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Code Issues Packages Projects Releases Wiki Activity

Group bulk export _since parameter issue (#4389) 

* Test + fix

* javadoc
This commit is contained in:
Qingyixia 2022-12-22 13:19:07 -05:00 committed by GitHub
parent e4ad370314
commit 51797c3c1e
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5 changed files with 68 additions and 14 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4387-group-bulk-export-since-parameter-error.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 4387
title: "Previously, when use group bulk export, if the group was referenced to a patient resource and the patient has not been updated after the _since parameter of the bulk export, none of their data/sub-resources comes through even if the sub-resources were qualified (By qualified, I mean the sub-resources were upadted/created after _since parameter).
Now, this issue has been fixed."

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java
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@ -149,7 +149,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
Set<String> patientSearchParams = SearchParameterUtil.getPatientSearchParamsForResourceType(myContext, theParams.getResourceType());
for (String patientSearchParam : patientSearchParams) {
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParams);
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParams, false);
for (SearchParameterMap map : maps) {
//Ensure users did not monkey with the patient compartment search parameter.
validateSearchParametersForPatient(map, theParams);
@ -196,7 +196,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
private LinkedHashSet<JpaPid> getPidsForSystemStyleExport(ExportPIDIteratorParameters theParams, String theJobId, RuntimeResourceDefinition theDef) {
LinkedHashSet<JpaPid> pids = new LinkedHashSet<>();
// System
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(theDef, theParams);
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(theDef, theParams, true);
ISearchBuilder<JpaPid> searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
for (SearchParameterMap map : maps) {
@ -311,7 +311,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
* possibly expanded by MDM, and don't have to go and fetch other resource DAOs.
*/
private LinkedHashSet<JpaPid> getExpandedPatientList(ExportPIDIteratorParameters theParameters) {
List<JpaPid> members = getMembersFromGroupWithFilter(theParameters);
List<JpaPid> members = getMembersFromGroupWithFilter(theParameters, true);
List<IIdType> ids = members.stream().map(member -> new IdDt("Patient/" + member)).collect(Collectors.toList());
ourLog.info("While extracting patients from a group, we found {} patients.", ids.size());
ourLog.info("Found patients: {}", ids.stream().map(id -> id.getValue()).collect(Collectors.joining(", ")));
@ -339,12 +339,11 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
*
* @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
*/
private List<JpaPid> getMembersFromGroupWithFilter(ExportPIDIteratorParameters theParameters) {
private List<JpaPid> getMembersFromGroupWithFilter(ExportPIDIteratorParameters theParameters, boolean theConsiderSince) {
RuntimeResourceDefinition def = myContext.getResourceDefinition("Patient");
List<String> pids = new ArrayList<>();
List<JpaPid> resPids = new ArrayList<>();
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParameters);
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParameters, theConsiderSince);
maps.forEach(map -> addMembershipToGroupClause(map, theParameters.getGroupId()));
@ -432,7 +431,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
//Build SP map
//First, inject the _typeFilters and _since from the export job
List<SearchParameterMap> expandedSpMaps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(theDef, theParams);
List<SearchParameterMap> expandedSpMaps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(theDef, theParams, true);
for (SearchParameterMap expandedSpMap : expandedSpMaps) {
//Since we are in a bulk job, we have to ensure the user didn't jam in a patient search param, since we need to manually set that.
@ -520,7 +519,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
//Now manually add the members of the group (its possible even with mdm expansion that some members dont have MDM matches,
//so would be otherwise skipped
List<JpaPid> membersFromGroupWithFilter = getMembersFromGroupWithFilter(theParams);
List<JpaPid> membersFromGroupWithFilter = getMembersFromGroupWithFilter(theParams, false);
ourLog.debug("Group with ID [{}] has been expanded to: {}", theParams.getGroupId(), membersFromGroupWithFilter);
expandedIds.addAll(membersFromGroupWithFilter);

