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Merge pull request #2558 from hapifhir/issue-2556-bulk-export-bug 

Issue 2556 bulk export bug
This commit is contained in:
Tadgh 2021-04-18 20:27:18 -04:00 committed by GitHub
parent d94611edf6 c54862e772
commit 48f93f5555
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11 changed files with 158 additions and 52 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2556-prevent-bulk-failure-while-partitioned.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 2556
title: "Fixed a bug which would cause Bulk Export to fail when run in a partitioned environment."

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkItemReader.java
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@ -29,6 +29,7 @@ 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.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
@ -118,7 +119,8 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
Set<Long> patientPidsToExport = new HashSet<>(pidsOrThrowException);
if (myMdmEnabled) {
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), srd);
Long pidOrNull = myIdHelperService.getPidOrNull(group);
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
goldenPidSourcePidTuple.forEach(tuple -> {
@ -178,13 +180,12 @@ 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 = SystemRequestDetails.newSystemRequestAllPartitions();
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 +195,8 @@ 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 = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), requestDetails);
Long pidOrNull = myIdHelperService.getPidOrNull(group);
//Attempt to perform MDM Expansion of membership

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceToFileWriter.java
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@ -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();
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java
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@ -42,6 +42,7 @@ import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -203,8 +204,8 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
ourLog.info("Purging bulk data file: {}", nextFile.getResourceId());
getBinaryDao().delete(toId(nextFile.getResourceId()));
getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), null);
getBinaryDao().delete(toId(nextFile.getResourceId()), new SystemRequestDetails());
getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), new SystemRequestDetails());
myBulkExportCollectionFileDao.deleteByPid(nextFile.getId());
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
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@ -65,7 +65,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
@ -655,16 +654,8 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
}
private void deleteAndExpungeResourceBinary(IIdType theResourceBinaryId, ExpungeOptions theOptions) {
if (myPartitionSettings.isPartitioningEnabled()) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
getBinaryDao().delete(theResourceBinaryId, requestDetails).getEntity();
getBinaryDao().forceExpungeInExistingTransaction(theResourceBinaryId, theOptions, requestDetails);
} else {
getBinaryDao().delete(theResourceBinaryId).getEntity();
getBinaryDao().forceExpungeInExistingTransaction(theResourceBinaryId, theOptions, null);
}
getBinaryDao().delete(theResourceBinaryId, new SystemRequestDetails()).getEntity();
getBinaryDao().forceExpungeInExistingTransaction(theResourceBinaryId, theOptions, new SystemRequestDetails());
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
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@ -347,7 +347,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private IBundleProvider searchResource(IFhirResourceDao theDao, SearchParameterMap theMap) {
if (myPartitionSettings.isPartitioningEnabled()) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
// requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
return theDao.search(theMap, requestDetails);
} else {
return theDao.search(theMap);

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java
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@ -35,6 +35,8 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
@ -44,11 +46,15 @@ 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;
import static org.slf4j.LoggerFactory.getLogger;
public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
private static final Logger ourLog = getLogger(RequestPartitionHelperSvc.class);
private final HashSet<Object> myNonPartitionableResourceNames;
@ -95,14 +101,18 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
public RequestPartitionId determineReadPartitionForRequest(@Nullable RequestDetails theRequest, String theResourceType) {
RequestPartitionId requestPartitionId;
boolean nonPartitionableResource = myNonPartitionableResourceNames.contains(theResourceType);
if (myPartitionSettings.isPartitioningEnabled()) {
// Handle system requests
if ((theRequest == null && myNonPartitionableResourceNames.contains(theResourceType))) {
//TODO GGG eventually, theRequest will not be allowed to be null here, and we will pass through SystemRequestDetails instead.
if (theRequest == null && nonPartitionableResource) {
return RequestPartitionId.defaultPartition();
}
if (theRequest instanceof SystemRequestDetails) {
requestPartitionId = getSystemRequestPartitionId(theRequest, nonPartitionableResource);
// Interceptor call: STORAGE_PARTITION_IDENTIFY_READ
if (hasHooks(Pointcut.STORAGE_PARTITION_IDENTIFY_READ, myInterceptorBroadcaster, theRequest)) {
} else if (hasHooks(Pointcut.STORAGE_PARTITION_IDENTIFY_READ, myInterceptorBroadcaster, theRequest)) {
HookParams params = new HookParams()
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest);
@ -119,6 +129,48 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
return RequestPartitionId.allPartitions();
}
/**
*
* For system requests, read partition from tenant ID if present, otherwise set to DEFAULT. If the resource they are attempting to partition
* is non-partitionable scream in the logs and set the partition to DEFAULT.
*
* @param theRequest
* @param theNonPartitionableResource
* @return
*/
@NotNull
private RequestPartitionId getSystemRequestPartitionId(@NotNull RequestDetails theRequest, boolean theNonPartitionableResource) {
RequestPartitionId requestPartitionId;
requestPartitionId = getSystemRequestPartitionId(theRequest);
if (theNonPartitionableResource && !requestPartitionId.isDefaultPartition()) {
throw new InternalErrorException("System call is attempting to write a non-partitionable resource to a partition! This is a bug!");
}
return requestPartitionId;
}
/**
* Determine the partition for a System Call (defined by the fact that the request is of type SystemRequestDetails)
*
* 1. If the tenant ID is set to the constant for all partitions, return all partitions
* 2. If there is a tenant ID set in the request, use it.
* 3. Otherwise, return the Default Partition.
*
* @param theRequest The {@link SystemRequestDetails}
* @return the {@link RequestPartitionId} to be used for this request.
*/
@NotNull
private RequestPartitionId getSystemRequestPartitionId(@NotNull RequestDetails theRequest) {
if (theRequest.getTenantId() != null) {
if (theRequest.getTenantId().equals(ALL_PARTITIONS_NAME)) {
return RequestPartitionId.allPartitions();
} else {
return RequestPartitionId.fromPartitionName(theRequest.getTenantId());
}
} else {
return RequestPartitionId.defaultPartition();
}
}
/**
* Invoke the {@link Pointcut#STORAGE_PARTITION_IDENTIFY_CREATE} interceptor pointcut to determine the tenant for a create request.
*/
@ -128,19 +180,23 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
RequestPartitionId requestPartitionId;
if (myPartitionSettings.isPartitioningEnabled()) {
boolean nonPartitionableResource = myNonPartitionableResourceNames.contains(theResourceType);
// Interceptor call: STORAGE_PARTITION_IDENTIFY_CREATE
HookParams params = new HookParams()
if (theRequest instanceof SystemRequestDetails) {
requestPartitionId = getSystemRequestPartitionId(theRequest, nonPartitionableResource);
} else {
//This is an external Request (e.g. ServletRequestDetails) so we want to figure out the partition via interceptor.
HookParams params = new HookParams()// Interceptor call: STORAGE_PARTITION_IDENTIFY_CREATE
.add(IBaseResource.class, theResource)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest);
requestPartitionId = (RequestPartitionId) doCallHooksAndReturnObject(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PARTITION_IDENTIFY_CREATE, params);
// Handle system requests
boolean nonPartitionableResource = myNonPartitionableResourceNames.contains(theResourceType);
//If the interceptors haven't selected a partition, and its a non-partitionable resource anyhow, send to DEFAULT
if (nonPartitionableResource && requestPartitionId == null) {
requestPartitionId = RequestPartitionId.defaultPartition();
}
}
String resourceName = myFhirContext.getResourceType(theResource);
validateSinglePartitionForCreate(requestPartitionId, resourceName, Pointcut.STORAGE_PARTITION_IDENTIFY_CREATE);

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/SystemRequestDetails.java
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@ -35,17 +35,15 @@ import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ImmutableListMultimap;
import com.google.common.collect.ImmutableMultimap;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.Multimap;
import com.google.common.collect.Multimaps;
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.nio.charset.Charset;
import java.util.List;
import java.util.Optional;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.ALL_PARTITIONS_NAME;
/**
* A default RequestDetails implementation that can be used for system calls to
@ -104,6 +102,11 @@ public class SystemRequestDetails extends RequestDetails {
}
myHeaders.put(theName, theValue);
}
public static SystemRequestDetails newSystemRequestAllPartitions() {
SystemRequestDetails systemRequestDetails = new SystemRequestDetails();
systemRequestDetails.setTenantId(ALL_PARTITIONS_NAME);
return systemRequestDetails;
}
@Override

70
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
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@ -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;
@ -116,7 +117,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
Binary b = new Binary();
b.setContent(new byte[]{0, 1, 2, 3});
String binaryId = myBinaryDao.create(b).getId().toUnqualifiedVersionless().getValue();
String binaryId = myBinaryDao.create(b, new SystemRequestDetails()).getId().toUnqualifiedVersionless().getValue();
BulkExportJobEntity job = new BulkExportJobEntity();
job.setStatus(BulkExportJobStatusEnum.COMPLETE);
@ -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
@ -523,7 +524,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
// Iterate over the files
for (IBulkDataExportSvc.FileEntry next : status.getFiles()) {
Binary nextBinary = myBinaryDao.read(next.getResourceId());
Binary nextBinary = myBinaryDao.read(next.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{}", next.getResourceType(), nextContents);
@ -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);
@ -1029,7 +1030,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
}
@Test
public void testCacheSettingIsRespectedWhenCreatingNewJobs() {
public void testCacheSettingIsRespectedWhenCreatingNewJobs() throws InterruptedException {
BulkDataExportOptions options = new BulkDataExportOptions();
options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM);
options.setResourceTypes(Sets.newHashSet("Procedure"));
@ -1048,6 +1049,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
IBulkDataExportSvc.JobInfo jobInfo6 = myBulkDataExportSvc.submitJob(options, false);
IBulkDataExportSvc.JobInfo jobInfo7 = myBulkDataExportSvc.submitJob(options, false);
IBulkDataExportSvc.JobInfo jobInfo8 = myBulkDataExportSvc.submitJob(options, false);
Thread.sleep(100L); //stupid commit timings.
IBulkDataExportSvc.JobInfo jobInfo9 = myBulkDataExportSvc.submitJob(options, false);
//First non-cached should retrieve new ID.
@ -1061,7 +1063,48 @@ 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"))));
myPartitionSettings.setPartitioningEnabled(false);
}
private void createResources() {
@ -1071,7 +1114,8 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
//Manually create a golden record
Patient goldenPatient = new Patient();
goldenPatient.setId("PAT999");
DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient);
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient, srd);
Long goldenPid = myIdHelperService.getPidOrNull(g1Outcome.getResource());
//Create our golden records' data.
@ -1098,12 +1142,12 @@ 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 +1176,14 @@ 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 +1201,7 @@ 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 +1212,7 @@ 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) {

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
View File

@ -642,7 +642,6 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
assertEquals(myPartitionId, resourceTable.getPartitionId().getPartitionId().intValue());
assertEquals(myPartitionDate, resourceTable.getPartitionId().getPartitionDate());
});
}
@Test

5
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java
View File

@ -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
*/