4030 bulk export to support fhir basepatientid$export endpoint (#4032)
* Refactored test helper method to be more generic, added new failing test for feature, and changed BulkDataExportOptions to fix compile error * added field to all objects needed in the bulk export pipeline for adding patient id, added new operation for the feature * added changelog * added support for patient parameter to patient export, changed patient id to a list to match the requirements for the patient parameter, added test for multiple id patient export * refactored methods, added new changes to changelog * code review changes * fix test error Co-authored-by: Steven Li <steven@smilecdr.com>
This commit is contained in:
StevenXLi
GitHub
parent
4d16a109de
commit
3b781022c1
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@ -0,0 +1,7 @@
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---
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type: add
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issue: 4030
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title: "Previously, Patient Bulk Export only supported endpoint [fhir base]/Patient/$export, which exports all patients.
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Now, Patient Export can be done at the instance level, following this format: `[fhir base]/Patient/[id]/$export`, which will export only the records for one patient.
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Additionally, added support for the `patient` parameter in Patient Bulk Export, which is another way to get the records of only one patient."
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@ -64,6 +64,7 @@ import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.annotation.Transactional;
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import javax.annotation.Nonnull;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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@ -75,6 +76,7 @@ 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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import static ca.uhn.fhir.rest.api.Constants.PARAM_ID;
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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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@ -146,9 +148,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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ISearchBuilder searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
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if (!resourceType.equalsIgnoreCase("Patient")) {
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map.add(patientSearchParam, new ReferenceParam().setMissing(false));
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}
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filterBySpecificPatient(theParams, resourceType, patientSearchParam, map);
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SearchRuntimeDetails searchRuntime = new SearchRuntimeDetails(null, jobId);
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IResultIterator resultIterator = searchBuilder.createQuery(map, searchRuntime, null, RequestPartitionId.allPartitions());
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@ -159,6 +159,31 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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return pids;
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}
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private static void filterBySpecificPatient(ExportPIDIteratorParameters theParams, String resourceType, String patientSearchParam, SearchParameterMap map) {
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if (resourceType.equalsIgnoreCase("Patient")) {
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if (theParams.getPatientIds() != null) {
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ReferenceOrListParam referenceOrListParam = getReferenceOrListParam(theParams);
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map.add(PARAM_ID, referenceOrListParam);
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}
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} else {
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if (theParams.getPatientIds() != null) {
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ReferenceOrListParam referenceOrListParam = getReferenceOrListParam(theParams);
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map.add(patientSearchParam, referenceOrListParam);
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} else {
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map.add(patientSearchParam, new ReferenceParam().setMissing(false));
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}
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}
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}
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@Nonnull
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private static ReferenceOrListParam getReferenceOrListParam(ExportPIDIteratorParameters theParams) {
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ReferenceOrListParam referenceOrListParam = new ReferenceOrListParam();
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for (String patientId : theParams.getPatientIds()) {
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referenceOrListParam.addOr(new ReferenceParam(patientId));
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}
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return referenceOrListParam;
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}
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private Set<ResourcePersistentId> getPidsForSystemStyleExport(ExportPIDIteratorParameters theParams, String theJobId, RuntimeResourceDefinition theDef) {
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Set<ResourcePersistentId> pids = new HashSet<>();
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// System
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@ -212,7 +237,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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private Set<ResourcePersistentId> getSingletonGroupList(ExportPIDIteratorParameters theParams) {
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IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(theParams.getGroupId()), SystemRequestDetails.newSystemRequestAllPartitions());
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ResourcePersistentId pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
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Set<ResourcePersistentId> pids = new HashSet<>();
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Set<ResourcePersistentId> pids = new HashSet<>();
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pids.add(pidOrNull);
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return pids;
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}
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@ -329,7 +354,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
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* This method takes an {@link SearchParameterMap} and adds a clause to it that will filter the search results to only
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* return members of the defined group.
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*
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* @param theMap the map to add the clause to.
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* @param theMap the map to add the clause to.
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* @param theGroupId the group ID to filter by.
