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Optmize prefetch for mass ingestion transactions (#6589) 

* Optmize prefetch for mass ingestion transactions

* Add changelog

* Spotless

* Resolve review comments and spotless
This commit is contained in:
James Agnew 2025-01-07 06:59:42 -05:00 committed by GitHub
parent d6b584b770
commit 12dd39342f
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6 changed files with 182 additions and 104 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6589_optimize_transactions_in_mass_ingestion_mode Normal file
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@ -0,0 +1,4 @@
---
type: perf
issue: 6589
title: "When performing data loading into a JPA repository using FHIR transactions with Mass Ingestion Mode enabled, the prefetch routine has been optimized to avoid loading the current resource body/contents, since these are not actually needed in Mass Ingestion mode. This avoids a redundant select statement being issued for each transaction and should improve performance."

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
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@ -206,12 +206,42 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
* However, for realistic average workloads, this should reduce the number of round trips.
*/
if (!idChunk.isEmpty()) {
List<ResourceTable> entityChunk = prefetchResourceTableAndHistory(idChunk);
List<ResourceTable> entityChunk = null;
/*
* Unless we're in Mass Ingestion mode, we will pre-fetch the current
* saved resource text in HFJ_RES_VER (ResourceHistoryTable). If we're
* in Mass Ingestion Mode, we don't need to do that because every update
* will generate a new version anyway so the system never needs to know
* the current contents.
*/
if (!myStorageSettings.isMassIngestionMode()) {
entityChunk = prefetchResourceTableAndHistory(idChunk);
}
if (thePreFetchIndexes) {
/*
* If we're in mass ingestion mode, then we still need to load the resource
* entries in HFJ_RESOURCE (ResourceTable). We combine that with the search
* for tokens (since token is the most likely kind of index to be populated
* for any arbitrary resource type).
*
* For all other index types, we only load indexes if at least one
* HFJ_RESOURCE row indicates that a resource we care about actually has
* index rows of the given type.
*/
if (entityChunk == null) {
String jqlQuery =
"SELECT r FROM ResourceTable r LEFT JOIN FETCH r.myParamsToken WHERE r.myPid IN ( :IDS )";
TypedQuery<ResourceTable> query = myEntityManager.createQuery(jqlQuery, ResourceTable.class);
query.setParameter("IDS", idChunk);
entityChunk = query.getResultList();
} else {
prefetchByField("token", "myParamsToken", ResourceTable::isParamsTokenPopulated, entityChunk);
}
prefetchByField("string", "myParamsString", ResourceTable::isParamsStringPopulated, entityChunk);
prefetchByField("token", "myParamsToken", ResourceTable::isParamsTokenPopulated, entityChunk);
prefetchByField("date", "myParamsDate", ResourceTable::isParamsDatePopulated, entityChunk);
prefetchByField(
"quantity", "myParamsQuantity", ResourceTable::isParamsQuantityPopulated, entityChunk);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
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@ -173,7 +173,7 @@ public class TransactionProcessor extends BaseTransactionProcessor {
* is for fast writing of data.
*
* Note that it's probably not necessary to reset it back, it should
* automatically go back to the default value after the transaction but
* automatically go back to the default value after the transaction, but
* we reset it just to be safe.
