Fix partition selection for system request details

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

@@ -29,6 +29,8 @@ import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
@@ -178,13 +180,13 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 	 * @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
 	 */
 	private List<String> getMembers() {
-		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setTenantId(JpaConstants.ALL_PARTITIONS_NAME);
+		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), requestDetails);
 		List<IPrimitiveType> evaluate = myContext.newFhirPath().evaluate(group, "member.entity.reference", IPrimitiveType.class);
 		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
@@ -194,7 +196,9 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
 	 */
 	private Set<String> expandAllPatientPidsFromGroup() {
 		Set<String> expandedIds = new HashSet<>();
-		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setTenantId(JpaConstants.ALL_PARTITIONS_NAME);
+		IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), new SystemRequestDetails());
 		Long pidOrNull = myIdHelperService.getPidOrNull(group);
 
 		//Attempt to perform MDM Expansion of membership

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

@@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.batch.log.Logs;
 import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
 import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.util.BinaryUtil;
@@ -100,7 +101,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 		IBaseBinary binary = BinaryUtil.newBinary(myFhirContext);
 		binary.setContentType(Constants.CT_FHIR_NDJSON);
 		binary.setContent(myOutputStream.toByteArray());
-		DaoMethodOutcome outcome = myBinaryDao.create(binary);
+		DaoMethodOutcome outcome = myBinaryDao.create(binary, new SystemRequestDetails());
 		return outcome.getResource().getIdElement();
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java

@@ -44,6 +44,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Objects;
 
+import static ca.uhn.fhir.jpa.model.util.JpaConstants.ALL_PARTITIONS_NAME;
 import static ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster.doCallHooks;
 import static ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster.doCallHooksAndReturnObject;
 import static ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster.hasHooks;
@@ -101,6 +102,19 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
 				return RequestPartitionId.defaultPartition();
 			}
 
+			//Shortcircuit and write system calls out to default partition.
+			if (theRequest instanceof SystemRequestDetails) {
+				if (theRequest.getTenantId() != null) {
+					if (theRequest.getTenantId().equals(ALL_PARTITIONS_NAME)) {
+						return RequestPartitionId.allPartitions();
+					} else {
+						return RequestPartitionId.fromPartitionName(theRequest.getTenantId());
+					}
+				} else {
+					return RequestPartitionId.defaultPartition();
+				}
+			}
+
 			// Interceptor call: STORAGE_PARTITION_IDENTIFY_READ
 			if (hasHooks(Pointcut.STORAGE_PARTITION_IDENTIFY_READ, myInterceptorBroadcaster, theRequest)) {
 				HookParams params = new HookParams()
@@ -129,7 +143,21 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
 
 		if (myPartitionSettings.isPartitioningEnabled()) {
 
-			// Interceptor call: STORAGE_PARTITION_IDENTIFY_CREATE
+			//Shortcircuit and write system calls out to default partition.
+			if (theRequest instanceof SystemRequestDetails) {
+				if (theRequest.getTenantId() != null) {
+					if (theRequest.getTenantId().equals(ALL_PARTITIONS_NAME)) {
+						return RequestPartitionId.allPartitions();
+					} else {
+						return RequestPartitionId.fromPartitionName(theRequest.getTenantId());
+					}
+				} else {
+					return RequestPartitionId.defaultPartition();
+				}
+			}
+
+
+				// Interceptor call: STORAGE_PARTITION_IDENTIFY_CREATE
 			HookParams params = new HookParams()
 				.add(IBaseResource.class, theResource)
 				.add(RequestDetails.class, theRequest)

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

@@ -18,6 +18,7 @@ import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
 import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
 import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
 import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
 import ca.uhn.fhir.parser.IParser;
@@ -494,7 +495,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 			Patient patient = new Patient();
 			patient.setId("PAT" + i);
 			patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
-			myPatientDao.update(patient).getId().toUnqualifiedVersionless();
+			myPatientDao.update(patient, new SystemRequestDetails()).getId().toUnqualifiedVersionless();
 		}
 
 		// Create a bulk job
@@ -848,7 +849,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 
 	public String getBinaryContents(IBulkDataExportSvc.JobInfo theJobInfo, int theIndex) {
 		// Iterate over the files
-		Binary nextBinary = myBinaryDao.read(theJobInfo.getFiles().get(theIndex).getResourceId());
+		Binary nextBinary = myBinaryDao.read(theJobInfo.getFiles().get(theIndex).getResourceId(), new SystemRequestDetails());
 		assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
 		String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
 		ourLog.info("Next contents for type {}:\n{}", nextBinary.getResourceType(), nextContents);
@@ -928,7 +929,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 
 
 		//Check Observation Content
-		Binary observationExportContent = myBinaryDao.read(jobInfo.getFiles().get(1).getResourceId());
+		Binary observationExportContent = myBinaryDao.read(jobInfo.getFiles().get(1).getResourceId(), new SystemRequestDetails());
 		assertEquals(Constants.CT_FHIR_NDJSON, observationExportContent.getContentType());
 		nextContents = new String(observationExportContent.getContent(), Constants.CHARSET_UTF8);
 		ourLog.info("Next contents for type {}:\n{}", observationExportContent.getResourceType(), nextContents);
@@ -1061,7 +1062,47 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 		//Now if we create another one and ask for the cache, we should get the most-recently-insert entry.
 		IBulkDataExportSvc.JobInfo jobInfo10 = myBulkDataExportSvc.submitJob(options, true);
 		assertThat(jobInfo10.getJobId(), is(equalTo(jobInfo9.getJobId())));
+	}
+	@Test
+	public void testBulkExportWritesToDEFAULTPartitionWhenPartitioningIsEnabled() {
+		myPartitionSettings.setPartitioningEnabled(true);
 