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessorTest.java
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@ -184,7 +184,7 @@ public class JpaBulkExportProcessorTest {
// when
when(myDaoConfig.getIndexMissingFields())
.thenReturn(DaoConfig.IndexEnabledEnum.ENABLED);
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters)))
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters), any(boolean.class)))
.thenReturn(maps);
// from getSearchBuilderForLocalResourceType
when(myDaoRegistry.getResourceDao(anyString()))
@ -259,7 +259,7 @@ public class JpaBulkExportProcessorTest {
ISearchBuilder searchBuilder = mock(ISearchBuilder.class);
// from getMembersFromGroupWithFilter
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters)))
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters), any(boolean.class)))
.thenReturn(Collections.singletonList(new SearchParameterMap()));
// from getSearchBuilderForLocalResourceType
when(myDaoRegistry.getResourceDao(not(eq("Group"))))
@ -355,7 +355,7 @@ public class JpaBulkExportProcessorTest {
.thenReturn(groupResource);
when(myIdHelperService.getPidOrNull(any(), eq(groupResource)))
.thenReturn(groupId);
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters)))
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters), any(boolean.class)))
.thenReturn(Collections.singletonList(new SearchParameterMap()));
when(myDaoRegistry.getResourceDao(not(eq("Group"))))
.thenReturn(mockDao);
@ -412,7 +412,8 @@ public class JpaBulkExportProcessorTest {
// when
when(myBulkExportHelperService.createSearchParameterMapsForResourceType(
any(RuntimeResourceDefinition.class),
any(ExportPIDIteratorParameters.class)
any(ExportPIDIteratorParameters.class),
any(boolean.class)
)).thenReturn(Collections.singletonList(new SearchParameterMap()));
when(myDaoRegistry.getResourceDao(eq("Patient")))
.thenReturn(dao);

42
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportTest.java
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@ -22,6 +22,7 @@ import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Location;
import org.hl7.fhir.r4.model.MedicationAdministration;
import org.hl7.fhir.r4.model.Observation;
@ -43,6 +44,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.io.StringReader;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@ -469,6 +471,46 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
verifyBulkExportResults(options, List.of("Patient/P1", obsId, provId, devId, devId2), List.of("Patient/P2", provId2, devId3));
}
@Test
public void testGroupBulkExport_QualifiedSubResourcesOfUnqualifiedPatientShouldShowUp() throws InterruptedException {
// Patient with lastUpdated before _since
Patient patient = new Patient();
patient.setId("A");
myClient.update().resource(patient).execute();
// Sleep for 1 sec
ourLog.info("Patient lastUpdated: " + InstantType.withCurrentTime().getValueAsString());
Thread.sleep(1000);
// LastUpdated since now
Date timeDate = InstantType.now().getValue();
ourLog.info(timeDate.toString());
// Group references to Patient/A
Group group = new Group();
group.setId("B");
group.addMember().getEntity().setReference("Patient/A");
myClient.update().resource(group).execute();
// Observation references to Patient/A
Observation observation = new Observation();
observation.setId("C");
observation.setSubject(new Reference("Patient/A"));
myClient.update().resource(observation).execute();
// Set the export options
BulkDataExportOptions options = new BulkDataExportOptions();
options.setResourceTypes(Sets.newHashSet("Patient", "Observation", "Group"));
options.setGroupId(new IdType("Group", "B"));
options.setFilters(new HashSet<>());
options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
options.setSince(timeDate);
options.setOutputFormat(Constants.CT_FHIR_NDJSON);
// Should get the sub-resource (Observation) even the patient hasn't been updated after the _since param
verifyBulkExportResults(options, List.of("Observation/C", "Group/B"), List.of("Patient/A"));
}
@Test
public void testPatientBulkExportWithReferenceToAuthor_ShouldShowUp() {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);

9
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkExportHelperService.java
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@ -47,7 +47,12 @@ public class BulkExportHelperService {
@Autowired
private FhirContext myContext;
public List<SearchParameterMap> createSearchParameterMapsForResourceType(RuntimeResourceDefinition theDef, ExportPIDIteratorParameters theParams) {
/**
* Given the parameters, create the search parameter map based on type filters and the _since parameter.
*
* The input boolean theConsiderSince determines whether to consider the lastUpdated date in the search parameter map.
*/
public List<SearchParameterMap> createSearchParameterMapsForResourceType(RuntimeResourceDefinition theDef, ExportPIDIteratorParameters theParams, boolean theConsiderSince) {
String resourceType = theDef.getName();
List<String> typeFilters = theParams.getFilters();
List<SearchParameterMap> spMaps = null;
@ -63,7 +68,9 @@ public class BulkExportHelperService {
//None of the _typeFilters applied to the current resource type, so just make a simple one.
if (spMaps.isEmpty()) {
SearchParameterMap defaultMap = new SearchParameterMap();
if (theConsiderSince) {
enhanceSearchParameterMapWithCommonParameters(defaultMap, theParams.getStartDate());
}
spMaps = Collections.singletonList(defaultMap);
}