value set expansion (#6286)

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

@@ -64,4 +64,12 @@
 			<property name="format" value="^(Base|Abstract).+$"/>
 		</module>
 	</module>
+
+	<!-- for suppression of rules; to use, surround code to exclude with comments: -->
+	<!-- CHECKSTYLE.OFF RuleToDisable   AND   CHECKSTYLE.ON RuleToDisable -->
+	<module name="SuppressWithPlainTextCommentFilter">
+		<property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)" />
+		<property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)" />
+	</module>
+
 </module>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6285-batch2-reindex-version2-added.yaml

@@ -0,0 +1,17 @@
+---
+type: fix
+issue: 6285
+title: "Updated the Reindex Batch2 job to allow
+        for an additional step that will check to ensure
+        that no pending 'reindex' work is needed.
+        This was done to prevent a bug in which
+        value set expansion would not return all
+        the existing CodeSystem Concepts after
+        a reindex call, due to some of the concepts
+        being deferred to future job runs.
+        
+        As such, `$reindex` operations on CodeSystems
+        will no longer result in incorrect value set
+        expansion when such an expansion is called
+        'too soon' after a $reindex operation.
+"

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

@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.api.IJobPartitionProvider;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.context.FhirVersionEnum;
@@ -158,6 +157,7 @@ import java.util.function.Supplier;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static java.util.Objects.isNull;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -1315,7 +1315,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			myJobPartitionProvider.getPartitionedUrls(theRequestDetails, urls).forEach(params::addPartitionedUrl);
 
 			JobInstanceStartRequest request = new JobInstanceStartRequest();
-			request.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+			request.setJobDefinitionId(JOB_REINDEX);
 			request.setParameters(params);
 			myJobCoordinator.startInstance(theRequestDetails, request);
 

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

@@ -27,7 +27,11 @@ import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
 import ca.uhn.fhir.context.support.LookupCodeRequest;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
+import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
+import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -176,6 +180,47 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
 		myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
 	}
 
+	/**
+	 * If there are more code systems to process
+	 * than {@link JpaStorageSettings#getDeferIndexingForCodesystemsOfSize()},
+	 * then these codes will have their processing deferred (for a later time).
+	 *
+	 * This can result in future reindex steps *skipping* these code systems (if
+	 * they're still deferred) and thus incorrect expansions resulting.
+	 *
+	 * So we override the reindex method for CodeSystems specifically to
+	 * force reindex batch jobs to wait until all code systems are processed before
+	 * moving on.
+	 */
+	@SuppressWarnings("rawtypes")
+	@Override
+	public ReindexOutcome reindex(
+			IResourcePersistentId thePid,
+			ReindexParameters theReindexParameters,
+			RequestDetails theRequest,
+			TransactionDetails theTransactionDetails) {
+		ReindexOutcome outcome = super.reindex(thePid, theReindexParameters, theRequest, theTransactionDetails);
+
+		if (outcome.getWarnings().isEmpty()) {
+			outcome.setHasPendingWork(true);
+		}
+		return outcome;
+	}
+
+	@Override
+	public ReindexJobStatus getReindexJobStatus() {
+		boolean isQueueEmpty = myTermDeferredStorageSvc.isStorageQueueEmpty(true);
+
+		ReindexJobStatus status = new ReindexJobStatus();
+		status.setHasReindexWorkPending(!isQueueEmpty);
+		if (status.isHasReindexWorkPending()) {
+			// force a run
+			myTermDeferredStorageSvc.saveDeferred();
+		}
+
+		return status;
+	}
+
 	@Override
 	public ResourceTable updateEntity(
 			RequestDetails theRequest,

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

@@ -593,7 +593,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		if (theStatisticsTracker.getUpdatedConceptCount() <= myStorageSettings.getDeferIndexingForCodesystemsOfSize()) {
 			saveConcept(conceptToAdd);
 			Long nextConceptPid = conceptToAdd.getId();
-			Validate.notNull(nextConceptPid);
+			Objects.requireNonNull(nextConceptPid);
 		} else {
 			myDeferredStorageSvc.addConceptToStorageQueue(conceptToAdd);
 		}

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

@@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.term;
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
-import ca.uhn.fhir.batch2.model.StatusEnum;
 import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
@@ -79,6 +78,8 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc, IHas
 	private static final long SAVE_ALL_DEFERRED_WARN_MINUTES = 1;
 	private static final long SAVE_ALL_DEFERRED_ERROR_MINUTES = 5;
 	private boolean myAllowDeferredTasksTimeout = true;
+	private static final List<String> BATCH_JOBS_TO_CARE_ABOUT =
+			List.of(TERM_CODE_SYSTEM_DELETE_JOB_NAME, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
 	private final List<TermCodeSystem> myDeferredCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
 	private final Queue<TermCodeSystemVersion> myDeferredCodeSystemVersionsDeletions = new ConcurrentLinkedQueue<>();
 	private final List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
@@ -436,7 +437,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc, IHas
 		return retVal;
 	}
 
-	private boolean isJobsExecuting() {
+	public boolean isJobsExecuting() {
 		cleanseEndedJobs();
 
 		return !myJobExecutions.isEmpty();
@@ -448,15 +449,18 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc, IHas
 		 * This is mostly a fail-safe
 		 * because "cancelled" jobs are never removed.
 		 */
-		List<String> executions = new ArrayList<>(myJobExecutions);
 		List<String> idsToDelete = new ArrayList<>();
-		for (String id : executions) {
+		for (String jobId : BATCH_JOBS_TO_CARE_ABOUT) {
-			// TODO - might want to consider a "fetch all instances"
+			List<JobInstance> jobInstanceInEndedState = myJobCoordinator.getInstancesbyJobDefinitionIdAndEndedStatus(
-			JobInstance instance = myJobCoordinator.getInstance(id);
+					jobId,
-			if (StatusEnum.getEndedStatuses().contains(instance.getStatus())) {
+					true, // ended = true (COMPLETED, FAILED, CANCELLED jobs only)
+					Math.max(myJobExecutions.size(), 1), // at most this many
+					0);
+			for (JobInstance instance : jobInstanceInEndedState) {
 				idsToDelete.add(instance.getInstanceId());
 			}
 		}
+
 		for (String id : idsToDelete) {
 			myJobExecutions.remove(id);
 		}

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

@@ -78,6 +78,8 @@ public interface ITermDeferredStorageSvc {
 
 	void logQueueForUnitTest();
 
+	boolean isJobsExecuting();
+
 	/**
 	 * Only to be used from tests - Disallow test timeouts on deferred tasks
 	 */

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java

@@ -1,14 +1,11 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
-import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -46,9 +43,11 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.jupiter.api.Assertions.fail;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.fail;
 
 
@@ -202,7 +201,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		mySearchParameterDao.create(fooSp, mySrd);
 
 		runInTransaction(()->{
-			List<JobInstance> allJobs = myBatch2JobHelper.findJobsByDefinition(ReindexAppCtx.JOB_REINDEX);
+			List<JobInstance> allJobs = myBatch2JobHelper.findJobsByDefinition(JOB_REINDEX);
 			assertEquals(1, allJobs.size());
 			assertEquals(1, allJobs.get(0).getParameters(ReindexJobParameters.class).getPartitionedUrls().size());
 			assertEquals("Patient?", allJobs.get(0).getParameters(ReindexJobParameters.class).getPartitionedUrls().get(0).getUrl());

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ComboUniqueParamTest.java

@@ -55,6 +55,7 @@ import java.util.List;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 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.assertj.core.api.Assertions.assertThat;
@@ -1075,7 +1076,7 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
 			parameters.addUrl(url);
 		}
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(mySrd, startRequest);
 		ourLog.info("Started reindex job with id {}", res.getInstanceId());

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4IndexStorageOptimizedTest.java

@@ -23,7 +23,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
 import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.model.util.SearchParamHash;
 import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
-import ca.uhn.fhir.jpa.reindex.ReindexStepTest;
+import ca.uhn.fhir.jpa.reindex.ReindexStepV1Test;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import ca.uhn.fhir.rest.param.BaseParam;
@@ -57,6 +57,7 @@ import org.springframework.data.jpa.repository.JpaRepository;
 
 import java.util.List;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -312,7 +313,7 @@ public class FhirResourceDaoR4IndexStorageOptimizedTest extends BaseJpaR4Test {
 			parameters.addUrl(url);
 		}
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(mySrd, startRequest);
 		ourLog.info("Started reindex job with id {}", res.getInstanceId());
@@ -321,7 +322,7 @@ public class FhirResourceDaoR4IndexStorageOptimizedTest extends BaseJpaR4Test {
 
 	// Additional existing tests with enabled IndexStorageOptimized
 	@Nested
-	public class IndexStorageOptimizedReindexStepTest extends ReindexStepTest {
+	public class IndexStorageOptimizedReindexStepTestV1 extends ReindexStepV1Test {
 		@BeforeEach
 		void setUp() {
 			myStorageSettings.setIndexStorageOptimized(true);

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

@@ -2,12 +2,15 @@ package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.batch2.api.IJobDataSink;
 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.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
 import ca.uhn.fhir.batch2.jobs.chunk.TypedPidJson;
 import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeStep;
+import ca.uhn.fhir.batch2.jobs.reindex.v1.ReindexStepV1;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
+import ca.uhn.fhir.batch2.model.JobInstance;
+import ca.uhn.fhir.batch2.model.WorkChunk;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
@@ -18,13 +21,13 @@ import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
 import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
-import ca.uhn.fhir.jpa.reindex.ReindexTestHelper;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
 import ca.uhn.fhir.jpa.interceptor.ForceOffsetSearchModeInterceptor;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
+import ca.uhn.fhir.jpa.reindex.ReindexTestHelper;
 import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.subscription.triggering.ISubscriptionTriggeringSvc;
@@ -146,7 +149,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 	@Autowired
 	private ISubscriptionTriggeringSvc mySubscriptionTriggeringSvc;
 	@Autowired
-	private ReindexStep myReindexStep;
+	private ReindexStepV1 myReindexStepV1;
 	@Autowired
 	private DeleteExpungeStep myDeleteExpungeStep;
 	@Autowired
@@ -1018,7 +1021,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		// insert to: HFJ_RESOURCE, HFJ_RES_VER, HFJ_RES_LINK
 		assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
-
 	}
 
 	@ParameterizedTest
@@ -1031,7 +1033,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 	})
 	public void testReindexJob_OptimizeStorage(boolean theOptimisticLock, ReindexParameters.OptimizeStorageModeEnum theOptimizeStorageModeEnum, int theExpectedSelectCount, int theExpectedUpdateCount) {
 		// Setup
-
 		ResourceIdListWorkChunkJson data = new ResourceIdListWorkChunkJson();
 		IIdType patientId = createPatient(withActiveTrue());
 		IIdType orgId = createOrganization(withName("MY ORG"));
@@ -1056,7 +1057,14 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		// execute
 		myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, mock(IJobDataSink.class), "123", "456", params);
+		JobInstance instance = new JobInstance();
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			mock(WorkChunk.class)
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, mock(IJobDataSink.class));
 