*/
FlushModeType initialFlushMode = myEntityManager.getFlushMode();

232
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
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@ -20,7 +20,6 @@ import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
@ -28,6 +27,7 @@ import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.interceptor.ForceOffsetSearchModeInterceptor;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
@ -80,6 +80,7 @@ import org.hl7.fhir.r4.model.Location;
import org.hl7.fhir.r4.model.Narrative;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
@ -107,11 +108,11 @@ import org.mockito.Mock;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.util.comparator.ComparableComparator;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@ -132,7 +133,6 @@ import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
/**
@ -229,14 +229,14 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
p.getMeta().addTag().setSystem("http://foo").setCode("bar");
p.setActive(true);
p.addName().setFamily("FOO");
myPatientDao.update(p).getId();
myPatientDao.update(p, mySrd);
for (int j = 0; j < 5; j++) {
p.setActive(!p.getActive());
myPatientDao.update(p);
myPatientDao.update(p, mySrd);
}
myPatientDao.delete(new IdType("Patient/TEST" + i));
myPatientDao.delete(new IdType("Patient/TEST" + i), mySrd);
}
myStorageSettings.setExpungeEnabled(true);
@ -344,7 +344,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
p.setManagingOrganization(new Reference(orgId));
return myPatientDao.create(p).getId().toUnqualified();
return myPatientDao.create(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
@ -353,7 +353,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
p.setId(id.getIdPart());
p.addIdentifier().setSystem("urn:system").setValue("2");
p.setManagingOrganization(new Reference(orgId));
myPatientDao.update(p);
myPatientDao.update(p, mySrd);
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(4);
@ -375,7 +375,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
p.setManagingOrganization(new Reference(orgId));
return myPatientDao.create(p).getId().toUnqualified();
return myPatientDao.create(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
@ -384,7 +384,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
p.setId(id.getIdPart());
p.addIdentifier().setSystem("urn:system").setValue("3");
p.setManagingOrganization(new Reference(orgId2));
myPatientDao.update(p).getResource();
assertNotNull(myPatientDao.update(p, mySrd).getResource());
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(5);
@ -458,19 +458,17 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.getMeta().addTag("http://system", "foo", "display");
p.addIdentifier().setSystem("urn:system").setValue("2");
return myPatientDao.create(p).getId().toUnqualified();
return myPatientDao.create(p, mySrd).getId().toUnqualified();
});
runInTransaction(() -> {
assertEquals(1, myResourceTagDao.count());
});
runInTransaction(() -> assertEquals(1, myResourceTagDao.count()));
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId(id.getIdPart());
p.addIdentifier().setSystem("urn:system").setValue("3");
IBaseResource newRes = myPatientDao.update(p).getResource();
IBaseResource newRes = myPatientDao.update(p, mySrd).getResource();
assertEquals(1, newRes.getMeta().getTag().size());
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
@ -628,12 +626,12 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
return myPatientDao.create(p).getId().toUnqualified();
return myPatientDao.create(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
myPatientDao.read(id.toVersionless());
myPatientDao.read(id.toVersionless(), mySrd);
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(2);
@ -916,6 +914,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(10, outcome.getDeletedEntities().size());
}
@SuppressWarnings("unchecked")
@Test
public void testDeleteExpungeStep() {
// Setup
@ -961,7 +960,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("123");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
});
@ -972,7 +971,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("456");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
@ -991,7 +990,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("789");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
@ -1043,7 +1042,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.clear();
observation = new Observation();
observation.getSubject().setReference("Patient/P");
myObservationDao.create(observation);
myObservationDao.create(observation, mySrd);
// select: lookup forced ID
assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@ -1067,7 +1066,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
patient.setActive(true);
myCaptureQueriesListener.clear();
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
/*
* Add a resource with a forced ID target link
@ -1076,7 +1075,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.clear();
Observation observation = new Observation();
observation.getSubject().setReference("Patient/P");
myObservationDao.create(observation);
myObservationDao.create(observation, mySrd);
myCaptureQueriesListener.logSelectQueries();
assertEquals(0, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@ -1092,7 +1091,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.clear();
observation = new Observation();
observation.getSubject().setReference("Patient/P");
myObservationDao.create(observation);
myObservationDao.create(observation, mySrd);
// select: no lookups needed because of cache
assertEquals(0, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@ -1219,16 +1218,16 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.setId("A");
p.addIdentifier().setSystem("urn:system").setValue("1");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
p = new Patient();
p.setId("B");
p.addIdentifier().setSystem("urn:system").setValue("2");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
myPatientDao.create(p).getId().toUnqualified();
myPatientDao.create(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
@ -1268,8 +1267,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
/**
* This could definitely stand to be optimized some, since we load tags individually
* for each resource
*/
/**
*
* See the class javadoc before changing the counts in this test!
