Merge fd56f1462f into a5f3878392

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6451-bulk-import-job-status-not-changing-after-activation.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6451
+jira: SMILE-9089
+title: "Previously, activating `BulkDataImport` job would not change jobs status to `RUNNING`, 
+causing it to be processed multiple times instead of single time. This has been fixed."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java

@@ -217,6 +217,12 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc, IHasScheduledJ
 		String biJobId = null;
 		try {
 			biJobId = processJob(bulkImportJobEntity);
+			// set job status to RUNNING so it would not be processed again
+			myTxTemplate.execute(t -> {
+				bulkImportJobEntity.setStatus(BulkImportJobStatusEnum.RUNNING);
+				myJobDao.save(bulkImportJobEntity);
+				return null;
+			});
 		} catch (Exception e) {
 			ourLog.error("Failure while preparing bulk export extract", e);
 			myTxTemplate.execute(t -> {
@@ -256,6 +262,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc, IHasScheduledJ
 	}
 
 	@Override
+	@Transactional
 	public JobInfo getJobStatus(String theBiJobId) {
 		BulkImportJobEntity theJob = findJobByBiJobId(theBiJobId);
 		return new JobInfo()

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

@@ -1162,10 +1162,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				}
 
 				if (myFulltextSearchSvc != null && !myFulltextSearchSvc.isDisabled() && changed.isChanged()) {
-					// set the lastUpdated dates so we can use them to search in lucene
-					if (theResource.getMeta().getLastUpdated() == null) {
-						theResource.getMeta().setLastUpdated(theTransactionDetails.getTransactionDate());
-					}
 					populateFullTextFields(myContext, theResource, entity, newParams);
 				}
 			} else {
@@ -1200,16 +1196,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		 * Save the resource itself
 		 */
 		if (entity.getId() == null) {
+			// create
 			myEntityManager.persist(entity);
 
 			postPersist(entity, (T) theResource, theRequest);
 
 		} else if (entity.getDeleted() != null) {
+			// delete
 			entity = myEntityManager.merge(entity);
 
 			postDelete(entity);
 
 		} else {
+			// update
 			entity = myEntityManager.merge(entity);
 
 			postUpdate(entity, (T) theResource, theRequest);
@@ -1863,7 +1862,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			theEntity.setContentText(parseContentTextIntoWords(theContext, theResource));
 			if (myStorageSettings.isAdvancedHSearchIndexing()) {
 				ExtendedHSearchIndexData hSearchIndexData =
-						myFulltextSearchSvc.extractLuceneIndexData(theResource, theNewParams);
+						myFulltextSearchSvc.extractLuceneIndexData(theResource, theEntity, theNewParams);
 				theEntity.setLuceneIndexData(hSearchIndexData);
 			}
 		}

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

@@ -135,12 +135,12 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 
 	@Override
 	public ExtendedHSearchIndexData extractLuceneIndexData(
-			IBaseResource theResource, ResourceIndexedSearchParams theNewParams) {
+			IBaseResource theResource, ResourceTable theEntity, ResourceIndexedSearchParams theNewParams) {
 		String resourceType = myFhirContext.getResourceType(theResource);
 		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(resourceType);
 		ExtendedHSearchIndexExtractor extractor = new ExtendedHSearchIndexExtractor(
 				myStorageSettings, myFhirContext, activeSearchParams, mySearchParamExtractor);
-		return extractor.extract(theResource, theNewParams);
+		return extractor.extract(theResource, theEntity, theNewParams);
 	}
 
 	@Override

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

@@ -89,7 +89,7 @@ public interface IFulltextSearchSvc {
 	boolean isDisabled();
 
 	ExtendedHSearchIndexData extractLuceneIndexData(
-			IBaseResource theResource, ResourceIndexedSearchParams theNewParams);
+			IBaseResource theResource, ResourceTable theEntity, ResourceIndexedSearchParams theNewParams);
 
 	/**
 	 * Returns true if the parameter map can be handled for hibernate search.

