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		// Setup
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 
 		// Execute
 
@@ -314,7 +314,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		// Setup
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(new BulkImportJobParameters());
 
 		// Execute
@@ -325,7 +325,10 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		} catch (InvalidRequestException e) {
 
 			// Verify
-			assertEquals("HAPI-2039: Failed to validate parameters for job of type BULK_IMPORT_PULL: [myNdJsonUrls At least one NDJSON URL must be provided]", e.getMessage());
+			String expected = """
+				HAPI-2039: Failed to validate parameters for job of type BULK_IMPORT_PULL:\s
+				 * myNdJsonUrls - At least one NDJSON URL must be provided""";
+			assertEquals(expected, e.getMessage());
 
 		}
 	}
@@ -338,7 +341,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		parameters.addNdJsonUrl("foo");
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(parameters);
 
 		// Execute
@@ -349,7 +352,10 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 		} catch (InvalidRequestException e) {
 
 			// Verify
-			assertEquals("HAPI-2039: Failed to validate parameters for job of type BULK_IMPORT_PULL: [myNdJsonUrls[0].<list element> Must be a valid URL]", e.getMessage());
+			String expected = """
+				HAPI-2039: Failed to validate parameters for job of type BULK_IMPORT_PULL:\s
+				 * myNdJsonUrls[0].<list element> - Must be a valid URL""";
+			assertEquals(expected, e.getMessage());
 
 		}
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
@@ -34,6 +36,8 @@ import static org.junit.jupiter.api.Assertions.fail;
 	JpaDstu2Config.class,
 	HapiJpaConfig.class,
 	TestJPAConfig.class,
+	JpaBatch2Config.class,
+	Batch2JobsConfig.class,
 	TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
 })
 public class TestDstu2Config {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
@@ -38,6 +40,8 @@ import static org.junit.jupiter.api.Assertions.fail;
 	JpaDstu3Config.class,
 	HapiJpaConfig.class,
 	TestJPAConfig.class,
+	JpaBatch2Config.class,
+	Batch2JobsConfig.class,
 	TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
 })
 public class TestDstu3Config {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
 import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
+import ca.uhn.fhir.jpa.util.Batch2JobHelper;
 import ca.uhn.fhir.test.utilities.BatchJobHelper;
 import org.springframework.batch.core.explore.JobExplorer;
 import org.springframework.context.annotation.Bean;
@@ -79,6 +80,11 @@ public class TestJPAConfig {
 		return new BatchJobHelper(theJobExplorer);
 	}
 
+	@Bean
+	public Batch2JobHelper batch2JobHelper() {
+		return new Batch2JobHelper();
+	}
+
 	@Bean
 	@Lazy
 	public IBinaryStorageSvc binaryStorage() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR5Config.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
 import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
 import ca.uhn.fhir.jpa.config.r5.JpaR5Config;
@@ -34,6 +36,8 @@ import static org.junit.jupiter.api.Assertions.fail;
 	JpaR5Config.class,
 	HapiJpaConfig.class,
 	TestJPAConfig.class,
+	JpaBatch2Config.class,
+	Batch2JobsConfig.class,
 	TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
 })
 public class TestR5Config {

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

@@ -56,6 +56,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.test.BaseTest;
+import ca.uhn.fhir.jpa.util.Batch2JobHelper;
 import ca.uhn.fhir.test.utilities.BatchJobHelper;
 import ca.uhn.fhir.test.utilities.LoggingExtension;
 import ca.uhn.fhir.test.utilities.ProxyUtil;
@@ -183,6 +184,8 @@ public abstract class BaseJpaTest extends BaseTest {
 	protected IFulltextSearchSvc myFulltestSearchSvc;
 	@Autowired(required = false)
 	protected BatchJobHelper myBatchJobHelper;
+	@Autowired(required = false)
+	protected Batch2JobHelper myBatch2JobHelper;
 	@Autowired
 	protected ITermConceptDao myTermConceptDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
-import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@@ -30,8 +29,6 @@ import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.client.api.IGenericClient;
-import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.NumberParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
@@ -40,13 +37,11 @@ import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
 import org.mockito.internal.util.collections.ListUtil;
 
 import java.util.List;
@@ -55,7 +50,6 @@ import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
-import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.fail;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -85,7 +85,6 @@ import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
-import java.util.Set;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
@@ -101,7 +100,7 @@ import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.Mockito.mock;
 
 @SuppressWarnings("unchecked")
-@ContextConfiguration(classes= TestHibernateSearchAddInConfig.NoFT.class)
+@ContextConfiguration(classes = TestHibernateSearchAddInConfig.NoFT.class)
 public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2SearchNoFtTest.class);
 	@Autowired
@@ -154,7 +153,7 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		IIdType moId = myMedicationOrderDao.create(mo, mySrd).getId().toUnqualifiedVersionless();
 
 		HttpServletRequest request = mock(HttpServletRequest.class);
-		IBundleProvider resp = myPatientDao.patientTypeEverything(request, null, null, null,  null, null, null, null, mySrd, null);
+		IBundleProvider resp = myPatientDao.patientTypeEverything(request, null, null, null, null, null, null, null, mySrd, null);
 		assertThat(toUnqualifiedVersionlessIds(resp), containsInAnyOrder(orgId, medId, patId, moId, patId2));
 
 		request = mock(HttpServletRequest.class);
@@ -1588,7 +1587,7 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		String methodName = "testSearchValueQuantity";
 
 		QuantityParam param;
-		Set<ResourcePersistentId> found;
+		List<ResourcePersistentId> found;
 		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
 		found = myObservationDao.searchForIds(new SearchParameterMap("value-quantity", param), null);
 		int initialSize = found.size();

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

@@ -290,7 +290,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			assertThat(toUnqualifiedVersionlessIdValues(found), hasItem(id2.getValue()));
 		}
 		{
-			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
+			List<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
 			assertThat(ResourcePersistentId.toLongList(found), not(hasItem(id2.getIdPartAsLong())));
 		}
 	}
@@ -1507,7 +1507,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 				"}\n";
 		//@formatter:on
 
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, inputStr);
@@ -2698,7 +2698,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 		assertThat(str.length(), greaterThan(ResourceIndexedSearchParamString.MAX_LENGTH));
 
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -2813,7 +2813,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 		String subStr1 = longStr1.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
 		String subStr2 = longStr2.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new IdentifierDt(subStr1, subStr2)), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new IdentifierDt(subStr1, subStr2)), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -2840,12 +2840,12 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 	public void testValidateAgainstDstu2Profile() throws Exception {
 		myDaoConfig.setAllowExternalReferences(true);
 
-		String stream = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_structuredefinition_dstu2.xml"), StandardCharsets.UTF_8);
+		String stream = loadResource("/binu_testpatient_structuredefinition_dstu2.xml");
 
 		StructureDefinition sd = myFhirContext.newXmlParser().parseResource(StructureDefinition.class, stream);
 		myStructureDefinitionDao.create(sd, mySrd);
 
-		String rawResource = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_resource.json"), StandardCharsets.UTF_8);
+		String rawResource = loadResource("/binu_testpatient_resource.json");
 		IBaseResource parsedResource = myFhirContext.newJsonParser().parseResource(rawResource);
 		try {
 			myPatientDao.validate((Patient) parsedResource, null, rawResource, EncodingEnum.JSON, ValidationModeEnum.UPDATE, null, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2UpdateTest.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
 import ca.uhn.fhir.i18n.Msg;
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
@@ -14,11 +13,10 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 
 import java.io.IOException;
@@ -41,7 +39,6 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2UpdateTest.class);
 
 
-
 	@Test
 	public void testUpdateByUrl() {
 		String methodName = "testUpdateByUrl";
@@ -100,7 +97,7 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
 		conformance.setId("");
 		myConformanceDao.create(conformance);
 
-		assertEquals(1, myConformanceDao.search(new SearchParameterMap().setLoadSynchronous(true)).size().intValue());
+		assertEquals(1, myConformanceDao.search(new SearchParameterMap().setLoadSynchronous(true)).sizeOrThrowNpe());
 	}
 
