More code review comments

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkItemReader.java

@@ -58,7 +58,7 @@ public class BulkItemReader implements ItemReader<List<ResourcePersistentId>> {
 	private void loadResourcePids() {
 		Optional<BulkExportJobEntity> jobOpt = myBulkExportJobDao.findByJobId(myJobUUID);
 		if (!jobOpt.isPresent()) {
-			ourLog.info("Job appears to be deleted");
+			ourLog.warn("Job appears to be deleted");
 			return;
 		}
 		myJobEntity = jobOpt.get();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceToFileWriter.java

@@ -27,7 +27,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 	private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
 
 	@Autowired
-	private FhirContext myContext;
+	private FhirContext myFhirContext;
 
 	@Autowired
 	private DaoRegistry myDaoRegistry;
@@ -52,7 +52,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 
 	@PostConstruct
 	public void start() {
-		myParser = myContext.newJsonParser().setPrettyPrint(false);
+		myParser = myFhirContext.newJsonParser().setPrettyPrint(false);
 		myBinaryDao = getBinaryDao();
 	}
 
@@ -73,7 +73,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 	}
 
 	private IIdType createBinaryFromOutputStream() {
-		IBaseBinary binary = BinaryUtil.newBinary(myContext);
+		IBaseBinary binary = BinaryUtil.newBinary(myFhirContext);
 		binary.setContentType(Constants.CT_FHIR_NDJSON);
 		binary.setContent(myOutputStream.toByteArray());
 
@@ -97,6 +97,8 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 		}
 
 		Optional<IIdType> createdId = flushToFiles();
-		createdId.ifPresent(theIIdType -> ourLog.warn("Created resources for bulk export file containing {} resources of type ", theIIdType.toUnqualifiedVersionless().getValue()));
+		if (createdId.isPresent()) {
+			ourLog.info("Created resources for bulk export file containing {} resources of type ", createdId.get().toUnqualifiedVersionless().getValue());
+		}
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceTypePartitioner.java

@@ -28,11 +28,7 @@ public class ResourceTypePartitioner implements Partitioner {
 		Map<String, ExecutionContext> partitionContextMap = new HashMap<>();
 
 		Map<Long, String> idToResourceType = myBulkExportDaoSvc.getBulkJobCollectionIdToResourceTypeMap(	myJobUUID);
-		//observation -> obs1.json, obs2.json, obs3.json BulkJobCollectionEntity
-		//bulk Collection Entity ID -> patient
 
-		// 123123-> Patient
-		// 91876389126-> Observation
 		idToResourceType.entrySet().stream()
 			.forEach(entry -> {
 				String resourceType = entry.getValue();

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

@@ -58,7 +58,7 @@ public class BulkExportDaoSvc {
 	private BulkExportJobEntity loadJob(String theJobUUID) {
 		Optional<BulkExportJobEntity> jobOpt = myBulkExportJobDao.findByJobId(theJobUUID);
 		if (!jobOpt.isPresent()) {
-			ourLog.info("Job appears to be deleted");
+			ourLog.warn("Job with UUID {} appears to be deleted", theJobUUID);
 			return null;
 		}
 		return jobOpt.get();

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

@@ -35,7 +35,4 @@ public interface IBulkExportCollectionDao extends JpaRepository<BulkExportCollec
 	@Modifying
 	@Query("DELETE FROM BulkExportCollectionEntity t WHERE t.myId = :pid")
 	void deleteByPid(@Param("pid") Long theId);
-
-//	@Query("SELECT BulkExportCollectionEntity ")
-//	void findByJobId(Long theId);
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java

@@ -33,6 +33,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
 import java.util.Date;
 import java.util.UUID;
 
+import static org.awaitility.Awaitility.await;
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.hamcrest.CoreMatchers.equalTo;
 import static org.junit.Assert.assertEquals;
@@ -264,7 +265,9 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 			.addLong("readChunkSize", 10L);
 		myBatchJobSubmitter.runJob(myBulkJob, paramBuilder.toJobParameters());
 
-		IBulkDataExportSvc.JobInfo jobInfo = awaitJobCompletion(jobDetails.getJobId());
+		awaitJobCompletion(jobDetails.getJobId());
+		IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
+
 		assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
 		assertThat(jobInfo.getFiles().size(), equalTo(2));
 	}
@@ -281,14 +284,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 	}
 
 	public IBulkDataExportSvc.JobInfo awaitJobCompletion(String theJobId) throws InterruptedException {
-		while(true) {
+		await().until(() -> myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(theJobId).getStatus() == BulkJobStatusEnum.COMPLETE);
-			IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(theJobId);
-			if (jobInfo.getStatus() != BulkJobStatusEnum.COMPLETE) {
-				Thread.sleep(1000L);
-			} else {
-				return jobInfo;
-			}
-		}
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java

@@ -8,14 +8,12 @@ import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
 import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
-import ca.uhn.fhir.model.dstu2.resource.Provenance;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
-import org.springframework.transaction.PlatformTransactionManager;
 
 import javax.persistence.EntityManagerFactory;
 
@@ -43,7 +41,8 @@ public class TestJPAConfig {
 	}
 
 	/*
-	I had to rename this bean as it was clashing with Spring Batch `transactionManager` in SimpleBatchConfiguration
+	Please do not rename this bean to "transactionManager()" as this will conflict with the transactionManager
+	provided by Spring Batch.
 	 */
 	@Bean
 	@Primary