Support forward references in Group Bulk Export (#3558)
* Preliminary test work to generate forward-reference data * Complete implementation * Permit Practitioner/Organization as forward references in bulk export group params * Wip * Fix test * Add error number * Address review comments * Update assert
This commit is contained in:
Tadgh
GitHub
parent
f9824d6b15
commit
53c8b067d5
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.batch.config;
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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.Set;
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public final class BatchConstants {
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@ -90,6 +91,8 @@ public final class BatchConstants {
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*/
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public static final String JOB_EXECUTION_RESOURCE_TYPE = "resourceType";
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public static final List<String> PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES = List.of("Practitioner", "Organization");
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/**
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* This Set contains the step names across all job types that are appropriate for
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* someone to look at the write count for that given step in order to determine the
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@ -0,0 +1,4 @@
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type: add
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issue: 3557
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jira: SMILE-4062
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title: "Group Bulk Export (e.g. Group/123/$export) now additionally supports Organization and Practitioner as valid _type parameters. This works internally by querying using a `_has` parameter"
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@ -34,14 +34,18 @@ import org.apache.commons.lang3.StringUtils;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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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.jetbrains.annotations.NotNull;
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import org.slf4j.Logger;
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import org.springframework.batch.item.ItemProcessor;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.lang.NonNull;
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import java.util.List;
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import java.util.Optional;
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import static ca.uhn.fhir.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
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/**
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* Reusable Item Processor which attaches an extension to any outgoing resource. This extension will contain a resource
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* reference to the golden resource patient of the given resources' patient. (e.g. Observation.subject, Immunization.patient, etc)
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@ -49,6 +53,7 @@ import java.util.Optional;
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public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBaseResource>, List<IBaseResource>> {
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private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
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@Value("#{stepExecutionContext['resourceType']}")
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private String myResourceType;
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@ -79,21 +84,34 @@ public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBa
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}
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@Override
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public List<IBaseResource> process(List<IBaseResource> theIBaseResources) throws Exception {
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//If MDM expansion is enabled, add this magic new extension, otherwise, return the resource as is.
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if (myMdmEnabled) {
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if (myRuntimeSearchParam == null) {
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populateRuntimeSearchParam();
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}
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if (myPatientFhirPath == null) {
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populatePatientFhirPath();
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}
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theIBaseResources.forEach(this::annotateClinicalResourceWithRelatedGoldenResourcePatient);
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public List<IBaseResource> process(@NonNull List<IBaseResource> theIBaseResources) throws Exception {
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if (shouldAnnotateResource()) {
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lazyLoadSearchParamsAndFhirPath();
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theIBaseResources.forEach(this::annotateBackwardsReferences);
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}
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return theIBaseResources;
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}
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private void annotateClinicalResourceWithRelatedGoldenResourcePatient(IBaseResource iBaseResource) {
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private void lazyLoadSearchParamsAndFhirPath() {
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if (myRuntimeSearchParam == null) {
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populateRuntimeSearchParam();
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}
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if (myPatientFhirPath == null) {
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populatePatientFhirPath();
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}
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}
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/**
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* If the resource is added via a forward-reference from a patient, e.g. Patient.managingOrganization, we have no way to fetch the patient at this point in time.
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* This is a shortcoming of including the forward reference types in a Group/Patient bulk export.
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*
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* @return true if the resource should be annotated with the golden resource patient reference
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*/
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private boolean shouldAnnotateResource() {
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return myMdmEnabled && !PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType);
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}
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private void annotateBackwardsReferences(IBaseResource iBaseResource) {
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Optional<String> patientReference = getPatientReference(iBaseResource);
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if (patientReference.isPresent()) {
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addGoldenResourceExtension(iBaseResource, patientReference.get());
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@ -104,13 +122,15 @@ public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBa
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}
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private Optional<String> getPatientReference(IBaseResource iBaseResource) {
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//In the case of patient, we will just use the raw ID.
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if (myResourceType.equalsIgnoreCase("Patient")) {
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return Optional.of(iBaseResource.getIdElement().getIdPart());
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//Otherwise, we will perform evaluation of the fhirPath.