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

@@ -25,6 +25,8 @@ import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
 import ca.uhn.fhir.jpa.model.entity.ResourceLink;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.entity.TagDefinition;
 import ca.uhn.fhir.jpa.model.search.CompositeSearchIndexData;
 import ca.uhn.fhir.jpa.model.search.DateSearchIndexData;
 import ca.uhn.fhir.jpa.model.search.ExtendedHSearchIndexData;
@@ -37,6 +39,7 @@ import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
 import ca.uhn.fhir.util.MetaUtil;
 import com.google.common.base.Strings;
 import jakarta.annotation.Nonnull;
+import org.apache.commons.lang3.ObjectUtils;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -73,9 +76,10 @@ public class ExtendedHSearchIndexExtractor {
 		mySearchParamExtractor = theSearchParamExtractor;
 	}
 
-	@Nonnull
-	public ExtendedHSearchIndexData extract(IBaseResource theResource, ResourceIndexedSearchParams theNewParams) {
-		ExtendedHSearchIndexData retVal = new ExtendedHSearchIndexData(myContext, myJpaStorageSettings, theResource);
+	public ExtendedHSearchIndexData extract(
+			IBaseResource theResource, ResourceTable theEntity, ResourceIndexedSearchParams theNewParams) {
+		ExtendedHSearchIndexData retVal =
+				new ExtendedHSearchIndexData(myContext, myJpaStorageSettings, theResource, theEntity);
 
 		if (myJpaStorageSettings.isStoreResourceInHSearchIndex()) {
 			retVal.setRawResourceData(myContext.newJsonParser().encodeResourceToString(theResource));
@@ -113,11 +117,27 @@ public class ExtendedHSearchIndexExtractor {
 				.filter(nextParam -> !nextParam.isMissing())
 				.forEach(nextParam -> retVal.addUriIndexData(nextParam.getParamName(), nextParam.getUri()));
 
-		theResource.getMeta().getTag().forEach(tag -> retVal.addTokenIndexData("_tag", tag));
+		theEntity.getTags().forEach(tag -> {
+			TagDefinition td = tag.getTag();
 
-		theResource.getMeta().getSecurity().forEach(sec -> retVal.addTokenIndexData("_security", sec));
-
-		theResource.getMeta().getProfile().forEach(prof -> retVal.addUriIndexData("_profile", prof.getValue()));
+			IBaseCoding coding = (IBaseCoding) myContext.getVersion().newCodingDt();
+			coding.setVersion(td.getVersion());
+			coding.setDisplay(td.getDisplay());
+			coding.setCode(td.getCode());
+			coding.setSystem(td.getSystem());
+			coding.setUserSelected(ObjectUtils.defaultIfNull(td.getUserSelected(), false));
+			switch (td.getTagType()) {
+				case TAG:
+					retVal.addTokenIndexData("_tag", coding);
+					break;
+				case PROFILE:
+					retVal.addUriIndexData("_profile", coding.getCode());
+					break;
+				case SECURITY_LABEL:
+					retVal.addTokenIndexData("_security", coding);
+					break;
+			}
+		});
 
 		String source = MetaUtil.getSource(myContext, theResource.getMeta());
 		if (isNotBlank(source)) {
@@ -127,20 +147,14 @@ public class ExtendedHSearchIndexExtractor {
 		theNewParams.myCompositeParams.forEach(nextParam ->
 				retVal.addCompositeIndexData(nextParam.getSearchParamName(), buildCompositeIndexData(nextParam)));
 
-		if (theResource.getMeta().getLastUpdated() != null) {
-			int ordinal = ResourceIndexedSearchParamDate.calculateOrdinalValue(
-							theResource.getMeta().getLastUpdated())
+		if (theEntity.getUpdated() != null && !theEntity.getUpdated().isEmpty()) {
+			int ordinal = ResourceIndexedSearchParamDate.calculateOrdinalValue(theEntity.getUpdatedDate())
 					.intValue();
 			retVal.addDateIndexData(
-					"_lastUpdated",
-					theResource.getMeta().getLastUpdated(),
-					ordinal,
-					theResource.getMeta().getLastUpdated(),
-					ordinal);
+					"_lastUpdated", theEntity.getUpdatedDate(), ordinal, theEntity.getUpdatedDate(), ordinal);
 		}
 
 		if (!theNewParams.myLinks.isEmpty()) {
-
 			// awkwardly, links are indexed by jsonpath, not by search param.
 			// so we re-build the linkage.
 			Map<String, List<String>> linkPathToParamName = new HashMap<>();