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*/
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private void addMembershipToGroupClause(SearchParameterMap theMap, String theGroupId) {
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@ -192,6 +192,10 @@ public class JpaConstants {
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* Parameter for the $export operation
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*/
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public static final String PARAM_EXPORT_TYPE_FILTER = "_typeFilter";
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/**
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* Parameter for the $export operation
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*/
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public static final String PARAM_EXPORT_PATIENT = "patient";
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/**
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* Parameter for the $import operation
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@ -1,5 +1,6 @@
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package ca.uhn.fhir.jpa.bulk;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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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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@ -11,10 +12,14 @@ 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.Encounter;
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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.Observation;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Reference;
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import org.junit.jupiter.api.AfterEach;
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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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@ -34,9 +39,17 @@ 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 DaoConfig myDaoConfig;
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@Autowired
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private IBatch2JobRunner myJobRunner;
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@AfterEach
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void afterEach() {
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myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
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}
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@Test
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public void testGroupBulkExportWithTypeFilter() {
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// Create some resources
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@ -59,7 +72,14 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
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group.addMember().getEntity().setReference("Patient/PM");
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myClient.update().resource(group).execute();
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verifyBulkExportResults("G", Sets.newHashSet("Patient?gender=female"), Collections.singletonList("\"PF\""), Collections.singletonList("\"PM\""));
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// set the export options
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Patient"));
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options.setGroupId(new IdType("Group", "G"));
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options.setFilters(Sets.newHashSet("Patient?gender=female"));
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options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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options.setOutputFormat(Constants.CT_FHIR_NDJSON);
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verifyBulkExportResults(options, Collections.singletonList("\"PF\""), Collections.singletonList("\"PM\""));
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}
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@Test
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@ -90,11 +110,18 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
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group.addMember().getEntity().setReference("Patient/PING2");
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myClient.update().resource(group).execute();
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verifyBulkExportResults("G2", new HashSet<>(), List.of("\"PING1\"", "\"PING2\""), Collections.singletonList("\"PNING3\""));
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// set the export options
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Patient"));
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options.setGroupId(new IdType("Group", "G2"));
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options.setFilters(new HashSet<>());
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options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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options.setOutputFormat(Constants.CT_FHIR_NDJSON);
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verifyBulkExportResults(options, List.of("\"PING1\"", "\"PING2\""), Collections.singletonList("\"PNING3\""));
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}
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@Test
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public void testTwoBulkExportsInArow() {
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public void testTwoBulkExportsInARow() {
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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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@ -107,29 +134,142 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
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group.setActive(true);
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group.addMember().getEntity().setReference("Patient/PING1");
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myClient.update().resource(group).execute();
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// set the export options
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Patient"));
