Enabling massIngestionMode causes incomplete resource deletion (#4476)

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4475-fix-incomplete-resource-deletion-with-massinjectionmode-enabled.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4475
+jira: SMILE-4961
+title: "Enabling mass ingestion mode alters the resource deletion process leaving resources partially deleted. The problem has been fixed."

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

@@ -143,7 +143,7 @@ import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.stream.Collectors;
 
-import static ca.uhn.fhir.jpa.model.util.JpaConstants.ALL_PARTITIONS_NAME;
+import static java.util.Objects.nonNull;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -601,7 +601,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 		} else {
 
-			theEntity.setHashSha256(null);
+			if(nonNull(theEntity.getHashSha256())){
+				theEntity.setHashSha256(null);
+				changed = true;
+			}
+
 			resourceBinary = null;
 			resourceText = null;
 			encoding = ResourceEncodingEnum.DEL;
@@ -939,7 +943,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			entity.setUpdated(theDeletedTimestampOrNull);
 			entity.setNarrativeText(null);
 			entity.setContentText(null);
-			entity.setHashSha256(null);
 			entity.setIndexStatus(INDEX_STATUS_INDEXED);
 			changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
 

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

@@ -2895,9 +2895,28 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 	}
 
-	private void printQueryCount(String theMessage){
+	@Test
-		
+	public void testDeleteResource_WithMassIngestionMode_enabled(){
-		ourLog.info("QueryCount {} is: ", theMessage);
+		myDaoConfig.setMassIngestionMode(true);
+
+		// given
+		Observation observation = new Observation()
+			.setStatus(Observation.ObservationStatus.FINAL)
+			.addCategory(new CodeableConcept().addCoding(new Coding("http://category-type", "12345", null)))
+			.setCode(new CodeableConcept().addCoding(new Coding("http://coverage-type", "12345", null)));
+
+		IIdType idDt = myObservationDao.create(observation, mySrd).getEntity().getIdDt();
+
+		// when
+		myCaptureQueriesListener.clear();
+		myObservationDao.delete(idDt, mySrd);
+
+		// then
+		assertQueryCount(3,1,1, 1);
+	}
+
+	private void printQueryCount(){
+
 		ourLog.info("\tselect: {}", myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 		ourLog.info("\tupdate: {}", myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
 		ourLog.info("\tinsert: {}", myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
@@ -2905,16 +2924,15 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 	}
 
-	private void assertQueryCount(int theExpectedSelect, int theExpectedUpdate, int theExpectedInsert, int theExpectedDelete){
+	private void assertQueryCount(int theExpectedSelectCount, int theExpectedUpdateCount, int theExpectedInsertCount, int theExpectedDeleteCount){
-		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 
-		assertEquals(theExpectedSelect, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+		assertEquals(theExpectedSelectCount, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 		myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
-		assertEquals(theExpectedUpdate, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
+		assertEquals(theExpectedUpdateCount, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
 		myCaptureQueriesListener.logInsertQueriesForCurrentThread();
-		assertEquals(theExpectedInsert, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
+		assertEquals(theExpectedInsertCount, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
 		myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
-		assertEquals(theExpectedDelete, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
+		assertEquals(theExpectedDeleteCount, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
 	}
 
 	private Group createGroup(List<IIdType> theIIdTypeList) {

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

@@ -175,6 +175,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		myDaoConfig.setInternalSynchronousSearchSize(new DaoConfig().getInternalSynchronousSearchSize());
 		myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
 		myDaoConfig.setHistoryCountMode(DaoConfig.DEFAULT_HISTORY_COUNT_MODE);
+		myDaoConfig.setMassIngestionMode(false);
 	}
 
 	private void assertGone(IIdType theId) {
@@ -2498,6 +2499,35 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testDeleteWithMassInjectionModeEnabled(){
+		myDaoConfig.setMassIngestionMode(true);
+
+		// given
+		Observation observation = new Observation()
+			.setStatus(ObservationStatus.FINAL)
+			.addCategory(newCodeableConcept("http://somesystem","somecode"))
+			.setCode(newCodeableConcept("http://loinc.org", "15074-8"));
+
+		// when
+		IIdType idDt = myObservationDao.create(observation, mySrd).getEntity().getIdDt();
+
+		myObservationDao.delete(idDt, mySrd);
+
+		// then
+		runInTransaction(() -> {
+			Long obsertionId = idDt.getIdPartAsLong();
+			Long resourceCurrentVersion = myResourceTableDao.findCurrentVersionByPid(obsertionId);
+			int resourceVersionCount = myResourceHistoryTableDao.findAllVersionsForResourceIdInOrder(obsertionId).size();
+			int indexedTokenCount = myResourceIndexedSearchParamTokenDao.countForResourceId(obsertionId);
+
+			assertThat(resourceCurrentVersion, equalTo(2L));
+			assertThat(resourceVersionCount, equalTo(2));
+			assertThat(indexedTokenCount, equalTo(0));
+
+		});
+	}
+
 	@Test
 	public void testPersistContactPoint() {
 		List<IAnyResource> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_TELECOM, new TokenParam(null, "555-123-4567")).setLoadSynchronous(true)));