3987 group bulk export does not apply typefilter searches to members of the group (#3988)
* Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient Co-authored-by: Steven Li <steven@smilecdr.com>
This commit is contained in:
StevenXLi
GitHub
parent
21cce44524
commit
a4a7fd9344
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@ -0,0 +1,6 @@
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---
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type: fix
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issue: 3987
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jira: SMILE-4921
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title: "Previously, bulk export for Group type with _typeFilter did not apply the filter if it was for the patients, and returned all members of the group.
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This has now been fixed, and the filter will apply."
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@ -61,6 +61,7 @@ import org.hl7.fhir.instance.model.api.IBaseReference;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.hl7.fhir.r4.model.Patient;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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@ -76,6 +77,8 @@ import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
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public class JpaBulkExportProcessor implements IBulkExportProcessor {
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private static final Logger ourLog = LoggerFactory.getLogger(JpaBulkExportProcessor.class);
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@ -150,8 +153,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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pids.add(resultIterator.next());
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}
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}
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}
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else if (theParams.getExportStyle() == BulkDataExportOptions.ExportStyle.GROUP) {
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} else if (theParams.getExportStyle() == BulkDataExportOptions.ExportStyle.GROUP) {
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// Group
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if (resourceType.equalsIgnoreCase("Patient")) {
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return getExpandedPatientIterator(theParams);
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@ -168,8 +170,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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queryChunker.chunk(new ArrayList<>(expandedMemberResourceIds), QUERY_CHUNK_SIZE, (idChunk) -> {
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queryResourceTypeWithReferencesToPatients(pids, idChunk, theParams, def);
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});
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}
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else {
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} else {
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// System
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List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParams);
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ISearchBuilder searchBuilder = getSearchBuilderForLocalResourceType(theParams);
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@ -256,7 +257,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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* possibly expanded by MDM, and don't have to go and fetch other resource DAOs.
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*/
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private Iterator<ResourcePersistentId> getExpandedPatientIterator(ExportPIDIteratorParameters theParameters) {
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List<String> members = getMembers(theParameters.getGroupId());
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List<String> members = getMembersFromGroupWithFilter(theParameters);
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List<IIdType> ids = members.stream().map(member -> new IdDt("Patient/" + member)).collect(Collectors.toList());
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// Are bulk exports partition aware or care about partition at all? This does
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@ -278,15 +279,36 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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}
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/**
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* Given the local myGroupId, read this group, and find all members' patient references.
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* Given the parameters, find all members' patient references in the group with the typeFilter applied.
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*
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* @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
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*/
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private List<String> getMembers(String theGroupId) {
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SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
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IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(theGroupId), requestDetails);
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List<IPrimitiveType> evaluate = myContext.newFhirPath().evaluate(group, "member.entity.reference", IPrimitiveType.class);
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return evaluate.stream().map(IPrimitiveType::getValueAsString).collect(Collectors.toList());
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private List<String> getMembersFromGroupWithFilter(ExportPIDIteratorParameters theParameters) {
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RuntimeResourceDefinition def = myContext.getResourceDefinition(theParameters.getResourceType());
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List<String> pids = new ArrayList<>();
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List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParameters);
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for (SearchParameterMap map : maps) {
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//Ensure users did not monkey with the patient compartment search parameter.
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validateSearchParametersForPatient(map, theParameters);
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ISearchBuilder searchBuilder = getSearchBuilderForLocalResourceType(theParameters);
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// Now, further filter the query with the group id.