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

@@ -146,8 +146,7 @@ public class ExtendedHSearchSearchBuilder {
 
 				// not yet supported in HSearch
 				myParams.getSearchContainedMode() == SearchContainedModeEnum.FALSE
-				&&
-				supportsLastUpdated(myParams)
+				&& supportsLastUpdated(myParams)
 				&& // ???
 				myParams.entrySet().stream()
 						.filter(e -> !ourUnsafeSearchParmeters.contains(e.getKey()))
@@ -164,8 +163,10 @@ public class ExtendedHSearchSearchBuilder {
 
 		DateRangeParam lastUpdated = theMap.getLastUpdated();
 
-		return lastUpdated.getLowerBound() != null && isParamTypeSupported(lastUpdated.getLowerBound())
-			&& lastUpdated.getUpperBound() != null && isParamTypeSupported(lastUpdated.getUpperBound());
+		return lastUpdated.getLowerBound() != null
+				&& isParamTypeSupported(lastUpdated.getLowerBound())
+				&& lastUpdated.getUpperBound() != null
+				&& isParamTypeSupported(lastUpdated.getUpperBound());
 	}
 
 	/**

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java

@@ -108,7 +108,6 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest implements I
 		when(mySrd.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE)).thenReturn(Boolean.TRUE);
 	}
 
-
 	@AfterEach
 	public void after() {
 		myStorageSettings.setMaximumExpansionSize(JpaStorageSettings.DEFAULT_MAX_EXPANSION_SIZE);
@@ -217,7 +216,6 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest implements I
 		}
 		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd(CS_URL, additions);
 
-
 		// Codes available exceeds the max
 		myStorageSettings.setMaximumExpansionSize(50);
 		ValueSet vs = new ValueSet();
@@ -236,7 +234,6 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest implements I
 		include.setSystem(CS_URL);
 		ValueSet outcome = myTermSvc.expandValueSet(null, vs);
 		assertThat(outcome.getExpansion().getContains()).hasSize(109);
-
 	}
 
 	@Test

hapi-fhir-jpaserver-elastic-test-utilities/src/test/resources/logback-test.xml

@@ -10,15 +10,15 @@
 	</root>
 <!--Uncomment the below if you are doing Elasticsearch debugging -->
 
-	<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="trace">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.elasticsearch.client" level="debug" additivity="false">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="tracer" level="TRACE" additivity="false">
-		<appender-ref ref="STDOUT" />
-	</logger>
+<!--	<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="trace">-->
+<!--		<appender-ref ref="STDOUT" />-->
+<!--	</logger>-->
+<!--	<logger name="org.elasticsearch.client" level="debug" additivity="false">-->
+<!--		<appender-ref ref="STDOUT" />-->
+<!--	</logger>-->
+<!--	<logger name="tracer" level="TRACE" additivity="false">-->
+<!--		<appender-ref ref="STDOUT" />-->
+<!--	</logger>-->
 
 
 </configuration>

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/ExtendedHSearchIndexData.java

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.jpa.model.search;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import com.google.common.collect.HashMultimap;
@@ -57,12 +58,17 @@ public class ExtendedHSearchIndexData {
 	private String myForcedId;
 	private String myResourceJSON;
 	private IBaseResource myResource;
+	private ResourceTable myEntity;
 
 	public ExtendedHSearchIndexData(
-			FhirContext theFhirContext, StorageSettings theStorageSettings, IBaseResource theResource) {
+			FhirContext theFhirContext,
+			StorageSettings theStorageSettings,
+			IBaseResource theResource,
+			ResourceTable theEntity) {
 		this.myFhirContext = theFhirContext;
 		this.myStorageSettings = theStorageSettings;
 		myResource = theResource;
+		myEntity = theEntity;
 	}
 
 	private <V> BiConsumer<String, V> ifNotContained(BiConsumer<String, V> theIndexWriter) {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java

@@ -17,6 +17,7 @@ import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
 import ca.uhn.fhir.jpa.bulk.imprt.model.ActivateJobResult;
 import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
 import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
+import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
 import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.subscription.channel.api.ChannelConsumerSettings;
@@ -166,6 +167,8 @@ public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuil
 
 		ActivateJobResult activateJobOutcome = mySvc.activateNextReadyJob();
 		assertTrue(activateJobOutcome.isActivated);
+		// validate that job changed status from READY to RUNNING
+		assertEquals(BulkImportJobStatusEnum.RUNNING, mySvc.getJobStatus(jobId).getStatus());
 
 		JobInstance instance = myBatch2JobHelper.awaitJobCompletion(activateJobOutcome.jobId, 60);
 		assertNotNull(instance);
@@ -196,6 +199,8 @@ public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuil
 
 			ActivateJobResult activateJobOutcome = mySvc.activateNextReadyJob();
 			assertTrue(activateJobOutcome.isActivated);
+			// validate that job changed status from READY to RUNNING
+			assertEquals(BulkImportJobStatusEnum.RUNNING, mySvc.getJobStatus(jobId).getStatus());
 
 			JobInstance instance = myBatch2JobHelper.awaitJobCompletion(activateJobOutcome.jobId);
 			assertNotNull(instance);

hapi-fhir-jpaserver-test-r4/src/test/resources/logback-test.xml

@@ -31,7 +31,7 @@
 	<logger name="ca.uhn.fhir.jpa.bulk" level="info"/>
 
 	<!-- more debugging -->
-<!--	&lt;!&ndash;-->
+<!--
 	<logger name="org.elasticsearch.client" level="trace"/>
 	<logger name="org.hibernate.search.elasticsearch.request" level="TRACE"/>
 	<logger name="ca.uhn.fhir.jpa.model.search" level="debug"/>
@@ -39,7 +39,7 @@
 	<logger name="org.hibernate.search" level="debug"/>
 	<logger name="org.hibernate.search.query" level="TRACE"/>
 	<logger name="org.hibernate.search.elasticsearch.request" level="TRACE"/>
-<!--	 &ndash;&gt;-->
+-->
 	<!-- See https://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/#backend-lucene-io-writer-infostream for lucene logging
 	<logger name="org.hibernate.search.backend.lucene.infostream" level="TRACE"/>  -->
 

hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_4_0/data/H2_EMBEDDED.sql

@@ -51,3 +51,33 @@ INSERT INTO TRM_CONCEPT_DESIG (
    54,
    150
 );
+
+INSERT INTO HFJ_RES_LINK (
+   PID,
+   PARTITION_DATE,
+   PARTITION_ID,
+   SRC_PATH,
+   SRC_RESOURCE_ID,
+   SOURCE_RESOURCE_TYPE,
+   TARGET_RESOURCE_ID,
+   TARGET_RESOURCE_TYPE,
+   TARGET_RESOURCE_URL,
+   TARGET_RESOURCE_VERSION,
+   SP_UPDATED,
+   TARGET_RES_PARTITION_ID,
+   TARGET_RES_PARTITION_DATE
+) VALUES (
+   702,
+   '2024-11-05',
+   1,
+   'Observation.subject.where(resolve() is Patient)',
+   1656,
+   'Observation',
+   1906,
+   'Patient',
+   'http://localhost:8000/Patient/123',
+   1,
+   '2024-11-01 18:01:12.921',
+   1,
+   '2024-11-05'
+);

hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_4_0/data/MSSQL_2012.sql

@@ -51,3 +51,33 @@ INSERT INTO TRM_CONCEPT_DESIG (
    54,
    150
 );
+
+INSERT INTO HFJ_RES_LINK (
+   PID,
+   PARTITION_DATE,
+   PARTITION_ID,
+   SRC_PATH,
+   SRC_RESOURCE_ID,
+   SOURCE_RESOURCE_TYPE,
+   TARGET_RESOURCE_ID,
+   TARGET_RESOURCE_TYPE,
+   TARGET_RESOURCE_URL,
+   TARGET_RESOURCE_VERSION,
+   SP_UPDATED,
+   TARGET_RES_PARTITION_ID,
+   TARGET_RES_PARTITION_DATE
+) VALUES (
+   702,
+   '2024-11-05',
+   1,
+   'Observation.subject.where(resolve() is Patient)',
+   1653,
+   'Observation',
+   1906,
+   'Patient',
+   'http://localhost:8000/Patient/123',
+   1,
+   '2024-11-01 18:01:12.921',
+   1,
+   '2024-11-05'
+);

hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_4_0/data/ORACLE_12C.sql

@@ -51,3 +51,33 @@ INSERT INTO TRM_CONCEPT_DESIG (
    54,
    150
 );
+
+INSERT INTO HFJ_RES_LINK (
+   PID,
+   PARTITION_DATE,
+   PARTITION_ID,
+   SRC_PATH,
+   SRC_RESOURCE_ID,
+   SOURCE_RESOURCE_TYPE,
+   TARGET_RESOURCE_ID,
+   TARGET_RESOURCE_TYPE,
+   TARGET_RESOURCE_URL,
+   TARGET_RESOURCE_VERSION,
+   SP_UPDATED,
+   TARGET_RES_PARTITION_ID,
+   TARGET_RES_PARTITION_DATE
+) VALUES (
+   702,
+   SYSDATE,
+   1,
+   'Observation.subject.where(resolve() is Patient)',
+   1653,
+   'Observation',
+   1906,
+   'Patient',
+   'http://localhost:8000/Patient/123',
+   1,
+   SYSDATE,
+   1,
+   SYSDATE
+);

hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_4_0/data/POSTGRES_9_4.sql

@@ -51,3 +51,33 @@ INSERT INTO TRM_CONCEPT_DESIG (
    54,
    150
 );
+
+INSERT INTO HFJ_RES_LINK (
+   PID,
+   PARTITION_DATE,
+   PARTITION_ID,
+   SRC_PATH,
+   SRC_RESOURCE_ID,
+   SOURCE_RESOURCE_TYPE,
+   TARGET_RESOURCE_ID,
+   TARGET_RESOURCE_TYPE,
+   TARGET_RESOURCE_URL,
+   TARGET_RESOURCE_VERSION,
+   SP_UPDATED,
+   TARGET_RES_PARTITION_ID,
+   TARGET_RES_PARTITION_DATE
+) VALUES (
+   702,
+   '2024-11-05',
+   1,
+   'Observation.subject.where(resolve() is Patient)',
+   1653,
+   'Observation',
+   1906,
+   'Patient',
+   'http://localhost:8000/Patient/123',
+   1,
+   '2024-11-01 18:01:12.921',
+   1,
+   '2024-11-05'
+);

hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/ILuceneSearchR4Test.java

@@ -74,6 +74,11 @@ public interface ILuceneSearchR4Test {
 		Patient patient = new Patient();
 		patient.getMeta()
 			.addTag(system, code, "");
+		patient.addName().addGiven("homer")
+			.setFamily("simpson");
+		patient.addAddress()
+			.setCity("springfield")
+			.addLine("742 evergreen terrace");
 		Long id = patientDao.create(patient, requestDeatils).getId().toUnqualifiedVersionless().getIdPartAsLong();
 
 		// create base search map

hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/search/ExtendedHSearchIndexExtractorTest.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.CompositeSearchIndexData;
 import ca.uhn.fhir.jpa.model.search.DateSearchIndexData;
 import ca.uhn.fhir.jpa.model.search.ExtendedHSearchIndexData;
@@ -54,7 +55,7 @@ class ExtendedHSearchIndexExtractorTest implements ITestDataBuilder.WithSupport
 		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams("Observation");
 		ExtendedHSearchIndexExtractor extractor = new ExtendedHSearchIndexExtractor(
 			myJpaStorageSettings, myFhirContext, activeSearchParams, mySearchParamExtractor);
-		ExtendedHSearchIndexData indexData = extractor.extract(new Observation(), extractedParams);
+		ExtendedHSearchIndexData indexData = extractor.extract(new Observation(), new ResourceTable(), extractedParams);
 
 		// validate
 		Set<CompositeSearchIndexData> spIndexData = indexData.getSearchParamComposites().get("component-code-value-concept");
@@ -77,14 +78,13 @@ class ExtendedHSearchIndexExtractorTest implements ITestDataBuilder.WithSupport
 		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams("Patient");
 		ExtendedHSearchIndexExtractor extractor = new ExtendedHSearchIndexExtractor(
 			myJpaStorageSettings, myFhirContext, activeSearchParams, mySearchParamExtractor);
-		ExtendedHSearchIndexData indexData = extractor.extract(new SearchParameter(), searchParams);
+		ExtendedHSearchIndexData indexData = extractor.extract(new SearchParameter(), new ResourceTable(), searchParams);
 
 		// validate
 		Set<DateSearchIndexData> dIndexData = indexData.getDateIndexData().get("Date");
 		assertThat(dIndexData).hasSize(0);
 		Set<QuantitySearchIndexData> qIndexData = indexData.getQuantityIndexData().get("Quantity");
 		assertThat(qIndexData).hasSize(0);
-
 	}
 
 	@Override

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/dstu3/EvaluateOperationConfig.java

@@ -21,15 +21,20 @@ package ca.uhn.fhir.cr.config.dstu3;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.cr.config.CrProcessorConfig;
 import ca.uhn.fhir.cr.config.ProviderLoader;
 import ca.uhn.fhir.cr.config.ProviderSelector;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 
 import java.util.Arrays;
 import java.util.Map;
 
+@Configuration
+@Import(CrProcessorConfig.class)
 public class EvaluateOperationConfig {
 	@Bean
 	ca.uhn.fhir.cr.dstu3.library.LibraryEvaluateProvider dstu3LibraryEvaluateProvider() {

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/r4/EvaluateOperationConfig.java

@@ -21,15 +21,20 @@ package ca.uhn.fhir.cr.config.r4;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.cr.config.CrProcessorConfig;
 import ca.uhn.fhir.cr.config.ProviderLoader;
 import ca.uhn.fhir.cr.config.ProviderSelector;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 
 import java.util.Arrays;
 import java.util.Map;
 
+@Configuration
+@Import(CrProcessorConfig.class)
 public class EvaluateOperationConfig {
 	@Bean
 	ca.uhn.fhir.cr.r4.library.LibraryEvaluateProvider r4LibraryEvaluateProvider() {

hapi-fhir-storage-test-utilities/src/main/java/ca/uhn/fhir/storage/test/DaoTestDataBuilder.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.test.utilities.ITestDataBuilder;
 import ca.uhn.fhir.util.BundleBuilder;
 import com.google.common.collect.HashMultimap;
@@ -66,18 +67,42 @@ public class DaoTestDataBuilder implements ITestDataBuilder.WithSupport, ITestDa
 		}
 		//noinspection rawtypes
 		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
+
+		// manipulate the transaction details to provide a fake transaction date
+		TransactionDetails details = null;
+		if (theResource.getMeta() != null && theResource.getMeta().getLastUpdated() != null) {
+			details = new TransactionDetails(theResource.getMeta().getLastUpdated());
+		} else {
+			details = new TransactionDetails();
+		}
+
 		//noinspection unchecked
-		IIdType id = dao.create(theResource, mySrd).getId().toUnqualifiedVersionless();
+		IIdType id = dao.create(theResource, null, true, mySrd, details)
+			.getId().toUnqualifiedVersionless();
 		myIds.put(theResource.fhirType(), id);
 		return id;
 	}
 
 	@Override
 	public IIdType doUpdateResource(IBaseResource theResource) {
+		// manipulate the transaction details to provdie a fake transaction date
+		TransactionDetails details = null;
+		if (theResource.getMeta() != null && theResource.getMeta().getLastUpdated() != null) {
+			details = new TransactionDetails(theResource.getMeta().getLastUpdated());
+		} else {
+			details = new TransactionDetails();
+		}
+
 		//noinspection rawtypes
 		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
+
 		//noinspection unchecked
-		IIdType id = dao.update(theResource, mySrd).getId().toUnqualifiedVersionless();
+		IIdType id = dao.update(theResource,
+			null,
+			true,
+			false,
+			mySrd,
+			details).getId().toUnqualifiedVersionless();
 		myIds.put(theResource.fhirType(), id);
 		return id;
 	}

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java

@@ -209,6 +209,12 @@ public interface ITestDataBuilder {
 		return t -> ((IBaseResource)t).getMeta().setLastUpdated(theLastUpdated);
 	}
 
+	/**
+	 * Sets a _lastUpdated value.
+	 *
+	 * This value will also be used to control the transaction time, which is what determines
+	 * what the Updated date is.
+	 */
 	default ICreationArgument withLastUpdated(String theIsoDate) {
 		return t -> ((IBaseResource)t).getMeta().setLastUpdated(new InstantType(theIsoDate).getValue());
 	}

pom.xml

@@ -1054,7 +1054,7 @@
 		<ucum_version>1.0.8</ucum_version>
 
 		<!-- Clinical Reasoning & CQL Support -->
-		<clinical-reasoning.version>3.13.0</clinical-reasoning.version>
+		<clinical-reasoning.version>3.13.1</clinical-reasoning.version>
 
 		<!-- Site properties -->
 		<fontawesomeVersion>5.4.1</fontawesomeVersion>