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options.setGroupId(new IdType("Group", "G2"));
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options.setFilters(new HashSet<>());
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options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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options.setOutputFormat(Constants.CT_FHIR_NDJSON);
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myCaptureQueriesListener.clear();
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verifyBulkExportResults("G2", new HashSet<>(), List.of("\"PING1\""), Collections.singletonList("\"PNING3\""));
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verifyBulkExportResults(options, List.of("\"PING1\""), Collections.singletonList("\"PNING3\""));
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myCaptureQueriesListener.logSelectQueries();
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ourLog.error("************");
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myCaptureQueriesListener.clear();
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try {
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verifyBulkExportResults("G2", new HashSet<>(), List.of("\"PING1\""), Collections.singletonList("\"PNING3\""));
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verifyBulkExportResults(options, List.of("\"PING1\""), Collections.singletonList("\"PNING3\""));
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} finally {
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myCaptureQueriesListener.logSelectQueries();
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}
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}
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@Test
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public void testPatientBulkExportWithSingleId() {
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myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
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// create some resources
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Patient patient = new Patient();
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patient.setId("P1");
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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private void verifyBulkExportResults(String theGroupId, HashSet<String> theFilters, List<String> theContainedList, List<String> theExcludedList) {
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Observation observation = new Observation();
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observation.setSubject(new Reference().setReference("Patient/P1"));
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observation.setStatus(Observation.ObservationStatus.PRELIMINARY);
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String obsId = myClient.create().resource(observation).execute().getId().getIdPart();
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Encounter encounter = new Encounter();
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encounter.setSubject(new Reference().setReference("Patient/P1"));
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encounter.setStatus(Encounter.EncounterStatus.INPROGRESS);
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String encId = myClient.create().resource(encounter).execute().getId().getIdPart();
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// diff patient
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patient = new Patient();
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patient.setId("P2");
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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observation = new Observation();
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observation.setSubject(new Reference().setReference("Patient/P2"));
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observation.setStatus(Observation.ObservationStatus.PRELIMINARY);
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String obsId2 = myClient.create().resource(observation).execute().getId().getIdPart();
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encounter = new Encounter();
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encounter.setSubject(new Reference().setReference("Patient/P2"));
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encounter.setStatus(Encounter.EncounterStatus.INPROGRESS);
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String encId2 = myClient.create().resource(encounter).execute().getId().getIdPart();
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observation = new Observation();
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observation.setStatus(Observation.ObservationStatus.PRELIMINARY);
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String obsId3 = myClient.create().resource(observation).execute().getId().getIdPart();
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// set the export options
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Patient"));
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options.setGroupId(new IdType("Group", theGroupId));
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options.setFilters(theFilters);
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options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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options.setResourceTypes(Sets.newHashSet("Patient", "Observation", "Encounter"));
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options.setPatientIds(Sets.newHashSet(new IdType("Patient", "P1")));
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options.setFilters(new HashSet<>());
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options.setExportStyle(BulkDataExportOptions.ExportStyle.PATIENT);
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options.setOutputFormat(Constants.CT_FHIR_NDJSON);
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Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(options));
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verifyBulkExportResults(options, List.of("\"P1\"", "\"" + obsId + "\"", "\"" + encId + "\""), List.of("\"P2\"", "\"" + obsId2 + "\"", "\"" + encId2 + "\"", "\"" + obsId3 + "\""));
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}
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@Test
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public void testPatientBulkExportWithMultiIds() {
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myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
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// create some resources
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Patient patient = new Patient();
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patient.setId("P1");
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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Observation observation = new Observation();
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observation.setSubject(new Reference().setReference("Patient/P1"));
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observation.setStatus(Observation.ObservationStatus.PRELIMINARY);
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String obsId = myClient.create().resource(observation).execute().getId().getIdPart();
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Encounter encounter = new Encounter();
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encounter.setSubject(new Reference().setReference("Patient/P1"));
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encounter.setStatus(Encounter.EncounterStatus.INPROGRESS);
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String encId = myClient.create().resource(encounter).execute().getId().getIdPart();
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// diff patient
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patient = new Patient();
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patient.setId("P2");
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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observation = new Observation();
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observation.setSubject(new Reference().setReference("Patient/P2"));
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observation.setStatus(Observation.ObservationStatus.PRELIMINARY);
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String obsId2 = myClient.create().resource(observation).execute().getId().getIdPart();
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encounter = new Encounter();
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encounter.setSubject(new Reference().setReference("Patient/P2"));
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encounter.setStatus(Encounter.EncounterStatus.INPROGRESS);
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String encId2 = myClient.create().resource(encounter).execute().getId().getIdPart();
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// yet another diff patient
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patient = new Patient();
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patient.setId("P3");
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patient.setActive(true);
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myClient.update().resource(patient).execute();
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observation = new Observation();
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observation.setSubject(new Reference().setReference("Patient/P3"));
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observation.setStatus(Observation.ObservationStatus.PRELIMINARY);
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String obsId3 = myClient.create().resource(observation).execute().getId().getIdPart();
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encounter = new Encounter();
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encounter.setSubject(new Reference().setReference("Patient/P3"));
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encounter.setStatus(Encounter.EncounterStatus.INPROGRESS);
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String encId3 = myClient.create().resource(encounter).execute().getId().getIdPart();
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// set the export options
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Patient", "Observation", "Encounter"));
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options.setPatientIds(Sets.newHashSet(new IdType("Patient", "P1"), new IdType("Patient", "P2")));
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options.setFilters(new HashSet<>());
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options.setExportStyle(BulkDataExportOptions.ExportStyle.PATIENT);
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options.setOutputFormat(Constants.CT_FHIR_NDJSON);
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verifyBulkExportResults(options, List.of("\"P1\"", "\"" + obsId + "\"", "\"" + encId + "\"", "\"P2\"", "\"" + obsId2 + "\"", "\"" + encId2 + "\""), List.of("\"P3\"", "\"" + obsId3 + "\"", "\"" + encId3 + "\""));
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}
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private void verifyBulkExportResults(BulkDataExportOptions theOptions, List<String> theContainedList, List<String> theExcludedList) {
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Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(theOptions));
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assertNotNull(startResponse);
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@ -141,22 +281,21 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
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// Iterate over the files
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String report = myJobRunner.getJobInfo(startResponse.getJobId()).getReport();
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BulkExportJobResults results = JsonUtil.deserialize(report, BulkExportJobResults.class);
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String contents = "";
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for (Map.Entry<String, List<String>> file : results.getResourceTypeToBinaryIds().entrySet()) {
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List<String> binaryIds = file.getValue();
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assertEquals(1, binaryIds.size());
