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Resolve NPE in group bulk export (#2476)

This commit is contained in:
James Agnew 2021-03-14 13:12:58 -04:00 committed by GitHub
parent f2baf9b8dc
commit 3a8881f913
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3 changed files with 53 additions and 5 deletions
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12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/provider/BulkDataExportProvider.java
View File

@ -132,12 +132,14 @@ public class BulkDataExportProvider {
}
private void validateResourceTypesAllContainPatientSearchParams(Set<String> theResourceTypes) {
List<String> badResourceTypes = theResourceTypes.stream()
.filter(resourceType -> !myBulkDataExportSvc.getPatientCompartmentResources().contains(resourceType))
.collect(Collectors.toList());
if (theResourceTypes != null) {
List<String> badResourceTypes = theResourceTypes.stream()
.filter(resourceType -> !myBulkDataExportSvc.getPatientCompartmentResources().contains(resourceType))
.collect(Collectors.toList());
if (!badResourceTypes.isEmpty()) {
throw new InvalidRequestException(String.format("Resource types [%s] are invalid for this type of export, as they do not contain search parameters that refer to patients.", String.join(",", badResourceTypes)));
if (!badResourceTypes.isEmpty()) {
throw new InvalidRequestException(String.format("Resource types [%s] are invalid for this type of export, as they do not contain search parameters that refer to patients.", String.join(",", badResourceTypes)));
}
}
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java
View File

@ -148,6 +148,7 @@ public class BulkDataExportProviderTest {
assertThat(options.getFilters(), containsInAnyOrder("Patient?identifier=foo"));
}
@Test
public void testSuccessfulInitiateBulkRequest_Get() throws IOException {
@ -432,6 +433,22 @@ public class BulkDataExportProviderTest {
assertThat(responseBody, is(containsString("Resource types [StructureDefinition] are invalid for this type of export, as they do not contain search parameters that refer to patients.")));
}
@Test
public void testInitiateGroupExportWithNoResourceTypes() throws IOException {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any(), any())).thenReturn(jobInfo);
String url = "http://localhost:" + myPort + "/" + "Group/123/" +JpaConstants.OPERATION_EXPORT
+ "?" + JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT + "=" + UrlUtil.escapeUrlParam(Constants.CT_FHIR_NDJSON);;
HttpGet get = new HttpGet(url);
get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
CloseableHttpResponse execute = myClient.execute(get);
assertThat(execute.getStatusLine().getStatusCode(), is(equalTo(202)));
}
@Test
public void testInitiateWithPostAndMultipleTypeFilters() throws IOException {

29
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
View File

@ -19,9 +19,11 @@ import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
@ -37,6 +39,7 @@ import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.Test;
@ -52,6 +55,7 @@ import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collection;
import java.util.Date;
@ -404,6 +408,31 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
}
}
@Test
public void testGroupExport_NoResourceTypesSpecified() {
createResources();
// Create a bulk job
BulkDataExportOptions bulkDataExportOptions = new BulkDataExportOptions();
bulkDataExportOptions.setOutputFormat(null);
bulkDataExportOptions.setSince(null);
bulkDataExportOptions.setFilters(null);
bulkDataExportOptions.setGroupId(myPatientGroupId);
bulkDataExportOptions.setExpandMdm(true);
bulkDataExportOptions.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
myBulkDataExportSvc.buildExportFiles();
awaitAllBulkJobCompletions();
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
assertThat(jobInfo.getFiles().size(), equalTo(5));
}
@Test
public void testGenerateBulkExport_WithHas() {