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Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625) 

* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation
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volodymyr-korzh 2024-01-26 08:49:12 -07:00 committed by GitHub
parent 1441a90a9f
commit 224e569317
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6 changed files with 178 additions and 32 deletions
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7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5619-fix-auto-version-reference-for-conditional-update-with-id-placeholder.yaml Normal file
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@ -0,0 +1,7 @@
---
type: fix
issue: 5619
jira: SMILE-7909
title: "Previously, when a transaction was posted with a resource that had placeholder references and auto versioning
references enabled for that path, if the target resource was included in the Bundle but not modified, the reference was
saved with a version number that didn't exist. This has been fixed."

4
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
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@ -3379,7 +3379,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(8, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(7, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(6, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
@ -3462,7 +3462,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(8, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(2, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(6, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(5, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
}

109
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
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@ -380,17 +380,11 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
observation.getEncounter().setReference(encounter.getId()); // not versioned
builder.addTransactionCreateEntry(observation);
Bundle outcome = mySystemDao.transaction(mySrd, (Bundle) builder.getBundle());
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("200 OK", outcome.getEntry().get(0).getResponse().getStatus());
assertEquals("200 OK", outcome.getEntry().get(1).getResponse().getStatus());
assertEquals("201 Created", outcome.getEntry().get(2).getResponse().getStatus());
Bundle outcome = createAndValidateBundle((Bundle) builder.getBundle(),
List.of("200 OK", "200 OK", "201 Created"), List.of("2", "1", "1"));
IdType patientId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
IdType encounterId = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
IdType observationId = new IdType(outcome.getEntry().get(2).getResponse().getLocation());
assertEquals("2", patientId.getVersionIdPart());
assertEquals("1", encounterId.getVersionIdPart());
assertEquals("1", observationId.getVersionIdPart());
// Read back and verify that reference is now versioned
observation = myObservationDao.read(observationId);
@ -429,14 +423,10 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
builder.addTransactionCreateEntry(observation);
myCaptureQueriesListener.clear();
Bundle outcome = mySystemDao.transaction(mySrd, (Bundle) builder.getBundle());
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("200 OK", outcome.getEntry().get(0).getResponse().getStatus());
assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
Bundle outcome = createAndValidateBundle((Bundle) builder.getBundle(),
List.of("200 OK", "201 Created"), List.of("3", "1"));
IdType patientId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
IdType observationId = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
assertEquals("3", patientId.getVersionIdPart());
assertEquals("1", observationId.getVersionIdPart());
// Make sure we're not introducing any extra DB operations
assertEquals(3, myCaptureQueriesListener.logSelectQueries().size());
@ -468,14 +458,10 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
myCaptureQueriesListener.clear();
Bundle outcome = mySystemDao.transaction(mySrd, (Bundle) builder.getBundle());
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("200 OK", outcome.getEntry().get(0).getResponse().getStatus());
assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
Bundle outcome = createAndValidateBundle((Bundle) builder.getBundle(),
List.of("200 OK", "201 Created"), List.of("3", "1"));
IdType patientId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
IdType observationId = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
assertEquals("3", patientId.getVersionIdPart());
assertEquals("1", observationId.getVersionIdPart());
// Make sure we're not introducing any extra DB operations
assertEquals(4, myCaptureQueriesListener.logSelectQueries().size());
@ -563,20 +549,91 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
BundleBuilder builder = new BundleBuilder(myFhirContext);
builder.addTransactionCreateEntry(messageHeader);
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(builder.getBundle()));
Bundle outcome = mySystemDao.transaction(mySrd, (Bundle) builder.getBundle());
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("201 Created", outcome.getEntry().get(0).getResponse().getStatus());
Bundle outcome = createAndValidateBundle((Bundle) builder.getBundle(),
List.of("201 Created"), List.of("1"));
IdType messageHeaderId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
assertEquals("2", patient.getIdElement().getVersionIdPart());
assertEquals("1", messageHeaderId.getVersionIdPart());
// read back and verify that reference is versioned
messageHeader = myMessageHeaderDao.read(messageHeaderId);
assertEquals(patient.getIdElement().getValue(), messageHeader.getFocus().get(0).getReference());
}
@Test
@DisplayName("#5619 Incorrect version of auto versioned reference for conditional update with urn id placeholder")
public void testInsertVersionedReferencesByPath_conditionalUpdateNoOpInTransaction_addsCorrectVersionToReference() {
Supplier<Bundle> supplier = () -> {
// create patient
Patient patient = new Patient();
patient.setActive(true);
patient.addIdentifier().setSystem("http://example.com").setValue("test");
// add patient to the Bundle - conditional update with placeholder url
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle.addEntry()
.setResource(patient)
.setFullUrl("urn:uuid:00001")
.getRequest()
.setMethod(Bundle.HTTPVerb.PUT)
.setUrl("Patient?identifier=http://example.com|test");
// create MessageHeader
MessageHeader messageHeader = new MessageHeader();
messageHeader.getMeta().setExtension(messageHeaderAutoVersionExtension);
// add reference
messageHeader.addFocus().setReference("urn:uuid:00001");
bundle.addEntry()
.setResource(messageHeader)
.getRequest()
.setMethod(Bundle.HTTPVerb.POST)
.setUrl("/MessageHeader");
return bundle;
};
// create bundle first time
Bundle outcome = createAndValidateBundle(supplier.get(),
List.of("201 Created", "201 Created"), List.of("1", "1"));
IdType patientId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
IdType messageHeaderId = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
// read back and verify that reference is versioned and correct
Patient patient = myPatientDao.read(patientId);
MessageHeader messageHeader = myMessageHeaderDao.read(messageHeaderId);
assertEquals(patient.getIdElement().getValue(), messageHeader.getFocus().get(0).getReference());
// create bundle second time
outcome = createAndValidateBundle(supplier.get(), List.of("200 OK", "201 Created"), List.of("1", "1"));
patientId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
messageHeaderId = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
// read back and verify that reference is versioned and correct
patient = myPatientDao.read(patientId);
messageHeader = myMessageHeaderDao.read(messageHeaderId);
assertEquals(patient.getIdElement().getValue(), messageHeader.getFocus().get(0).getReference());
}
private Bundle createAndValidateBundle(Bundle theBundle, List<String> theOutcomeStatuses,
List<String> theOutcomeVersions) {
assertEquals(theBundle.getEntry().size(), theOutcomeStatuses.size(),
"Size of OutcomeStatuses list is incorrect");
assertEquals(theBundle.getEntry().size(), theOutcomeVersions.size(),
"Size of OutcomeVersions list is incorrect");
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(theBundle));
Bundle result = mySystemDao.transaction(mySrd, theBundle);
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(theBundle));
for (int i = 0; i < result.getEntry().size(); i++) {
assertEquals(theOutcomeStatuses.get(i), result.getEntry().get(i).getResponse().getStatus());
IIdType resultId = new IdType(result.getEntry().get(i).getResponse().getLocation());
assertEquals(theOutcomeVersions.get(i), resultId.getVersionIdPart());
}
return result;
}
private Patient createAndUpdatePatient(String thePatientId) {
Patient patient = new Patient();
patient.setId(thePatientId);

5
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
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@ -1806,10 +1806,7 @@ public abstract class BaseTransactionProcessor {
theDaoMethodOutcome.setId(newId);
IIdType target = theIdSubstitutions.getForSource(newId);
if (target != null) {
target.setValue(newId.getValue());
}
theIdSubstitutions.updateTargets(newId);
if (theDaoMethodOutcome.getOperationOutcome() != null) {
IBase responseEntry = entriesToProcess.getResponseBundleEntryWithVersionlessComparison(newId);

17
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/IdSubstitutionMap.java
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@ -27,6 +27,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;
public class IdSubstitutionMap {
@ -87,6 +88,22 @@ public class IdSubstitutionMap {
return myMap.isEmpty();
}
/**
* Updates all targets of the map with a new id value if the input id has
* the same ResourceType and IdPart as the target id.
*/
public void updateTargets(IIdType theNewId) {
if (theNewId == null) {
return;
}
String newUnqualifiedVersionLessId = theNewId.toUnqualifiedVersionless().getValue();
entrySet().stream()
.map(Pair::getValue)
.filter(targetId ->
Objects.equals(targetId.toUnqualifiedVersionless().getValue(), newUnqualifiedVersionLessId))
.forEach(targetId -> targetId.setValue(theNewId.getValue()));
}
private static class Entry {
private final String myUnversionedId;

68
hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/dao/IdSubstitutionMapTest.java Normal file
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@ -0,0 +1,68 @@
package ca.uhn.fhir.jpa.dao;
import org.hl7.fhir.r4.model.IdType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.junit.jupiter.MockitoExtension;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ExtendWith(MockitoExtension.class)
public class IdSubstitutionMapTest {
private IdSubstitutionMap idSubstitutions;
@BeforeEach
void setUp() {
idSubstitutions = new IdSubstitutionMap();
}
@ParameterizedTest
@CsvSource({
"Patient/123/_history/3, Patient/123/_history/2",
"Patient/123/_history/3, Patient/123"
})
void testUpdateTargets_inputMatchesTarget_onlyMatchedTargetUpdated(String theInputId, String theTargetId) {
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType(theTargetId));
idSubstitutions.put(new IdType("urn:uuid:5000"), new IdType("Patient/5000"));
idSubstitutions.put(new IdType("urn:uuid:6000"), new IdType("Patient/6000_history/3"));
idSubstitutions.updateTargets(new IdType(theInputId));
assertEquals(theInputId, idSubstitutions.getForSource("urn:uuid:1234").getValue());
assertEquals("Patient/5000", idSubstitutions.getForSource("urn:uuid:5000").getValue());
assertEquals("Patient/6000_history/3", idSubstitutions.getForSource("urn:uuid:6000").getValue());
}
@Test
void testUpdateTargets_inputMatchesAllTargets_allTargetsUpdated() {
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123/_history/1"));
idSubstitutions.put(new IdType("urn:uuid:5000"), new IdType("Patient/123/_history/2"));
idSubstitutions.put(new IdType("urn:uuid:6000"), new IdType("Patient/123/_history/4"));
idSubstitutions.updateTargets(new IdType("Patient/123/_history/3"));
assertEquals("Patient/123/_history/3", idSubstitutions.getForSource("urn:uuid:1234").getValue());
assertEquals("Patient/123/_history/3", idSubstitutions.getForSource("urn:uuid:5000").getValue());
assertEquals("Patient/123/_history/3", idSubstitutions.getForSource("urn:uuid:6000").getValue());
}
@ParameterizedTest
@ValueSource(strings = {"Patient/124", "Patient/124/_history/3", "Patient", ""})
void testUpdateTargets_noMatchingTarget_noUpdate(String theInputId) {
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123/_history/3"));
idSubstitutions.updateTargets(new IdType(theInputId));
assertEquals("Patient/123/_history/3", idSubstitutions.getForSource("urn:uuid:1234").getValue());
}
@Test
void testUpdateTargets_nullInputId_noExceptionAndNoUpdate() {
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123/_history/3"));
idSubstitutions.updateTargets(null);
assertEquals("Patient/123/_history/3", idSubstitutions.getForSource("urn:uuid:1234").getValue());
}
}