Fix indexing bug

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

@@ -876,6 +876,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	@Override
 	public T read(IIdType theId, RequestDetails theRequestDetails) {
+		return read(theId, theRequestDetails, false);
+	}
+
+		@Override
+	public T read(IIdType theId, RequestDetails theRequestDetails, boolean theDeletedOk) {
 		validateResourceTypeAndThrowIllegalArgumentException(theId);
 
 		// Notify interceptors
@@ -891,10 +896,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		T retVal = toResource(myResourceType, entity, null, false);
 
-		if (entity.getDeleted() != null) {
+		if (theForHistory == false) {
-			throw new ResourceGoneException("Resource was deleted at " + new InstantType(entity.getDeleted()).getValueAsString());
+			if (entity.getDeleted() != null) {
+				throw new ResourceGoneException("Resource was deleted at " + new InstantType(entity.getDeleted()).getValueAsString());
+			}
 		}
 
+
 		ourLog.debug("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
 		return retVal;
 	}

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

@@ -171,6 +171,12 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	T read(IIdType theId, RequestDetails theRequestDetails);
 
+	/**
+	 * Should deleted resources be returned successfully. This should be false for
+	 * a normal FHIR read.
+	 */
+	T read(IIdType theId, RequestDetails theRequestDetails, boolean theDeletedOk);
+
 	BaseHasResource readEntity(IIdType theId);
 
 	/**

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

@@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.annotations.VisibleForTesting;
@@ -460,7 +461,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 
 						IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceTable.getResourceType());
 						long expectedVersion = resourceTable.getVersion();
-						IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless());
+						IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless(), null,true);
 						if (resource == null) {
 							throw new InternalErrorException("Could not find resource version " + resourceTable.getIdDt().toUnqualified().getValue() + " in database");
 						}

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

@@ -237,7 +237,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		runInTransaction(() -> {
 			Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
 			assertTrue(tableOpt.isPresent());
-			assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED, tableOpt.get().getIndexStatus().longValue());
+			assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, tableOpt.get().getIndexStatus().longValue());
 			assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), not(greaterThan(0)));
 		});
 

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

@@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.Before;
@@ -197,22 +198,22 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
 			"Patient"
 		};
 		List<IBaseResource> resources = Arrays.asList(
-			new Patient().setId("Patient/0"),
+			new Patient().setId("Patient/0/_history/1"),
-			new Patient().setId("Patient/1"),
+			new Patient().setId("Patient/1/_history/1"),
-			new Patient().setId("Patient/2"),
+			new Patient().setId("Patient/2/_history/1"),
-			new Patient().setId("Patient/3")
+			new Patient().setId("Patient/3/_history/1")
 		);
 		mockWhenResourceTableFindById(updatedTimes, resourceTypes);
 		when(myDaoRegistry.getResourceDao(eq("Patient"))).thenReturn(myResourceDao);
 		when(myDaoRegistry.getResourceDao(eq(Patient.class))).thenReturn(myResourceDao);
 		when(myDaoRegistry.getResourceDao(eq("Observation"))).thenReturn(myResourceDao);
 		when(myDaoRegistry.getResourceDao(eq(Observation.class))).thenReturn(myResourceDao);
-		when(myResourceDao.toResource(any(), anyBoolean())).thenAnswer(t -> {
+		when(myResourceDao.read(any())).thenAnswer(t->{
-			ResourceTable table = (ResourceTable) t.getArguments()[0];
+			IIdType id = (IIdType) t.getArguments()[0];
-			Long id = table.getId();
+			return resources.get(id.getIdPartAsLong().intValue());
-			return resources.get(id.intValue());
 		});
 
+
 		int count = mySvc.forceReindexingPass();
 		assertEquals(4, count);
 
@@ -258,20 +259,19 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
 			"Observation"
 		};
 		List<IBaseResource> resources = Arrays.asList(
-			new Patient().setId("Patient/0"),
+			new Patient().setId("Patient/0/_history/1"),
-			new Patient().setId("Patient/1"),
+			new Patient().setId("Patient/1/_history/1"),
-			new Observation().setId("Observation/2"),
+			new Observation().setId("Observation/2/_history/1"),
-			new Observation().setId("Observation/3")
+			new Observation().setId("Observation/3/_history/1")
 		);
 		mockWhenResourceTableFindById(updatedTimes, resourceTypes);
 		when(myDaoRegistry.getResourceDao(eq("Patient"))).thenReturn(myResourceDao);
 		when(myDaoRegistry.getResourceDao(eq(Patient.class))).thenReturn(myResourceDao);
 		when(myDaoRegistry.getResourceDao(eq("Observation"))).thenReturn(myResourceDao);
 		when(myDaoRegistry.getResourceDao(eq(Observation.class))).thenReturn(myResourceDao);
-		when(myResourceDao.toResource(any(), anyBoolean())).thenAnswer(t -> {
+		when(myResourceDao.read(any())).thenAnswer(t->{
-			ResourceTable table = (ResourceTable) t.getArguments()[0];
+			IIdType id = (IIdType) t.getArguments()[0];
-			Long id = table.getId();
+			return resources.get(id.getIdPartAsLong().intValue());
-			return resources.get(id.intValue());
 		});
 	}