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Ensure that source resource type of Provenance is also excluded from the $everything linkage. (#4692)

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Luke deGruchy 2023-03-28 10:41:24 -04:00 committed by GitHub
parent b2c0a48915
commit 479e412786
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4691-everything-two-patients-linked-by-provenance-and-composition.yaml Normal file
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@ -0,0 +1,5 @@
---
type: change
issue: 4691
title: "When calling $everything on a Patient instance, the jpa server no longer traverses into other patients.
Previously it was possible to pull in data from another patient for example, via Provenance and Composition resources."

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
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@ -1176,6 +1176,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
// (e.g. via Provenance, List, or Group) when in an $everything operation
if (myParams != null && myParams.getEverythingMode() == SearchParameterMap.EverythingModeEnum.PATIENT_INSTANCE) {
sqlBuilder.append(" AND r.myTargetResourceType != 'Patient'");
sqlBuilder.append(" AND r.mySourceResourceType != 'Provenance'");
}
String sql = sqlBuilder.toString();

50
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -99,6 +99,7 @@ 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.Composition;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.Coverage;
@ -3799,6 +3800,55 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
assertThat(ids, containsInAnyOrder(goodPid, oid, provid));
}
@Test
public void testEverythingDoesNotEnterSecondPatientLinkedByProvenanceAndComposition() {
final Patient desiredPatient = new Patient();
desiredPatient.setActive(true);
final String desiredPid = myPatientDao.create(desiredPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
final Patient notDesiredPatient = new Patient();
desiredPatient.setActive(true);
final String notDesiredPid = myPatientDao.create(notDesiredPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
final Observation desiredObservation = new Observation();
desiredObservation.getSubject().setReference(desiredPid);
desiredObservation.addIdentifier().setSystem("foo").setValue("1");
final String desiredObservationId = myObservationDao.create(desiredObservation, mySrd).getId().toUnqualifiedVersionless().getValue();
final Observation notDesiredObservation = new Observation();
notDesiredObservation.getSubject().setReference(notDesiredPid);
notDesiredObservation.addIdentifier().setSystem("foo").setValue("1");
final String notDesiredObservationId = myObservationDao.create(notDesiredObservation, mySrd).getId().toUnqualifiedVersionless().getValue();
final Composition composition = new Composition();
final Reference referenceToNotDesiredPatient = new Reference();
referenceToNotDesiredPatient.setReference(notDesiredPid);
composition.setSubject(referenceToNotDesiredPatient);
final String compositionId = myCompositionDao.create(composition, mySrd).getId().toUnqualifiedVersionless().getValue();
final Provenance desiredProvenance = new Provenance();
desiredProvenance.addTarget().setReference(desiredPid);
desiredProvenance.addTarget().setReference(compositionId);
final String desiredProvenanceId = myProvenanceDao.create(desiredProvenance, mySrd).getId().toUnqualifiedVersionless().getValue();
final Provenance notDesiredProvenance = new Provenance();
notDesiredProvenance.addTarget().setReference(notDesiredPid);
notDesiredProvenance.addTarget().setReference(compositionId);
final String notDesiredProvenanceId = myProvenanceDao.create(notDesiredProvenance, mySrd).getId().toUnqualifiedVersionless().getValue();
final Bundle response = myClient
.operation()
.onInstance(new IdType(desiredPid))
.named("everything")
.withNoParameters(Parameters.class)
.returnResourceType(Bundle.class)
.execute();
final List<String> actualResourceIds = toUnqualifiedVersionlessIdValues(response);
// We should not pick up other resources via the notDesiredProvenance
assertThat(actualResourceIds, containsInAnyOrder(desiredPid, desiredObservationId, desiredProvenanceId));
}
@Test
public void testIncludeRecurseFromProvenanceDoesTraverse() {
Patient goodPatient = new Patient();

4
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java
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@ -125,6 +125,7 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.Communication;
import org.hl7.fhir.r4.model.CommunicationRequest;
import org.hl7.fhir.r4.model.CompartmentDefinition;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
@ -380,6 +381,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Qualifier("myObservationDaoR4")
protected IFhirResourceDao<Observation> myObservationDao;
@Autowired
@Qualifier("myCompositionDaoR4")
protected IFhirResourceDao<Composition> myCompositionDao;
@Autowired
@Qualifier("myOperationDefinitionDaoR4")
protected IFhirResourceDao<OperationDefinition> myOperationDefinitionDao;
@Autowired