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for (String binaryId : binaryIds) {
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Binary binary = myBinaryDao.read(new IdType(binaryId));
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assertEquals(Constants.CT_FHIR_NDJSON, binary.getContentType());
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String contents = new String(binary.getContent(), Constants.CHARSET_UTF8);
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ourLog.info("Next contents for type {} :\n{}", binary.getResourceType(), contents);
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for (String containedString : theContainedList) {
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assertThat(contents, Matchers.containsString(containedString));
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Binary binary = myBinaryDao.read(new IdType(binaryIds.get(0)));
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assertEquals(Constants.CT_FHIR_NDJSON, binary.getContentType());
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contents += new String(binary.getContent(), Constants.CHARSET_UTF8) + "\n";
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ourLog.info("Next contents for type {} :\n{}", binary.getResourceType(), new String(binary.getContent(), Constants.CHARSET_UTF8));
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}
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}
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for (String excludedString : theExcludedList) {
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assertThat(contents, not(Matchers.containsString(excludedString)));
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}
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}
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for (String containedString : theContainedList) {
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assertThat(contents, Matchers.containsString(containedString));
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}
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for (String excludedString : theExcludedList) {
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assertThat(contents, not(Matchers.containsString(excludedString)));
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}
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}
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@ -43,6 +43,7 @@ public class BulkDataExportOptions {
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private ExportStyle myExportStyle;
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private boolean myExpandMdm;
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private IIdType myGroupId;
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private Set<IIdType> myPatientIds;
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public void setOutputFormat(String theOutputFormat) {
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myOutputFormat = theOutputFormat;
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@ -99,4 +100,12 @@ public class BulkDataExportOptions {
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public void setGroupId(IIdType theGroupId) {
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myGroupId = theGroupId;
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}
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public Set<IIdType> getPatientIds() {
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return myPatientIds;
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}
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public void setPatientIds(Set<IIdType> thePatientIds) {
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myPatientIds = thePatientIds;
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}
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}
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|
|
@ -62,6 +62,7 @@ public class FetchResourceIdsStep implements IFirstJobStepWorker<BulkExportJobPa
|
|||
providerParams.setStartDate(params.getStartDate());
|
||||
providerParams.setExportStyle(params.getExportStyle());
|
||||
providerParams.setGroupId(params.getGroupId());
|
||||
providerParams.setPatientIds(params.getPatientIds());
|
||||
providerParams.setExpandMdm(params.isExpandMdm());
|
||||
|
||||
int submissionCount = 0;
|
||||
|
|
|
|||
|
|
@ -56,6 +56,9 @@ public class BulkExportJobParameters extends BulkExportJobBase {
|
|||
@JsonProperty("exportStyle")
|
||||
private BulkDataExportOptions.ExportStyle myExportStyle;
|
||||
|
||||
@JsonProperty("patientIds")
|
||||
private List<String> myPatientIds;
|
||||
|
||||
// Stuff for group export only
|
||||
|
||||
/**
|
||||
|
|
@ -107,6 +110,14 @@ public class BulkExportJobParameters extends BulkExportJobBase {
|
|||
myExportStyle = theExportStyle;
|
||||
}
|
||||
|
||||
public List<String> getPatientIds() {
|
||||
return myPatientIds;
|
||||
}
|
||||
|
||||
public void setPatientIds(List<String> thePatientIds) {
|
||||
myPatientIds = thePatientIds;
|
||||
}
|
||||
|
||||
public String getGroupId() {
|
||||
return myGroupId;
|
||||
}
|
||||
|
|
@ -132,6 +143,7 @@ public class BulkExportJobParameters extends BulkExportJobBase {
|
|||
params.setOutputFormat(theParameters.getOutputFormat());
|
||||
params.setStartDate(theParameters.getStartDate());
|
||||
params.setExpandMdm(theParameters.isExpandMdm());
|
||||
params.setPatientIds(theParameters.getPatientIds());
|
||||
return params;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -70,6 +70,11 @@ public class BulkExportParameters extends Batch2BaseJobParameters {
|
|||
*/
|
||||
private boolean myExpandMdm;
|
||||
|
||||
/**
|
||||
* Patient id(s)
|
||||
*/
|
||||
private List<String> myPatientIds;
|
||||
|
||||
public boolean isExpandMdm() {
|
||||
return myExpandMdm;
|
||||
}
|
||||
|
|
@ -132,4 +137,12 @@ public class BulkExportParameters extends Batch2BaseJobParameters {
|
|||
public void setOutputFormat(String theOutputFormat) {
|
||||
myOutputFormat = theOutputFormat;
|
||||
}
|
||||
|
||||
public List<String> getPatientIds() {
|
||||
return myPatientIds;
|
||||
}
|
||||
|
||||
public void setPatientIds(List<String> thePatientIds) {
|
||||
myPatientIds = thePatientIds;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -68,6 +68,11 @@ public class ExportPIDIteratorParameters {
|
|||
*/
|
||||
private boolean myExpandMdm;
|
||||
|
||||
/**
|
||||
* The patient id
|
||||
*/
|
||||
private List<String> myPatientIds;
|
||||
|
||||
public String getResourceType() {
|
||||
return myResourceType;
|
||||
}
|
||||
|
|
@ -124,6 +129,14 @@ public class ExportPIDIteratorParameters {
|
|||
myExpandMdm = theExpandMdm;
|
||||
}
|
||||
|
||||
public List<String> getPatientIds() {
|
||||
return myPatientIds;
|
||||
}
|
||||
|
||||
public void setPatientIds(List<String> thePatientIds) {
|
||||
myPatientIds = thePatientIds;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return ToStringBuilder.reflectionToString(this, ToStringStyle.SHORT_PREFIX_STYLE);
|
||||
|
|
|
|||
|
|
@ -21,8 +21,6 @@ package ca.uhn.fhir.jpa.bulk.export.provider;
|
|||
*/
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||
import ca.uhn.fhir.context.RuntimeSearchParam;
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.interceptor.api.HookParams;
|
||||
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
||||
|
|
@ -67,6 +65,7 @@ import org.springframework.beans.factory.annotation.Autowired;
|
|||
import javax.servlet.http.HttpServletResponse;
|
||||
import java.io.IOException;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.Date;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
|
|
@ -169,7 +168,7 @@ public class BulkDataExportProvider {
|
|||
}
|
||||
|
||||
/**
|
||||
* Group/Id/$export
|
||||
* Group/[id]/$export
|
||||
*/
|
||||
@Operation(name = JpaConstants.OPERATION_EXPORT, manualResponse = true, idempotent = true, typeName = "Group")
|
||||
public void groupExport(
|
||||
|
|
@ -230,10 +229,30 @@ public class BulkDataExportProvider {
|
|||
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theTypeFilter,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_PATIENT, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> thePatient,
|
||||
ServletRequestDetails theRequestDetails
|
||||
) throws Exception {
|
||||
validatePreferAsyncHeader(theRequestDetails, JpaConstants.OPERATION_EXPORT);
|
||||
BulkDataExportOptions bulkDataExportOptions = buildPatientBulkExportOptions(theOutputFormat, theType, theSince, theTypeFilter);
|
||||
BulkDataExportOptions bulkDataExportOptions = buildPatientBulkExportOptions(theOutputFormat, theType, theSince, theTypeFilter, thePatient);
|
||||
validateResourceTypesAllContainPatientSearchParams(bulkDataExportOptions.getResourceTypes());
|
||||
|
||||
startJob(theRequestDetails, bulkDataExportOptions);
|
||||
}
|
||||
|
||||
/**
|
||||
* Patient/[id]/$export
|
||||
*/
|
||||
@Operation(name = JpaConstants.OPERATION_EXPORT, manualResponse = true, idempotent = true, typeName = "Patient")
|
||||
public void patientInstanceExport(
|
||||
@IdParam IIdType theIdParam,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
|
||||
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theTypeFilter,
|
||||
ServletRequestDetails theRequestDetails
|
||||
) throws Exception {
|
||||
validatePreferAsyncHeader(theRequestDetails, JpaConstants.OPERATION_EXPORT);
|
||||
BulkDataExportOptions bulkDataExportOptions = buildPatientBulkExportOptions(theOutputFormat, theType, theSince, theTypeFilter, theIdParam);
|
||||
validateResourceTypesAllContainPatientSearchParams(bulkDataExportOptions.getResourceTypes());
|
||||
|
||||
startJob(theRequestDetails, bulkDataExportOptions);
|
||||
|
|
@ -364,8 +383,18 @@ public class BulkDataExportProvider {
|
|||
return bulkDataExportOptions;
|
||||
}
|
||||
|
||||
private BulkDataExportOptions buildPatientBulkExportOptions(IPrimitiveType<String> theOutputFormat, IPrimitiveType<String> theType, IPrimitiveType<Date> theSince, List<IPrimitiveType<String>> theTypeFilter) {
|
||||
return buildBulkDataExportOptions(theOutputFormat, theType, theSince, theTypeFilter, BulkDataExportOptions.ExportStyle.PATIENT);
|
||||
private BulkDataExportOptions buildPatientBulkExportOptions(IPrimitiveType<String> theOutputFormat, IPrimitiveType<String> theType, IPrimitiveType<Date> theSince, List<IPrimitiveType<String>> theTypeFilter, List<IPrimitiveType<String>> thePatientIds) {
|
||||
BulkDataExportOptions bulkDataExportOptions = buildBulkDataExportOptions(theOutputFormat, theType, theSince, theTypeFilter, BulkDataExportOptions.ExportStyle.PATIENT);
|
||||
if (thePatientIds != null) {
|
||||
bulkDataExportOptions.setPatientIds(thePatientIds.stream().map((pid) -> new IdType(pid.getValueAsString())).collect(Collectors.toSet()));
|
||||
}
|
||||
return bulkDataExportOptions;
|
||||
}
|
||||
|
||||
private BulkDataExportOptions buildPatientBulkExportOptions(IPrimitiveType<String> theOutputFormat, IPrimitiveType<String> theType, IPrimitiveType<Date> theSince, List<IPrimitiveType<String>> theTypeFilter, IIdType thePatientId) {
|
||||
BulkDataExportOptions bulkDataExportOptions = buildBulkDataExportOptions(theOutputFormat, theType, theSince, theTypeFilter, BulkDataExportOptions.ExportStyle.PATIENT);
|
||||
bulkDataExportOptions.setPatientIds(Collections.singleton(thePatientId));
|
||||
return bulkDataExportOptions;
|
||||
}
|
||||
|
||||
private BulkDataExportOptions buildBulkDataExportOptions(IPrimitiveType<String> theOutputFormat, IPrimitiveType<String> theType, IPrimitiveType<Date> theSince, List<IPrimitiveType<String>> theTypeFilter, BulkDataExportOptions.ExportStyle theExportStyle) {
|
||||
|
|
|
|||
|
|
@ -23,8 +23,10 @@ package ca.uhn.fhir.jpa.util;
|
|||
import ca.uhn.fhir.jpa.api.model.BulkExportParameters;
|
||||
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
|
||||
import ca.uhn.fhir.util.Batch2JobDefinitionConstants;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
public class BulkExportUtils {
|
||||
private BulkExportUtils() {}
|
||||
|
|
@ -47,6 +49,9 @@ public class BulkExportUtils {
|
|||
if (theOptions.getResourceTypes() != null) {
|
||||
parameters.setResourceTypes(new ArrayList<>(theOptions.getResourceTypes()));
|
||||
}
|
||||
if (theOptions.getPatientIds() != null) {
|
||||
parameters.setPatientIds(theOptions.getPatientIds().stream().map(IIdType::getValue).collect(Collectors.toList()));
|
||||
}
|
||||
parameters.setExpandMdm(theOptions.isExpandMdm());
|
||||
parameters.setUseExistingJobsFirst(true);
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue