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4190 offset count and total are wrong for some queries offset produces short pages and repeats results on different pages (#4193) 

* created failing test

* implemented the fix, added more tests

* added change log

Co-authored-by: Steven Li <steven@smilecdr.com>
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StevenXLi 2022-10-25 09:42:54 -04:00 committed by GitHub
parent 51627fb873
commit e1e33df38c
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5 changed files with 167 additions and 2 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4190-offset-count-and-total-are-wrong-for-some-queries-_offset-produces-short-pages-and-repeats-results-on-different-pages.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 4190
title: "Previously, when using _offset, the queries will result in short pages, and repeats results on different pages.
This has now been fixed."

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
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@ -951,6 +951,11 @@ public class QueryStack {
}
}
public void addGrouping() {
BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
mySqlBuilder.getSelect().addGroupings(firstPredicateBuilder.getResourceIdColumn());
}
private class ChainElement {
private final String myResourceType;
private final String mySearchParameterName;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
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@ -648,6 +648,10 @@ public class SearchBuilder implements ISearchBuilder {
createSort(queryStack3, sort);
}
if (theOffset != null) {
queryStack3.addGrouping();
}
/*
* Now perform the search
*/

84
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4FilterTest.java
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@ -2,20 +2,32 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CarePlan;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.DecimalType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.HealthcareService;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Location;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.PractitionerRole;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.RiskAssessment;
import org.hl7.fhir.r4.model.SearchParameter;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@ -23,6 +35,7 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.List;
import java.util.stream.Collectors;
@ -39,6 +52,9 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4FilterTest.class);
@Autowired
private IResourceHistoryProvenanceDao myResourceProvenanceDao;
@Autowired
@Qualifier("myHealthcareServiceDaoR4")
protected IFhirResourceDao<HealthcareService> myHealthcareServiceDao;
@AfterEach
public void after() {
@ -349,7 +365,6 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
}
@Test
public void testStringComparatorCo() {
@ -1238,5 +1253,72 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchWithChainingForNonExistingReference() {
SearchParameter searchParameter = new SearchParameter();
searchParameter.setId("isplaceholder");
searchParameter.setUrl("http://hl7.org/fhir/SearchParameter/isplaceholder");
searchParameter.setName("isplaceholder");
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameter.setVersion("1.0.1");
searchParameter.setDescription("Custom SearchParameter for HCSC");
searchParameter.setCode("isplaceholder");
searchParameter.addBase("PractitionerRole");
searchParameter.addBase("Organization");
searchParameter.addBase("OrganizationAffiliation");
searchParameter.addBase("Location");
searchParameter.addBase("Practitioner");
searchParameter.addBase("HealthcareService");
searchParameter.setType(Enumerations.SearchParamType.TOKEN);
searchParameter.setExpression("extension.where(url='http://hapifhir.io/fhir/StructureDefinition/resource-placeholder').exists()");
searchParameter.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
mySearchParameterDao.update(searchParameter);
mySearchParamRegistry.forceRefresh();
Location l = new Location();
l.setId("loc-real");
l.setMeta(new Meta().addTag("http://www.smilecdr.com/custom_tag/uuid",
"51f922e6-1ae6-48c4-a41e-0f978326000dSP1975060918", ""));
myLocationDao.update(l);
HealthcareService hs = new HealthcareService();
hs.setId("hs-real");
hs.setMeta(new Meta().addTag("http://www.smilecdr.com/custom_tag/uuid",
"51f922e6-1ae6-48c4-a41e-0f978326000dSP1975060918", ""));
hs.setActive(true);
myHealthcareServiceDao.update(hs);
Practitioner p = new Practitioner();
p.setId("prac-real");
Identifier identifier = new Identifier();
identifier.setSystem("http://hl7.org/fhir/sid/us-npi");
identifier.setValue("1234567890");
p.setActive(true);
p.setGender(Enumerations.AdministrativeGender.MALE);
p.addIdentifier(identifier);
myPractitionerDao.update(p);
{
for (int i = 0; i < 5; i++) {
PractitionerRole pr = new PractitionerRole();
pr.setId("ref" + i + 1 + "-prac-loc-hcs");
pr.setMeta(new Meta().addTag("http://www.smilecdr.com/custom_tag/uuid",
"51f922e6-1ae6-48c4-a41e-0f978326000dSP1975060918", ""));
pr.setPractitioner(new Reference("Practitioner/prac-real"));
pr.addLocation(new Reference("Location/loc-real"));
pr.addHealthcareService(new Reference("HealthcareService/hs-real"));
myPractitionerRoleDao.create(pr, mySrd).getId().toUnqualifiedVersionless().getValue();
}
}
SearchParameterMap spMap;
List<IBaseResource> actual;
spMap = SearchParameterMap.newSynchronous();
spMap.add(Constants.PARAM_TAG, new TokenParam("51f922e6-1ae6-48c4-a41e-0f978326000dSP1975060918"));
spMap.add(Constants.PARAM_FILTER, new StringParam("service.isplaceholder eq false or organization.isplaceholder eq false or practitioner.isplaceholder eq false or location.isplaceholder eq false"));
spMap.setOffset(0);
IBundleProvider search = myPractitionerRoleDao.search(spMap);
actual = search.getResources(0, 100);
assertEquals(5, actual.size());
}
}

71
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
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@ -34,6 +34,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
@ -83,6 +84,7 @@ import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.MolecularSequence;
@ -133,6 +135,7 @@ import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.MatcherAssert.assertThat;
@ -336,7 +339,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
}
@Tag("intermittent")
@Tag("intermittent")
// @Test
public void testTermConceptReindexingDoesntDuplicateData() {
myDaoConfig.setSchedulingDisabled(true);
@ -4260,6 +4263,72 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
assertNotEquals(uuid, results.getUuid());
}
@Test
public void testSearchWithReverseChainingAndOffset() {
int amountOfPatients = 5;
{
for (int i = 0; i < amountOfPatients; i++) {
Patient p = new Patient();
p.setActive(true);
String pid = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless().getValue();
for (int j = 0; j < 20; j++) {
Observation o = new Observation();
o.setSubject(new Reference().setReference(pid));
o.setCode(new CodeableConcept().addCoding(new Coding().setCode("sample")));
myObservationDao.create(o, mySrd);
}
}
}
SearchParameterMap spMap;
List<IBaseResource> actual;
spMap = SearchParameterMap.newSynchronous();
spMap.add(PARAM_HAS, new HasParam("Observation", "patient", "code", "sample"));
spMap.setOffset(0);
spMap.setCount(5);
IBundleProvider search = myPatientDao.search(spMap);
actual = search.getResources(0, 100);
assertEquals(amountOfPatients, actual.size());
}
@Test
public void testSearchWithReverseChainingOffsetAndSort() {
int amountOfPatients = 5;
String[] namesNotInAlpha = {"Charlie", "Tim", "Adam", "Dan", "Bob"};
String[] namesInAlpha = {"Adam", "Bob", "Charlie", "Dan", "Tim"};
{
for (int i = 0; i < amountOfPatients; i++) {
Patient p = new Patient();
p.setActive(true);
p.addName(new HumanName().addGiven(namesNotInAlpha[i]));
String pid = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless().getValue();
for (int j = 0; j < 20; j++) {
Observation o = new Observation();
o.setSubject(new Reference().setReference(pid));
o.setCode(new CodeableConcept().addCoding(new Coding().setCode("sample")));
myObservationDao.create(o, mySrd);
}
}
}
SearchParameterMap spMap;
List<IBaseResource> actual;
spMap = SearchParameterMap.newSynchronous();
spMap.add(PARAM_HAS, new HasParam("Observation", "patient", "code", "sample"));
spMap.setOffset(0);
spMap.setCount(5);
spMap.setSort(new SortSpec(Patient.SP_GIVEN));
IBundleProvider search = myPatientDao.search(spMap);
actual = search.getResources(0, 100);
List<String> actualNameList = actual.stream().map((resource) -> ((Patient) resource).getName().get(0).getGiven().get(0).toString()).toList();
ourLog.info("Results: {}", actualNameList);
assertEquals(amountOfPatients, actual.size());
assertThat(actualNameList, contains(namesInAlpha));
}
public static void assertConflictException(String theResourceType, ResourceVersionConflictException e) {
assertThat(e.getMessage(), matchesPattern(
Msg.code(550) + Msg.code(515) + "Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource " + theResourceType + "/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+"));