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hapi-fhir
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This commit is contained in:
Tadgh 2020-06-09 19:18:06 -07:00
parent 942fc313ec
commit c36e1d2899
7 changed files with 15 additions and 25 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkItemReader.java
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@ -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();

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceToFileWriter.java
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@ -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());
}
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceTypePartitioner.java
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@ -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();

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/svc/BulkExportDaoSvc.java
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@ -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();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBulkExportCollectionDao.java
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@ -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);
}

14
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
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@ -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) {
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(theJobId);
if (jobInfo.getStatus() != BulkJobStatusEnum.COMPLETE) {
Thread.sleep(1000L);
} else {
return jobInfo;
}
}
await().until(() -> myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(theJobId).getStatus() == BulkJobStatusEnum.COMPLETE);
}
@Test

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java
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@ -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