 	/**
@@ -171,7 +168,7 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
 		p2.addName().addFamily("Tester").addGiven("testUpdateMaintainsSearchParamsDstu2BBB");
 		myPatientDao.create(p2, mySrd);
 
-		Set<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsDstu2AAA")), null);
+		List<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsDstu2AAA")), null);
 		assertEquals(1, ids.size());
 		assertThat(ResourcePersistentId.toLongList(ids), contains(p1id.getIdPartAsLong()));
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -117,7 +117,7 @@ import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
-@SuppressWarnings({"unchecked", "deprecation"})
+@SuppressWarnings({"unchecked"})
 public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3Test.class);
@@ -161,8 +161,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	private List<String> extractNames(IBundleProvider theSearch) {
-		ArrayList<String> retVal = new ArrayList<String>();
+		ArrayList<String> retVal = new ArrayList<>();
-		for (IBaseResource next : theSearch.getResources(0, theSearch.size())) {
+		for (IBaseResource next : theSearch.getResources(0, theSearch.sizeOrThrowNpe())) {
 			Patient nextPt = (Patient) next;
 			retVal.add(nextPt.getName().get(0).getNameAsSingleString());
 		}
@@ -187,7 +187,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	private List<UriType> sortIds(List<UriType> theProfiles) {
-		ArrayList<UriType> retVal = new ArrayList<UriType>(theProfiles);
+		ArrayList<UriType> retVal = new ArrayList<>(theProfiles);
 		retVal.sort(Comparator.comparing(PrimitiveType::getValue));
 		return retVal;
 	}
@@ -199,7 +199,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		org.setLanguageElement(new CodeType("EN_ca"));
 		org.setName(methodName);
 
-		ArrayList<Coding> tl = new ArrayList<Coding>();
+		ArrayList<Coding> tl = new ArrayList<>();
 		tl.add(new Coding().setSystem(methodName).setCode(methodName));
 		org.getMeta().getTag().addAll(tl);
 
@@ -254,11 +254,11 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		IIdType id2 = myObservationDao.create(o2, mySrd).getId();
 
 		{
-			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
+			List<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
 			assertThat(ResourcePersistentId.toLongList(found), hasItem(id2.getIdPartAsLong()));
 		}
 		{
-			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
+			List<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
 			assertThat(ResourcePersistentId.toLongList(found), not(hasItem(id2.getIdPartAsLong())));
 		}
 	}
@@ -1914,7 +1914,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 				"}\n";
 		//@formatter:on
 
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, inputStr);
@@ -3165,7 +3165,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		assertThat(str.length(), greaterThan(ResourceIndexedSearchParamString.MAX_LENGTH));
 
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -3266,8 +3266,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		assertEquals("http://profile/1", profiles.get(0).getValue());
 		assertEquals("http://profile/2", profiles.get(1).getValue());
 
-		myPatientDao.metaAddOperation(patientId, new Meta().addTag( "http://foo", "Cat", "Kittens"), null);
+		myPatientDao.metaAddOperation(patientId, new Meta().addTag("http://foo", "Cat", "Kittens"), null);
-		myPatientDao.metaAddOperation(patientId, new Meta().addTag( "http://foo", "Cow", "Calves"), null);
+		myPatientDao.metaAddOperation(patientId, new Meta().addTag("http://foo", "Cow", "Calves"), null);
 
 		retrieved = myPatientDao.read(patientId, mySrd);
 		published = (ArrayList<Coding>) retrieved.getMeta().getTag();
@@ -3344,7 +3344,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		String subStr1 = longStr1.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
 		String subStr2 = longStr2.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -3368,7 +3368,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	@Test
-	public void testUpdateRejectsIdWhichPointsToForcedId() throws InterruptedException {
+	public void testUpdateRejectsIdWhichPointsToForcedId() {
 		Patient p1 = new Patient();
 		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsIdWhichPointsToForcedId01");
 		p1.addName().setFamily("Tester").addGiven("testUpdateRejectsIdWhichPointsToForcedId01");
@@ -3416,7 +3416,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	private static List<String> toStringList(List<UriType> theUriType) {
-		ArrayList<String> retVal = new ArrayList<String>();
+		ArrayList<String> retVal = new ArrayList<>();
 		for (UriType next : theUriType) {
 			retVal.add(next.getValue());
 		}

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

@@ -466,7 +466,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 		p2.addName().setFamily("Tester").addGiven("testUpdateMaintainsSearchParamsDstu2BBB");
 		myPatientDao.create(p2, mySrd).getId();
 
-		Set<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
+		List<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
 		assertEquals(1, ids.size());
 		assertThat(ResourcePersistentId.toLongList(ids), contains(p1id.getIdPartAsLong()));
 

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

@@ -476,11 +476,11 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		IIdType id2 = myObservationDao.create(o2, mySrd).getId();
 
 		{
-			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
+			List<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
 			assertThat(ResourcePersistentId.toLongList(found), hasItem(id2.getIdPartAsLong()));
 		}
 		{
-			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
+			List<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
 			assertThat(ResourcePersistentId.toLongList(found), not(hasItem(id2.getIdPartAsLong())));
 		}
 	}
@@ -2481,7 +2481,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 				"}\n";
 		//@formatter:on
 
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, inputStr);
@@ -3914,7 +3914,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		assertThat(str.length(), greaterThan(ResourceIndexedSearchParamString.MAX_LENGTH));
 
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -4093,7 +4093,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		String subStr1 = longStr1.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
 		String subStr2 = longStr2.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
-		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
+		List<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java

@@ -724,7 +724,7 @@ public class FhirResourceDaoR4UpdateTest extends BaseJpaR4Test {
 		p2.addName().setFamily("Tester").addGiven("testUpdateMaintainsSearchParamsDstu2BBB");
 		myPatientDao.create(p2, mySrd).getId();
 
-		Set<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
+		List<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
 		assertEquals(1, ids.size());
 		assertThat(ResourcePersistentId.toLongList(ids), contains(p1id.getIdPartAsLong()));
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

@@ -1,54 +1,26 @@
 package ca.uhn.fhir.jpa.delete.job;
 
-import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.batch2.api.IJobCoordinator;
-import ca.uhn.fhir.jpa.batch.CommonBatchJobConfig;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
-import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
-import ca.uhn.fhir.jpa.batch.config.BatchConstants;
+import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
-import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
-import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
-import ca.uhn.fhir.test.utilities.BatchJobHelper;
-import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.batch.core.Job;
-import org.springframework.batch.core.JobExecution;
-import org.springframework.batch.core.JobParameter;
-import org.springframework.batch.core.JobParameters;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
 
 import javax.annotation.PostConstruct;
-import java.util.Date;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.hasSize;
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class ReindexJobTest extends BaseJpaR4Test {
-	private static final Logger ourLog = LoggerFactory.getLogger(ReindexJobTest.class);
-
 	@Autowired
-	private IBatchJobSubmitter myBatchJobSubmitter;
+	private IJobCoordinator myJobCoordinator;
-	@Autowired
-	@Qualifier(BatchConstants.REINDEX_JOB_NAME)
-	private Job myReindexJob;
-	@Autowired
-	@Qualifier(BatchConstants.REINDEX_EVERYTHING_JOB_NAME)
-	private Job myReindexEverythingJob;
-	@Autowired
-	private BatchJobHelper myBatchJobHelper;
 
 	private ReindexTestHelper myReindexTestHelper;
 
@@ -58,128 +30,61 @@ public class ReindexJobTest extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testReindexJob() throws Exception {
+	public void testReindex_ByUrl() {
 		// setup
 