 		// validate
 		assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(theExpectedSelectCount);
@@ -1064,7 +1072,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		assertThat(myCaptureQueriesListener.getInsertQueriesForCurrentThread()).isEmpty();
 		assertThat(myCaptureQueriesListener.getDeleteQueriesForCurrentThread()).isEmpty();
 		assertEquals(10, outcome.getRecordsProcessed());
-
 	}
 
 	@Test
@@ -1095,7 +1102,14 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
         // execute
         myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, mock(IJobDataSink.class), "123", "456", params);
+		JobInstance instance = new JobInstance();
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			mock(WorkChunk.class)
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, mock(IJobDataSink.class));
 		assertEquals(20, outcome.getRecordsProcessed());
 
         // validate
@@ -1103,10 +1117,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
         assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
         assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
         assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
-
     }
 
-
 	public void assertNoPartitionSelectors() {
 		List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
 		for (SqlQuery next : selectQueries) {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.phonetic.PhoneticEncoderEnum;
@@ -22,7 +21,6 @@ import ca.uhn.fhir.rest.param.NumberParam;
 import ca.uhn.fhir.rest.param.ReferenceOrListParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.TokenOrListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -70,6 +68,7 @@ import org.springframework.transaction.support.TransactionTemplate;
 import java.util.List;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -441,11 +440,11 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		fooSp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
 
-		List<JobInstance> initialJobs = myBatch2JobHelper.findJobsByDefinition(ReindexAppCtx.JOB_REINDEX);
+		List<JobInstance> initialJobs = myBatch2JobHelper.findJobsByDefinition(JOB_REINDEX);
 
 		mySearchParameterDao.create(fooSp, mySrd);
 
-		List<JobInstance> finalJobs = myBatch2JobHelper.findJobsByDefinition(ReindexAppCtx.JOB_REINDEX);
+		List<JobInstance> finalJobs = myBatch2JobHelper.findJobsByDefinition(JOB_REINDEX);
 		List<JobInstance> newJobs = finalJobs.stream().filter(t -> !initialJobs.contains(t)).collect(Collectors.toList());
 		assertThat(newJobs.size()).as("number of jobs created").isEqualTo(1);
 	}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/tx/ReindexStepV1Test.java

@@ -6,7 +6,7 @@ import ca.uhn.fhir.batch2.api.VoidModel;
 import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
 import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrl;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
+import ca.uhn.fhir.batch2.jobs.reindex.v1.ReindexStepV1;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -26,7 +26,7 @@ import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
-public class ReindexStepTest {
+public class ReindexStepV1Test {
 
 	@Mock
 	private HapiTransactionService myHapiTransactionService;
@@ -34,7 +34,7 @@ public class ReindexStepTest {
 	private IJobDataSink<VoidModel> myDataSink;
 
 	@InjectMocks
-	private ReindexStep myReindexStep;
+	private ReindexStepV1 myReindexStepV1;
 
 	@Captor
 	private ArgumentCaptor<HapiTransactionService.ExecutionBuilder> builderArgumentCaptor;
@@ -51,7 +51,7 @@ public class ReindexStepTest {
 		when(myHapiTransactionService.buildExecutionBuilder(any())).thenCallRealMethod();
 
 		// when
-		myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", reindexJobParameters);
+		myReindexStepV1.doReindex(data, myDataSink, "index-id", "chunk-id", reindexJobParameters);
 
 		// then
 		assertMethodArgumentRequestPartitionId(expectedPartitionId);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java

@@ -1,8 +1,5 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.i18n.Msg;
@@ -60,9 +57,11 @@ import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.jupiter.api.Assertions.fail;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.fail;
 
 
@@ -244,7 +243,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 		runInTransaction(() -> {
 			myBatch2JobHelper.forceRunMaintenancePass();
 
-			List<JobInstance> allJobs = myBatch2JobHelper.findJobsByDefinition(ReindexAppCtx.JOB_REINDEX);
+			List<JobInstance> allJobs = myBatch2JobHelper.findJobsByDefinition(JOB_REINDEX);
 			assertEquals(1, allJobs.size());
 			assertEquals(1, allJobs.get(0).getParameters(ReindexJobParameters.class).getPartitionedUrls().size());
 			assertEquals("Patient?", allJobs.get(0).getParameters(ReindexJobParameters.class).getPartitionedUrls().get(0).getUrl());

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexStepV1Test.java

@@ -2,10 +2,13 @@ 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.StepExecutionDetails;
 import ca.uhn.fhir.batch2.api.VoidModel;
 import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
+import ca.uhn.fhir.batch2.jobs.reindex.v1.ReindexStepV1;
+import ca.uhn.fhir.batch2.model.JobInstance;
+import ca.uhn.fhir.batch2.model.WorkChunk;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
@@ -25,13 +28,14 @@ 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.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
-public class ReindexStepTest extends BaseJpaR4Test {
+public class ReindexStepV1Test extends BaseJpaR4Test {
 
 	@Autowired
-	private ReindexStep myReindexStep;
+	private ReindexStepV1 myReindexStepV1;
 
 	@Mock
 	private IJobDataSink<VoidModel> myDataSink;
@@ -46,9 +50,7 @@ public class ReindexStepTest extends BaseJpaR4Test {
 
 	@Test
 	public void testReindex_NoActionNeeded() {
-
 		// Setup
-
 		Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
 		Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
 
@@ -57,9 +59,19 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		data.addTypedPid("Patient", id1);
 
 		// Execute
-
+		ReindexJobParameters params = new ReindexJobParameters();
 		myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
+		JobInstance instance = new JobInstance();
+		instance.setInstanceId("index-id");
+		WorkChunk chunk = new WorkChunk();
+		chunk.setId("chunk-id");
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			chunk
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
 
 		// Verify
 		assertEquals(2, outcome.getRecordsProcessed());
@@ -72,12 +84,9 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
 	}
 
-
 	@Test
 	public void testReindex_NoActionNeeded_IndexMissingFieldsEnabled() {
-
 		// Setup
-
 		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.ENABLED);
 
 		Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
@@ -88,9 +97,16 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		data.addTypedPid("Patient", id1);
 
 		// Execute
-
+		ReindexJobParameters params = new ReindexJobParameters();
 		myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
+		JobInstance instance = new JobInstance();
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			mock(WorkChunk.class)
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
 
 		// Verify
 		assertEquals(2, outcome.getRecordsProcessed());
@@ -121,9 +137,16 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		});
 
 		// Execute
-
+		ReindexJobParameters params = new ReindexJobParameters();
 		myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
+		JobInstance instance = new JobInstance();
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			mock(WorkChunk.class)
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
 
 		// Verify
 		assertEquals(2, outcome.getRecordsProcessed());
@@ -136,12 +159,9 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		assertEquals(0, myCaptureQueriesListener.getRollbackCount());
 	}
 
-
 	@Test
 	public void testReindex_IndexesAddedAndRemoved_IndexMissingFieldsEnabled() {
-
 		// Setup
-
 		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.ENABLED);
 		boolean markResourcesForReindexingUponSearchParameterChange = myStorageSettings.isMarkResourcesForReindexingUponSearchParameterChange();
 		myStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false);	// if this were true, it would set up a lot of reindex jobs extraneous to the one we're trying to test
@@ -189,9 +209,16 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		mySearchParamRegistry.forceRefresh();
 
 		// Execute
-
+		ReindexJobParameters params = new ReindexJobParameters();
 		myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
+		JobInstance instance = new JobInstance();
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			mock(WorkChunk.class)
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
 
 		// Verify
 		assertEquals(2, outcome.getRecordsProcessed());
@@ -207,9 +234,7 @@ public class ReindexStepTest extends BaseJpaR4Test {
 
 	@Test
 	public void testReindex_OneResourceReindexFailedButOthersSucceeded() {
-
 		// Setup
-
 		Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
 		Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
 		Long idPatientToInvalidate = createPatient().getIdPartAsLong();
@@ -234,9 +259,19 @@ public class ReindexStepTest extends BaseJpaR4Test {
 		});
 
 		// Execute
-
+		ReindexJobParameters params = new ReindexJobParameters();
 		myCaptureQueriesListener.clear();
-		RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
+		JobInstance instance = new JobInstance();
+		instance.setInstanceId("index-id");
+		WorkChunk workChunk = new WorkChunk();
+		workChunk.setId("workid");
+		StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
+			params,
+			data,
+			instance,
+			workChunk
+		);
+		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
 
 		// Verify
 		assertEquals(4, outcome.getRecordsProcessed());

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

@@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.reindex;
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.api.IJobPersistence;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
@@ -39,6 +38,7 @@ import java.util.Date;
 import java.util.List;
 import java.util.stream.Stream;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -47,7 +47,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
 @SuppressWarnings("SqlDialectInspection")
-public class ReindexJobTest extends BaseJpaR4Test {
+public class ReindexTaskTest extends BaseJpaR4Test {
 
 	@Autowired
 	private IJobCoordinator myJobCoordinator;
@@ -101,7 +101,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(
 			new ReindexJobParameters()
 				.setOptimizeStorage(ReindexParameters.OptimizeStorageModeEnum.CURRENT_VERSION)
@@ -158,7 +158,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(
 			new ReindexJobParameters()
 				.setOptimizeStorage(ReindexParameters.OptimizeStorageModeEnum.ALL_VERSIONS)
@@ -217,7 +217,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(
 			new ReindexJobParameters()
 				.setOptimizeStorage(ReindexParameters.OptimizeStorageModeEnum.ALL_VERSIONS)
@@ -252,7 +252,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(
 			new ReindexJobParameters()
 				.setOptimizeStorage(ReindexParameters.OptimizeStorageModeEnum.CURRENT_VERSION)
@@ -294,7 +294,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(mySrd, startRequest);
 		myBatch2JobHelper.awaitJobCompletion(res);
@@ -325,7 +325,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(startRequest);
 		JobInstance jobInstance = myBatch2JobHelper.awaitJobCompletion(res);
@@ -356,7 +356,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 		parameters.addUrl("Observation?status=final");
 
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(mySrd, startRequest);
 		myBatch2JobHelper.awaitJobCompletion(res);
@@ -387,7 +387,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(new ReindexJobParameters());
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(mySrd, startRequest);
 		myBatch2JobHelper.awaitJobCompletion(startResponse);
@@ -406,7 +406,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 		DaoMethodOutcome searchParameter = myReindexTestHelper.createUniqueCodeSearchParameter();
 
