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Fix partition selection for system request details

This commit is contained in:
Tadgh 2021-04-16 11:12:40 -04:00
parent d94611edf6
commit 7cabcbd772
5 changed files with 95 additions and 16 deletions
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12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkItemReader.java
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@ -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

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();
}

30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java
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@ -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)

61
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;
@ -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) {

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