+		createResources();
+
+		//Only get COVID-19 vaccinations
+		Set<String> filters = new HashSet<>();
+		filters.add("Immunization?vaccine-code=vaccines|COVID-19");
+
+		BulkDataExportOptions bulkDataExportOptions = new BulkDataExportOptions();
+		bulkDataExportOptions.setOutputFormat(null);
+		bulkDataExportOptions.setResourceTypes(Sets.newHashSet("Immunization"));
+		bulkDataExportOptions.setSince(null);
+		bulkDataExportOptions.setFilters(filters);
+		bulkDataExportOptions.setGroupId(myPatientGroupId);
+		bulkDataExportOptions.setExpandMdm(true);
+		bulkDataExportOptions.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
+		IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
+
+		myBulkDataExportSvc.buildExportFiles();
+		awaitAllBulkJobCompletions();
+
+		IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
+
+		assertThat(jobInfo.getStatus(), equalTo(BulkExportJobStatusEnum.COMPLETE));
+		assertThat(jobInfo.getFiles().size(), equalTo(1));
+		assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
+
+		// Check immunization Content
+		String nextContents = getBinaryContents(jobInfo, 0);
+
+		assertThat(nextContents, is(containsString("IMM1")));
+		assertThat(nextContents, is(containsString("IMM3")));
+		assertThat(nextContents, is(containsString("IMM5")));
+		assertThat(nextContents, is(containsString("IMM7")));
+		assertThat(nextContents, is(containsString("IMM9")));
+		assertThat(nextContents, is(containsString("IMM999")));
+
+		assertThat(nextContents, is(not(containsString("Flu"))));
 	}
 
 	private void createResources() {
@@ -1071,7 +1112,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 		//Manually create a golden record
 		Patient goldenPatient = new Patient();
 		goldenPatient.setId("PAT999");
-		DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient);
+		DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient, new SystemRequestDetails());
 		Long goldenPid = myIdHelperService.getPidOrNull(g1Outcome.getResource());
 
 		//Create our golden records' data.
@@ -1098,12 +1139,12 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 			createCareTeamWithIndex(i, patId);
 		}
 
-		myPatientGroupId = myGroupDao.update(group).getId();
+		myPatientGroupId = myGroupDao.update(group, new SystemRequestDetails()).getId();
 
 		//Manually create another golden record
 		Patient goldenPatient2 = new Patient();
 		goldenPatient2.setId("PAT888");
-		DaoMethodOutcome g2Outcome = myPatientDao.update(goldenPatient2);
+		DaoMethodOutcome g2Outcome = myPatientDao.update(goldenPatient2, new SystemRequestDetails());
 		Long goldenPid2 = myIdHelperService.getPidOrNull(g2Outcome.getResource());
 
 		//Create some nongroup patients MDM linked to a different golden resource. They shouldnt be included in the query.
@@ -1132,14 +1173,14 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 		patient.setGender(i % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
 		patient.addName().setFamily("FAM" + i);
 		patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
-		return myPatientDao.update(patient);
+		return myPatientDao.update(patient, new SystemRequestDetails());
 	}
 
 	private void createCareTeamWithIndex(int i, IIdType patId) {
 		CareTeam careTeam = new CareTeam();
 		careTeam.setId("CT" + i);
 		careTeam.setSubject(new Reference(patId)); // This maps to the "patient" search parameter on CareTeam
-		myCareTeamDao.update(careTeam);
+		myCareTeamDao.update(careTeam, new SystemRequestDetails());
 	}
 
 	private void createImmunizationWithIndex(int i, IIdType patId) {
@@ -1157,7 +1198,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 			cc.addCoding().setSystem("vaccines").setCode("COVID-19");
 			immunization.setVaccineCode(cc);
 		}
-		myImmunizationDao.update(immunization);
+		myImmunizationDao.update(immunization, new SystemRequestDetails());
 	}
 
 	private void createObservationWithIndex(int i, IIdType patId) {
@@ -1168,7 +1209,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
 		if (patId != null) {
 			obs.getSubject().setReference(patId.getValue());
 		}
-		myObservationDao.update(obs);
+		myObservationDao.update(obs, new SystemRequestDetails());
 	}
 
 	public void linkToGoldenResource(Long theGoldenPid, Long theSourcePid) {

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java

@@ -218,6 +218,11 @@ public class JpaConstants {
 	 */
 	public static final String DEFAULT_PARTITION_NAME = "DEFAULT";
 
+	/**
+	 * The name of the collection of all partitions
+	 */
+	public static final String ALL_PARTITIONS_NAME = "ALL_PARTITIONS";
+
 	/**
 	 * Parameter for the $expand operation
 	 */