Add test for exporting patients from group

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java

@@ -37,7 +37,9 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.ReferenceOrListParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.springframework.batch.item.ItemReader;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -80,6 +82,11 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 	Iterator<ResourcePersistentId> getResourcePidIterator() {
 		List<ResourcePersistentId> myReadPids = new ArrayList<>();
 
+		//Short circuit out if we detect we are attempting to extract patients
+		if (myResourceType.equalsIgnoreCase("Patient")) {
+			return getExpandedPatientIterator();
+		}
+
 		//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.
 		Set<String> expandedMemberResourceIds = expandAllPatientPidsFromGroup();
 		if (ourLog.isDebugEnabled()) {
@@ -99,6 +106,31 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 		return myReadPids.iterator();
 	}
 
+	/**
+	 * In case we are doing a Group Bulk Export and resourceType `Patient` is requested, we can just return the group members,
+	 * possibly expanded by MDM, and don't have to go and fetch other resource DAOs.
+	 */
+	private Iterator<ResourcePersistentId> getExpandedPatientIterator() {
+		Set<Long> patientPidsToExport = new HashSet<>();
+		//This gets all member pids
+		List<String> members = getMembers();
+		List<IIdType> ids = members.stream().map(member -> new IdDt("Patient/" + member)).collect(Collectors.toList());
+		List<Long> pidsOrThrowException = myIdHelperService.getPidsOrThrowException(ids);
+		patientPidsToExport.addAll(pidsOrThrowException);
+
+		if (Boolean.parseBoolean(myMdmEnabled)) {
+			IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
+			Long pidOrNull = myIdHelperService.getPidOrNull(group);
+			List<List<Long>> lists = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
+			lists.forEach(patientPidsToExport::addAll);
+		}
+		List<ResourcePersistentId> resourcePersistentIds = patientPidsToExport
+			.stream()
+			.map(ResourcePersistentId::new)
+			.collect(Collectors.toList());
+		return resourcePersistentIds.iterator();
+	}
+
 	/**
 	 * Given the local myGroupId, read this group, and find all members' patient references.
 	 * @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
@@ -109,6 +141,8 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 		return  evaluate.stream().map(IPrimitiveType::getValueAsString).collect(Collectors.toList());
 	}
 
+
+
 	/**
 	 * Given the local myGroupId, perform an expansion to retrieve all resource IDs of member patients.
 	 * if myMdmEnabled is set to true, we also reach out to the IMdmLinkDao to attempt to also expand it into matched
@@ -122,7 +156,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 		Long pidOrNull = myIdHelperService.getPidOrNull(group);
 
 		//Attempt to perform MDM Expansion of membership
-		if (Boolean.valueOf(myMdmEnabled)) {
+		if (Boolean.parseBoolean(myMdmEnabled)) {
 			List<List<Long>> goldenPidTargetPidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
 			//Now lets translate these pids into resource IDs
 			Set<Long> uniquePids = new HashSet<>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IMdmLinkDao.java

@@ -40,7 +40,7 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
 	@Query("DELETE FROM MdmLink f WHERE (myGoldenResourcePid = :pid OR mySourcePid = :pid) AND myMatchResult <> :matchResult")
 	int deleteWithAnyReferenceToPidAndMatchResultNot(@Param("pid") Long thePid, @Param("matchResult") MdmMatchResultEnum theMatchResult);
 
-	@Query("SELECT f.mySourcePid FROM MdmLink f WHERE f.myMatchResult=:matchResult AND f.myGoldenResourcePid IN (:pids)")
+	@Query("SELECT f.myGoldenResourcePid, f.mySourcePid FROM MdmLink f WHERE f.myMatchResult=:matchResult AND f.myGoldenResourcePid IN (:pids)")
 	List<Long> expandGoldenResourcePids(@Param("pids")List<Long> theGoldenResourcePids, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
 
 	@Query("SELECT f.myGoldenResourcePid FROM MdmLink f WHERE f.mySourcePid IN (:pids)")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java

@@ -610,6 +610,32 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 		}
 	}
 
+
+	@Test
+	public void testMdmExpansionSuccessfullyExtractsPatients() throws JobParametersInvalidException {
+		createResources();
+
+		// Create a bulk job
+		IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(null, Sets.newHashSet("Patient"), null, null, myPatientGroupId, true));
+
+		myBulkDataExportSvc.buildExportFiles();
+		awaitAllBulkJobCompletions();
+
+		IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
+		assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
+		assertThat(jobInfo.getFiles().size(), equalTo(1));
+		assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Patient")));
+
+		Binary patientExportContent = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
+		assertEquals(Constants.CT_FHIR_NDJSON, patientExportContent.getContentType());
+		String nextContents = new String(patientExportContent.getContent(), Constants.CHARSET_UTF8);
+		ourLog.info("Next contents for type {}:\n{}", patientExportContent.getResourceType(), nextContents);
+		assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Patient")));
+
+		//Output contains The entire group, plus the Mdm expansion, plus the golden resource
+		assertEquals(11, nextContents.split("\n").length);
+	}
+
 	@Test
 	public void testMdmExpansionWorksForGroupExportOnMatchedPatients() throws JobParametersInvalidException {
 		createResources();