*/
@Test
@ -1282,20 +1280,20 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
p.getMeta().addTag("system", "code2", "displaY2");
p.setId("A");
p.addIdentifier().setSystem("urn:system").setValue("1");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
p = new Patient();
p.getMeta().addTag("system", "code1", "displaY1");
p.getMeta().addTag("system", "code2", "displaY2");
p.setId("B");
p.addIdentifier().setSystem("urn:system").setValue("2");
myPatientDao.update(p).getId().toUnqualified();
myPatientDao.update(p, mySrd).getId().toUnqualified();
p = new Patient();
p.getMeta().addTag("system", "code1", "displaY1");
p.getMeta().addTag("system", "code2", "displaY2");
p.addIdentifier().setSystem("urn:system").setValue("2");
myPatientDao.create(p).getId().toUnqualified();
myPatientDao.create(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
@ -1347,16 +1345,16 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
}
assertThat(foundIds).hasSize(ids.size());
ids.sort(new ComparableComparator<>());
foundIds.sort(new ComparableComparator<>());
ids.sort(Comparator.naturalOrder());
foundIds.sort(Comparator.naturalOrder());
assertEquals(ids, foundIds);
// This really generates a surprising number of selects and commits. We
// could stand to reduce this!
myCaptureQueriesListener.logSelectQueries();
assertEquals(56, myCaptureQueriesListener.countSelectQueries());
assertEquals(71, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
assertEquals(71, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
}
/**
@ -1375,13 +1373,13 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
search = myPagingProvider.retrieveResultList(mySrd, search.getUuid());
}
ids.sort(new ComparableComparator<>());
foundIds.sort(new ComparableComparator<>());
ids.sort(Comparator.naturalOrder());
foundIds.sort(Comparator.naturalOrder());
assertEquals(ids, foundIds);
assertEquals(22, myCaptureQueriesListener.countSelectQueries());
assertEquals(21, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
assertEquals(21, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
}
/**
@ -1399,13 +1397,13 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
nextChunk.forEach(t -> foundIds.add(t.getIdElement().toUnqualifiedVersionless().getValue()));
}
ids.sort(new ComparableComparator<>());
foundIds.sort(new ComparableComparator<>());
ids.sort(Comparator.naturalOrder());
foundIds.sort(Comparator.naturalOrder());
assertEquals(ids, foundIds);
assertEquals(2, myCaptureQueriesListener.countSelectQueries());
assertEquals(1, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
assertEquals(1, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
}
@Nonnull
@ -1532,18 +1530,18 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setId("P");
patient.setActive(true);
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
Observation obs = new Observation();
obs.getSubject().setReference("Patient/P");
myObservationDao.create(obs);
myObservationDao.create(obs, mySrd);
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("subject", new ReferenceParam("Patient/P"));
myCaptureQueriesListener.clear();
assertEquals(1, myObservationDao.search(map).size().intValue());
assertEquals(1, myObservationDao.search(map, mySrd).sizeOrThrowNpe());
// (not resolve forced ID), Perform search, load result
assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertNoPartitionSelectors();
@ -1556,7 +1554,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
*/
myCaptureQueriesListener.clear();
assertEquals(1, myObservationDao.search(map).size().intValue());
assertEquals(1, myObservationDao.search(map, mySrd).sizeOrThrowNpe());
myCaptureQueriesListener.logAllQueriesForCurrentThread();
// (not resolve forced ID), Perform search, load result (this time we reuse the cached forced-id resolution)
assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
@ -1576,18 +1574,18 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setId("P");
patient.setActive(true);
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
Observation obs = new Observation();
obs.getSubject().setReference("Patient/P");
myObservationDao.create(obs);
myObservationDao.create(obs, mySrd);
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("subject", new ReferenceParam("Patient/P"));
myCaptureQueriesListener.clear();
assertEquals(1, myObservationDao.search(map).size().intValue());
assertEquals(1, myObservationDao.search(map, mySrd).sizeOrThrowNpe());
myCaptureQueriesListener.logAllQueriesForCurrentThread();
// (not Resolve forced ID), Perform search, load result
assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
@ -1600,7 +1598,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
*/
myCaptureQueriesListener.clear();
assertEquals(1, myObservationDao.search(map).size().intValue());
assertEquals(1, myObservationDao.search(map, mySrd).sizeOrThrowNpe());
myCaptureQueriesListener.logAllQueriesForCurrentThread();
// (NO resolve forced ID), Perform search, load result
assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
@ -1618,16 +1616,16 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setId("P");
patient.addIdentifier().setSystem("sys").setValue("val");
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
Observation obs = new Observation();
obs.setId("O");
obs.getSubject().setReference("Patient/P");
myObservationDao.update(obs);
myObservationDao.update(obs, mySrd);
SearchParameterMap map = SearchParameterMap.newSynchronous(Observation.SP_SUBJECT, new ReferenceParam("identifier", "sys|val"));
myCaptureQueriesListener.clear();
IBundleProvider outcome = myObservationDao.search(map);
IBundleProvider outcome = myObservationDao.search(map, mySrd);
assertThat(toUnqualifiedVersionlessIdValues(outcome)).containsExactlyInAnyOrder("Observation/O");
assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
@ -1650,32 +1648,32 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
patient.getMeta().addTag("http://system", "value1", "display");
patient.setId("P1");
patient.getNameFirstRep().setFamily("FAM1");
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
patient = new Patient();
patient.setId("P2");
patient.getMeta().addTag("http://system", "value1", "display");
patient.getNameFirstRep().setFamily("FAM2");
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
for (int i = 0; i < 3; i++) {
CareTeam ct = new CareTeam();
ct.setId("CT1-" + i);
ct.getMeta().addTag("http://system", "value11", "display");
ct.getSubject().setReference("Patient/P1");
myCareTeamDao.update(ct);
myCareTeamDao.update(ct, mySrd);
ct = new CareTeam();
ct.setId("CT2-" + i);
ct.getMeta().addTag("http://system", "value22", "display");
ct.getSubject().setReference("Patient/P2");
myCareTeamDao.update(ct);
myCareTeamDao.update(ct, mySrd);
}
SearchParameterMap map = SearchParameterMap.newSynchronous().addRevInclude(CareTeam.INCLUDE_SUBJECT).setSort(new SortSpec(Patient.SP_NAME));
myCaptureQueriesListener.clear();
IBundleProvider outcome = myPatientDao.search(map);
IBundleProvider outcome = myPatientDao.search(map, mySrd);
assertEquals(SimpleBundleProvider.class, outcome.getClass());
assertThat(toUnqualifiedVersionlessIdValues(outcome)).containsExactlyInAnyOrder("Patient/P1", "CareTeam/CT1-0", "CareTeam/CT1-1", "CareTeam/CT1-2", "Patient/P2", "CareTeam/CT2-0", "CareTeam/CT2-1", "CareTeam/CT2-2");
@ -1924,7 +1922,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Practitioner pract = new Practitioner();
pract.addIdentifier().setSystem("foo").setValue("bar");
myPractitionerDao.create(pract);
myPractitionerDao.create(pract, mySrd);
runInTransaction(() -> assertEquals(1, myResourceTableDao.count(), () -> myResourceTableDao.findAll().stream().map(t -> t.getIdDt().toUnqualifiedVersionless().getValue()).collect(Collectors.joining(","))));
// First pass
@ -2127,7 +2125,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
outcome = mySystemDao.transaction(mySrd, input.get());
ourLog.debug("Resp: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
myCaptureQueriesListener.logSelectQueries();
assertEquals(4, myCaptureQueriesListener.countSelectQueries());
assertEquals(3, myCaptureQueriesListener.countSelectQueries());
myCaptureQueriesListener.logInsertQueries();
assertEquals(2, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.logUpdateQueries();
@ -2210,7 +2208,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
outcome = mySystemDao.transaction(mySrd, input.get());
ourLog.debug("Resp: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
myCaptureQueriesListener.logSelectQueries();
assertEquals(5, myCaptureQueriesListener.countSelectQueries());
assertEquals(4, myCaptureQueriesListener.countSelectQueries());
myCaptureQueriesListener.logInsertQueries();
assertEquals(5, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.logUpdateQueries();
@ -2334,7 +2332,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient pt = new Patient();
pt.setId("ABC");
pt.setActive(true);
myPatientDao.update(pt);
myPatientDao.update(pt, mySrd);
Location loc = new Location();
loc.setId("LOC");
@ -2522,7 +2520,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
outcome = mySystemDao.transaction(mySrd, input.get());
ourLog.debug("Resp: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
myCaptureQueriesListener.logSelectQueries();
assertEquals(7, myCaptureQueriesListener.countSelectQueries());
assertEquals(6, myCaptureQueriesListener.countSelectQueries());
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.logUpdateQueries();
@ -2537,7 +2535,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
outcome = mySystemDao.transaction(mySrd, input.get());
ourLog.debug("Resp: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
myCaptureQueriesListener.logSelectQueries();
assertEquals(5, myCaptureQueriesListener.countSelectQueries());
assertEquals(4, myCaptureQueriesListener.countSelectQueries());
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.logUpdateQueries();
@ -2579,7 +2577,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(() -> {
List<String> types = myResourceTableDao.findAll().stream().map(t -> t.getResourceType()).collect(Collectors.toList());
List<String> types = myResourceTableDao.findAll().stream().map(ResourceTable::getResourceType).collect(Collectors.toList());
assertThat(types).containsExactlyInAnyOrder("Patient", "Observation");
});
@ -2593,7 +2591,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(() -> {
List<String> types = myResourceTableDao.findAll().stream().map(t -> t.getResourceType()).collect(Collectors.toList());
List<String> types = myResourceTableDao.findAll().stream().map(ResourceTable::getResourceType).collect(Collectors.toList());
assertThat(types).containsExactlyInAnyOrder("Patient", "Observation", "Observation");
});
@ -2606,7 +2604,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(() -> {
List<String> types = myResourceTableDao.findAll().stream().map(t -> t.getResourceType()).collect(Collectors.toList());
List<String> types = myResourceTableDao.findAll().stream().map(ResourceTable::getResourceType).collect(Collectors.toList());
assertThat(types).containsExactlyInAnyOrder("Patient", "Observation", "Observation", "Observation");
});
@ -2644,7 +2642,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(() -> {
List<String> types = myResourceTableDao.findAll().stream().map(t -> t.getResourceType()).collect(Collectors.toList());
List<String> types = myResourceTableDao.findAll().stream().map(ResourceTable::getResourceType).collect(Collectors.toList());
assertThat(types).containsExactlyInAnyOrder("Patient", "Observation");
});
@ -2663,7 +2661,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertThat(matchUrlQuery).contains("fetch first '2'");
runInTransaction(() -> {
List<String> types = myResourceTableDao.findAll().stream().map(t -> t.getResourceType()).collect(Collectors.toList());
List<String> types = myResourceTableDao.findAll().stream().map(ResourceTable::getResourceType).collect(Collectors.toList());
assertThat(types).containsExactlyInAnyOrder("Patient", "Observation", "Observation");
});
@ -2676,7 +2674,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(() -> {
List<String> types = myResourceTableDao.findAll().stream().map(t -> t.getResourceType()).collect(Collectors.toList());
List<String> types = myResourceTableDao.findAll().stream().map(ResourceTable::getResourceType).collect(Collectors.toList());
assertThat(types).containsExactlyInAnyOrder("Patient", "Observation", "Observation", "Observation");
});
@ -2848,12 +2846,12 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setId("Patient/A");
patient.setActive(true);
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
Practitioner practitioner = new Practitioner();
practitioner.setId("Practitioner/B");
practitioner.setActive(true);
myPractitionerDao.update(practitioner);
myPractitionerDao.update(practitioner, mySrd);
// Create transaction
@ -2921,11 +2919,11 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setActive(true);
IIdType patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
IIdType patientId = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
Practitioner practitioner = new Practitioner();
practitioner.setActive(true);
IIdType practitionerId = myPractitionerDao.create(practitioner).getId().toUnqualifiedVersionless();
IIdType practitionerId = myPractitionerDao.create(practitioner, mySrd).getId().toUnqualifiedVersionless();
// Create transaction
Bundle input = new Bundle();
@ -2994,12 +2992,12 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setId("Patient/A");
patient.setActive(true);
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
Practitioner practitioner = new Practitioner();
practitioner.setId("Practitioner/B");
practitioner.setActive(true);
myPractitionerDao.update(practitioner);
myPractitionerDao.update(practitioner, mySrd);
// Create transaction
@ -3067,11 +3065,11 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setActive(true);
IIdType patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
IIdType patientId = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
Practitioner practitioner = new Practitioner();
practitioner.setActive(true);
IIdType practitionerId = myPractitionerDao.create(practitioner).getId().toUnqualifiedVersionless();
IIdType practitionerId = myPractitionerDao.create(practitioner, mySrd).getId().toUnqualifiedVersionless();
// Create transaction
Bundle input = new Bundle();
@ -3139,12 +3137,12 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient patient = new Patient();
patient.setId("Patient/A");
patient.setActive(true);
myPatientDao.update(patient);
myPatientDao.update(patient, mySrd);
Practitioner practitioner = new Practitioner();
practitioner.setId("Practitioner/B");
practitioner.setActive(true);
myPractitionerDao.update(practitioner);
myPractitionerDao.update(practitioner, mySrd);
// Create transaction
@ -3750,7 +3748,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.clear();
Bundle outcome = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
myCaptureQueriesListener.logSelectQueries();
assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(5, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(7, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
@ -3773,7 +3771,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.clear();
outcome = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(5, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(6, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
@ -3834,11 +3832,65 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.clear();
mySystemDao.transaction(new SystemRequestDetails(), loadResourceFromClasspath(Bundle.class, "r4/transaction-perf-bundle-smallchanges.json"));
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(5, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(2, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(6, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(1, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testMassIngestionMode_TransactionWithManyUpdates() {
myStorageSettings.setMassIngestionMode(true);
for (int i = 0; i < 10; i++) {
Organization org = new Organization();
org.setId("ORG" + i);
org.setName("ORG " + i);
myOrganizationDao.update(org, mySrd);
}
for (int i = 0; i < 5; i++) {
Patient patient = new Patient();
patient.setId("PT" + i);
patient.setActive(true);
patient.setManagingOrganization(new Reference("Organization/ORG" + i));
myPatientDao.update(patient, mySrd);
}
Supplier<Bundle> supplier = () -> {
BundleBuilder bb = new BundleBuilder(myFhirContext);
for (int i = 0; i < 10; i++) {
Patient patient = new Patient();
patient.setId("PT" + i);
// Flip this value
patient.setActive(false);
patient.addIdentifier().setSystem("http://foo").setValue("bar");
patient.setManagingOrganization(new Reference("Organization/ORG" + i));
bb.addTransactionUpdateEntry(patient);
}
return (Bundle) bb.getBundle();
};
// Test
myCaptureQueriesListener.clear();
myMemoryCacheService.invalidateAllCaches();
mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
myCaptureQueriesListener.logSelectQueries();
myCaptureQueriesListener.logInsertQueries();
assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(40, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(10, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countInsertQueriesRepeated());
}
/**
@ -3860,7 +3912,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(3, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
runInTransaction(() -> {
ResourceTable version = myResourceTableDao.findById(patientId.getIdPartAsLong()).orElseThrow();
ResourceTable version = myResourceTableDao.findById(JpaPid.fromId(patientId.getIdPartAsLong())).orElseThrow();
assertFalse(version.isParamsTokenPopulated());
assertFalse(version.isHasLinks());
assertEquals(0, myResourceIndexedSearchParamTokenDao.count());
@ -3882,7 +3934,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
IIdType idDt = myObservationDao.create(observation, mySrd).getEntity().getIdDt();
runInTransaction(() -> {
assertEquals(4, myResourceIndexedSearchParamTokenDao.count());
ResourceTable version = myResourceTableDao.findById(idDt.getIdPartAsLong()).orElseThrow();
ResourceTable version = myResourceTableDao.findById(JpaPid.fromId(idDt.getIdPartAsLong())).orElseThrow();
assertTrue(version.isParamsTokenPopulated());
});
@ -3894,7 +3946,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertQueryCount(3, 1, 1, 2);
runInTransaction(() -> {
assertEquals(0, myResourceIndexedSearchParamTokenDao.count());
ResourceTable version = myResourceTableDao.findById(idDt.getIdPartAsLong()).orElseThrow();
ResourceTable version = myResourceTableDao.findById(JpaPid.fromId(idDt.getIdPartAsLong())).orElseThrow();
assertFalse(version.isParamsTokenPopulated());
});
}
@ -3950,12 +4002,10 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
String encoded;
IIdType id = null;
int initialAdditionalSelects = 0;
if (theStoredInRepository) {
id = myPatientDao.create(resource, mySrd).getId();
resource = null;
encoded = null;
initialAdditionalSelects = 1;
} else {
resource.setId("A");
encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource);
@ -4149,7 +4199,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Patient p = new Patient();
p.getMeta().addTag("http://system", "foo", "display");
p.addIdentifier().setSystem("urn:system").setValue("2");
return myPatientDao.create(p).getId().toUnqualified();
return myPatientDao.create(p, mySrd).getId().toUnqualified();
});
}

6
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
View File

@ -116,7 +116,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
@BeforeEach
public void disableAdvanceIndexing() {
myStorageSettings.setAdvancedHSearchIndexing(false);
myStorageSettings.setHibernateSearchIndexSearchParams(false);
// ugh - somewhere the hibernate round trip is mangling LocalDate to h2 date column unless the tz=GMT
TimeZone.setDefault(TimeZone.getTimeZone("GMT"));
ourLog.info("Running with Timezone {}", TimeZone.getDefault().getID());
@ -3053,7 +3053,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
outcome = mySystemDao.transaction(mySrd, input.get());
ourLog.debug("Resp: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(7, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
@ -3069,7 +3069,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
outcome = mySystemDao.transaction(mySrd, input.get());
ourLog.debug("Resp: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(5, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();

8
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/subscription/websocket/WebsocketWithSubscriptionIdR5Test.java
View File

@ -112,13 +112,7 @@ public class WebsocketWithSubscriptionIdR5Test extends BaseSubscriptionsR5Test {
// Then
List<String> messages = myWebsocketClientExtension.getMessages();
await().until(() -> !messages.isEmpty());
// Log it
ourLog.info("Messages: {}", messages);
// Verify a ping message shall be returned
Assertions.assertTrue(messages.contains("ping " + subscriptionId));
await().until(() -> messages, t -> t.contains("ping " + subscriptionId));
}
@Test