 		IIdType obsFinalId = myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.FINAL);
-		IIdType obsCancelledId = myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.CANCELLED);
+		myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.CANCELLED);
 
 		myReindexTestHelper.createAlleleSearchParameter();
 
 		assertEquals(2, myObservationDao.search(SearchParameterMap.newSynchronous()).size());
-		// The searchparam value is on the observation, but it hasn't been indexed yet
+		// The search param value is on the observation, but it hasn't been indexed yet
 		assertThat(myReindexTestHelper.getAlleleObservationIds(), hasSize(0));
 
 		// Only reindex one of them
-		JobParameters jobParameters = MultiUrlJobParameterUtil.buildJobParameters("Observation?status=final");
+		ReindexJobParameters parameters = new ReindexJobParameters();
+		parameters.addUrl("Observation?status=final");
 
 		// execute
-		JobExecution jobExecution = myBatchJobSubmitter.runJob(myReindexJob, jobParameters);
+		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-
+		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
-		myBatchJobHelper.awaitJobCompletion(jobExecution);
+		startRequest.setParameters(parameters);
+		String id = myJobCoordinator.startInstance(startRequest);
+		myBatch2JobHelper.awaitJobCompletion(id);
 
 		// validate
 		assertEquals(2, myObservationDao.search(SearchParameterMap.newSynchronous()).size());
+
 		// Now one of them should be indexed
 		List<String> alleleObservationIds = myReindexTestHelper.getAlleleObservationIds();
 		assertThat(alleleObservationIds, hasSize(1));
 		assertEquals(obsFinalId.getIdPart(), alleleObservationIds.get(0));
 	}
 
-	private long generateAndReturnTimeGap() {
-		long start_time = System.currentTimeMillis();
-		sleepUntilTimeChanges();
-		long end_time = System.currentTimeMillis();
-		return end_time - start_time;
-	}
-
 	@Test
-	public void testReindexJobLastUpdatedFilter() throws Exception {
+	public void testReindex_Everything() {
-		// Given
-		DaoMethodOutcome T1_Patient = myReindexTestHelper.createEyeColourPatient(true);
-		long timeGap1 = generateAndReturnTimeGap();
-		DaoMethodOutcome T3_Patient = myReindexTestHelper.createEyeColourPatient(true);
-		long timeGap2 = generateAndReturnTimeGap();
-		DaoMethodOutcome T6_Patient = myReindexTestHelper.createEyeColourPatient(true);
-
-		// Setup cutoff
-		Date firstPatientLastUpdated = T1_Patient.getResource().getMeta().getLastUpdated();
-		Date secondPatientLastUpdated = T3_Patient.getResource().getMeta().getLastUpdated();
-		Date T2_Date = DateUtils.addMilliseconds(firstPatientLastUpdated, (int) (timeGap1 / 2));
-		Date T4_Date = DateUtils.addMilliseconds(secondPatientLastUpdated, (int) (timeGap2 / 2));
-		ourLog.info("Older lastUpdated: {}", firstPatientLastUpdated);
-		ourLog.info("Newer lastUpdated: {}", secondPatientLastUpdated);
-		ourLog.info("Cutoff Lowerbound: {}", T2_Date);
-		ourLog.info("Cutoff Upperbound: {}", T4_Date);
-		assertTrue(T2_Date.after(firstPatientLastUpdated));
-		assertTrue(T2_Date.before(secondPatientLastUpdated));
-		assertTrue(T4_Date.after(secondPatientLastUpdated));
-
-		//Create our new SP.
-		myReindexTestHelper.createEyeColourSearchParameter();
-
-		//There exists 3 patients
-		assertEquals(3, myPatientDao.search(SearchParameterMap.newSynchronous()).size());
-		// The searchparam value is on the patient, but it hasn't been indexed yet, so the call to search for all with eye-colour returns 0
-		assertThat(myReindexTestHelper.getEyeColourPatientIds(), hasSize(0));
-
-		// Only reindex one of them
-		String T2_DateString = new DateTimeDt(T2_Date).setPrecision(TemporalPrecisionEnum.MILLI).getValueAsString();
-		String T4_DateString = new DateTimeDt(T4_Date).setPrecision(TemporalPrecisionEnum.MILLI).getValueAsString();
-		JobParameters T3_Patient_JobParams = MultiUrlJobParameterUtil.buildJobParameters("Patient?_lastUpdated=ge" +
-			T2_DateString + "&_lastUpdated=le" + T4_DateString);
-		JobParameters T1_Patient_JobParams = MultiUrlJobParameterUtil.buildJobParameters("Patient?_lastUpdated=le" + T2_DateString);
-		JobParameters T6_Patient_JobParams = MultiUrlJobParameterUtil.buildJobParameters("Patient?_lastUpdated=ge" + T4_DateString);
-
-		// execute
-		JobExecution jobExecution = myBatchJobSubmitter.runJob(myReindexJob, T3_Patient_JobParams);
-		myBatchJobHelper.awaitJobCompletion(jobExecution);
-
-		// Now one of them should be indexed for the eye colour SP
-		List<String> eyeColourPatientIds = myReindexTestHelper.getEyeColourPatientIds();
-		assertThat(eyeColourPatientIds, hasSize(1));
-		assertEquals(T3_Patient.getId().getIdPart(), eyeColourPatientIds.get(0));
-
-		// execute
-		JobExecution jobExecutionT1 = myBatchJobSubmitter.runJob(myReindexJob, T1_Patient_JobParams);
-		myBatchJobHelper.awaitJobCompletion(jobExecution);
-
-		// Now one of them should be indexed for the eye colour SP
-		eyeColourPatientIds = myReindexTestHelper.getEyeColourPatientIds();
-		assertThat(eyeColourPatientIds, hasSize(2));
-		assertThat(eyeColourPatientIds, hasItem(T3_Patient.getId().getIdPart()));
-
-		// execute
-		JobExecution jobExecutionT6 = myBatchJobSubmitter.runJob(myReindexJob, T6_Patient_JobParams);
-		myBatchJobHelper.awaitJobCompletion(jobExecution);
-
-		// Now one of them should be indexed for the eye colour SP
-		eyeColourPatientIds = myReindexTestHelper.getEyeColourPatientIds();
-		assertThat(eyeColourPatientIds, hasSize(3));
-		assertThat(eyeColourPatientIds, hasItem(T6_Patient.getId().getIdPart()));
-	}
-
-	@Test
-	public void testReindexEverythingJob() throws Exception {
 		// setup
 
 		for (int i = 0; i < 50; ++i) {
 			myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.FINAL);
 		}
 
+		sleepUntilTimeChanges();
+
 		myReindexTestHelper.createAlleleSearchParameter();
 		mySearchParamRegistry.forceRefresh();
 
 		assertEquals(50, myObservationDao.search(SearchParameterMap.newSynchronous()).size());
-		// The searchparam value is on the observation, but it hasn't been indexed yet
+		// The search param value is on the observation, but it hasn't been indexed yet
 		assertThat(myReindexTestHelper.getAlleleObservationIds(), hasSize(0));
 
-		JobParameters jobParameters = buildEverythingJobParameters(3L);
-
 		// execute
-		JobExecution jobExecution = myBatchJobSubmitter.runJob(myReindexEverythingJob, jobParameters);
+		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-
+		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
-		myBatchJobHelper.awaitJobCompletion(jobExecution);
+		startRequest.setParameters(new ReindexJobParameters());
+		String id = myJobCoordinator.startInstance(startRequest);
+		myBatch2JobHelper.awaitJobCompletion(id);
 
 		// validate
 		assertEquals(50, myObservationDao.search(SearchParameterMap.newSynchronous()).size());
@@ -187,13 +92,4 @@ public class ReindexJobTest extends BaseJpaR4Test {
 		assertThat(myReindexTestHelper.getAlleleObservationIds(), hasSize(50));
 	}
 
-	private JobParameters buildEverythingJobParameters(Long theBatchSize) {
-		Map<String, JobParameter> map = new HashMap<>();
-		map.put(CronologicalBatchAllResourcePidReader.JOB_PARAM_START_TIME, new JobParameter(DateUtils.addMinutes(new Date(), CommonBatchJobConfig.MINUTES_IN_FUTURE_TO_PROCESS_FROM)));
-		map.put(CronologicalBatchAllResourcePidReader.JOB_PARAM_BATCH_SIZE, new JobParameter(theBatchSize.longValue()));
-		JobParameters parameters = new JobParameters(map);
-		return parameters;
-	}
-
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java