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(new ReindexJobParameters());
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(new SystemRequestDetails(), startRequest);
 		JobInstance myJob = myBatch2JobHelper.awaitJobCompletion(startResponse);
@@ -436,7 +436,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// Run a reindex
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(new ReindexJobParameters());
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(new SystemRequestDetails(), startRequest);
 		JobInstance myJob = myBatch2JobHelper.awaitJobCompletion(startResponse.getInstanceId(), 999);
@@ -469,7 +469,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// Run a reindex
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(new ReindexJobParameters());
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(new SystemRequestDetails(), startRequest);
 		JobInstance myJob = myBatch2JobHelper.awaitJobCompletion(startResponse.getInstanceId(), 999);
@@ -500,7 +500,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(new ReindexJobParameters());
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(mySrd, startRequest);
 		JobInstance outcome = myBatch2JobHelper.awaitJobCompletion(startResponse);
@@ -528,7 +528,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(new ReindexJobParameters());
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(new SystemRequestDetails(), startRequest);
 		JobInstance outcome = myBatch2JobHelper.awaitJobFailure(startResponse);
@@ -541,7 +541,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 
 	@Test
 	public void testReindex_withReindexingUponSearchParameterChangeEnabled_reindexJobCompleted() {
-		List<JobInstance> jobInstances = myJobPersistence.fetchInstancesByJobDefinitionId(ReindexAppCtx.JOB_REINDEX, 10, 0);
+		List<JobInstance> jobInstances = myJobPersistence.fetchInstancesByJobDefinitionId(JOB_REINDEX, 10, 0);
 		assertThat(jobInstances).isEmpty();
 
 		// make sure the resources auto-reindex after the search parameter update is enabled
@@ -552,7 +552,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
 		myReindexTestHelper.createCodeSearchParameter();
 
 		// check that reindex job was created
-		jobInstances = myJobPersistence.fetchInstancesByJobDefinitionId(ReindexAppCtx.JOB_REINDEX, 10, 0);
+		jobInstances = myJobPersistence.fetchInstancesByJobDefinitionId(JOB_REINDEX, 10, 0);
 		assertThat(jobInstances).hasSize(1);
 
 		// check that the job is completed (not stuck in QUEUED status)

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

@@ -1,9 +1,8 @@
 package ca.uhn.fhir.jpa.reindex;
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
-import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrlJobParameters;
 import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrl;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
+import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrlJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
@@ -25,9 +24,10 @@ import org.springframework.beans.factory.annotation.Autowired;
 import java.util.List;
 import java.util.stream.Stream;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.assertj.core.api.Assertions.assertThat;
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
-public class ReindexJobWithPartitioningTest extends BaseJpaR4Test {
+public class ReindexTaskWithPartitioningTest extends BaseJpaR4Test {
 
 	@Autowired
 	private IJobCoordinator myJobCoordinator;
@@ -133,7 +133,7 @@ public class ReindexJobWithPartitioningTest extends BaseJpaR4Test {
 
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(new SystemRequestDetails(), startRequest);
 		JobInstance jobInstance = myBatch2JobHelper.awaitJobCompletion(res);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.jpa.term;
 
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils;
+import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.support.ConceptValidationOptions;
@@ -9,6 +12,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
@@ -25,7 +29,10 @@ import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.jpa.util.SqlQuery;
 import ca.uhn.fhir.jpa.util.ValueSetTestUtil;
+import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import com.google.common.collect.Lists;
@@ -51,10 +58,16 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import java.io.IOException;
+import java.time.Duration;
+import java.time.temporal.ChronoUnit;
+import java.util.Collection;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static ca.uhn.fhir.util.HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.awaitility.Awaitility.await;
@@ -2081,7 +2094,172 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test implements IValueSet
 		outcome = myValueSetDao.validateCode(vs.getUrlElement(), null, new StringType("A"), cs.getUrlElement(), null, null, null, mySrd);
 		assertEquals(false, outcome.isOk());
 		assertThat(outcome.getMessage()).contains("Code validation occurred using a ValueSet expansion that was pre-calculated");
-
 	}
 
+	@Test
+	public void reindexCodeSystems_withDeferredCodeSystems_reindexesAllCodeSystems() {
+		// setup
+		int deferredIndexingDefault = myStorageSettings.getDeferIndexingForCodesystemsOfSize();
+
+		try {
+			/**
+			 * The deferred count must be less than the number of
+			 * concepts we are going to be uploading.
+			 * That way, when we do the reindex, it will defer
+			 * the additional code systems for a later job run.
+			 *
+			 * See {@link TermCodeSystemStorageSvcImpl#addConceptInHierarchy(TermCodeSystemVersion, Collection, TermConcept, UploadStatistics, Map, int)}
+			 *
+			 * Our CodeSystem below only has 6 Concepts to add.
+			 * So we'll set the deferred count to 3 (so 3 will be deferred)
+			 */
+			myStorageSettings.setDeferIndexingForCodesystemsOfSize(3);
+			/*
+			 * We're also setting our retry delay to a short timeframe
+			 * so this test doesn't run too long.
+			 */
+			ReindexUtils.setRetryDelay(Duration.of(300, ChronoUnit.MILLIS));
+
+			IParser parser = myFhirContext.newJsonParser();
+
+			RequestDetails rq = new SystemRequestDetails();
+			CodeSystem cs;
+			ValueSet vs;
+			String csStr;
+			{
+				String vsStr = """
+						{
+						    "resourceType": "ValueSet",
+						    "id": "0447bffa-01fa-4405-828a-96192e74a5d8",
+						    "meta": {
+						        "versionId": "2",
+						        "lastUpdated": "2024-04-09T15:06:24.025+00:00",
+						        "source": "#f4491e490a6a2900"
+						    },
+						    "url": "https://health.gov.on.ca/idms/fhir/ValueSet/IDMS-Submission-Types",
+						    "version": "1.0.0",
+						    "name": "IDMS-SUBMISSION-TYPES",
+						    "title": "IDMS Submission Types",
+						    "status": "active",
+						    "experimental": false,
+						    "date": "2023-09-28",
+						    "publisher": "IDMS",
+						    "description": "List of Submission Types",
+						    "compose": {
+						        "include": [
+						            {
+						                "system": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types"
+						            }
+						        ]
+						    }
+						}
+					""";
+				vs = parser.parseResource(ValueSet.class, vsStr);
+				csStr = """
+					{
+						        "resourceType": "CodeSystem",
+						        "id": "d9acd5b8-9533-4fa1-bb70-b4380957a8c3",
+						        "meta": {
+						            "versionId": "14",
+						            "lastUpdated": "2024-06-03T17:49:56.580+00:00",
+						            "source": "#261a82258b0978a8"
+						        },
+						        "url": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types",
+						        "version": "1.0.0",
+						        "name": "IDMS-Internal-Submission-Types",
+						        "status": "active",
+						        "date": "2023-09-07",
+						        "publisher": "IDMS",
+						        "description": "This contains a lists of codes Submission Type Codes.",
+						        "content": "complete",
+						        "concept": [
+						            {
+						                "code": "SUB-BRAND-PRODUCT",
+						                "display": "New Brand Product (Non-New Chemical Entity)"
+						            },
+						            {
+						                "code": "SUB-CLASSIFICATION",
+						                "display": "Classification Change"
+						            },
+						            {
+						                "code": "SUB-CLINICIAN-LED-SUBMISSIONS",
+						                "display": "Clinician-Led Submissions"
+						            },
+						            {
+						                "code": "SUB-DELISTING",
+						                "display": "Delisting"
+						            },
+						            {
+						                "code": "SUB-DIN-CHANGE",
+						                "display": "Drug Identification Number (DIN) Change"
+						            },
+						            {
+						                "code": "SUB-DISTRIBUTOR",
+						                "display": "Distributor Change"
+						            }
+						        ]
+						    }
+					""";
+				cs = parser.parseResource(CodeSystem.class, csStr);
+			}
+
+			// create our ValueSet
+			myValueSetDao.update(vs, rq);
+
+			// and the code system
+			myCodeSystemDao.update(cs, rq);
+
+			// sanity check to make sure our code system was actually created
+			SearchParameterMap spMap = new SearchParameterMap();
+			spMap.setLoadSynchronous(true);
+			IBundleProvider bp = myCodeSystemDao.search(spMap, rq);
+			assertEquals(1, bp.getAllResources().size());
+			IBaseResource baseResource = bp.getAllResources().get(0);
+			CodeSystem cssaved;
+			if (baseResource instanceof CodeSystem saved) {
+				cssaved = saved;
+			} else {
+				fail("Should be a code system");
+				return;
+			}
+			assertEquals(cs.getConcept().size(), cssaved.getConcept().size());
+
+			// test
+			// perform the reindex (we'll only target the CodeSystem here)
+			ReindexJobParameters params = new ReindexJobParameters();
+			params.addUrl("CodeSystem?");
+			JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
+			startRequest.setJobDefinitionId(JOB_REINDEX);
+			startRequest.setParameters(params);
+
+			// and wait for it to complete
+			Batch2JobStartResponse response = myJobCoordinator.startInstance(rq, startRequest);
+			myBatch2JobHelper.awaitJobCompletion(response);
+
+			// verify by doing the value expansion
+			ValueSetExpansionOptions options = new ValueSetExpansionOptions();
+			options.setCount(200); // this is way more than exist, so it's ok
+			ValueSet expanded = myValueSetDao.expand(vs, options);
+			assertNotNull(expanded);
+
+			/*
+			 * If the reindex was performed correctly, the expanded ValueSet
+			 * should contain all the CodeSystem concepts that we originally
+			 * uploaded (and nothing else).
+			 */
+			HashSet<String> all = new HashSet<>();
+			for (CodeSystem.ConceptDefinitionComponent set : cs.getConcept()) {
+				all.add(set.getCode());
+			}
+			for (ValueSet.ValueSetExpansionContainsComponent v : expanded.getExpansion().getContains()) {
+				all.remove(v.getCode());
+			}
+			assertTrue(all.isEmpty(), String.join(", ", all));
+			assertEquals(cs.getConcept().size(), expanded.getExpansion().getTotal());
+		} finally {
+			// set back to standard values
+			myStorageSettings.setDeferIndexingForCodesystemsOfSize(deferredIndexingDefault);
+			ReindexUtils.setRetryDelay(null);
+		}
+	}
 }

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/DuplicateIndexR5Test.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.dao.r5;
 
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
@@ -19,6 +18,7 @@ import org.hl7.fhir.r5.model.Reference;
 import org.hl7.fhir.r5.model.SearchParameter;
 import org.junit.jupiter.api.Test;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class DuplicateIndexR5Test extends BaseJpaR5Test {
@@ -149,7 +149,7 @@ public class DuplicateIndexR5Test extends BaseJpaR5Test {
 		ReindexJobParameters parameters = new ReindexJobParameters();
 		parameters.addUrl("Patient?");
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 		startRequest.setParameters(parameters);
 		Batch2JobStartResponse res = myJobCoordinator.startInstance(mySrd, startRequest);
 		myBatch2JobHelper.awaitJobCompletion(res.getInstanceId());

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5Test.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.provider.r5;
 
 import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrl;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
@@ -67,6 +66,7 @@ import java.util.List;
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.apache.commons.lang3.StringUtils.leftPad;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -374,7 +374,7 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
 			ReindexJobParameters jobParameters = new ReindexJobParameters();
 			jobParameters.addPartitionedUrl(new PartitionedUrl().setRequestPartitionId(RequestPartitionId.allPartitions()));
 			JobInstanceStartRequest request = new JobInstanceStartRequest();
-			request.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+			request.setJobDefinitionId(JOB_REINDEX);
 			request.setParameters(jobParameters);
 			Batch2JobStartResponse response = myJobCoordinator.startInstance(new SystemRequestDetails(), request);
 

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java

@@ -19,6 +19,7 @@
  */
 package ca.uhn.fhir.jpa.test;
 
+import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
 import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
 import ca.uhn.fhir.context.FhirContext;
@@ -559,6 +560,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 
 	@Autowired
 	protected IJobMaintenanceService myJobMaintenanceService;
+	@Autowired
+	protected IJobCoordinator myJobCoordinator;
 
 	@RegisterExtension
 	private final PreventDanglingInterceptorsExtension myPreventDanglingInterceptorsExtension = new PreventDanglingInterceptorsExtension(()-> myInterceptorRegistry);

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

@@ -38,6 +38,7 @@ import org.junit.jupiter.params.provider.Arguments;
 import java.util.List;
 import java.util.stream.Stream;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.fail;
@@ -170,7 +171,7 @@ public class PatientReindexTestHelper {
 
 	private JobInstanceStartRequest createPatientReindexRequest(int theBatchSize) {
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
-		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setJobDefinitionId(JOB_REINDEX);
 
 		ReindexJobParameters reindexJobParameters = new ReindexJobParameters();
 		reindexJobParameters.setBatchSize(Math.max(theBatchSize,1));

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

@@ -17,11 +17,15 @@ import org.springframework.test.util.ReflectionTestUtils;
 import org.springframework.transaction.PlatformTransactionManager;
 
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 
+import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.anyInt;
 import static org.mockito.ArgumentMatchers.anyLong;
+import static org.mockito.ArgumentMatchers.anyString;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.ArgumentMatchers.same;
 import static org.mockito.Mockito.times;
@@ -67,8 +71,15 @@ public class TermDeferredStorageSvcImplTest {
 
 		ReflectionTestUtils.setField(mySvc, "myJobExecutions", mockExecutions);
 
-		when(myJobCoordinator.getInstance(eq(jobId)))
+		when(myJobCoordinator.getInstancesbyJobDefinitionIdAndEndedStatus(
-			.thenReturn(instance);
+			eq(TERM_CODE_SYSTEM_DELETE_JOB_NAME),
+			eq(true),
+			anyInt(),
+			eq(0)
+		))
+			.thenReturn(List.of()) // first nothing
+			.thenReturn(List.of(instance)); // then the list with the instance
+
 		assertFalse(mySvc.isStorageQueueEmpty(true));
 		instance.setStatus(StatusEnum.COMPLETED);
 		assertTrue(mySvc.isStorageQueueEmpty(true));

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

@@ -21,69 +21,37 @@ package ca.uhn.fhir.batch2.jobs.reindex;
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.api.IJobPartitionProvider;
-import ca.uhn.fhir.batch2.api.IJobStepWorker;
+import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
-import ca.uhn.fhir.batch2.api.VoidModel;
+import ca.uhn.fhir.batch2.jobs.reindex.v1.ReindexV1Config;
-import ca.uhn.fhir.batch2.jobs.chunk.ChunkRangeJson;
+import ca.uhn.fhir.batch2.jobs.reindex.v2.ReindexV2Config;
-import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
-import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
-import ca.uhn.fhir.batch2.jobs.step.GenerateRangeChunksStep;
-import ca.uhn.fhir.batch2.jobs.step.LoadIdsStep;
-import ca.uhn.fhir.batch2.model.JobDefinition;
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import ca.uhn.fhir.rest.server.provider.ProviderConstants;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 
 @Configuration
+@Import({ReindexV1Config.class, ReindexV2Config.class})
 public class ReindexAppCtx {
 
-	public static final String JOB_REINDEX = "REINDEX";
+	@Autowired
+	private HapiTransactionService myHapiTransactionService;
 
-	@Bean
+	@Autowired
-	public JobDefinition<ReindexJobParameters> reindexJobDefinition(IBatch2DaoSvc theBatch2DaoSvc) {
+	private IFhirSystemDao<?, ?> mySystemDao;
-		return JobDefinition.newBuilder()
-				.setJobDefinitionId(JOB_REINDEX)
-				.setJobDescription("Reindex resources")
-				.setJobDefinitionVersion(1)
-				.setParametersType(ReindexJobParameters.class)
-				.setParametersValidator(reindexJobParametersValidator(theBatch2DaoSvc))
-				.gatedExecution()
-				.addFirstStep(
-						"generate-ranges",
-						"Generate data ranges to reindex",
-						ChunkRangeJson.class,
-						reindexGenerateRangeChunksStep())
-				.addIntermediateStep(
-						"load-ids",
-						"Load IDs of resources to reindex",
-						ResourceIdListWorkChunkJson.class,
-						reindexLoadIdsStep(theBatch2DaoSvc))
-				.addLastStep("reindex", "Perform the resource reindex", reindexStep())
-				.build();
-	}
 
-	@Bean
+	@Autowired
-	public IJobStepWorker<ReindexJobParameters, VoidModel, ChunkRangeJson> reindexGenerateRangeChunksStep() {
+	private DaoRegistry myRegistry;
-		return new GenerateRangeChunksStep<>();
-	}
 
-	@Bean
+	@Autowired
-	public IJobStepWorker<ReindexJobParameters, ChunkRangeJson, ResourceIdListWorkChunkJson> reindexLoadIdsStep(
+	private IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
-			IBatch2DaoSvc theBatch2DaoSvc) {
-		return new LoadIdsStep<>(theBatch2DaoSvc);
-	}
 
-	@Bean
+	/* Shared services */
-	public ReindexJobParametersValidator reindexJobParametersValidator(IBatch2DaoSvc theBatch2DaoSvc) {
-		return new ReindexJobParametersValidator(
-				new UrlListValidator(ProviderConstants.OPERATION_REINDEX, theBatch2DaoSvc));
-	}
-
-	@Bean
-	public ReindexStep reindexStep() {
-		return new ReindexStep();
-	}
 
 	@Bean
 	public ReindexProvider reindexProvider(
@@ -92,4 +60,9 @@ public class ReindexAppCtx {
 			IJobPartitionProvider theJobPartitionHandler) {
 		return new ReindexProvider(theFhirContext, theJobCoordinator, theJobPartitionHandler);
 	}
+
+	@Bean
+	public ReindexJobService jobService() {
+		return new ReindexJobService(myRegistry);
+	}
 }

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

@@ -44,6 +44,7 @@ import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters.OPTIMIZE_STORAGE;
 import static ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters.REINDEX_SEARCH_PARAMETERS;
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 
 public class ReindexProvider {
 
@@ -127,7 +128,7 @@ public class ReindexProvider {
 		myJobPartitionProvider.getPartitionedUrls(theRequestDetails, urls).forEach(params::addPartitionedUrl);
 
 		JobInstanceStartRequest request = new JobInstanceStartRequest();
-		request.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		request.setJobDefinitionId(JOB_REINDEX);
 		request.setParameters(params);
 		Batch2JobStartResponse response = myJobCoordinator.startInstance(theRequestDetails, request);
 

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

@@ -1,203 +0,0 @@
-/*-
- * #%L
- * hapi-fhir-storage-batch2-jobs
- * %%
- * Copyright (C) 2014 - 2024 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-package ca.uhn.fhir.batch2.jobs.reindex;
-
-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.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
-import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
-import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
-import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
-import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
-import ca.uhn.fhir.parser.DataFormatException;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.util.StopWatch;
-import jakarta.annotation.Nonnull;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.TransactionStatus;
-import org.springframework.transaction.support.TransactionCallback;
-
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
-public class ReindexStep implements IJobStepWorker<ReindexJobParameters, ResourceIdListWorkChunkJson, VoidModel> {
-
-	public static final int REINDEX_MAX_RETRIES = 10;
-
-	private static final Logger ourLog = LoggerFactory.getLogger(ReindexStep.class);
-
-	@Autowired
-	private HapiTransactionService myHapiTransactionService;
-
-	@Autowired
-	private IFhirSystemDao<?, ?> mySystemDao;
-
-	@Autowired
-	private DaoRegistry myDaoRegistry;
-
-	@Autowired
-	private IIdHelperService<IResourcePersistentId> myIdHelperService;
-
-	@Nonnull
-	@Override
-	public RunOutcome run(
-			@Nonnull StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails,
-			@Nonnull IJobDataSink<VoidModel> theDataSink)
-			throws JobExecutionFailedException {
-
-		ResourceIdListWorkChunkJson data = theStepExecutionDetails.getData();
-		ReindexJobParameters jobParameters = theStepExecutionDetails.getParameters();
-
-		return doReindex(
-				data,
-				theDataSink,
-				theStepExecutionDetails.getInstance().getInstanceId(),
-				theStepExecutionDetails.getChunkId(),
-				jobParameters);
-	}
-
-	@Nonnull
-	public RunOutcome doReindex(
-			ResourceIdListWorkChunkJson data,
-			IJobDataSink<VoidModel> theDataSink,
-			String theInstanceId,
-			String theChunkId,
-			ReindexJobParameters theJobParameters) {
-		RequestDetails requestDetails = new SystemRequestDetails();
-		requestDetails.setRetry(true);
-		requestDetails.setMaxRetries(REINDEX_MAX_RETRIES);
-		TransactionDetails transactionDetails = new TransactionDetails();
-		ReindexJob reindexJob = new ReindexJob(
-				data, requestDetails, transactionDetails, theDataSink, theInstanceId, theChunkId, theJobParameters);
-
-		myHapiTransactionService
-				.withRequest(requestDetails)
-				.withTransactionDetails(transactionDetails)
-				.withRequestPartitionId(data.getRequestPartitionId())
-				.execute(reindexJob);
-
-		return new RunOutcome(data.size());
-	}
-
-	private class ReindexJob implements TransactionCallback<Void> {
-		private final ResourceIdListWorkChunkJson myData;
-		private final RequestDetails myRequestDetails;
-		private final TransactionDetails myTransactionDetails;
-		private final IJobDataSink<VoidModel> myDataSink;
-		private final String myChunkId;
-		private final String myInstanceId;
-		private final ReindexJobParameters myJobParameters;
-
-		public ReindexJob(
-				ResourceIdListWorkChunkJson theData,
-				RequestDetails theRequestDetails,
-				TransactionDetails theTransactionDetails,
-				IJobDataSink<VoidModel> theDataSink,
-				String theInstanceId,
-				String theChunkId,
-				ReindexJobParameters theJobParameters) {
-			myData = theData;
-			myRequestDetails = theRequestDetails;
-			myTransactionDetails = theTransactionDetails;
-			myDataSink = theDataSink;
-			myInstanceId = theInstanceId;
-			myChunkId = theChunkId;
-			myJobParameters = theJobParameters;
-			myDataSink.setWarningProcessor(new ReindexWarningProcessor());
-		}
-
-		@Override
-		public Void doInTransaction(@Nonnull TransactionStatus theStatus) {
-
-			List<IResourcePersistentId> persistentIds = myData.getResourcePersistentIds(myIdHelperService);
-
-			ourLog.info(
-					"Starting reindex work chunk with {} resources - Instance[{}] Chunk[{}]",
-					persistentIds.size(),
-					myInstanceId,
-					myChunkId);
-			StopWatch sw = new StopWatch();
-
-			// Prefetch Resources from DB
-
-			boolean reindexSearchParameters =
-					myJobParameters.getReindexSearchParameters() != ReindexParameters.ReindexSearchParametersEnum.NONE;
-			mySystemDao.preFetchResources(persistentIds, reindexSearchParameters);
-			ourLog.info(
-					"Prefetched {} resources in {} - Instance[{}] Chunk[{}]",
-					persistentIds.size(),
-					sw,
-					myInstanceId,
-					myChunkId);
-
-			ReindexParameters parameters = new ReindexParameters()
-					.setReindexSearchParameters(myJobParameters.getReindexSearchParameters())
-					.setOptimizeStorage(myJobParameters.getOptimizeStorage())
-					.setOptimisticLock(myJobParameters.getOptimisticLock());
-
-			// Reindex
-
-			sw.restart();
-			for (int i = 0; i < myData.size(); i++) {
-
-				String nextResourceType = myData.getResourceType(i);
-				IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextResourceType);
-				IResourcePersistentId<?> resourcePersistentId = persistentIds.get(i);
-				try {
-
-					ReindexOutcome outcome =
-							dao.reindex(resourcePersistentId, parameters, myRequestDetails, myTransactionDetails);
-					outcome.getWarnings().forEach(myDataSink::recoveredError);
-
-				} catch (BaseServerResponseException | DataFormatException e) {
-					String resourceForcedId = myIdHelperService
-							.translatePidIdToForcedIdWithCache(resourcePersistentId)
-							.orElse(resourcePersistentId.toString());
-					String resourceId = nextResourceType + "/" + resourceForcedId;
-					ourLog.debug("Failure during reindexing {}", resourceId, e);
-					myDataSink.recoveredError("Failure reindexing " + resourceId + ": " + e.getMessage());
-				}
-			}
-
-			ourLog.info(
-					"Finished reindexing {} resources in {} - {}/sec - Instance[{}] Chunk[{}]",
-					persistentIds.size(),
-					sw,
-					sw.formatThroughput(persistentIds.size(), TimeUnit.SECONDS),
-					myInstanceId,
-					myChunkId);
-
-			return null;
-		}
-	}
-}

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

@@ -0,0 +1,39 @@
+package ca.uhn.fhir.batch2.jobs.reindex;
+
+import com.google.common.annotations.VisibleForTesting;
+
+import java.time.Duration;
+import java.time.temporal.ChronoUnit;
+
+public class ReindexUtils {
+
+	/**
+	 * The reindex job definition id
+	 */
+	public static final String JOB_REINDEX = "REINDEX";
+
+	public static final int REINDEX_MAX_RETRIES = 10;
+
+	private static final Duration RETRY_DELAY = Duration.of(30, ChronoUnit.SECONDS);
+
+	private static Duration myDelay;
+
+	/**
+	 * Returns the retry delay for reindex jobs that require polling.
+	 */
+	public static Duration getRetryLaterDelay() {
+		if (myDelay != null) {
+			return myDelay;
+		}
+		return RETRY_DELAY;
+	}
+
+	/**
+	 * Sets the retry delay to use for reindex jobs.
+	 * Do not use this in production code! Only test code.
+	 */
+	@VisibleForTesting
+	public static void setRetryDelay(Duration theDuration) {
+		myDelay = theDuration;
+	}
+}

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

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.batch2.jobs.reindex.models;
+
+import ca.uhn.fhir.model.api.IModelJson;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.HashMap;
+
+public class ReindexResults implements IModelJson {
+
+	/**
+	 * A map of resource type : whether or not the reindex is completed;
+	 * true = more work needed. false (or omitted) = reindex is done
+	 */
+	@JsonProperty("resource2NeedsWork")
+	private HashMap<String, Boolean> myResourceToHasWorkToComplete;
+
+	public ReindexResults() {}
+
+	public HashMap<String, Boolean> getResourceToHasWorkToComplete() {
+		if (myResourceToHasWorkToComplete == null) {
+			myResourceToHasWorkToComplete = new HashMap<>();
+		}
+		return myResourceToHasWorkToComplete;
+	}
+
+	public void addResourceTypeToCompletionStatus(String theResourceType, boolean theRequiresMoreWork) {
+		getResourceToHasWorkToComplete().put(theResourceType, theRequiresMoreWork);
+	}
+}

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

@@ -0,0 +1,38 @@
+package ca.uhn.fhir.batch2.jobs.reindex.svcs;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
+
+import java.util.Map;
+
+public class ReindexJobService {
+
+	private final DaoRegistry myDaoRegistry;
+
+	public ReindexJobService(DaoRegistry theRegistry) {
+		myDaoRegistry = theRegistry;
+	}
+
+	/**
+	 * Checks if any of the resource types in the map have any pending reindex work waiting.
+	 * This will return true after the first such encounter, and only return false if no
+	 * reindex work is required for any resource.
+	 * @param theResourceTypesToCheckFlag map of resourceType:whether or not to check
+	 * @return true if there's reindex work pending, false otherwise
+	 */
+	public boolean anyResourceHasPendingReindexWork(Map<String, Boolean> theResourceTypesToCheckFlag) {
+		for (String resourceType : theResourceTypesToCheckFlag.keySet()) {
+			boolean toCheck = theResourceTypesToCheckFlag.get(resourceType);
+			if (toCheck) {
+				IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
+
+				ReindexJobStatus status = dao.getReindexJobStatus();
+				if (status.isHasReindexWorkPending()) {
+					return true;
+				}
+			}
+		}
+		return false;
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v1/ReindexJobParametersValidatorV1.java

@@ -0,0 +1,57 @@
+/*-
+ * #%L
+ * hapi-fhir-storage-batch2-jobs
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package ca.uhn.fhir.batch2.jobs.reindex.v1;
+
+import ca.uhn.fhir.batch2.api.IJobParametersValidator;
+import ca.uhn.fhir.batch2.jobs.parameters.IUrlListValidator;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Deprecated(forRemoval = true, since = "7.6.0")
+public class ReindexJobParametersValidatorV1 implements IJobParametersValidator<ReindexJobParameters> {
+
+	private final IUrlListValidator myUrlListValidator;
+
+	public ReindexJobParametersValidatorV1(IUrlListValidator theUrlListValidator) {
+		myUrlListValidator = theUrlListValidator;
+	}
+
+	@Nullable
+	@Override
+	public List<String> validate(RequestDetails theRequestDetails, @Nonnull ReindexJobParameters theParameters) {
+		List<String> errors = myUrlListValidator.validateUrls(theParameters.getUrls());
+
+		if (errors == null || errors.isEmpty()) {
+			// only check if there's no other errors (new list to fix immutable issues)
+			errors = new ArrayList<>();
+			for (String url : theParameters.getUrls()) {
+				if (url.contains(" ") || url.contains("\n") || url.contains("\t")) {
+					errors.add("Invalid URL. URL cannot contain spaces : " + url);
+				}
+			}
+		}
+		return errors;
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v1/ReindexStepV1.java

@@ -0,0 +1,117 @@
+/*-
+ * #%L
+ * hapi-fhir-storage-batch2-jobs
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package ca.uhn.fhir.batch2.jobs.reindex.v1;
+
+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.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import jakarta.annotation.Nonnull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.REINDEX_MAX_RETRIES;
+
+@Deprecated(forRemoval = true, since = "7.6.0")
+public class ReindexStepV1 implements IJobStepWorker<ReindexJobParameters, ResourceIdListWorkChunkJson, VoidModel> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ReindexStepV1.class);
+
+	private final HapiTransactionService myHapiTransactionService;
+
+	private final IFhirSystemDao<?, ?> mySystemDao;
+
+	private final DaoRegistry myDaoRegistry;
+
+	private final IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
+
+	public ReindexStepV1(
+			HapiTransactionService theHapiTransactionService,
+			IFhirSystemDao<?, ?> theSystemDao,
+			DaoRegistry theRegistry,
+			IIdHelperService<IResourcePersistentId<?>> theIdHelperService) {
+		myDaoRegistry = theRegistry;
+		myHapiTransactionService = theHapiTransactionService;
+		mySystemDao = theSystemDao;
+		myIdHelperService = theIdHelperService;
+	}
+
+	@Nonnull
+	@Override
+	public RunOutcome run(
+			@Nonnull StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails,
+			@Nonnull IJobDataSink<VoidModel> theDataSink)
+			throws JobExecutionFailedException {
+
+		ResourceIdListWorkChunkJson data = theStepExecutionDetails.getData();
+		ReindexJobParameters jobParameters = theStepExecutionDetails.getParameters();
+
+		doReindex(
+				data,
+				theDataSink,
+				theStepExecutionDetails.getInstance().getInstanceId(),
+				theStepExecutionDetails.getChunkId(),
+				jobParameters);
+
+		return new RunOutcome(data.size());
+	}
+
+	public ReindexResults doReindex(
+			ResourceIdListWorkChunkJson data,
+			IJobDataSink<?> theDataSink,
+			String theInstanceId,
+			String theChunkId,
+			ReindexJobParameters theJobParameters) {
+		RequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setRetry(true);
+		requestDetails.setMaxRetries(REINDEX_MAX_RETRIES);
+
+		TransactionDetails transactionDetails = new TransactionDetails();
+		ReindexTaskV1.JobParameters jp = new ReindexTaskV1.JobParameters();
+		jp.setData(data)
+				.setRequestDetails(requestDetails)
+				.setTransactionDetails(transactionDetails)
+				.setDataSink(theDataSink)
+				.setInstanceId(theInstanceId)
+				.setChunkId(theChunkId)
+				.setJobParameters(theJobParameters);
+
+		ReindexTaskV1 reindexJob = new ReindexTaskV1(jp, myDaoRegistry, mySystemDao, myIdHelperService);
+
+		return myHapiTransactionService
+				.withRequest(requestDetails)
+				.withTransactionDetails(transactionDetails)
+				.withRequestPartitionId(data.getRequestPartitionId())
+				.execute(reindexJob);
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v1/ReindexTaskV1.java

@@ -0,0 +1,202 @@
+package ca.uhn.fhir.batch2.jobs.reindex.v1;
+
+import ca.uhn.fhir.batch2.api.IJobDataSink;
+import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexWarningProcessor;
+import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
+import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.util.StopWatch;
+import jakarta.annotation.Nonnull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallback;
+
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+@Deprecated(forRemoval = true, since = "7.6.0")
+public class ReindexTaskV1 implements TransactionCallback<ReindexResults> {
+	private static final Logger ourLog = LoggerFactory.getLogger(ReindexTaskV1.class);
+
+	public static class JobParameters {
+		private ResourceIdListWorkChunkJson myData;
+		private RequestDetails myRequestDetails;
+		private TransactionDetails myTransactionDetails;
+		private IJobDataSink<?> myDataSink;
+		private String myChunkId;
+		private String myInstanceId;
+		private ReindexJobParameters myJobParameters;
+
+		public ResourceIdListWorkChunkJson getData() {
+			return myData;
+		}
+
+		public JobParameters setData(ResourceIdListWorkChunkJson theData) {
+			myData = theData;
+			return this;
+		}
+
+		public RequestDetails getRequestDetails() {
+			return myRequestDetails;
+		}
+
+		public JobParameters setRequestDetails(RequestDetails theRequestDetails) {
+			myRequestDetails = theRequestDetails;
+			return this;
+		}
+
+		public TransactionDetails getTransactionDetails() {
+			return myTransactionDetails;
+		}
+
+		public JobParameters setTransactionDetails(TransactionDetails theTransactionDetails) {
+			myTransactionDetails = theTransactionDetails;
+			return this;
+		}
+
+		public IJobDataSink<?> getDataSink() {
+			return myDataSink;
+		}
+
+		public JobParameters setDataSink(IJobDataSink<?> theDataSink) {
+			myDataSink = theDataSink;
+			return this;
+		}
+
+		public String getChunkId() {
+			return myChunkId;
+		}
+
+		public JobParameters setChunkId(String theChunkId) {
+			myChunkId = theChunkId;
+			return this;
+		}
+
+		public String getInstanceId() {
+			return myInstanceId;
+		}
+
+		public JobParameters setInstanceId(String theInstanceId) {
+			myInstanceId = theInstanceId;
+			return this;
+		}
+
+		public ReindexJobParameters getJobParameters() {
+			return myJobParameters;
+		}
+
+		public JobParameters setJobParameters(ReindexJobParameters theJobParameters) {
+			myJobParameters = theJobParameters;
+			return this;
+		}
+	}
+
+	private final DaoRegistry myDaoRegistry;
+	private final IFhirSystemDao<?, ?> mySystemDao;
+
+	private final IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
+
+	private final ResourceIdListWorkChunkJson myData;
+	private final RequestDetails myRequestDetails;
+	private final TransactionDetails myTransactionDetails;
+	private final IJobDataSink<?> myDataSink;
+	private final String myChunkId;
+	private final String myInstanceId;
+	private final ReindexJobParameters myJobParameters;
+
+	public ReindexTaskV1(
+			JobParameters theJobParameters,
+			DaoRegistry theRegistry,
+			IFhirSystemDao<?, ?> theSystemDao,
+			IIdHelperService<IResourcePersistentId<?>> theIdHelperService) {
+		myDaoRegistry = theRegistry;
+		mySystemDao = theSystemDao;
+		myIdHelperService = theIdHelperService;
+
+		myData = theJobParameters.getData();
+		myRequestDetails = theJobParameters.getRequestDetails();
+		myTransactionDetails = theJobParameters.getTransactionDetails();
+		myDataSink = theJobParameters.getDataSink();
+		myInstanceId = theJobParameters.getInstanceId();
+		myChunkId = theJobParameters.getChunkId();
+		myJobParameters = theJobParameters.getJobParameters();
+		myDataSink.setWarningProcessor(new ReindexWarningProcessor());
+	}
+
+	@Override
+	public ReindexResults doInTransaction(@Nonnull TransactionStatus theStatus) {
+		List<IResourcePersistentId<?>> persistentIds = myData.getResourcePersistentIds(myIdHelperService);
+
+		ourLog.info(
+				"Starting reindex work chunk with {} resources - Instance[{}] Chunk[{}]",
+				persistentIds.size(),
+				myInstanceId,
+				myChunkId);
+		StopWatch sw = new StopWatch();
+		ReindexResults reindexResults = new ReindexResults();
+
+		// Prefetch Resources from DB
+		boolean reindexSearchParameters =
+				myJobParameters.getReindexSearchParameters() != ReindexParameters.ReindexSearchParametersEnum.NONE;
+		mySystemDao.preFetchResources(persistentIds, reindexSearchParameters);
+		ourLog.info(
+				"Prefetched {} resources in {} - Instance[{}] Chunk[{}]",
+				persistentIds.size(),
+				sw,
+				myInstanceId,
+				myChunkId);
+
+		ReindexParameters parameters = new ReindexParameters()
+				.setReindexSearchParameters(myJobParameters.getReindexSearchParameters())
+				.setOptimizeStorage(myJobParameters.getOptimizeStorage())
+				.setOptimisticLock(myJobParameters.getOptimisticLock());
+
+		// Reindex
+
+		sw.restart();
+		for (int i = 0; i < myData.size(); i++) {
+
+			String nextResourceType = myData.getResourceType(i);
+			IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextResourceType);
+			IResourcePersistentId<?> resourcePersistentId = persistentIds.get(i);
+			try {
+
+				ReindexOutcome outcome =
+						dao.reindex(resourcePersistentId, parameters, myRequestDetails, myTransactionDetails);
+
+				outcome.getWarnings().forEach(myDataSink::recoveredError);
+				reindexResults.addResourceTypeToCompletionStatus(nextResourceType, outcome.isHasPendingWork());
+
+			} catch (BaseServerResponseException | DataFormatException e) {
+				String resourceForcedId = myIdHelperService
+						.translatePidIdToForcedIdWithCache(resourcePersistentId)
+						.orElse(resourcePersistentId.toString());
+				String resourceId = nextResourceType + "/" + resourceForcedId;
+				ourLog.error("Failure during reindexing {}", resourceId, e);
+				myDataSink.recoveredError("Failure reindexing " + resourceId + ": " + e.getMessage());
+			}
+		}
+
+		ourLog.info(
+				"Finished reindexing {} resources in {} - {}/sec - Instance[{}] Chunk[{}]",
+				persistentIds.size(),
+				sw,
+				sw.formatThroughput(persistentIds.size(), TimeUnit.SECONDS),
+				myInstanceId,
+				myChunkId);
+
+		return reindexResults;
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v1/ReindexV1Config.java

@@ -0,0 +1,101 @@
+package ca.uhn.fhir.batch2.jobs.reindex.v1;
+
+import ca.uhn.fhir.batch2.api.IJobStepWorker;
+import ca.uhn.fhir.batch2.api.VoidModel;
+import ca.uhn.fhir.batch2.jobs.chunk.ChunkRangeJson;
+import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
+import ca.uhn.fhir.batch2.jobs.step.GenerateRangeChunksStep;
+import ca.uhn.fhir.batch2.jobs.step.LoadIdsStep;
+import ca.uhn.fhir.batch2.model.JobDefinition;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.server.provider.ProviderConstants;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
+
+@Deprecated(forRemoval = true, since = "7.6.0")
+@Configuration
+public class ReindexV1Config {
+	@Autowired
+	private ReindexJobService myReindexJobService;
+
+	@Autowired
+	private HapiTransactionService myHapiTransactionService;
+
+	@Autowired
+	private IFhirSystemDao<?, ?> mySystemDao;
+
+	@Autowired
+	private DaoRegistry myRegistry;
+
+	@Autowired
+	private IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
+
+	@Autowired
+	@Qualifier("reindexGenerateRangeChunkStepV1")
+	private IJobStepWorker<ReindexJobParameters, VoidModel, ChunkRangeJson> myReindexGenerateRangeChunkStep;
+
+	@Autowired
+	@Qualifier("reindexLoadIdsStepV1")
+	private IJobStepWorker<ReindexJobParameters, ChunkRangeJson, ResourceIdListWorkChunkJson> myReindexLoadIdsStep;
+
+	@Autowired
+	private ReindexJobParametersValidatorV1 myReindexJobParametersValidatorV1;
+
+	// Version 1
+	@Bean
+	public JobDefinition<ReindexJobParameters> reindexJobDefinitionV1() {
+		return JobDefinition.newBuilder()
+				.setJobDefinitionId(JOB_REINDEX)
+				.setJobDescription("Reindex resources")
+				.setJobDefinitionVersion(1)
+				.setParametersType(ReindexJobParameters.class)
+				.setParametersValidator(myReindexJobParametersValidatorV1)
+				.gatedExecution()
+				.addFirstStep(
+						"generate-ranges",
+						"Generate data ranges to reindex",
+						ChunkRangeJson.class,
+						myReindexGenerateRangeChunkStep)
+				.addIntermediateStep(
+						"load-ids",
+						"Load IDs of resources to reindex",
+						ResourceIdListWorkChunkJson.class,
+						myReindexLoadIdsStep)
+				.addLastStep("reindex-start", "Start the resource reindex", reindexStepV1())
+				.build();
+	}
+
+	@Bean
+	public ReindexStepV1 reindexStepV1() {
+		return new ReindexStepV1(myHapiTransactionService, mySystemDao, myRegistry, myIdHelperService);
+	}
+
+	@Bean("reindexGenerateRangeChunkStepV1")
+	public IJobStepWorker<ReindexJobParameters, VoidModel, ChunkRangeJson> reindexGenerateRangeChunksStep() {
+		return new GenerateRangeChunksStep<>();
+	}
+
+	@Bean("reindexLoadIdsStepV1")
+	public IJobStepWorker<ReindexJobParameters, ChunkRangeJson, ResourceIdListWorkChunkJson> reindexLoadIdsStep(
+			IBatch2DaoSvc theBatch2DaoSvc) {
+		return new LoadIdsStep<>(theBatch2DaoSvc);
+	}
+
+	@Bean
+	public ReindexJobParametersValidatorV1 reindexJobParametersValidatorV1(IBatch2DaoSvc theBatch2DaoSvc) {
+		return new ReindexJobParametersValidatorV1(
+				new UrlListValidator(ProviderConstants.OPERATION_REINDEX, theBatch2DaoSvc));
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v2/CheckPendingReindexWorkStep.java

@@ -0,0 +1,42 @@
+package ca.uhn.fhir.batch2.jobs.reindex.v2;
+
+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.RetryChunkLaterException;
+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.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils;
+import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
+import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
+import ca.uhn.fhir.i18n.Msg;
+import jakarta.annotation.Nonnull;
+
+public class CheckPendingReindexWorkStep implements IJobStepWorker<ReindexJobParameters, ReindexResults, VoidModel> {
+
+	private final ReindexJobService myReindexJobService;
+
+	public CheckPendingReindexWorkStep(ReindexJobService theReindexJobService) {
+		myReindexJobService = theReindexJobService;
+	}
+
+	@Nonnull
+	@Override
+	public RunOutcome run(
+			@Nonnull StepExecutionDetails<ReindexJobParameters, ReindexResults> theStepExecutionDetails,
+			@Nonnull IJobDataSink<VoidModel> theDataSink)
+			throws JobExecutionFailedException {
+
+		ReindexResults results = theStepExecutionDetails.getData();
+
+		if (!results.getResourceToHasWorkToComplete().isEmpty()) {
+			if (myReindexJobService.anyResourceHasPendingReindexWork(results.getResourceToHasWorkToComplete())) {
+				throw new RetryChunkLaterException(Msg.code(2553), ReindexUtils.getRetryLaterDelay());
+			}
+		}
+
+		return RunOutcome.SUCCESS;
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v2/ReindexJobParametersValidatorV2.java

@@ -17,10 +17,11 @@
  * limitations under the License.
  * #L%
  */
-package ca.uhn.fhir.batch2.jobs.reindex;
+package ca.uhn.fhir.batch2.jobs.reindex.v2;
 
 import ca.uhn.fhir.batch2.api.IJobParametersValidator;
 import ca.uhn.fhir.batch2.jobs.parameters.IUrlListValidator;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import jakarta.annotation.Nonnull;
 import jakarta.annotation.Nullable;
@@ -28,11 +29,11 @@ import jakarta.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.List;
 
-public class ReindexJobParametersValidator implements IJobParametersValidator<ReindexJobParameters> {
+public class ReindexJobParametersValidatorV2 implements IJobParametersValidator<ReindexJobParameters> {
 
 	private final IUrlListValidator myUrlListValidator;
 
-	public ReindexJobParametersValidator(IUrlListValidator theUrlListValidator) {
+	public ReindexJobParametersValidatorV2(IUrlListValidator theUrlListValidator) {
 		myUrlListValidator = theUrlListValidator;
 	}
 

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v2/ReindexStepV2.java

@@ -0,0 +1,118 @@
+package ca.uhn.fhir.batch2.jobs.reindex.v2;
+
+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.RetryChunkLaterException;
+import ca.uhn.fhir.batch2.api.RunOutcome;
+import ca.uhn.fhir.batch2.api.StepExecutionDetails;
+import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils;
+import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
+import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
+import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import jakarta.annotation.Nonnull;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.REINDEX_MAX_RETRIES;
+
+public class ReindexStepV2
+		implements IJobStepWorker<ReindexJobParameters, ResourceIdListWorkChunkJson, ReindexResults> {
+
+	private final ReindexJobService myReindexJobService;
+	private final HapiTransactionService myHapiTransactionService;
+
+	private final IFhirSystemDao<?, ?> mySystemDao;
+
+	private final DaoRegistry myDaoRegistry;
+
+	private final IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
+
+	public ReindexStepV2(
+			ReindexJobService theJobService,
+			HapiTransactionService theHapiTransactionService,
+			IFhirSystemDao<?, ?> theSystemDao,
+			DaoRegistry theRegistry,
+			IIdHelperService<IResourcePersistentId<?>> theIdHelperService) {
+		myDaoRegistry = theRegistry;
+		myHapiTransactionService = theHapiTransactionService;
+		mySystemDao = theSystemDao;
+		myIdHelperService = theIdHelperService;
+		myReindexJobService = theJobService;
+	}
+
+	@Nonnull
+	@Override
+	public RunOutcome run(
+			@Nonnull StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails,
+			@Nonnull IJobDataSink<ReindexResults> theDataSink)
+			throws JobExecutionFailedException {
+		ResourceIdListWorkChunkJson data = theStepExecutionDetails.getData();
+		ReindexJobParameters jobParameters = theStepExecutionDetails.getParameters();
+
+		// This is not strictly necessary;
+		// but we'll ensure that no outstanding "reindex work"
+		// is waiting to be completed, so that when we do
+		// our reindex work here, it won't skip over that data
+		Map<String, Boolean> resourceTypesToCheckFlag = new HashMap<>();
+		data.getTypedPids().forEach(id -> {
+			// we don't really care about duplicates; we check by resource type
+			resourceTypesToCheckFlag.put(id.getResourceType(), true);
+		});
+		if (myReindexJobService.anyResourceHasPendingReindexWork(resourceTypesToCheckFlag)) {
+
+			throw new RetryChunkLaterException(Msg.code(2552), ReindexUtils.getRetryLaterDelay());
+		}
+
+		ReindexResults results = doReindex(
+				data,
+				theDataSink,
+				theStepExecutionDetails.getInstance().getInstanceId(),
+				theStepExecutionDetails.getChunkId(),
+				jobParameters);
+
+		theDataSink.accept(results);
+
+		return new RunOutcome(data.size());
+	}
+
+	public ReindexResults doReindex(
+			ResourceIdListWorkChunkJson data,
+			IJobDataSink<?> theDataSink,
+			String theInstanceId,
+			String theChunkId,
+			ReindexJobParameters theJobParameters) {
+		RequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setRetry(true);
+		requestDetails.setMaxRetries(REINDEX_MAX_RETRIES);
+
+		TransactionDetails transactionDetails = new TransactionDetails();
+		ReindexTaskV2.JobParameters jp = new ReindexTaskV2.JobParameters();
+		jp.setData(data)
+				.setRequestDetails(requestDetails)
+				.setTransactionDetails(transactionDetails)
+				.setDataSink(theDataSink)
+				.setInstanceId(theInstanceId)
+				.setChunkId(theChunkId)
+				.setJobParameters(theJobParameters);
+
+		ReindexTaskV2 reindexJob = new ReindexTaskV2(jp, myDaoRegistry, mySystemDao, myIdHelperService);
+
+		return myHapiTransactionService
+				.withRequest(requestDetails)
+				.withTransactionDetails(transactionDetails)
+				.withRequestPartitionId(data.getRequestPartitionId())
+				.execute(reindexJob);
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v2/ReindexTaskV2.java

@@ -0,0 +1,201 @@
+package ca.uhn.fhir.batch2.jobs.reindex.v2;
+
+import ca.uhn.fhir.batch2.api.IJobDataSink;
+import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexWarningProcessor;
+import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
+import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.util.StopWatch;
+import jakarta.annotation.Nonnull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallback;
+
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+public class ReindexTaskV2 implements TransactionCallback<ReindexResults> {
+	private static final Logger ourLog = LoggerFactory.getLogger(ReindexTaskV2.class);
+
+	public static class JobParameters {
+		private ResourceIdListWorkChunkJson myData;
+		private RequestDetails myRequestDetails;
+		private TransactionDetails myTransactionDetails;
+		private IJobDataSink<?> myDataSink;
+		private String myChunkId;
+		private String myInstanceId;
+		private ReindexJobParameters myJobParameters;
+
+		public ResourceIdListWorkChunkJson getData() {
+			return myData;
+		}
+
+		public JobParameters setData(ResourceIdListWorkChunkJson theData) {
+			myData = theData;
+			return this;
+		}
+
+		public RequestDetails getRequestDetails() {
+			return myRequestDetails;
+		}
+
+		public JobParameters setRequestDetails(RequestDetails theRequestDetails) {
+			myRequestDetails = theRequestDetails;
+			return this;
+		}
+
+		public TransactionDetails getTransactionDetails() {
+			return myTransactionDetails;
+		}
+
+		public JobParameters setTransactionDetails(TransactionDetails theTransactionDetails) {
+			myTransactionDetails = theTransactionDetails;
+			return this;
+		}
+
+		public IJobDataSink<?> getDataSink() {
+			return myDataSink;
+		}
+
+		public JobParameters setDataSink(IJobDataSink<?> theDataSink) {
+			myDataSink = theDataSink;
+			return this;
+		}
+
+		public String getChunkId() {
+			return myChunkId;
+		}
+
+		public JobParameters setChunkId(String theChunkId) {
+			myChunkId = theChunkId;
+			return this;
+		}
+
+		public String getInstanceId() {
+			return myInstanceId;
+		}
+
+		public JobParameters setInstanceId(String theInstanceId) {
+			myInstanceId = theInstanceId;
+			return this;
+		}
+
+		public ReindexJobParameters getJobParameters() {
+			return myJobParameters;
+		}
+
+		public JobParameters setJobParameters(ReindexJobParameters theJobParameters) {
+			myJobParameters = theJobParameters;
+			return this;
+		}
+	}
+
+	private final DaoRegistry myDaoRegistry;
+	private final IFhirSystemDao<?, ?> mySystemDao;
+
+	private final IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
+
+	private final ResourceIdListWorkChunkJson myData;
+	private final RequestDetails myRequestDetails;
+	private final TransactionDetails myTransactionDetails;
+	private final IJobDataSink<?> myDataSink;
+	private final String myChunkId;
+	private final String myInstanceId;
+	private final ReindexJobParameters myJobParameters;
+
+	public ReindexTaskV2(
+			JobParameters theJobParameters,
+			DaoRegistry theRegistry,
+			IFhirSystemDao<?, ?> theSystemDao,
+			IIdHelperService<IResourcePersistentId<?>> theIdHelperService) {
+		myDaoRegistry = theRegistry;
+		mySystemDao = theSystemDao;
+		myIdHelperService = theIdHelperService;
+
+		myData = theJobParameters.getData();
+		myRequestDetails = theJobParameters.getRequestDetails();
+		myTransactionDetails = theJobParameters.getTransactionDetails();
+		myDataSink = theJobParameters.getDataSink();
+		myInstanceId = theJobParameters.getInstanceId();
+		myChunkId = theJobParameters.getChunkId();
+		myJobParameters = theJobParameters.getJobParameters();
+		myDataSink.setWarningProcessor(new ReindexWarningProcessor());
+	}
+
+	@Override
+	public ReindexResults doInTransaction(@Nonnull TransactionStatus theStatus) {
+		List<IResourcePersistentId<?>> persistentIds = myData.getResourcePersistentIds(myIdHelperService);
+
+		ourLog.info(
+				"Starting reindex work chunk with {} resources - Instance[{}] Chunk[{}]",
+				persistentIds.size(),
+				myInstanceId,
+				myChunkId);
+		StopWatch sw = new StopWatch();
+		ReindexResults reindexResults = new ReindexResults();
+
+		// Prefetch Resources from DB
+		boolean reindexSearchParameters =
+				myJobParameters.getReindexSearchParameters() != ReindexParameters.ReindexSearchParametersEnum.NONE;
+		mySystemDao.preFetchResources(persistentIds, reindexSearchParameters);
+		ourLog.info(
+				"Prefetched {} resources in {} - Instance[{}] Chunk[{}]",
+				persistentIds.size(),
+				sw,
+				myInstanceId,
+				myChunkId);
+
+		ReindexParameters parameters = new ReindexParameters()
+				.setReindexSearchParameters(myJobParameters.getReindexSearchParameters())
+				.setOptimizeStorage(myJobParameters.getOptimizeStorage())
+				.setOptimisticLock(myJobParameters.getOptimisticLock());
+
+		// Reindex
+
+		sw.restart();
+		for (int i = 0; i < myData.size(); i++) {
+
+			String nextResourceType = myData.getResourceType(i);
+			IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextResourceType);
+			IResourcePersistentId<?> resourcePersistentId = persistentIds.get(i);
+			try {
+
+				ReindexOutcome outcome =
+						dao.reindex(resourcePersistentId, parameters, myRequestDetails, myTransactionDetails);
+
+				outcome.getWarnings().forEach(myDataSink::recoveredError);
+				reindexResults.addResourceTypeToCompletionStatus(nextResourceType, outcome.isHasPendingWork());
+
+			} catch (BaseServerResponseException | DataFormatException e) {
+				String resourceForcedId = myIdHelperService
+						.translatePidIdToForcedIdWithCache(resourcePersistentId)
+						.orElse(resourcePersistentId.toString());
+				String resourceId = nextResourceType + "/" + resourceForcedId;
+				ourLog.error("Failure during reindexing {}", resourceId, e);
+				myDataSink.recoveredError("Failure reindexing " + resourceId + ": " + e.getMessage());
+			}
+		}
+
+		ourLog.info(
+				"Finished reindexing {} resources in {} - {}/sec - Instance[{}] Chunk[{}]",
+				persistentIds.size(),
+				sw,
+				sw.formatThroughput(persistentIds.size(), TimeUnit.SECONDS),
+				myInstanceId,
+				myChunkId);
+
+		return reindexResults;
+	}
+}

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/v2/ReindexV2Config.java

@@ -0,0 +1,110 @@
+package ca.uhn.fhir.batch2.jobs.reindex.v2;
+
+import ca.uhn.fhir.batch2.api.IJobStepWorker;
+import ca.uhn.fhir.batch2.api.VoidModel;
+import ca.uhn.fhir.batch2.jobs.chunk.ChunkRangeJson;
+import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
+import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
+import ca.uhn.fhir.batch2.jobs.step.GenerateRangeChunksStep;
+import ca.uhn.fhir.batch2.jobs.step.LoadIdsStep;
+import ca.uhn.fhir.batch2.model.JobDefinition;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.server.provider.ProviderConstants;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
+
+@Configuration
+public class ReindexV2Config {
+
+	@Autowired
+	private ReindexJobService myReindexJobService;
+
+	@Autowired
+	private HapiTransactionService myHapiTransactionService;
+
+	@Autowired
+	private IFhirSystemDao<?, ?> mySystemDao;
+
+	@Autowired
+	private DaoRegistry myRegistry;
+
+	@Autowired
+	private IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
+
+	@Autowired
+	@Qualifier("reindexGenerateRangeChunkStepV2")
+	private IJobStepWorker<ReindexJobParameters, VoidModel, ChunkRangeJson> myReindexGenerateRangeChunkStep;
+
+	@Autowired
+	@Qualifier("reindexLoadIdsStepV2")
+	private IJobStepWorker<ReindexJobParameters, ChunkRangeJson, ResourceIdListWorkChunkJson> myReindexLoadIdsStep;
+
+	@Autowired
+	private ReindexJobParametersValidatorV2 myReindexJobParametersValidator;
+
+	// Version 2
+	@Bean
+	public JobDefinition<ReindexJobParameters> reindexJobDefinitionV2() {
+		return JobDefinition.newBuilder()
+				.setJobDefinitionId(JOB_REINDEX)
+				.setJobDescription("Reindex resources")
+				.setJobDefinitionVersion(2)
+				.setParametersType(ReindexJobParameters.class)
+				.setParametersValidator(myReindexJobParametersValidator)
+				.gatedExecution()
+				.addFirstStep(
+						"generate-ranges",
+						"Generate data ranges to reindex",
+						ChunkRangeJson.class,
+						myReindexGenerateRangeChunkStep)
+				.addIntermediateStep(
+						"load-ids",
+						"Load IDs of resources to reindex",
+						ResourceIdListWorkChunkJson.class,
+						myReindexLoadIdsStep)
+				.addIntermediateStep(
+						"reindex-start", "Perform the resource reindex", ReindexResults.class, reindexStepV2())
+				.addLastStep("reindex-pending-work", "Waits for reindex work to complete.", pendingWorkStep())
+				.build();
+	}
+
+	@Bean
+	public CheckPendingReindexWorkStep pendingWorkStep() {
+		return new CheckPendingReindexWorkStep(myReindexJobService);
+	}
+
+	@Bean
+	public ReindexStepV2 reindexStepV2() {
+		return new ReindexStepV2(
+				myReindexJobService, myHapiTransactionService, mySystemDao, myRegistry, myIdHelperService);
+	}
+
+	@Bean("reindexGenerateRangeChunkStepV2")
+	public IJobStepWorker<ReindexJobParameters, VoidModel, ChunkRangeJson> reindexGenerateRangeChunksStep() {
+		return new GenerateRangeChunksStep<>();
+	}
+
+	@Bean("reindexLoadIdsStepV2")
+	public IJobStepWorker<ReindexJobParameters, ChunkRangeJson, ResourceIdListWorkChunkJson> reindexLoadIdsStep(
+			IBatch2DaoSvc theBatch2DaoSvc) {
+		return new LoadIdsStep<>(theBatch2DaoSvc);
+	}
+
+	@Bean
+	public ReindexJobParametersValidatorV2 reindexJobParametersValidatorV2(IBatch2DaoSvc theBatch2DaoSvc) {
+		return new ReindexJobParametersValidatorV2(
+				new UrlListValidator(ProviderConstants.OPERATION_REINDEX, theBatch2DaoSvc));
+	}
+}

hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexTaskParametersValidatorTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.batch2.jobs.reindex;
 
 import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
+import ca.uhn.fhir.batch2.jobs.reindex.v1.ReindexJobParametersValidatorV1;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
@@ -13,13 +14,13 @@ import java.util.List;
 import static org.assertj.core.api.Assertions.assertThat;
 
 @ExtendWith(MockitoExtension.class)
-public class ReindexJobParametersValidatorTest {
+public class ReindexTaskParametersValidatorTest {
 
 	@Mock
 	private UrlListValidator myListValidator;
 
 	@InjectMocks
-	private ReindexJobParametersValidator myValidator;
+	private ReindexJobParametersValidatorV1 myValidator;
 
 	@ParameterizedTest
 	@ValueSource(strings = { "\n", " ", "\t" })

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/RetryChunkLaterException.java

@@ -38,11 +38,18 @@ public class RetryChunkLaterException extends RuntimeException {
 	private final Duration myNextPollDuration;
 
 	public RetryChunkLaterException() {
-		this(ONE_MINUTE);
+		this("", ONE_MINUTE);
 	}
 
+	/**
+	 * For HAPI exceptions, use {@link RetryChunkLaterException#RetryChunkLaterException(String, Duration)}
+	 */
 	public RetryChunkLaterException(Duration theDuration) {
-		super();
+		this("", theDuration);
+	}
+
+	public RetryChunkLaterException(String theCode, Duration theDuration) {
+		super(theCode);
 		this.myNextPollDuration = theDuration;
 	}
 

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/chunk/ResourceIdListWorkChunkJson.java

@@ -62,7 +62,7 @@ public class ResourceIdListWorkChunkJson implements IModelJson {
 		return myRequestPartitionId;
 	}
 
-	private List<TypedPidJson> getTypedPids() {
+	public List<TypedPidJson> getTypedPids() {
 		if (myTypedPids == null) {
 			myTypedPids = new ArrayList<>();
 		}

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
 import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
+import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -315,12 +316,24 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 * @param theResourcePersistentId The ID
 	 * @return
 	 */
+	@SuppressWarnings("rawtypes")
 	ReindexOutcome reindex(
 			IResourcePersistentId theResourcePersistentId,
 			ReindexParameters theReindexParameters,
 			RequestDetails theRequest,
 			TransactionDetails theTransactionDetails);
 
+	/**
+	 * Returns ReindexJobStatus information object that tells the caller
+	 * if a reindex job is still in progress or not.
+	 *
+	 * If the implementing DAO requires additional work during reindexing,
+	 * this is the method to override.
+	 */
+	default ReindexJobStatus getReindexJobStatus() {
+		return ReindexJobStatus.NO_WORK_NEEDED;
+	}
+
 	void removeTag(
 			IIdType theId, TagTypeEnum theTagType, String theSystem, String theCode, RequestDetails theRequestDetails);
 

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

@@ -29,6 +29,11 @@ public class ReindexOutcome {
 
 	private List<String> myWarnings;
 
+	/**
+	 * True if there is additional (async) work to wait on.
+	 */
+	private boolean myHasPendingWork;
+
 	public List<String> getWarnings() {
 		return defaultIfNull(myWarnings, Collections.emptyList());
 	}
@@ -39,4 +44,12 @@ public class ReindexOutcome {
 		}
 		myWarnings.add(theWarning);
 	}
+
+	public boolean isHasPendingWork() {
+		return myHasPendingWork;
+	}
+
+	public void setHasPendingWork(boolean theHasPendingWork) {
+		myHasPendingWork = theHasPendingWork;
+	}
 }

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/model/ReindexJobStatus.java

@@ -0,0 +1,16 @@
+package ca.uhn.fhir.jpa.api.model;
+
+public class ReindexJobStatus {
+
+	public static ReindexJobStatus NO_WORK_NEEDED = new ReindexJobStatus();
+
+	private boolean myHasReindexWorkPending;
+
+	public boolean isHasReindexWorkPending() {
+		return myHasReindexWorkPending;
+	}
+
+	public void setHasReindexWorkPending(boolean theHasReindexWorkPending) {
+		myHasReindexWorkPending = theHasReindexWorkPending;
+	}
+}