Fix a crash when reindexing deleted resources

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

@@ -1772,8 +1772,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
 		theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+		Validate.notNull(theEntity);
+		Validate.isTrue(theDeletedTimestampOrNull != null || theResource != null, "Must have either a resource[{}] or a deleted timestamp[{}] for resource PID[{}]", theDeletedTimestampOrNull != null, theResource != null, theEntity.getId());
+
 		ourLog.debug("Starting entity update");
 
+
 		/*
 		 * This should be the very first thing..
 		 */
@@ -1863,6 +1867,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			theEntity.setNarrativeTextParsedIntoWords(null);
 			theEntity.setContentTextParsedIntoWords(null);
 			theEntity.setHashSha256(null);
+			theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
 			changed = populateResourceIntoEntity(theRequest, theResource, theEntity, true);
 
 		} else {

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

@@ -927,10 +927,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	@Override
 	public void reindex(T theResource, ResourceTable theEntity) {
-		ourLog.debug("Indexing resource {} - PID {}", theResource.getIdElement().getValue(), theEntity.getId());
+		ourLog.debug("Indexing resource {} - PID {}", theEntity.getIdDt().getValue(), theEntity.getId());
-		CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
+		if (theResource != null) {
-		updateEntity(null, theResource, theEntity, null, true, false, theEntity.getUpdatedDate(), true, false);
+			CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
-		CURRENTLY_REINDEXING.put(theResource, null);
+		}
+		updateEntity(null, theResource, theEntity, theEntity.getDeleted(), true, false, theEntity.getUpdatedDate(), true, false);
+		if (theResource != null) {
+			CURRENTLY_REINDEXING.put(theResource, null);
+		}
 	}
 
 	@Override
@@ -1062,6 +1066,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		mySecondaryPrimaryKeyParamName = theSecondaryPrimaryKeyParamName;
 	}
 
+	@PostConstruct
+	public void start() {
+		ourLog.debug("Starting resource DAO for type: {}", getResourceName());
+	}
+
 	protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) {
 		MT retVal;
 		try {
@@ -1333,9 +1342,4 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 	}
 
-	@PostConstruct
-	public void start() {
-		ourLog.debug("Starting resource DAO for type: {}", getResourceName());
-	}
-
 }

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

@@ -23,7 +23,12 @@ package ca.uhn.fhir.jpa.dao.data;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
 public interface IResourceIndexedSearchParamStringDao extends JpaRepository<ResourceIndexedSearchParamString, Long> {
-	// nothing yet
+
+	@Query("select count(*) from ResourceIndexedSearchParamString t WHERE t.myResourcePid = :resid")
+	int countForResourceId(@Param("resid") Long theResourcePid);
+
 }

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

@@ -20,10 +20,14 @@ package ca.uhn.fhir.jpa.dao.data;
  * #L%
  */
 
-import org.springframework.data.jpa.repository.JpaRepository;
-
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
 public interface IResourceIndexedSearchParamTokenDao extends JpaRepository<ResourceIndexedSearchParamToken, Long> {
-	// nothing yet
+
+	@Query("select count(*) from ResourceIndexedSearchParamToken t WHERE t.myResourcePid = :resid")
+	int countForResourceId(@Param("resid") Long theResourcePid);
+
 }

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

@@ -1,10 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.*;
-import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
+import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
-import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
@@ -152,6 +149,42 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		return retVal;
 	}
 
+
+	@Test
+	public void testDeletedResourcesAreReindexed() {
+		myDaoConfig.setSchedulingDisabled(true);
+
+		Patient pt1 = new Patient();
+		pt1.setActive(true);
+		pt1.addName().setFamily("FAM");
+		IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
+
+		runInTransaction(()->{
+			assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), greaterThan(0));
+		});
+
+		runInTransaction(()->{
+			Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
+			assertTrue(tableOpt.isPresent());
+			ResourceTable table = tableOpt.get();
+			table.setIndexStatus(null);
+			table.setDeleted(new Date());
+		});
+
+		mySystemDao.performReindexingPass(1000);
+		mySystemDao.performReindexingPass(1000);
+
+		runInTransaction(()->{
+			Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
+			assertTrue(tableOpt.isPresent());
+			assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, tableOpt.get().getIndexStatus().longValue());
+			assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), not(greaterThan(0)));
+		});
+
+
+	}
+
+
 	@Test
 	public void testCantSearchForDeletedResourceByLanguageOrTag() {
 		String methodName = "testCantSearchForDeletedResourceByLanguageOrTag";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java

@@ -1,9 +1,11 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.SearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedCompositeStringUnique;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.util.JpaConstants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -27,6 +29,7 @@ import org.springframework.transaction.support.TransactionTemplate;
 import javax.annotation.Nonnull;
 import java.util.Collections;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 
 import static org.hamcrest.Matchers.*;

src/changes/changes.xml

@@ -134,6 +134,10 @@
 				A crash was fixed when deleting a ConceptMap resource in the
 				JPA server. This crash was a regression in HAPI FHIR 3.4.0.
 			</action>
+			<action type="fix">
+				A crash in the JPA server when performing a manual reindex of a deleted resource
+				was fixed.
+			</action>
 		</release>
 		<release version="3.4.0" date="2018-05-28">
 			<action type="add">