@@ -25,7 +25,7 @@ import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
-import ca.uhn.fhir.rest.server.provider.ReindexProvider;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
 import ca.uhn.fhir.test.utilities.JettyUtil;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

@@ -21,6 +21,7 @@ import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DecimalType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.StringType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -128,6 +129,9 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
 		myTenantClientInterceptor.setTenantId(TENANT_B);
 		IIdType obsFinalB = doCreateResource(reindexTestHelper.buildObservationWithAlleleExtension());
 
+		myTenantClientInterceptor.setTenantId(DEFAULT_PARTITION_NAME);
+		IIdType obsFinalD = doCreateResource(reindexTestHelper.buildObservationWithAlleleExtension());
+
 		reindexTestHelper.createAlleleSearchParameter();
 
 		// The searchparam value is on the observation, but it hasn't been indexed yet
@@ -135,13 +139,11 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
 		assertThat(reindexTestHelper.getAlleleObservationIds(myClient), hasSize(0));
 		myTenantClientInterceptor.setTenantId(TENANT_B);
 		assertThat(reindexTestHelper.getAlleleObservationIds(myClient), hasSize(0));
+		myTenantClientInterceptor.setTenantId(DEFAULT_PARTITION_NAME);
+		assertThat(reindexTestHelper.getAlleleObservationIds(myClient), hasSize(0));
+
 		// setup
 		Parameters input = new Parameters();
-		Integer batchSize = 2401;
-		input.addParameter(ProviderConstants.OPERATION_REINDEX_PARAM_BATCH_SIZE, new DecimalType(batchSize));
-		input.addParameter(ProviderConstants.OPERATION_REINDEX_PARAM_EVERYTHING, new BooleanType(true));
-
-		ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
 
 		// reindex all of Tenant A
 		myTenantClientInterceptor.setTenantId(TENANT_A);
@@ -152,9 +154,9 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
 			.withParameters(input)
 			.execute();
 		ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
-		DecimalType jobId = (DecimalType) response.getParameter(ProviderConstants.OPERATION_REINDEX_RESPONSE_JOB_ID);
+		StringType jobId = (StringType) response.getParameter(ProviderConstants.OPERATION_REINDEX_RESPONSE_JOB_ID);
 
-		myBatchJobHelper.awaitJobExecution(jobId.getValueAsNumber().longValue());
+		myBatch2JobHelper.awaitJobCompletion(jobId.getValue());
 
 		// validate
 		List<String> alleleObservationIds = reindexTestHelper.getAlleleObservationIds(myClient);
@@ -164,6 +166,25 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
 		assertEquals(obsFinalA.getIdPart(), alleleObservationIds.get(0));
 		myTenantClientInterceptor.setTenantId(TENANT_B);
 		assertThat(reindexTestHelper.getAlleleObservationIds(myClient), hasSize(0));
+		myTenantClientInterceptor.setTenantId(DEFAULT_PARTITION_NAME);
+		assertThat(reindexTestHelper.getAlleleObservationIds(myClient), hasSize(0));
+
+		// Reindex default partition
+		myTenantClientInterceptor.setTenantId(DEFAULT_PARTITION_NAME);
+		response = myClient
+			.operation()
+			.onServer()
+			.named(ProviderConstants.OPERATION_REINDEX)
+			.withParameters(input)
+			.execute();
+		ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
+		jobId = (StringType) response.getParameter(ProviderConstants.OPERATION_REINDEX_RESPONSE_JOB_ID);
+
+		myBatch2JobHelper.awaitJobCompletion(jobId.getValue());
+
+
+		myTenantClientInterceptor.setTenantId(DEFAULT_PARTITION_NAME);
+		assertThat(reindexTestHelper.getAlleleObservationIds(myClient), hasSize(1));
 	}
 
 	@Test
@@ -187,8 +208,6 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
 
 		// setup
 		Parameters input = new Parameters();
-		Integer batchSize = 2401;
-		input.addParameter(ProviderConstants.OPERATION_REINDEX_PARAM_BATCH_SIZE, new DecimalType(batchSize));
 		input.addParameter(ProviderConstants.OPERATION_REINDEX_PARAM_URL, "Observation?status=final");
 
 		ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
@@ -202,9 +221,9 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
 			.withParameters(input)
 			.execute();
 		ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
-		DecimalType jobId = (DecimalType) response.getParameter(ProviderConstants.OPERATION_REINDEX_RESPONSE_JOB_ID);
+		StringType jobId = (StringType) response.getParameter(ProviderConstants.OPERATION_REINDEX_RESPONSE_JOB_ID);
 
-		myBatchJobHelper.awaitJobExecution(jobId.getValueAsNumber().longValue());
+		myBatch2JobHelper.awaitJobCompletion(jobId.getValue());
 
 		// validate
 		List<String> alleleObservationIds = reindexTestHelper.getAlleleObservationIds(myClient);

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

@@ -0,0 +1,153 @@
+package ca.uhn.fhir.jpa.reindex;
+
+import ca.uhn.fhir.batch2.api.IJobDataSink;
+import ca.uhn.fhir.batch2.api.RunOutcome;
+import ca.uhn.fhir.batch2.api.VoidModel;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexChunkIds;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
+import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import org.hl7.fhir.r4.model.IdType;
+import org.junit.jupiter.api.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.Mock;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.INDEX_STATUS_INDEXED;
+import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+public class ReindexStepTest extends BaseJpaR4Test {
+
+	@Autowired
+	private ReindexStep myReindexStep;
+
+	@Mock
+	private IJobDataSink<VoidModel> myDataSink;
+
+	@Captor
+	private ArgumentCaptor<String> myErrorCaptor;
+
+	@Test
+	public void testReindex_NoActionNeeded() {
+
+		// Setup
+
+		Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
+		Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
+
+		ReindexChunkIds data = new ReindexChunkIds();
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id0.toString()));
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id1.toString()));
+
+		// Execute
+
+		myCaptureQueriesListener.clear();
+		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id");
+
+		// Verify
+		assertEquals(2, outcome.getRecordsProcessed());
+		assertEquals(4, myCaptureQueriesListener.logSelectQueries().size());
+		assertEquals(0, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.getCommitCount());
+		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
+	}
+
+
+	@Test
+	public void testReindex_IndexesWereMissing() {
+
+		// Setup
+
+		Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
+		Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
+
+		ReindexChunkIds data = new ReindexChunkIds();
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id0.toString()));
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id1.toString()));
+
+		runInTransaction(() -> {
+			myResourceIndexedSearchParamStringDao.deleteByResourceId(id0);
+			myResourceIndexedSearchParamTokenDao.deleteByResourceId(id0);
+		});
+
+		// Execute
+
+		myCaptureQueriesListener.clear();
+		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id");
+
+		// Verify
+		assertEquals(2, outcome.getRecordsProcessed());
+		assertEquals(4, myCaptureQueriesListener.logSelectQueries().size());
+		// name, family, phonetic, deceased, active
+		assertEquals(5, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.getCommitCount());
+		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
+	}
+
+
+	@Test
+	public void testReindex_OneResourceReindexFailedButOthersSucceeded() {
+
+		// Setup
+
+		Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
+		Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
+		Long idPatientToInvalidate = createPatient().getIdPartAsLong();
+		Long idObservation = createObservation(withSubject(new IdType("Patient/" + idPatientToInvalidate))).getIdPartAsLong();
+
+		ReindexChunkIds data = new ReindexChunkIds();
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id0.toString()));
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id1.toString()));
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(idPatientToInvalidate.toString()));
+		data.getIds().add(new ReindexChunkIds.Id().setResourceType("Observation").setId(idObservation.toString()));
+
+		runInTransaction(() -> {
+			// Swap in some invalid text, which will cause an error when we go to reindex
+			assertEquals(1, myEntityManager.createNativeQuery("UPDATE HFJ_RES_VER SET RES_TEXT = null WHERE RES_ID = " + idPatientToInvalidate).executeUpdate());
+			assertEquals(1, myEntityManager.createNativeQuery("UPDATE HFJ_RES_VER SET RES_TEXT_VC = 'ABCDEFG' WHERE RES_ID = " + idPatientToInvalidate).executeUpdate());
+
+			// Also set the current index status to errored on one, so it can be reset
+			assertEquals(1, myEntityManager.createNativeQuery("UPDATE HFJ_RESOURCE SET SP_INDEX_STATUS = 2 WHERE RES_ID = " + id0).executeUpdate());
+
+			myResourceIndexedSearchParamStringDao.deleteByResourceId(id0);
+			myResourceIndexedSearchParamTokenDao.deleteByResourceId(id0);
+		});
+
+		// Execute
+
+		myCaptureQueriesListener.clear();
+		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id");
+
+		// Verify
+		assertEquals(4, outcome.getRecordsProcessed());
+		assertEquals(6, myCaptureQueriesListener.logSelectQueries().size());
+		assertEquals(5, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(2, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.getCommitCount());
+		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
+
+		verify(myDataSink, times(1)).recoveredError(myErrorCaptor.capture());
+		String message = myErrorCaptor.getValue();
+		message = message.replace("Observation.subject.where(resolve() is Patient)", "Observation.subject"); // depending on whether subject or patient gets indexed first
+		assertEquals("Failure reindexing Patient/" + idPatientToInvalidate + ": HAPI-0928: Failed to parse database resource[Patient/" + idPatientToInvalidate + " (pid " + idPatientToInvalidate + ", version R4): HAPI-1861: Failed to parse JSON encoded FHIR content: HAPI-1859: Content does not appear to be FHIR JSON, first non-whitespace character was: 'A' (must be '{')", message);
+
+		runInTransaction(() -> {
+			ResourceTable table = myResourceTableDao.findById(idPatientToInvalidate).orElseThrow();
+			assertEquals(INDEX_STATUS_INDEXING_FAILED, table.getIndexStatus());
+
+			table = myResourceTableDao.findById(id0).orElseThrow();
+			assertEquals(INDEX_STATUS_INDEXED, table.getIndexStatus());
+		});
+	}
+
+
+}

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

@@ -0,0 +1,151 @@
+package ca.uhn.fhir.jpa.reindex;
+
+import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
+import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+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.Date;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+@SuppressWarnings("unchecked")
+@TestMethodOrder(value = MethodOrderer.MethodName.class)
+public class ResourceReindexSvcImplTest extends BaseJpaR4Test {
+
+	@Autowired
+	private IResourceReindexSvc mySvc;
+
+	@Test
+	public void testFetchResourceIdsPage_NoUrl_WithData() {
+
+		// Setup
+
+		createPatient(withActiveFalse());
+		sleepUntilTimeChanges();
+
+		Date start = new Date();
+
+		Long id0 = createPatient(withActiveFalse()).getIdPartAsLong();
+		sleepUntilTimeChanges();
+		Long id1 = createPatient(withActiveFalse()).getIdPartAsLong();
+		sleepUntilTimeChanges();
+		Date beforeLastInRange = new Date();
+		sleepUntilTimeChanges();
+		Long id2 = createObservation(withObservationCode("http://foo", "bar")).getIdPartAsLong();
+		sleepUntilTimeChanges();
+
+		Date end = new Date();
+
+		sleepUntilTimeChanges();
+
+		createPatient(withActiveFalse());
+
+		// Execute
+
+		myCaptureQueriesListener.clear();
+		IResourceReindexSvc.IdChunk page = mySvc.fetchResourceIdsPage(start, end, null, null);
+
+		// Verify
+
+		assertThat(page.getResourceTypes().toString(), page.getResourceTypes(), contains("Patient", "Patient", "Observation"));
+		assertThat(page.getIds(), contains(new ResourcePersistentId(id0), new ResourcePersistentId(id1), new ResourcePersistentId(id2)));
+		assertTrue(page.getLastDate().after(beforeLastInRange));
+		assertTrue(page.getLastDate().before(end));
+
+		assertEquals(1, myCaptureQueriesListener.logSelectQueries().size());
+		assertEquals(0, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.getCommitCount());
+		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
+
+	}
+
+
+	@Test
+	public void testFetchResourceIdsPage_NoUrl_NoData() {
+
+		// Setup
+
+		Date start = new Date();
+		Date end = new Date();
+
+		// Execute
+
+		myCaptureQueriesListener.clear();
+		IResourceReindexSvc.IdChunk page = mySvc.fetchResourceIdsPage(start, end, null, null);
+
+		// Verify
+
+		assertEquals(0, page.getResourceTypes().size());
+		assertEquals(0, page.getIds().size());
+		assertNull(page.getLastDate());
+
+		assertEquals(1, myCaptureQueriesListener.logSelectQueries().size());
+		assertEquals(0, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.getCommitCount());
+		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
+
+	}
+
+
+	@Test
+	public void testFetchResourceIdsPage_WithUrl_WithData() {
+
+		// Setup
+
+		createPatient(withActiveFalse());
+		sleepUntilTimeChanges();
+
+		// Start of resources within range
+		Date start = new Date();
+		sleepUntilTimeChanges();
+		Long id0 = createPatient(withActiveFalse()).getIdPartAsLong();
+		createObservation(withObservationCode("http://foo", "bar"));
+		createObservation(withObservationCode("http://foo", "bar"));
+		sleepUntilTimeChanges();
+		Date beforeLastInRange = new Date();
+		sleepUntilTimeChanges();
+		Long id1 = createPatient(withActiveFalse()).getIdPartAsLong();
+		sleepUntilTimeChanges();
+		Date end = new Date();
+		sleepUntilTimeChanges();
+		// End of resources within range
+
+		createObservation(withObservationCode("http://foo", "bar"));
+		createPatient(withActiveFalse());
+		sleepUntilTimeChanges();
+
+		// Execute
+
+		myCaptureQueriesListener.clear();
+		IResourceReindexSvc.IdChunk page = mySvc.fetchResourceIdsPage(start, end, null, "Patient?active=false");
+
+		// Verify
+
+		assertThat(page.getResourceTypes().toString(), page.getResourceTypes(), contains("Patient", "Patient"));
+		assertThat(page.getIds(), contains(new ResourcePersistentId(id0), new ResourcePersistentId(id1)));
+		assertTrue(page.getLastDate().after(beforeLastInRange));
+		assertTrue(page.getLastDate().before(end));
+
+		assertEquals(3, myCaptureQueriesListener.logSelectQueries().size());
+		assertEquals(0, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.getCommitCount());
+		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
+
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/reindex/job/ReindexWriterTest.java

@@ -1,51 +0,0 @@
-package ca.uhn.fhir.jpa.reindex.job;
-
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.InjectMocks;
-import org.mockito.Mock;
-import org.mockito.junit.jupiter.MockitoExtension;
-import org.springframework.transaction.PlatformTransactionManager;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import static org.mockito.ArgumentMatchers.anyLong;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.verifyNoMoreInteractions;
-import static org.mockito.Mockito.when;
-
-@ExtendWith(MockitoExtension.class)
-public class ReindexWriterTest {
-
-	@Mock
-	private DaoConfig myDaoConfig;
-	@Mock
-	private PlatformTransactionManager myPlatformTransactionManager;
-	@Mock
-	ResourceReindexer myResourceReindexer;
-
-	@InjectMocks
-	private ReindexWriter myReindexWriter;
-
-	@Test
-	public void testReindexSplitsPidList() throws Exception {
-		when(myDaoConfig.getReindexBatchSize()).thenReturn(5);
-		when(myDaoConfig.getReindexThreadCount()).thenReturn(4);
-
-		List<Long> pidList = new ArrayList<>();
-		int count = 20;
-		for (long i = 0; i < count; ++i) {
-			pidList.add(i);
-		}
-		List<List<Long>> pidListList = new ArrayList<>();
-		pidListList.add(pidList);
-		myReindexWriter.write(pidListList);
-
-		verify(myResourceReindexer, times(count)).readAndReindexResourceByPid(anyLong());
-		verifyNoMoreInteractions(myResourceReindexer);
-	}
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/Batch2JobHelper.java

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.jpa.util;
+
+import ca.uhn.fhir.batch2.api.IJobCleanerService;
+import ca.uhn.fhir.batch2.api.IJobCoordinator;
+import ca.uhn.fhir.batch2.model.StatusEnum;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.concurrent.TimeUnit;
+
+import static org.awaitility.Awaitility.await;
+import static org.hamcrest.Matchers.equalTo;
+
+public class Batch2JobHelper {
+
+	@Autowired
+	private IJobCleanerService myJobCleanerService;
+
+	@Autowired
+	private IJobCoordinator myJobCoordinator;
+
+	public void awaitJobCompletion(String theId) {
+		await().until(() -> {
+			myJobCleanerService.runCleanupPass();
+			return myJobCoordinator.getInstance(theId).getStatus();
+		}, equalTo(StatusEnum.COMPLETED));
+	}
+
+}

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -73,9 +73,9 @@ import java.util.stream.Collectors;
 @Indexed(routingBinder= @RoutingBinderRef(type = ResourceTableRoutingBinder.class))
 @Entity
 @Table(name = "HFJ_RESOURCE", uniqueConstraints = {}, indexes = {
+	// Do not reuse previously used index name: IDX_INDEXSTATUS
 	@Index(name = "IDX_RES_DATE", columnList = "RES_UPDATED"),
 	@Index(name = "IDX_RES_TYPE", columnList = "RES_TYPE"),
-	@Index(name = "IDX_INDEXSTATUS", columnList = "SP_INDEX_STATUS")
 })
 @NamedEntityGraph(name = "Resource.noJoins")
 public class ResourceTable extends BaseHasResource implements Serializable, IBasePersistedResource, IResourceLookup {

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -195,14 +195,6 @@
 						</webApp>
 					</configuration>
 				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<configuration>
-						<source>1.8</source>
-						<target>1.8</target>
-					</configuration>
-				</plugin>
 				<!--This plugin's configuration is used to store Eclipse m2e settings 
 					only. It has no influence on the Maven build itself. -->
 				<plugin>

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhirtest;
 
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
@@ -268,6 +269,12 @@ public class TestRestfulServer extends RestfulServer {
 		 */
 		registerProvider(myAppCtx.getBean(BulkDataExportProvider.class));
 
+		/*
+		 * $reindex
+		 */
+		registerProvider(myAppCtx.getBean(ReindexProvider.class));
+
+
 		/*
 		 * $diff operation
 		 */

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

@@ -1,6 +1,8 @@
 package ca.uhn.fhirtest.config;
 
+import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
+import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -19,7 +21,9 @@ import org.springframework.context.annotation.Import;
 	WebsocketDispatcherConfig.class,
 	SubscriptionChannelConfig.class,
 	SubscriptionProcessorConfig.class,
-	SubscriptionSubmitterConfig.class
+	SubscriptionSubmitterConfig.class,
+	JpaBatch2Config.class,
+	Batch2JobsConfig.class
 })
 public class CommonConfig {
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -43,9 +43,7 @@ import java.util.concurrent.TimeUnit;
 @Import({CommonConfig.class, JpaDstu3Config.class, HapiJpaConfig.class})
 @EnableTransactionManagement()
 public class TestDstu3Config {
-	public static final String FHIR_DB_USERNAME = "${fhir.db.username}";
+	public static final String FHIR_LUCENE_LOCATION_DSTU3 = "fhir.lucene.location.dstu3";
-	public static final String FHIR_DB_PASSWORD = "${fhir.db.password}";
-	public static final String FHIR_LUCENE_LOCATION_DSTU3 = "${fhir.lucene.location.dstu3}";
 
 	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);
 	private String myDbPassword = System.getProperty(TestR5Config.FHIR_DB_PASSWORD);

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -43,9 +43,7 @@ import java.util.concurrent.TimeUnit;
 @Import({CommonConfig.class, JpaR4Config.class, HapiJpaConfig.class})
 @EnableTransactionManagement()
 public class TestR4Config {
-	public static final String FHIR_DB_USERNAME = "${fhir.db.username}";
+	public static final String FHIR_LUCENE_LOCATION_R4 = "fhir.lucene.location.r4";
-	public static final String FHIR_DB_PASSWORD = "${fhir.db.password}";
-	public static final String FHIR_LUCENE_LOCATION_R4 = "${fhir.lucene.location.r4}";
 	public static final Integer COUNT_SEARCH_RESULTS_UP_TO = 50000;
 
 	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -45,9 +45,9 @@ import java.util.concurrent.TimeUnit;
 @Import({CommonConfig.class, JpaR5Config.class, HapiJpaConfig.class})
 @EnableTransactionManagement()
 public class TestR5Config {
-	public static final String FHIR_DB_USERNAME = "${fhir.db.username}";
+	public static final String FHIR_DB_USERNAME = "fhir.db.username";
-	public static final String FHIR_DB_PASSWORD = "${fhir.db.password}";
+	public static final String FHIR_DB_PASSWORD = "fhir.db.password";
-	public static final String FHIR_LUCENE_LOCATION_R5 = "${fhir.lucene.location.r5}";
+	public static final String FHIR_LUCENE_LOCATION_R5 = "fhir.lucene.location.r5";
 	public static final Integer COUNT_SEARCH_RESULTS_UP_TO = 50000;
 	private static final Logger ourLog = LoggerFactory.getLogger(TestR5Config.class);
 	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);

hapi-fhir-jpaserver-uhnfhirtest/src/test/java/ca/uhn/fhirtest/UhnFhirTestApp.java

@@ -12,6 +12,8 @@ import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
 import org.hl7.fhir.instance.model.api.IIdType;
 
+import static ca.uhn.fhirtest.config.TestDstu3Config.FHIR_LUCENE_LOCATION_DSTU3;
+
 public class UhnFhirTestApp {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UhnFhirTestApp.class);

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server-openapi/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/ResourcePersistentId.java

@@ -33,7 +33,6 @@ import java.util.Optional;
  * a Long, a String, or something else.
  */
 public class ResourcePersistentId {
-	private static final String RESOURCE_PID = "RESOURCE_PID";
 	private Object myId;
 	private Long myVersion;
 	private IIdType myAssociatedResourceId;
@@ -91,6 +90,9 @@ public class ResourcePersistentId {
 	}
 
 	public Long getIdAsLong() {
+		if (myId instanceof String) {
+			return Long.parseLong((String) myId);
+		}
 		return (Long) myId;
 	}
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/provider/ProviderConstants.java

@@ -157,7 +157,7 @@ public class ProviderConstants {
 	public static final String OPERATION_BATCH_RESPONSE_JOB_ID = "jobId";
 
 	/**
-	 * Operation name for the $delete-expunge operation
+	 * Operation name for the $reindex operation
 	 */
 	public static final String OPERATION_REINDEX = "$reindex";
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/provider/ReindexProvider.java

@@ -1,86 +0,0 @@
-package ca.uhn.fhir.rest.server.provider;
-
-/*-
- * #%L
- * HAPI FHIR - Server Framework
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.i18n.Msg;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.Operation;
-import ca.uhn.fhir.rest.annotation.OperationParam;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.IReindexJobSubmitter;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.ParametersUtil;
-import org.hl7.fhir.instance.model.api.IBaseParameters;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.springframework.batch.core.JobExecution;
-import org.springframework.batch.core.JobParametersInvalidException;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import javax.annotation.Nullable;
-import java.math.BigDecimal;
-import java.util.List;
-import java.util.stream.Collectors;
-
-public class ReindexProvider {
-	private final FhirContext myFhirContext;
-	private final IReindexJobSubmitter myReindexJobSubmitter;
-	private final MultiUrlProcessor myMultiUrlProcessor;
-
-	public ReindexProvider(FhirContext theFhirContext, IReindexJobSubmitter theReindexJobSubmitter) {
-		myFhirContext = theFhirContext;
-		myMultiUrlProcessor = new MultiUrlProcessor(theFhirContext, theReindexJobSubmitter);
-		myReindexJobSubmitter = theReindexJobSubmitter;
-	}
-
-	@Operation(name = ProviderConstants.OPERATION_REINDEX, idempotent = false)
-	public IBaseParameters Reindex(
-		@OperationParam(name = ProviderConstants.OPERATION_REINDEX_PARAM_URL, typeName = "string", min = 0, max = 1) List<IPrimitiveType<String>> theUrlsToReindex,
-		@OperationParam(name = ProviderConstants.OPERATION_REINDEX_PARAM_BATCH_SIZE, typeName = "decimal", min = 0, max = 1) IPrimitiveType<BigDecimal> theBatchSize,
-		@OperationParam(name = ProviderConstants.OPERATION_REINDEX_PARAM_EVERYTHING, typeName = "boolean", min = 0, max = 1) IPrimitiveType<Boolean> theEverything,
-		RequestDetails theRequestDetails
-	) {
-		boolean everything = theEverything != null && theEverything.getValue();
-		@Nullable Integer batchSize = myMultiUrlProcessor.getBatchSize(theBatchSize);
-		if (everything) {
-			return processEverything(batchSize, theRequestDetails);
-		} else if (theUrlsToReindex != null && !theUrlsToReindex.isEmpty()) {
-			List<String> urls = theUrlsToReindex.stream().map(IPrimitiveType::getValue).collect(Collectors.toList());
-			return myMultiUrlProcessor.processUrls(urls, batchSize, theRequestDetails);
-		} else {
-			throw new InvalidRequestException(Msg.code(318) + ProviderConstants.OPERATION_REINDEX + " must specify either everything=true or provide at least one value for " + ProviderConstants.OPERATION_REINDEX_PARAM_URL);
-		}
-	}
-
-	private IBaseParameters processEverything(Integer theBatchSize, RequestDetails theRequestDetails) {
-		try {
-			JobExecution jobExecution = myReindexJobSubmitter.submitEverythingJob(theBatchSize, theRequestDetails);
-			IBaseParameters retVal = ParametersUtil.newInstance(myFhirContext);
-			ParametersUtil.addParameterToParametersLong(myFhirContext, retVal, ProviderConstants.OPERATION_BATCH_RESPONSE_JOB_ID, jobExecution.getJobId());
-			return retVal;
-		} catch (JobParametersInvalidException e) {
-			throw new InvalidRequestException(Msg.code(319) + "Invalid job parameters: " + e.getMessage(), e);
-		}
-	}
-
-
-}

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-samples</artifactId>

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

@@ -5,7 +5,7 @@
    <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>6.0.0-PRE6-SNAPSHOT</version>
+      <version>6.0.0-PRE8-SNAPSHOT</version>
       <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
 

hapi-fhir-spring-boot/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-sql-migrate/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -123,16 +123,6 @@
 				</executions>
 			</plugin>
 
-			<!-- Tell Maven which Java source version you want to use -->
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<configuration>
-					<source>8</source>
-					<target>8</target>
-				</configuration>
-			</plugin>
-
 			<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

hapi-fhir-storage-batch2-jobs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE6-SNAPSHOT</version>
+		<version>6.0.0-PRE8-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/config/Batch2JobsConfig.java

@@ -20,14 +20,16 @@ package ca.uhn.fhir.batch2.jobs.config;
  * #L%
  */
 
-import ca.uhn.fhir.batch2.jobs.imprt.BulkImport2AppCtx;
+import ca.uhn.fhir.batch2.jobs.imprt.BulkImportAppCtx;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 
 //When you define a new batch job, add it here.
 @Configuration
 @Import({
-	BulkImport2AppCtx.class
+	BulkImportAppCtx.class,
+	ReindexAppCtx.class
 })
 public class Batch2JobsConfig {
 	// nothing

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/imprt/BulkDataImportProvider.java

@@ -159,7 +159,7 @@ public class BulkDataImportProvider {
 		}
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(BulkImport2AppCtx.JOB_BULK_IMPORT_PULL);
+		request.setJobDefinitionId(BulkImportAppCtx.JOB_BULK_IMPORT_PULL);
 		request.setParameters(jobParameters);
 
 		ourLog.info("Requesting Bulk Import Job ($import by Manifest) with {} urls", typeAndUrls.size());

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/imprt/BulkImportAppCtx.java

@@ -27,7 +27,7 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
 @Configuration
-public class BulkImport2AppCtx {
+public class BulkImportAppCtx {
 
 	public static final String JOB_BULK_IMPORT_PULL = "BULK_IMPORT_PULL";
 	public static final int PARAM_MAXIMUM_BATCH_SIZE_DEFAULT = 800; // Avoid the 1000 SQL param limit
@@ -48,7 +48,6 @@ public class BulkImport2AppCtx {
 			.addLastStep(
 				"process-files",
 				"Process files",
-				NdJsonFileJson.class,
 				bulkImport2ConsumeFiles())
 			.build();
 	}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/imprt/BulkImportJobParameters.java

@@ -32,6 +32,10 @@ import javax.validation.constraints.Size;
 import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * This class is the parameters model object for starting a
+ * bulk import job.
+ */
 public class BulkImportJobParameters implements IModelJson {
 
 	@JsonProperty(value = "ndJsonUrls", required = true)

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/imprt/ConsumeFilesStep.java

@@ -23,6 +23,7 @@ package ca.uhn.fhir.batch2.jobs.imprt;
 import ca.uhn.fhir.batch2.api.IJobDataSink;
 import ca.uhn.fhir.batch2.api.ILastJobStepWorker;
 import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
+import ca.uhn.fhir.batch2.api.RunOutcome;
 import ca.uhn.fhir.batch2.api.StepExecutionDetails;
 import ca.uhn.fhir.batch2.api.VoidModel;
 import ca.uhn.fhir.context.FhirContext;
@@ -48,6 +49,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
 import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -70,8 +72,9 @@ public class ConsumeFilesStep implements ILastJobStepWorker<BulkImportJobParamet
 	@Autowired
 	private IFhirSystemDao<?, ?> mySystemDao;
 
+	@Nonnull
 	@Override
-	public RunOutcome run(StepExecutionDetails<BulkImportJobParameters, NdJsonFileJson> theStepExecutionDetails, IJobDataSink<VoidModel> theDataSink) {
+	public RunOutcome run(@Nonnull StepExecutionDetails<BulkImportJobParameters, NdJsonFileJson> theStepExecutionDetails, @Nonnull IJobDataSink<VoidModel> theDataSink) {
 
 		String ndjson = theStepExecutionDetails.getData().getNdJsonText();
 		String sourceName = theStepExecutionDetails.getData().getSourceName();

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/imprt/FetchFilesStep.java

@@ -22,8 +22,8 @@ package ca.uhn.fhir.batch2.jobs.imprt;
 
 import ca.uhn.fhir.batch2.api.IFirstJobStepWorker;
 import ca.uhn.fhir.batch2.api.IJobDataSink;
-import ca.uhn.fhir.batch2.api.IJobStepWorker;
 import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
+import ca.uhn.fhir.batch2.api.RunOutcome;
 import ca.uhn.fhir.batch2.api.StepExecutionDetails;
 import ca.uhn.fhir.batch2.api.VoidModel;
 import ca.uhn.fhir.i18n.Msg;
@@ -42,6 +42,7 @@ import org.apache.http.impl.client.HttpClientBuilder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -53,14 +54,15 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class FetchFilesStep implements IFirstJobStepWorker<BulkImportJobParameters, NdJsonFileJson> {
 	private static final Logger ourLog = LoggerFactory.getLogger(FetchFilesStep.class);
 
+	@Nonnull
 	@Override
-	public RunOutcome run(StepExecutionDetails<BulkImportJobParameters, VoidModel> theStepExecutionDetails, IJobDataSink<NdJsonFileJson> theDataSink) {
+	public RunOutcome run(@Nonnull StepExecutionDetails<BulkImportJobParameters, VoidModel> theStepExecutionDetails, @Nonnull IJobDataSink<NdJsonFileJson> theDataSink) {
 
 		Integer maxBatchResourceCount = theStepExecutionDetails
 			.getParameters()
 			.getMaxBatchResourceCount();
 		if (maxBatchResourceCount == null || maxBatchResourceCount <= 0) {
-			maxBatchResourceCount = BulkImport2AppCtx.PARAM_MAXIMUM_BATCH_SIZE_DEFAULT;
+			maxBatchResourceCount = BulkImportAppCtx.PARAM_MAXIMUM_BATCH_SIZE_DEFAULT;
 		}
 
 		try (CloseableHttpClient httpClient = newHttpClient(theStepExecutionDetails)) {

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/GenerateRangeChunksStep.java

@@ -0,0 +1,72 @@
+package ca.uhn.fhir.batch2.jobs.reindex;
+
+/*-
+ * #%L
+ * hapi-fhir-storage-batch2-jobs
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.batch2.api.IFirstJobStepWorker;
+import ca.uhn.fhir.batch2.api.IJobDataSink;
+import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
+import ca.uhn.fhir.batch2.api.RunOutcome;
+import ca.uhn.fhir.batch2.api.StepExecutionDetails;
+import ca.uhn.fhir.batch2.api.VoidModel;
+import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
+import org.hl7.fhir.r4.model.InstantType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nonnull;
+import java.util.Date;
+
+public class GenerateRangeChunksStep implements IFirstJobStepWorker<ReindexJobParameters, ReindexChunkRange> {
+	private static final Logger ourLog = LoggerFactory.getLogger(GenerateRangeChunksStep.class);
+
+	@Autowired
+	private IResourceReindexSvc myResourceReindexSvc;
+
+	@Nonnull
+	@Override
+	public RunOutcome run(@Nonnull StepExecutionDetails<ReindexJobParameters, VoidModel> theStepExecutionDetails, @Nonnull IJobDataSink<ReindexChunkRange> theDataSink) throws JobExecutionFailedException {
+		ReindexJobParameters params = theStepExecutionDetails.getParameters();
+
+		Date start = new InstantType("2000-01-01T00:00:00Z").getValue();
+		Date end = new Date();
+
+		if (params.getUrl().isEmpty()) {
+			ourLog.info("Initiating reindex of All Resources from {} to {}", start, end);
+			ReindexChunkRange nextRange = new ReindexChunkRange();
+			nextRange.setStart(start);
+			nextRange.setEnd(end);
+			theDataSink.accept(nextRange);
+		} else {
+			for (String nextUrl : params.getUrl()) {
+				ourLog.info("Initiating reindex of [{}]] from {} to {}", nextUrl, start, end);
+				ReindexChunkRange nextRange = new ReindexChunkRange();
+				nextRange.setUrl(nextUrl);
+				nextRange.setStart(start);
+				nextRange.setEnd(end);
+				theDataSink.accept(nextRange);
+			}
+		}
+
+		return RunOutcome.SUCCESS;
+	}
+
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/LoadIdsStep.java

@@ -0,0 +1,139 @@
+package ca.uhn.fhir.batch2.jobs.reindex;
+
+/*-
+ * #%L
+ * hapi-fhir-storage-batch2-jobs
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.batch2.api.IJobDataSink;
+import ca.uhn.fhir.batch2.api.IJobStepWorker;
+import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
+import ca.uhn.fhir.batch2.api.RunOutcome;
+import ca.uhn.fhir.batch2.api.StepExecutionDetails;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
+import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nonnull;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+public class LoadIdsStep implements IJobStepWorker<ReindexJobParameters, ReindexChunkRange, ReindexChunkIds> {
+	private static final Logger ourLog = LoggerFactory.getLogger(LoadIdsStep.class);
+
+	@Autowired
+	private IResourceReindexSvc myResourceReindexSvc;
+
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
+	@Autowired
+	private MatchUrlService myMatchUrlService;
+
+	@Nonnull
+	@Override
+	public RunOutcome run(@Nonnull StepExecutionDetails<ReindexJobParameters, ReindexChunkRange> theStepExecutionDetails, @Nonnull IJobDataSink<ReindexChunkIds> theDataSink) throws JobExecutionFailedException {
+
+		ReindexChunkRange data = theStepExecutionDetails.getData();
+
+		Date start = data.getStart();
+		Date end = data.getEnd();
+
+		ourLog.info("Beginning scan for reindex IDs in range {} to {}", start, end);
+
+		Date nextStart = start;
+		RequestPartitionId requestPartitionId = theStepExecutionDetails.getParameters().getRequestPartitionId();
+		Set<ReindexChunkIds.Id> idBuffer = new HashSet<>();
+		long previousLastTime = 0L;
+		int totalIdsFound = 0;
+		int chunkCount = 0;
+		while (true) {
+			String url = theStepExecutionDetails.getData().getUrl();
+
+			ourLog.info("Fetching resource ID chunk for URL {} - Range {} - {}", url, nextStart, end);
+			IResourceReindexSvc.IdChunk nextChunk = myResourceReindexSvc.fetchResourceIdsPage(nextStart, end, requestPartitionId, url);
+
+			if (nextChunk.getIds().isEmpty()) {
+				ourLog.info("No data returned");
+				break;
+			}
+
+			ourLog.info("Found {} IDs from {} to {}", nextChunk.getIds().size(), nextStart, nextChunk.getLastDate());
+
+			// If we get the same last time twice in a row, we've clearly reached the end
+			if (nextChunk.getLastDate().getTime() == previousLastTime) {
+				ourLog.info("Matching final timestamp of {}, loading is completed", new Date(previousLastTime));
+				break;
+			}
+			previousLastTime = nextChunk.getLastDate().getTime();
+
+			for (int i = 0; i < nextChunk.getIds().size(); i++) {
+				ReindexChunkIds.Id nextId = new ReindexChunkIds.Id();
+				nextId.setResourceType(nextChunk.getResourceTypes().get(i));
+				nextId.setId(nextChunk.getIds().get(i).getId().toString());
+				idBuffer.add(nextId);
+			}
+
+			nextStart = nextChunk.getLastDate();
+
+			if (idBuffer.size() >= 1000) {
+
+				List<ReindexChunkIds.Id> submissionIds = new ArrayList<>();
+				for (Iterator<ReindexChunkIds.Id> iter = idBuffer.iterator(); iter.hasNext(); ) {
+					submissionIds.add(iter.next());
+					iter.remove();
+					if (submissionIds.size() >= 1000) {
+						break;
+					}
+				}
+
+				totalIdsFound += submissionIds.size();
+				chunkCount++;
+				submitWorkChunk(submissionIds, theDataSink);
+			}
+		}
+
+		totalIdsFound += idBuffer.size();
+		chunkCount++;
+		submitWorkChunk(idBuffer, theDataSink);
+
+		ourLog.info("Submitted {} chunks with {} resource IDs", chunkCount, totalIdsFound);
+		return RunOutcome.SUCCESS;
+	}
+
+	private void submitWorkChunk(Collection<ReindexChunkIds.Id> theIdBuffer, IJobDataSink<ReindexChunkIds> theDataSink) {
+		if (theIdBuffer.isEmpty()) {
+			return;
+		}
+		ourLog.info("Submitting work chunk with {} IDs", theIdBuffer.size());
+
+		ReindexChunkIds data = new ReindexChunkIds();
+		data.getIds().addAll(theIdBuffer);
+		theDataSink.accept(data);
+	}
+
+}