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} else {
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Optional<IBaseReference> optionalReference = getFhirParser().evaluateFirst(iBaseResource, myPatientFhirPath, IBaseReference.class);
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return optionalReference.map(theIBaseReference -> theIBaseReference.getReferenceElement().getIdPart());
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if (optionalReference.isPresent()) {
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return optionalReference.map(theIBaseReference -> theIBaseReference.getReferenceElement().getIdPart());
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} else {
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return Optional.empty();
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}
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}
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}
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@ -38,6 +38,8 @@ import ca.uhn.fhir.jpa.util.QueryChunker;
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import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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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 ca.uhn.fhir.rest.param.ReferenceOrListParam;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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@ -58,6 +60,8 @@ 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.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
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/**
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* Bulk Item reader for the Group Bulk Export job.
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* Instead of performing a normal query on the resource type using type filters, we instead
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@ -87,13 +91,14 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
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@Override
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protected Iterator<ResourcePersistentId> getResourcePidIterator() {
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Set<ResourcePersistentId> myReadPids = new HashSet<>();
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//Short circuit out if we detect we are attempting to extract patients
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if (myResourceType.equalsIgnoreCase("Patient")) {
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return getExpandedPatientIterator();
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}
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//First lets expand the group so we get a list of all patient IDs of the group, and MDM-matched patient IDs of the group.
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Set<String> expandedMemberResourceIds = expandAllPatientPidsFromGroup();
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if (ourLog.isDebugEnabled()) {
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@ -102,15 +107,16 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
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//Next, let's search for the target resources, with their correct patient references, chunked.
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//The results will be jammed into myReadPids
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Set<ResourcePersistentId> myExpandedMemberPids = new HashSet<>();
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QueryChunker<String> queryChunker = new QueryChunker<>();
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queryChunker.chunk(new ArrayList<>(expandedMemberResourceIds), QUERY_CHUNK_SIZE, (idChunk) -> {
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queryResourceTypeWithReferencesToPatients(myReadPids, idChunk);
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queryResourceTypeWithReferencesToPatients(myExpandedMemberPids, idChunk);
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});
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if (ourLog.isDebugEnabled()) {
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ourLog.debug("Resource PIDs to be Bulk Exported: [{}]", myReadPids.stream().map(ResourcePersistentId::toString).collect(Collectors.joining(",")));
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ourLog.debug("Resource PIDs to be Bulk Exported: {}", myExpandedMemberPids);
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}
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return myReadPids.iterator();
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return myExpandedMemberPids.iterator();
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}
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/**
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@ -243,6 +249,7 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
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}
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private void queryResourceTypeWithReferencesToPatients(Set<ResourcePersistentId> myReadPids, List<String> idChunk) {
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//Build SP map
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//First, inject the _typeFilters and _since from the export job
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List<SearchParameterMap> expandedSpMaps = createSearchParameterMapsForResourceType();
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@ -251,12 +258,16 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
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//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.
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validateSearchParameters(expandedSpMap);
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// Now, further filter the query with patient references defined by the chunk of IDs we have.
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filterSearchByResourceIds(idChunk, expandedSpMap);
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// Fetch and cache a search builder for this resource type
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ISearchBuilder searchBuilder = getSearchBuilderForLocalResourceType();
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// Now, further filter the query with patient references defined by the chunk of IDs we have.
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if (PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType)) {
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filterSearchByHasParam(idChunk, expandedSpMap);
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} else {
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filterSearchByResourceIds(idChunk, expandedSpMap);
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}
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//Execute query and all found pids to our local iterator.
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IResultIterator resultIterator = searchBuilder.createQuery(expandedSpMap, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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while (resultIterator.hasNext()) {
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@ -265,17 +276,41 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
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}
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}
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/**
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*
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* @param idChunk
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* @param expandedSpMap
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*/
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private void filterSearchByHasParam(List<String> idChunk, SearchParameterMap expandedSpMap) {
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HasOrListParam hasOrListParam = new HasOrListParam();
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idChunk.stream().forEach(id -> hasOrListParam.addOr(buildHasParam(id)));
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expandedSpMap.add("_has", hasOrListParam);
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}
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private HasParam buildHasParam(String theId) {
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if ("Practitioner".equalsIgnoreCase(myResourceType)) {
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return new HasParam("Patient", "general-practitioner", "_id", theId);
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} else if ("Organization".equalsIgnoreCase(myResourceType)) {
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return new HasParam("Patient", "organization", "_id", theId);
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} else {
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throw new IllegalArgumentException(Msg.code(2077) + " We can't handle forward references onto type " + myResourceType);
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}
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}
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private void filterSearchByResourceIds(List<String> idChunk, SearchParameterMap expandedSpMap) {
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ReferenceOrListParam orList = new ReferenceOrListParam();
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idChunk.forEach(id -> orList.add(new ReferenceParam(id)));
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expandedSpMap.add(getPatientSearchParamForCurrentResourceType().getName(), orList);
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}
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private RuntimeSearchParam validateSearchParameters(SearchParameterMap expandedSpMap) {
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RuntimeSearchParam runtimeSearchParam = getPatientSearchParamForCurrentResourceType();
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if (expandedSpMap.get(runtimeSearchParam.getName()) != null) {
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throw new IllegalArgumentException(Msg.code(792) + String.format("Group Bulk Export manually modifies the Search Parameter called [%s], so you may not include this search parameter in your _typeFilter!", runtimeSearchParam.getName()));
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private void validateSearchParameters(SearchParameterMap expandedSpMap) {
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if (PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType)) {
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return;
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} else {
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RuntimeSearchParam runtimeSearchParam = getPatientSearchParamForCurrentResourceType();
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if (expandedSpMap.get(runtimeSearchParam.getName()) != null) {
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throw new IllegalArgumentException(Msg.code(792) + String.format("Group Bulk Export manually modifies the Search Parameter called [%s], so you may not include this search parameter in your _typeFilter!", runtimeSearchParam.getName()));
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}
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}
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return runtimeSearchParam;
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}
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}
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@ -49,7 +49,9 @@ import org.hl7.fhir.r4.model.Group;
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import org.hl7.fhir.r4.model.Immunization;
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import org.hl7.fhir.r4.model.InstantType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Organization;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Practitioner;
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import org.hl7.fhir.r4.model.Reference;
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import org.junit.jupiter.api.Test;
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import org.mockito.ArgumentCaptor;
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@ -63,6 +65,7 @@ import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Date;
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import java.util.HashSet;
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import java.util.List;
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@ -423,7 +426,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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// Fetch the job again
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status = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
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assertEquals(BulkExportJobStatusEnum.COMPLETE, status.getStatus());
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assertEquals(5, status.getFiles().size());
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assertEquals(7, status.getFiles().size());
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// Iterate over the files
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for (IBulkDataExportSvc.FileEntry next : status.getFiles()) {
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@ -443,6 +446,12 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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} else if ("CareTeam".equals(next.getResourceType())) {
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assertThat(nextContents, containsString("\"id\":\"CT0\""));
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assertEquals(16, nextContents.split("\n").length);
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} else if ("Practitioner".equals(next.getResourceType())) {
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assertThat(nextContents, containsString("\"id\":\"PRACT0\""));
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assertEquals(11, nextContents.split("\n").length);
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} else if ("Organization".equals(next.getResourceType())) {
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assertThat(nextContents, containsString("\"id\":\"ORG0\""));
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assertEquals(11, nextContents.split("\n").length);
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} else if ("Group".equals(next.getResourceType())) {
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assertThat(nextContents, containsString("\"id\":\"G0\""));
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assertEquals(1, nextContents.split("\n").length);
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@ -702,7 +711,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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bulkDataExportOptions.setSince(null);
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bulkDataExportOptions.setFilters(null);
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bulkDataExportOptions.setGroupId(myPatientGroupId);
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bulkDataExportOptions.setExpandMdm(true);
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bulkDataExportOptions.setExpandMdm(false);
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bulkDataExportOptions.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
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@ -727,6 +736,58 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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assertThat(nextContents, is(containsString("IMM8")));
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}
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@Test
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public void testGroupBatchJobFindsForwardReferencesIfNeeded() {
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createResources();
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// Create a bulk job
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BulkDataExportOptions bulkDataExportOptions = new BulkDataExportOptions();
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bulkDataExportOptions.setOutputFormat(null);
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bulkDataExportOptions.setResourceTypes(Sets.newHashSet("Practitioner","Organization", "Observation"));
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bulkDataExportOptions.setSince(null);
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bulkDataExportOptions.setFilters(null);
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bulkDataExportOptions.setGroupId(myPatientGroupId);
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bulkDataExportOptions.setExpandMdm(false);
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//FIXME GGG Make sure this works with MDM Enabled as well.
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bulkDataExportOptions.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
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myBulkDataExportJobSchedulingHelper.startSubmittedJobs();
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awaitAllBulkJobCompletions();
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IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
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assertThat(jobInfo.getStatus(), equalTo(BulkExportJobStatusEnum.COMPLETE));
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assertThat(jobInfo.getFiles().size(), equalTo(3));
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// Iterate over the files
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String nextContents = getBinaryContents(jobInfo, 0);
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Practitioner")));
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assertThat(nextContents, is(containsString("PRACT0")));
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assertThat(nextContents, is(containsString("PRACT2")));
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assertThat(nextContents, is(containsString("PRACT4")));
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assertThat(nextContents, is(containsString("PRACT6")));
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assertThat(nextContents, is(containsString("PRACT8")));
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nextContents = getBinaryContents(jobInfo, 1);
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assertThat(jobInfo.getFiles().get(1).getResourceType(), is(equalTo("Organization")));
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assertThat(nextContents, is(containsString("ORG0")));
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assertThat(nextContents, is(containsString("ORG2")));
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assertThat(nextContents, is(containsString("ORG4")));
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assertThat(nextContents, is(containsString("ORG6")));
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assertThat(nextContents, is(containsString("ORG8")));
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//Ensure _backwards_ references still work
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nextContents = getBinaryContents(jobInfo, 2);
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assertThat(jobInfo.getFiles().get(2).getResourceType(), is(equalTo("Observation")));
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assertThat(nextContents, is(containsString("OBS0")));
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assertThat(nextContents, is(containsString("OBS2")));
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assertThat(nextContents, is(containsString("OBS4")));
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assertThat(nextContents, is(containsString("OBS6")));
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assertThat(nextContents, is(containsString("OBS8")));
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}
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@Test
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public void testGroupBatchJobMdmExpansionIdentifiesGoldenResources() {
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createResources();
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@ -867,6 +928,14 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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assertThat(nextContents, is(containsString("CT4")));
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assertThat(nextContents, is(containsString("CT6")));
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assertThat(nextContents, is(containsString("CT8")));
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//These should be brought in via MDM.
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assertThat(nextContents, is(containsString("CT1")));
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assertThat(nextContents, is(containsString("CT3")));
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assertThat(nextContents, is(containsString("CT5")));
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assertThat(nextContents, is(containsString("CT7")));
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assertThat(nextContents, is(containsString("CT9")));
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}
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@ -1209,13 +1278,23 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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}
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private void createResources() {
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SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
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Group group = new Group();
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group.setId("G0");
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//Manually create a Practitioner
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IIdType goldenPractId = createPractitionerWithIndex(999);
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//Manually create an Organization
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IIdType goldenOrgId = createOrganizationWithIndex(999);
|
||||
|
||||
//Manually create a golden record
|
||||
Patient goldenPatient = new Patient();
|
||||
|
||||
goldenPatient.setId("PAT999");
|
||||
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
|
||||
goldenPatient.setGeneralPractitioner(Collections.singletonList(new Reference(goldenPractId.toVersionless())));
|
||||
goldenPatient.setManagingOrganization(new Reference(goldenOrgId.toVersionless()));
|
||||
|
||||
DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient, srd);
|
||||
Long goldenPid = runInTransaction(() -> myIdHelperService.getPidOrNull(g1Outcome.getResource()));
|
||||
|
||||
|
|
@ -1225,7 +1304,9 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
createCareTeamWithIndex(999, g1Outcome.getId());
|
||||
|
||||
for (int i = 0; i < 10; i++) {
|
||||
DaoMethodOutcome patientOutcome = createPatientWithIndex(i);
|
||||
IIdType orgId = createOrganizationWithIndex(i);
|
||||
IIdType practId = createPractitionerWithIndex(i);
|
||||
DaoMethodOutcome patientOutcome = createPatientWithIndexAndGPAndManagingOrganization(i, practId, orgId);
|
||||
IIdType patId = patientOutcome.getId().toUnqualifiedVersionless();
|
||||
Long sourcePid = runInTransaction(() -> myIdHelperService.getPidOrNull(patientOutcome.getResource()));
|
||||
|
||||
|
|
@ -1254,7 +1335,9 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
//Create some nongroup patients MDM linked to a different golden resource. They shouldnt be included in the query.
|
||||
for (int i = 0; i < 5; i++) {
|
||||
int index = 1000 + i;
|
||||
DaoMethodOutcome patientOutcome = createPatientWithIndex(index);
|
||||
IIdType orgId = createOrganizationWithIndex(i);
|
||||
IIdType practId = createPractitionerWithIndex(i);
|
||||
DaoMethodOutcome patientOutcome = createPatientWithIndexAndGPAndManagingOrganization(index, practId, orgId);
|
||||
IIdType patId = patientOutcome.getId().toUnqualifiedVersionless();
|
||||
Long sourcePid = runInTransaction(() -> myIdHelperService.getPidOrNull(patientOutcome.getResource()));
|
||||
linkToGoldenResource(goldenPid2, sourcePid);
|
||||
|
|
@ -1271,12 +1354,26 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
}
|
||||
}
|
||||
|
||||
private DaoMethodOutcome createPatientWithIndex(int i) {
|
||||
private IIdType createPractitionerWithIndex(int theIndex) {
|
||||
Practitioner pract = new Practitioner();
|
||||
pract.setId("PRACT" + theIndex);
|
||||
return myPractitionerDao.update(pract, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition())).getId();
|
||||
}
|
||||
|
||||
private IIdType createOrganizationWithIndex(int theIndex) {
|
||||
Organization org = new Organization();
|
||||
org.setId("ORG" + theIndex);
|
||||
return myOrganizationDao.update(org, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition())).getId();
|
||||
}
|
||||
|
||||
private DaoMethodOutcome createPatientWithIndexAndGPAndManagingOrganization(int theIndex, IIdType thePractId, IIdType theOrgId) {
|
||||
Patient patient = new Patient();
|
||||
patient.setId("PAT" + i);
|
||||
patient.setGender(i % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
|
||||
patient.addName().setFamily("FAM" + i);
|
||||
patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
|
||||
patient.setId("PAT" + theIndex);
|
||||
patient.setGender(theIndex % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
|
||||
patient.addName().setFamily("FAM" + theIndex);
|
||||
patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + theIndex);
|
||||
patient.setManagingOrganization(new Reference(theOrgId.toVersionless()));
|
||||
patient.setGeneralPractitioner(Collections.singletonList(new Reference(thePractId.toVersionless())));
|
||||
return myPatientDao.update(patient, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition()));
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -56,6 +56,7 @@ import java.util.List;
|
|||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
|
||||
import static org.slf4j.LoggerFactory.getLogger;
|
||||
|
||||
|
||||
|
|
@ -135,6 +136,7 @@ public class BulkDataExportProvider {
|
|||
private void validateResourceTypesAllContainPatientSearchParams(Set<String> theResourceTypes) {
|
||||
if (theResourceTypes != null) {
|
||||
List<String> badResourceTypes = theResourceTypes.stream()
|
||||
.filter(resourceType -> !PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(resourceType))
|
||||
.filter(resourceType -> !myBulkDataExportSvc.getPatientCompartmentResources().contains(resourceType))
|
||||
.collect(Collectors.toList());
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue