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FhirResourceDaoR4QueryCountTest.java
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FhirResourceDaoR4QueryCountTest.java
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package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.chunk.TypedPidJson;
import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeStep;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
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.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.subscription.submit.svc.ResourceModifiedSubmitterSvc;
import ca.uhn.fhir.jpa.subscription.triggering.ISubscriptionTriggeringSvc;
import ca.uhn.fhir.jpa.subscription.triggering.SubscriptionTriggeringSvcImpl;
import ca.uhn.fhir.jpa.term.TermReadSvcImpl;
import ca.uhn.fhir.jpa.test.util.SubscriptionTestUtil;
import ca.uhn.fhir.jpa.util.SqlQuery;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.auth.PolicyEnum;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.test.utilities.ProxyUtil;
import ca.uhn.fhir.test.utilities.server.HashMapResourceProviderExtension;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import ca.uhn.fhir.util.BundleBuilder;
import jakarta.annotation.Nonnull;
import org.hamcrest.CoreMatchers;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CareTeam;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
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.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Provenance;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.ServiceRequest;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.Subscription;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.MethodOrderer;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestMethodOrder;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
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.Date;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import static ca.uhn.fhir.jpa.subscription.FhirR4Util.createSubscription;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
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;
/**
* Note about this test class:
* <p>
* This entire test class is a regression test - The aim here is to make sure that
* changes we make don't inadvertently add additional database operations. The
* various test perform different kinds of actions and then check the numbers of
* SQL selects, inserts, etc. The various numbers are arbitrary, but the point of
* this test is that if you make a change and suddenly one of these tests shows
* that a new SQL statement has been added, it is critical that you identify why
* that change has happened and work out if it is absolutely necessary. Every
* single individual SQL statement adds up when we're doing operations at scale,
* so don't ever blindly adjust numbers in this test without figuring out why.
*/
@SuppressWarnings("JavadocBlankLines")
@TestMethodOrder(MethodOrderer.MethodName.class)
public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test {
@RegisterExtension
@Order(0)
public static final RestfulServerExtension ourServer = new RestfulServerExtension(FhirContext.forR4Cached())
.keepAliveBetweenTests();
@RegisterExtension
@Order(1)
public static final HashMapResourceProviderExtension<Patient> ourPatientProvider = new HashMapResourceProviderExtension<>(ourServer, Patient.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4QueryCountTest.class);
@Autowired
private ISearchParamPresentDao mySearchParamPresentDao;
@Autowired
private ISubscriptionTriggeringSvc mySubscriptionTriggeringSvc;
@Autowired
private ResourceModifiedSubmitterSvc myResourceModifiedSubmitterSvc;
@Autowired
private ReindexStep myReindexStep;
@Autowired
private DeleteExpungeStep myDeleteExpungeStep;
@Autowired
protected SubscriptionTestUtil mySubscriptionTestUtil;
@AfterEach
public void afterResetDao() {
myStorageSettings.clearSupportedSubscriptionTypesForUnitTest();
myStorageSettings.setAllowMultipleDelete(new JpaStorageSettings().isAllowMultipleDelete());
myStorageSettings.setAutoCreatePlaceholderReferenceTargets(new JpaStorageSettings().isAutoCreatePlaceholderReferenceTargets());
myStorageSettings.setAutoVersionReferenceAtPaths(new JpaStorageSettings().getAutoVersionReferenceAtPaths());
myStorageSettings.setDeleteEnabled(new JpaStorageSettings().isDeleteEnabled());
myStorageSettings.setHistoryCountMode(JpaStorageSettings.DEFAULT_HISTORY_COUNT_MODE);
myStorageSettings.setIndexMissingFields(new JpaStorageSettings().getIndexMissingFields());
myStorageSettings.setInlineResourceTextBelowSize(new JpaStorageSettings().getInlineResourceTextBelowSize());
myStorageSettings.setMassIngestionMode(new JpaStorageSettings().isMassIngestionMode());
myStorageSettings.setMatchUrlCacheEnabled(new JpaStorageSettings().isMatchUrlCacheEnabled());
myStorageSettings.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(new JpaStorageSettings().isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets());
myStorageSettings.setResourceClientIdStrategy(new JpaStorageSettings().getResourceClientIdStrategy());
myStorageSettings.setResourceMetaCountHardLimit(new JpaStorageSettings().getResourceMetaCountHardLimit());
myStorageSettings.setRespectVersionsForSearchIncludes(new JpaStorageSettings().isRespectVersionsForSearchIncludes());
myStorageSettings.setTagStorageMode(new JpaStorageSettings().getTagStorageMode());
myStorageSettings.setExpungeEnabled(false);
myFhirContext.getParserOptions().setStripVersionsFromReferences(true);
TermReadSvcImpl.setForceDisableHibernateSearchForUnitTest(false);
mySubscriptionTestUtil.unregisterSubscriptionInterceptor();
}
@Override
@BeforeEach
public void before() throws Exception {
super.before();
// Pre-cache all StructureDefinitions so that query doesn't affect other counts
myValidationSupport.invalidateCaches();
myValidationSupport.fetchAllStructureDefinitions();
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testExpungeAllVersionsWithTagsDeletesRow() {
// Setup
// Create then delete
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setId("TEST" + i);
p.getMeta().addTag().setSystem("http:https://foo").setCode("bar");
p.setActive(true);
p.addName().setFamily("FOO");
myPatientDao.update(p).getId();
for (int j = 0; j < 5; j++) {
p.setActive(!p.getActive());
myPatientDao.update(p);
}
myPatientDao.delete(new IdType("Patient/TEST" + i));
}
myStorageSettings.setExpungeEnabled(true);
runInTransaction(() -> assertThat(myResourceTableDao.findAll(), not(empty())));
runInTransaction(() -> assertThat(myResourceHistoryTableDao.findAll(), not(empty())));
logAllResources();
// Test
myCaptureQueriesListener.clear();
myPatientDao.expunge(new ExpungeOptions()
.setExpungeDeletedResources(true), null);
// Verify
/*
* Note: $expunge is still pretty inefficient. We load all the HFJ_RESOURCE entities
* in one shot, but we then load HFJ_RES_VER entities one by one and delete the FK
* constraints on both HFJ_RESOURCE and HFJ_RES_VER one by one. This could definitely
* stand to be optimized. The one gotcha is that we call an interceptor for each
* version being deleted (I think so that MDM can do cleanup?) so we need to be careful
* about any batch deletes.
*/
assertEquals(47, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(80, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
runInTransaction(() -> assertThat(myResourceTableDao.findAll(), empty()));
runInTransaction(() -> assertThat(myResourceHistoryTableDao.findAll(), empty()));
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateWithNoChanges() {
IIdType orgId = createOrganization(withName("MY ORG"));
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
p.setManagingOrganization(new Reference(orgId));
return myPatientDao.create(p).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId(id.getIdPart());
p.addIdentifier().setSystem("urn:system").setValue("2");
p.setManagingOrganization(new Reference(orgId));
myPatientDao.update(p);
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(5, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertThat(myCaptureQueriesListener.getInsertQueriesForCurrentThread(), empty());
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateWithChanges() {
IIdType orgId = createOrganization(withName("MY ORG"));
IIdType orgId2 = createOrganization(withName("MY ORG 2"));
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
p.setManagingOrganization(new Reference(orgId));
return myPatientDao.create(p).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId(id.getIdPart());
p.addIdentifier().setSystem("urn:system").setValue("3");
p.setManagingOrganization(new Reference(orgId2));
myPatientDao.update(p).getResource();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(6, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateGroup_withAddedReferences_willSucceed() {
int initialPatientsCount = 30;
int newPatientsCount = 5;
int allPatientsCount = initialPatientsCount + newPatientsCount;
List<IIdType> patientList = createPatients(allPatientsCount);
myCaptureQueriesListener.clear();
Group group = createGroup(patientList.subList(0, initialPatientsCount));
assertQueryCount(31, 0, 3, 0);
myCaptureQueriesListener.clear();
group = updateGroup(group, patientList.subList(initialPatientsCount, allPatientsCount));
assertQueryCount(10, 1, 2, 0);
assertEquals(allPatientsCount, group.getMember().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateGroup_NoChangesToReferences() {
List<IIdType> patientList = createPatients(30);
myCaptureQueriesListener.clear();
Group group = createGroup(patientList);
assertQueryCount(31, 0, 3, 0);
// Make a change to the group, but don't touch any references in it
myCaptureQueriesListener.clear();
group.addIdentifier().setValue("foo");
group = updateGroup(group, Collections.emptyList());
myCaptureQueriesListener.logSelectQueries();
assertQueryCount(5, 1, 2, 0);
assertEquals(30, group.getMember().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateWithChangesAndTags() {
myStorageSettings.setTagStorageMode(JpaStorageSettings.TagStorageModeEnum.NON_VERSIONED);
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.getMeta().addTag("http:https://system", "foo", "display");
p.addIdentifier().setSystem("urn:system").setValue("2");
return myPatientDao.create(p).getId().toUnqualified();
});
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();
assertEquals(1, newRes.getMeta().getTag().size());
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(4, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(2, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateWithIndexMissingFieldsEnabled() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.ENABLED);
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
p.addName().setFamily("FAMILY");
myCaptureQueriesListener.clear();
return myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
});
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertEquals(6, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
assertEquals(1, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
runInTransaction(() -> {
assertEquals(9, myResourceIndexedSearchParamStringDao.count());
assertEquals(9, myResourceIndexedSearchParamTokenDao.count());
assertEquals(3, mySearchParamPresentDao.count());
});
// Now update with one additional string index
runInTransaction(() -> {
Patient p = new Patient();
p.setId(id);
p.addIdentifier().setSystem("urn:system").setValue("2");
p.addName().setFamily("FAMILY").addGiven("GIVEN");
myCaptureQueriesListener.clear();
myPatientDao.update(p, mySrd);
});
assertEquals(6, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
assertEquals(2, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertEquals(2, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
assertEquals(1, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
runInTransaction(() -> {
assertEquals(11, myResourceIndexedSearchParamStringDao.count());
assertEquals(9, myResourceIndexedSearchParamTokenDao.count());
assertEquals(3, mySearchParamPresentDao.count());
});
// Now update with no changes
runInTransaction(() -> {
Patient p = new Patient();
p.setId(id);
p.addIdentifier().setSystem("urn:system").setValue("2");
p.addName().setFamily("FAMILY").addGiven("GIVEN");
myCaptureQueriesListener.clear();
myPatientDao.update(p, mySrd);
});
assertEquals(5, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
assertEquals(1, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
runInTransaction(() -> {
assertEquals(11, myResourceIndexedSearchParamStringDao.count());
assertEquals(9, myResourceIndexedSearchParamTokenDao.count());
assertEquals(3, mySearchParamPresentDao.count());
});
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdate_DeletesSearchUrlOnlyWhenPresent() {
Patient p = new Patient();
p.setActive(false);
p.addIdentifier().setSystem("http:https://foo").setValue("123");
myCaptureQueriesListener.clear();
IIdType id = myPatientDao.create(p, "Patient?identifier=http:https://foo|123", mySrd).getId();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(1L, id.getVersionIdPartAsLong());
// Update 1 - Should delete search URL
p.setActive(true);
myCaptureQueriesListener.clear();
id = myPatientDao.update(p, "Patient?identifier=http:https://foo|123", mySrd).getId();
assertEquals(1, myCaptureQueriesListener.countDeleteQueries());
assertEquals(2L, id.getVersionIdPartAsLong());
// Update 2 - Should not try to delete search URL
p.setActive(false);
myCaptureQueriesListener.clear();
id = myPatientDao.update(p, "Patient?identifier=http:https://foo|123", mySrd).getId();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(3L, id.getVersionIdPartAsLong());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdate_DeletesSearchUrlOnlyWhenPresent_NonConditional() {
Patient p = new Patient();
p.setActive(false);
p.addIdentifier().setSystem("http:https://foo").setValue("123");
myCaptureQueriesListener.clear();
IIdType id = myPatientDao.create(p, mySrd).getId();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(1L, id.getVersionIdPartAsLong());
// Update 1 - Should not try to delete search URL since none should exist
p.setActive(true);
myCaptureQueriesListener.clear();
id = myPatientDao.update(p, "Patient?identifier=http:https://foo|123", mySrd).getId();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(2L, id.getVersionIdPartAsLong());
// Update 2 - Should not try to delete search URL
p.setActive(false);
myCaptureQueriesListener.clear();
id = myPatientDao.update(p, "Patient?identifier=http:https://foo|123", mySrd).getId();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(3L, id.getVersionIdPartAsLong());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testRead() {
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
return myPatientDao.create(p).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
myPatientDao.read(id.toVersionless());
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(2, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testValidate() {
CodeSystem cs = new CodeSystem();
cs.setUrl("http:https://foo/cs");
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.addConcept().setCode("bar-1").setDisplay("Bar 1");
cs.addConcept().setCode("bar-2").setDisplay("Bar 2");
myCodeSystemDao.create(cs);
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(cs));
Observation obs = new Observation();
// obs.getMeta().addProfile("http:https://example.com/fhir/StructureDefinition/vitalsigns-2");
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED).setDivAsString("<div>Hello</div>");
obs.getCategoryFirstRep().addCoding().setSystem("http:https://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
obs.setSubject(new Reference("Patient/123"));
obs.addPerformer(new Reference("Practitioner/123"));
obs.setEffective(DateTimeType.now());
obs.setStatus(Observation.ObservationStatus.FINAL);
obs.setValue(new StringType("This is the value"));
obs.getCode().addCoding().setSystem("http:https://foo/cs").setCode("bar-1");
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
// Validate once
myCaptureQueriesListener.clear();
try {
myObservationDao.validate(obs, null, null, null, null, null, null);
} catch (PreconditionFailedException e) {
fail(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(14, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
assertEquals(12, myCaptureQueriesListener.getCommitCount());
// Validate again (should rely only on caches)
myCaptureQueriesListener.clear();
myObservationDao.validate(obs, null, null, null, null, null, null);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(6, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
assertEquals(6, myCaptureQueriesListener.getCommitCount());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testVRead() {
IIdType id = runInTransaction(() -> {
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("2");
return myPatientDao.create(p).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
myPatientDao.read(id.withVersion("1"));
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(2, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testCreateWithClientAssignedId() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
runInTransaction(() -> {
Patient p = new Patient();
p.getMaritalStatus().setText("123");
return myPatientDao.create(p).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("123");
return myPatientDao.update(p).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
runInTransaction(() -> {
List<ResourceTable> resources = myResourceTableDao.findAll();
assertEquals(2, resources.size());
assertEquals(1, resources.get(0).getVersion());
assertEquals(1, resources.get(1).getVersion());
});
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testCreateWithServerAssignedId_AnyClientAssignedIdStrategy() {
myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
myCaptureQueriesListener.clear();
IIdType resourceId = runInTransaction(() -> {
Patient p = new Patient();
p.setUserData("ABAB", "ABAB");
p.getMaritalStatus().setText("123");
return myPatientDao.create(p).getId().toUnqualifiedVersionless();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
runInTransaction(() -> {
List<ResourceTable> resources = myResourceTableDao.findAll();
String versions = "Resource Versions:\n * " + resources.stream().map(t -> "Resource " + t.getIdDt() + " has version: " + t.getVersion()).collect(Collectors.joining("\n * "));
for (ResourceTable next : resources) {
assertEquals(1, next.getVersion(), versions);
assertNotNull(next.getResourceId());
assertNotNull(next.getFhirId());
}
});
runInTransaction(() -> {
Patient patient = myPatientDao.read(resourceId, mySrd);
assertEquals(resourceId.getIdPart(), patient.getIdElement().getIdPart());
assertEquals("123", patient.getMaritalStatus().getText());
assertEquals("1", patient.getIdElement().getVersionIdPart());
});
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testCreateWithClientAssignedId_AnyClientAssignedIdStrategy() {
myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
runInTransaction(() -> {
Patient p = new Patient();
p.setUserData("ABAB", "ABAB");
p.getMaritalStatus().setText("123");
return myPatientDao.create(p).getId().toUnqualified();
});
runInTransaction(() -> {
Patient p = new Patient();
p.setId("BBB");
p.getMaritalStatus().setText("123");
myPatientDao.update(p);
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("123");
myPatientDao.update(p);
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
runInTransaction(() -> {
List<ResourceTable> resources = myResourceTableDao.findAll();
String versions = "Resource Versions:\n * " + resources.stream().map(t -> "Resource " + t.getIdDt() + " has version: " + t.getVersion()).collect(Collectors.joining("\n * "));
for (ResourceTable next : resources) {
assertEquals(1, next.getVersion(), versions);
assertNotNull(next.getResourceId());
assertNotNull(next.getFhirId());
}
});
runInTransaction(() -> {
Patient patient = myPatientDao.read(new IdType("Patient/AAA"), mySrd);
assertEquals("AAA", patient.getIdElement().getIdPart());
assertEquals("123", patient.getMaritalStatus().getText());
assertEquals("1", patient.getIdElement().getVersionIdPart());
});
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testCreateWithClientAssignedId_CheckDisabledMode() {
when(mySrd.getHeader(eq(JpaConstants.HEADER_UPSERT_EXISTENCE_CHECK))).thenReturn(JpaConstants.HEADER_UPSERT_EXISTENCE_CHECK_DISABLED);
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("123");
return myPatientDao.update(p, mySrd).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
@Test
public void testDeleteMultiple() {
for (int i = 0; i < 10; i++) {
createPatient(withId("PT" + i), withActiveTrue(), withIdentifier("http:https://foo", "id" + i), withFamily("Family" + i));
}
myStorageSettings.setAllowMultipleDelete(true);
// Test
myCaptureQueriesListener.clear();
DeleteMethodOutcome outcome = myPatientDao.deleteByUrl("Patient?active=true", new SystemRequestDetails());
// Validate
assertEquals(12, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(10, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(10, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(30, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(10, outcome.getDeletedEntities().size());
}
@Test
public void testDeleteExpungeStep() {
// Setup
for (int i = 0; i < 10; i++) {
createPatient(
withId("PT" + i),
withActiveTrue(),
withIdentifier("http:https://foo", "id" + i),
withFamily("Family" + i),
withTag("http:https://foo", "blah"));
}
List<TypedPidJson> pids = runInTransaction(() -> myResourceTableDao
.findAll()
.stream()
.map(t -> new TypedPidJson(t.getResourceType(), Long.toString(t.getResourceId())))
.collect(Collectors.toList()));
runInTransaction(()-> assertEquals(10, myResourceTableDao.count()));
IJobDataSink<VoidModel> sink = mock(IJobDataSink.class);
// Test
myCaptureQueriesListener.clear();
RunOutcome outcome = myDeleteExpungeStep.doDeleteExpunge(new ResourceIdListWorkChunkJson(pids, null), sink, "instance-id", "chunk-id", false, null);
// Verify
assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(29, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(10, outcome.getRecordsProcessed());
runInTransaction(()-> assertEquals(0, myResourceTableDao.count()));
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testUpdateWithClientAssignedId_DeletesDisabled() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
myStorageSettings.setDeleteEnabled(false);
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("123");
myPatientDao.update(p).getId().toUnqualified();
});
// Second time
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("456");
myPatientDao.update(p).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
// Third time (caches all loaded by now)
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("789");
myPatientDao.update(p).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testReferenceToForcedId() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
Patient patient = new Patient();
patient.setId("P");
patient.setActive(true);
myCaptureQueriesListener.clear();
myPatientDao.update(patient);
/*
* Add a resource with a forced ID target link
*/
myCaptureQueriesListener.clear();
Observation observation = new Observation();
observation.getSubject().setReference("Patient/P");
myObservationDao.create(observation);
myCaptureQueriesListener.logAllQueriesForCurrentThread();
// select: lookup forced ID
assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
// insert to: HFJ_RESOURCE, HFJ_RES_VER, HFJ_RES_LINK (subject/patient)
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
/*
* Add another
*/
myCaptureQueriesListener.clear();
observation = new Observation();
observation.getSubject().setReference("Patient/P");
myObservationDao.create(observation);
// select: lookup forced ID
assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
// insert to: HFJ_RESOURCE, HFJ_RES_VER, HFJ_RES_LINK (subject/patient)
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
}
/**
* See the class javadoc before changing the counts in this test!
*/
@Test
public void testReferenceToForcedId_DeletesDisabled() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
myStorageSettings.setDeleteEnabled(false);
Patient patient = new Patient();
patient.setId("P");
patient.setActive(true);
myCaptureQueriesListener.clear();
myPatientDao.update(patient);
/*
* Add a resource with a forced ID target link
*/
myCaptureQueriesListener.clear();
Observation observation = new Observation();
observation.getSubject().setReference("Patient/P");
myObservationDao.create(observation);
myCaptureQueriesListener.logAllQueriesForCurrentThread();