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Resolve 5602 bulk export would fail if type parameter is not provided (#5605) 

* default _type to all resource types in the patient compartment for patient type&instance level bulk export

* parametrized test so that it calls both type and instance level

* added change log and spotless check

* resolved code review comments
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TynerGjs 2024-01-19 15:05:32 -05:00 committed by GitHub
parent 6a370c60cb
commit 6e1a56d520
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3 changed files with 26 additions and 7 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5602-bulk-export-would-fail-if-type-parameter-is-not-provided.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 5602
title: "Previously, instance-level Patient Bulk Export batch job would fail if the `_type` parameter was empty. This is
now fixed and `_type` will default to all resource types in the Patient Compartment plus Device."

17
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java
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@ -29,6 +29,7 @@ import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import ca.uhn.fhir.test.utilities.HttpClientExtension;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import ca.uhn.fhir.util.JsonUtil;
import ca.uhn.fhir.util.SearchParameterUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
@ -49,6 +50,7 @@ import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.CsvSource;
import org.junit.jupiter.params.provider.MethodSource;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.ArgumentCaptor;
import org.mockito.InjectMocks;
import org.mockito.Mock;
@ -60,13 +62,16 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Stream;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.arrayContainingInAnyOrder;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
@ -799,8 +804,9 @@ public class BulkDataExportProviderTest {
assertThat(bp.getFilters(), containsInAnyOrder("Patient?gender=male", "Patient?gender=female"));
}
@Test
public void testInitiateBulkExportOnPatient_noTypeParam_addsTypeBeforeBulkExport() throws IOException {
@ParameterizedTest
@ValueSource(strings = {"/Patient/" + ProviderConstants.OPERATION_EXPORT, "/Patient/p1/" + ProviderConstants.OPERATION_EXPORT})
public void testInitiateBulkExportOnPatient_noTypeParam_addsTypeBeforeBulkExport(String mode) throws IOException {
// when
when(myJobCoordinator.startInstance(isNotNull(), any()))
.thenReturn(createJobStartResponse());
@ -809,7 +815,7 @@ public class BulkDataExportProviderTest {
input.addParameter(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, new StringType(Constants.CT_FHIR_NDJSON));
// call
HttpPost post = new HttpPost(myServer.getBaseUrl() + "/Patient/" + ProviderConstants.OPERATION_EXPORT);
HttpPost post = new HttpPost(myServer.getBaseUrl() + mode);
post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
post.setEntity(new ResourceEntity(myCtx, input));
ourLog.info("Request: {}", post);
@ -820,9 +826,12 @@ public class BulkDataExportProviderTest {
assertEquals(myServer.getBaseUrl() + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
}
// verify
Set<String> expectedResourceTypes = new HashSet<>(SearchParameterUtil.getAllResourceTypesThatAreInPatientCompartment(myCtx));
expectedResourceTypes.add("Device");
BulkExportJobParameters bp = verifyJobStartAndReturnParameters();
assertEquals(Constants.CT_FHIR_NDJSON, bp.getOutputFormat());
assertThat(bp.getResourceTypes(), containsInAnyOrder("Patient"));
assertThat(bp.getResourceTypes(), containsInAnyOrder(expectedResourceTypes.toArray()));
}
@Test

11
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/BulkDataExportProvider.java
View File

@ -647,8 +647,8 @@ public class BulkDataExportProvider {
List<IPrimitiveType<String>> theTypePostFetchFilterUrl) {
IPrimitiveType<String> type = theType;
if (type == null) {
// Type is optional, but the job requires it
type = new StringDt("Patient");
// set type to all patient compartment resources if it is null
type = new StringDt(String.join(",", getPatientCompartmentResources()));
}
BulkExportJobParameters BulkExportJobParameters = buildBulkExportJobParameters(
theOutputFormat,
@ -673,9 +673,14 @@ public class BulkDataExportProvider {
IPrimitiveType<String> theExportIdentifier,
IIdType thePatientId,
List<IPrimitiveType<String>> theTypePostFetchFilterUrl) {
IPrimitiveType<String> type = theType;
if (type == null) {
// set type to all patient compartment resources if it is null
type = new StringDt(String.join(",", getPatientCompartmentResources()));
}
BulkExportJobParameters BulkExportJobParameters = buildBulkExportJobParameters(
theOutputFormat,
theType,
type,
theSince,
theTypeFilter,
theExportIdentifier,