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HasOrListParam hasOrListParam = new HasOrListParam();
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hasOrListParam.addOr(new HasParam("Group", "member", "_id", theParameters.getGroupId()));
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map.add(PARAM_HAS, hasOrListParam);
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IResultIterator resultIterator = searchBuilder.createQuery(map,
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new SearchRuntimeDetails(null, theParameters.getJobId()),
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null,
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RequestPartitionId.allPartitions());
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while (resultIterator.hasNext()) {
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pids.add(resultIterator.next().toString());
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}
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}
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return pids;
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}
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/**
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@ -435,7 +457,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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//Now manually add the members of the group (its possible even with mdm expansion that some members dont have MDM matches,
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//so would be otherwise skipped
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expandedIds.addAll(getMembers(theParams.getGroupId()));
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expandedIds.addAll(getMembersFromGroupWithFilter(theParams));
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return expandedIds;
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}
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@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.bulk.export.svc;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.fhirpath.IFhirPath;
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import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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@ -13,7 +12,6 @@ import ca.uhn.fhir.jpa.bulk.export.model.ExportPIDIteratorParameters;
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import ca.uhn.fhir.jpa.dao.IResultIterator;
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import ca.uhn.fhir.jpa.dao.ISearchBuilder;
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import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
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import ca.uhn.fhir.jpa.dao.index.IJpaIdHelperService;
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import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
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import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
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import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
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@ -24,6 +22,9 @@ import ca.uhn.fhir.mdm.model.MdmPidTuple;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.rest.param.HasOrListParam;
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import ca.uhn.fhir.rest.param.HasParam;
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import ch.qos.logback.classic.spi.ILoggingEvent;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.hl7.fhir.r4.model.Group;
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@ -33,6 +34,7 @@ import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.junit.jupiter.params.ParameterizedTest;
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import org.junit.jupiter.params.provider.ValueSource;
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import org.mockito.ArgumentMatcher;
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import org.mockito.InjectMocks;
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import org.mockito.Mock;
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import org.mockito.Spy;
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@ -50,15 +52,17 @@ import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.AdditionalMatchers.not;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.ArgumentMatchers.anyList;
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import static org.mockito.ArgumentMatchers.anyLong;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.ArgumentMatchers.argThat;
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import static org.mockito.ArgumentMatchers.eq;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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@ -242,9 +246,7 @@ public class JpaBulkExportProcessorTest {
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}
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@ParameterizedTest
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@ValueSource(
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booleans = { true, false }
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)
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@ValueSource(booleans = {true, false})
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public void getResourcePidIterator_groupExportStyleWithPatientResource_returnsIterator(boolean theMdm) {
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// setup
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ExportPIDIteratorParameters parameters = createExportParameters(BulkDataExportOptions.ExportStyle.GROUP);
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@ -265,23 +267,37 @@ public class JpaBulkExportProcessorTest {
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MdmPidTuple tuple = createTuple(groupId.getIdAsLong(), groupGoldenPid);
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IFhirResourceDao<Group> groupDao = mock(IFhirResourceDao.class);
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IFhirPath path = mock(IFhirPath.class);
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parameters.setExpandMdm(theMdm); // set mdm expansion
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// extra mocks
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IFhirResourceDao<?> mockDao = mock(IFhirResourceDao.class);
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ISearchBuilder searchBuilder = mock(ISearchBuilder.class);
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// when
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// getMembers
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when(myDaoRegistry.getResourceDao(eq("Group")))
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.thenReturn(groupDao);
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when(groupDao.read(eq(new IdDt(parameters.getGroupId())), any(SystemRequestDetails.class)))
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.thenReturn(groupResource);
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when(myFhirContext.newFhirPath())
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.thenReturn(path);
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when(path.evaluate(eq(groupResource), anyString(), any(Class.class)))
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.thenReturn(patientTypes);
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when(myIdHelperService.getPidsOrThrowException(any(), anyList()))
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.thenReturn(pids);
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// from getMembersFromGroupWithFilter
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when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters)))
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.thenReturn(Collections.singletonList(new SearchParameterMap()));
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// from getSearchBuilderForLocalResourceType
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when(myDaoRegistry.getResourceDao(not(eq("Group"))))
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.thenReturn(mockDao);
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when(mySearchBuilderFactory.newSearchBuilder(eq(mockDao), eq(parameters.getResourceType()), any()))
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.thenReturn(searchBuilder);
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// ret
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when(searchBuilder.createQuery(
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any(SearchParameterMap.class),
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any(SearchRuntimeDetails.class),
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any(),
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eq(RequestPartitionId.allPartitions())))
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.thenReturn(new ListResultIterator(pids));
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// mdm expansion stuff
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if (theMdm) {
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when(myDaoRegistry.getResourceDao(eq("Group")))
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.thenReturn(groupDao);
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when(groupDao.read(eq(new IdDt(parameters.getGroupId())), any(SystemRequestDetails.class)))
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.thenReturn(groupResource);
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when(myIdHelperService.translatePidsToForcedIds(any(Set.class)))
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.thenAnswer(params -> {
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Set<ResourcePersistentId> uniqPids = params.getArgument(0);
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@ -322,7 +338,7 @@ public class JpaBulkExportProcessorTest {
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}
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@ParameterizedTest
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@ValueSource(booleans = { false, true })
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@ValueSource(booleans = {false, true})
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public void getResourcePidIterator_groupExportNonPatient_returnsIterator(boolean theMdm) {
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// setup
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ExportPIDIteratorParameters parameters = createExportParameters(BulkDataExportOptions.ExportStyle.GROUP);
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@ -345,17 +361,33 @@ public class JpaBulkExportProcessorTest {
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IFhirResourceDao<Group> groupDao = mock(IFhirResourceDao.class);
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IFhirResourceDao<Observation> observationDao = mock(IFhirResourceDao.class);
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parameters.setExpandMdm(theMdm); // set mdm expansion
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IFhirPath path = mock(IFhirPath.class);
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// extra mocks
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IFhirResourceDao<?> mockDao = mock(IFhirResourceDao.class);
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ISearchBuilder searchBuilder = mock(ISearchBuilder.class);
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// when
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// getMembers
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when(myDaoRegistry.getResourceDao(eq("Group")))
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.thenReturn(groupDao);
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when(groupDao.read(any(IIdType.class), any(SystemRequestDetails.class)))
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.thenReturn(groupResource);
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when(myIdHelperService.getPidOrNull(any(), eq(groupResource)))
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.thenReturn(groupId);
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when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), eq(parameters)))
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.thenReturn(Collections.singletonList(new SearchParameterMap()));
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when(myDaoRegistry.getResourceDao(not(eq("Group"))))
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.thenReturn(mockDao);
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when(mySearchBuilderFactory.newSearchBuilder(eq(mockDao), not(eq("Group")), any()))
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.thenReturn(searchBuilder);
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// ret
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when(searchBuilder.createQuery(
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any(SearchParameterMap.class),
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any(SearchRuntimeDetails.class),
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any(),
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eq(RequestPartitionId.allPartitions())))
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.thenReturn(new ListResultIterator(Collections.singletonList(pid)))
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.thenReturn(resultIterator);
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if (theMdm) {
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when(myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(any(ResourcePersistentId.class), eq(MdmMatchResultEnum.MATCH)))
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@ -370,21 +402,6 @@ public class JpaBulkExportProcessorTest {
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return new PersistentIdToForcedIdMap(answer);
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});
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}
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when(myFhirContext.newFhirPath())
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.thenReturn(path);
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when(path.evaluate(eq(groupResource), anyString(), any(Class.class)))
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.thenReturn(patientTypes);
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when(myBulkExportHelperService.createSearchParameterMapsForResourceType(any(RuntimeResourceDefinition.class), any(ExportPIDIteratorParameters.class)))
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.thenReturn(Collections.singletonList(new SearchParameterMap()));
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when(myDaoRegistry.getResourceDao(eq("Observation")))
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.thenReturn(observationDao);
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when(mySearchBuilderFactory.newSearchBuilder(any(), eq("Observation"), any()))
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.thenReturn(searchBuilder);
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when(searchBuilder.createQuery(any(SearchParameterMap.class),
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any(SearchRuntimeDetails.class),
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any(),
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eq(RequestPartitionId.allPartitions())))
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.thenReturn(resultIterator);
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// test
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Iterator<ResourcePersistentId> pidIterator = myProcessor.getResourcePidIterator(parameters);
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@ -0,0 +1,136 @@
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package ca.uhn.fhir.jpa.bulk;
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import ca.uhn.fhir.jpa.api.model.BulkExportJobResults;
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import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
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import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
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import ca.uhn.fhir.jpa.provider.r4.BaseResourceProviderR4Test;
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import ca.uhn.fhir.jpa.util.BulkExportUtils;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
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import ca.uhn.fhir.util.JsonUtil;
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import com.google.common.collect.Sets;
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import org.hamcrest.Matchers;
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import org.hl7.fhir.r4.model.Binary;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.Group;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Patient;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import static org.awaitility.Awaitility.await;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.not;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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public class BulkDataExportTest extends BaseResourceProviderR4Test {
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private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportTest.class);
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@Autowired
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private IBatch2JobRunner myJobRunner;
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@Test
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public void testGroupBulkExportWithTypeFilter() {
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// Create some resources
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Patient patient = new Patient();
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patient.setId("PF");
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patient.setGender(Enumerations.AdministrativeGender.FEMALE);
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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patient = new Patient();
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patient.setId("PM");
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patient.setGender(Enumerations.AdministrativeGender.MALE);
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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Group group = new Group();
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group.setId("Group/G");
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group.setActive(true);
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group.addMember().getEntity().setReference("Patient/PF");
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group.addMember().getEntity().setReference("Patient/PM");
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myClient.update().resource(group).execute();
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varifyBulkExportResults("G", Sets.newHashSet("Patient?gender=female"), Collections.singletonList("\"PF\""), Collections.singletonList("\"PM\""));
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}
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@Test
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public void testGroupBulkExportNotInGroup_DoeNotShowUp() {
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// Create some resources
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Patient patient = new Patient();
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patient.setId("PING1");
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patient.setGender(Enumerations.AdministrativeGender.FEMALE);
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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patient = new Patient();
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patient.setId("PING2");
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patient.setGender(Enumerations.AdministrativeGender.MALE);
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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patient = new Patient();
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patient.setId("PNING3");
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patient.setGender(Enumerations.AdministrativeGender.MALE);
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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Group group = new Group();
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group.setId("Group/G2");
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group.setActive(true);
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group.addMember().getEntity().setReference("Patient/PING1");
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group.addMember().getEntity().setReference("Patient/PING2");
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myClient.update().resource(group).execute();
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varifyBulkExportResults("G2", new HashSet<>(), List.of("\"PING1\"", "\"PING2\""), Collections.singletonList("\"PNING3\""));
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}
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|
||||
private void varifyBulkExportResults(String theGroupId, HashSet<String> theFilters, List<String> theContainedList, List<String> theExcludedList) {
|
||||
BulkDataExportOptions options = new BulkDataExportOptions();
|
||||
options.setResourceTypes(Sets.newHashSet("Patient"));
|
||||
options.setGroupId(new IdType("Group", theGroupId));
|
||||
options.setFilters(theFilters);
|
||||
options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
|
||||
options.setOutputFormat(Constants.CT_FHIR_NDJSON);
|
||||
|
||||
Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(options));
|
||||
|
||||
assertNotNull(startResponse);
|
||||
|
||||
// Run a scheduled pass to build the export
|
||||
myBatch2JobHelper.awaitJobCompletion(startResponse.getJobId());
|
||||
|
||||
await().until(() -> myJobRunner.getJobInfo(startResponse.getJobId()).getReport() != null);
|
||||
|
||||
// Iterate over the files
|
||||
String report = myJobRunner.getJobInfo(startResponse.getJobId()).getReport();
|
||||
BulkExportJobResults results = JsonUtil.deserialize(report, BulkExportJobResults.class);
|
||||
for (Map.Entry<String, List<String>> file : results.getResourceTypeToBinaryIds().entrySet()) {
|
||||
List<String> binaryIds = file.getValue();
|
||||
assertEquals(1, binaryIds.size());
|
||||
for (String binaryId : binaryIds) {
|
||||
Binary binary = myBinaryDao.read(new IdType(binaryId));
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, binary.getContentType());
|
||||
String contents = new String(binary.getContent(), Constants.CHARSET_UTF8);
|
||||
ourLog.info("Next contents for type {} :\n{}", binary.getResourceType(), contents);
|
||||
for (String containedString : theContainedList) {
|
||||
assertThat(contents, Matchers.containsString(containedString));
|
||||
|
||||
}
|
||||
for (String excludedString : theExcludedList) {
|
||||
assertThat(contents, not(Matchers.containsString(excludedString)));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue