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Resolve 5336 Mdm Link History Would Fail If Provided with Unknown Ids On Postgres (#5337) 

* - Added checks in MdmLinkDaoJpaImpl to make sure no empty IN clauses are sent to database.
- Implemented tests for the above change.

* modified changelog
This commit is contained in:
TynerGjs 2023-09-27 15:01:45 -04:00 committed by GitHub
parent a2204654df
commit c3ff3dae82
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3 changed files with 210 additions and 4 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5336-mdm-link-history-would-fail-if-provided-with-unknown-ids-on-postgres.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 5336
jira: SMILE-7406
title: "Previously, on PostgreSQL, the $mdm-link-history operation would fail if all ids provided to a parameter are
unknown, and the error will persist for all subsequent requests. This is now fixed."

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkDaoJpaImpl.java
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@ -40,6 +40,7 @@ import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.ListUtils;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.Validate;
import org.hibernate.envers.AuditReader;
import org.hibernate.envers.RevisionType;
@ -371,21 +372,39 @@ public class MdmLinkDaoJpaImpl implements IMdmLinkDao<JpaPid, MdmLink> {
final AuditQueryCreator auditQueryCreator = myAuditReader.createQuery();
try {
final AuditCriterion goldenResourceIdCriterion = AuditEntity.property(GOLDEN_RESOURCE_PID_NAME)
.in(convertToLongIds(theMdmHistorySearchParameters.getGoldenResourceIds()));
final AuditCriterion resourceIdCriterion = AuditEntity.property(SOURCE_PID_NAME)
.in(convertToLongIds(theMdmHistorySearchParameters.getSourceIds()));
final AuditCriterion goldenResourceIdCriterion = buildAuditCriterionOrNull(
theMdmHistorySearchParameters.getGoldenResourceIds(), GOLDEN_RESOURCE_PID_NAME);
final AuditCriterion resourceIdCriterion =
buildAuditCriterionOrNull(theMdmHistorySearchParameters.getSourceIds(), SOURCE_PID_NAME);
final AuditCriterion goldenResourceAndOrResourceIdCriterion;
if (!theMdmHistorySearchParameters.getGoldenResourceIds().isEmpty()
&& !theMdmHistorySearchParameters.getSourceIds().isEmpty()) {
// Make sure the criterion does not contain empty IN clause, e.g. id IN (), which postgres (likely other
// sql servers) do not like. Directly return empty result instead.
if (ObjectUtils.anyNull(goldenResourceIdCriterion, resourceIdCriterion)) {
return new ArrayList<>();
}
goldenResourceAndOrResourceIdCriterion =
AuditEntity.and(goldenResourceIdCriterion, resourceIdCriterion);
} else if (!theMdmHistorySearchParameters.getGoldenResourceIds().isEmpty()) {
if (ObjectUtils.anyNull(goldenResourceIdCriterion)) {
return new ArrayList<>();
}
goldenResourceAndOrResourceIdCriterion = goldenResourceIdCriterion;
} else if (!theMdmHistorySearchParameters.getSourceIds().isEmpty()) {
if (ObjectUtils.anyNull(resourceIdCriterion)) {
return new ArrayList<>();
}
goldenResourceAndOrResourceIdCriterion = resourceIdCriterion;
} else {
throw new IllegalArgumentException(Msg.code(2298)
+ "$mdm-link-history Golden resource and source query IDs cannot both be empty.");
@ -420,6 +439,12 @@ public class MdmLinkDaoJpaImpl implements IMdmLinkDao<JpaPid, MdmLink> {
.collect(Collectors.toUnmodifiableList());
}
private AuditCriterion buildAuditCriterionOrNull(
List<IIdType> theMdmHistorySearchParameterIds, String theProperty) {
List<Long> longIds = convertToLongIds(theMdmHistorySearchParameterIds);
return longIds.isEmpty() ? null : AuditEntity.property(theProperty).in(longIds);
}
private MdmLinkWithRevision<MdmLink> buildRevisionFromObjectArray(Object[] theArray) {
final Object mdmLinkUncast = theArray[0];
final Object revisionUncast = theArray[1];

175
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvcTest.java
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@ -20,6 +20,8 @@ import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -276,6 +278,179 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
assertEquals(2, actualMdmLinkRevisions.size(), "Both Patient/p123 and Practitioner/p123 should be returned");
}
@ParameterizedTest
@ValueSource(strings = {"allUnknown", "someUnknown"})
public void testHistoryForUnknownIdsSourceIdOnly(String mode) {
// setup
final List<MdmLink> mdmLinksWithLinkedPatients1 = createMdmLinksWithLinkedPatients(MdmMatchResultEnum.MATCH, 3);
final List<MdmLink> mdmLinksWithLinkedPatients2 = createMdmLinksWithLinkedPatients(MdmMatchResultEnum.MATCH, 4);
MdmHistorySearchParameters mdmHistorySearchParameters = null;
List<MdmLinkWithRevision<MdmLink>> expectedMdLinkRevisions = null;
switch (mode) {
// $mdm-link-history?resourceId=Patient/unknown
case "allUnknown" -> {
mdmHistorySearchParameters = new MdmHistorySearchParameters().setSourceIds(List.of("unknown"));
expectedMdLinkRevisions = new ArrayList<>();
}
// $mdm-link-history?resourceId=Patient/1,Patient/2,Patient/unknown
case "someUnknown" -> {
List<String> resourceIdsWithSomeUnknown = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getSourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
resourceIdsWithSomeUnknown.add("unknown");
mdmHistorySearchParameters = new MdmHistorySearchParameters().setSourceIds(resourceIdsWithSomeUnknown);
final JpaPid goldenResourceId1 = mdmLinksWithLinkedPatients1.get(0).getGoldenResourcePersistenceId();
final JpaPid goldenResourceId2 = mdmLinksWithLinkedPatients2.get(0).getGoldenResourcePersistenceId();
final JpaPid sourceId1_1 = mdmLinksWithLinkedPatients1.get(0).getSourcePersistenceId();
final JpaPid sourceId2_1 = mdmLinksWithLinkedPatients2.get(0).getSourcePersistenceId();
expectedMdLinkRevisions = List.of(
buildMdmLinkWithRevision(1, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId1, sourceId1_1),
buildMdmLinkWithRevision(4, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId2, sourceId2_1)
);
}
}
// execute
final List<MdmLinkWithRevision<MdmLink>> actualMdmLinkRevisions = myMdmLinkDaoSvc.findMdmLinkHistory(mdmHistorySearchParameters);
// verify
assert expectedMdLinkRevisions != null;
assertMdmRevisionsEqual(expectedMdLinkRevisions, actualMdmLinkRevisions);
}
@ParameterizedTest
@ValueSource(strings = {"allUnknown", "someUnknown"})
public void testHistoryForUnknownIdsGoldenResourceIdOnly(String mode) {
// setup
final List<MdmLink> mdmLinksWithLinkedPatients1 = createMdmLinksWithLinkedPatients(MdmMatchResultEnum.MATCH, 3);
final List<MdmLink> mdmLinksWithLinkedPatients2 = createMdmLinksWithLinkedPatients(MdmMatchResultEnum.MATCH, 4);
MdmHistorySearchParameters mdmHistorySearchParameters = null;
List<MdmLinkWithRevision<MdmLink>> expectedMdLinkRevisions = null;
switch (mode) {
// $mdm-link-history?goldenResourceId=Patient/unknown
case "allUnknown" -> {
mdmHistorySearchParameters = new MdmHistorySearchParameters().setGoldenResourceIds(List.of("unknown"));
expectedMdLinkRevisions = new ArrayList<>();
}
// $mdm-link-history?goldenResourceId=Patient/1,Patient/2,Patient/unknown
case "someUnknown" -> {
List<String> resourceIdsWithSomeUnknown = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getGoldenResourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
resourceIdsWithSomeUnknown.add("unknown");
mdmHistorySearchParameters = new MdmHistorySearchParameters().setGoldenResourceIds(resourceIdsWithSomeUnknown);
final JpaPid goldenResourceId1 = mdmLinksWithLinkedPatients1.get(0).getGoldenResourcePersistenceId();
final JpaPid goldenResourceId2 = mdmLinksWithLinkedPatients2.get(0).getGoldenResourcePersistenceId();
final JpaPid sourceId1_1 = mdmLinksWithLinkedPatients1.get(0).getSourcePersistenceId();
final JpaPid sourceId1_2 = mdmLinksWithLinkedPatients1.get(1).getSourcePersistenceId();
final JpaPid sourceId1_3 = mdmLinksWithLinkedPatients1.get(2).getSourcePersistenceId();
final JpaPid sourceId2_1 = mdmLinksWithLinkedPatients2.get(0).getSourcePersistenceId();
final JpaPid sourceId2_2 = mdmLinksWithLinkedPatients2.get(1).getSourcePersistenceId();
final JpaPid sourceId2_3 = mdmLinksWithLinkedPatients2.get(2).getSourcePersistenceId();
final JpaPid sourceId2_4 = mdmLinksWithLinkedPatients2.get(3).getSourcePersistenceId();
expectedMdLinkRevisions = List.of(
buildMdmLinkWithRevision(1, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId1, sourceId1_1),
buildMdmLinkWithRevision(2, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId1, sourceId1_2),
buildMdmLinkWithRevision(3, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId1, sourceId1_3),
buildMdmLinkWithRevision(4, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId2, sourceId2_1),
buildMdmLinkWithRevision(5, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId2, sourceId2_2),
buildMdmLinkWithRevision(6, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId2, sourceId2_3),
buildMdmLinkWithRevision(7, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId2, sourceId2_4)
);
}
}
// execute
final List<MdmLinkWithRevision<MdmLink>> actualMdmLinkRevisions = myMdmLinkDaoSvc.findMdmLinkHistory(mdmHistorySearchParameters);
// verify
assert expectedMdLinkRevisions != null;
assertMdmRevisionsEqual(expectedMdLinkRevisions, actualMdmLinkRevisions);
}
@ParameterizedTest
@ValueSource(strings = {
"allUnknownSourceId",
"allUnknownGoldenId",
"allUnknownBoth",
"someUnknownSourceId",
"someUnknownGoldenId",
"someUnknownBoth"
})
public void testHistoryForUnknownIdsBothSourceAndGoldenResourceId(String mode) {
// setup
final List<MdmLink> mdmLinksWithLinkedPatients1 = createMdmLinksWithLinkedPatients(MdmMatchResultEnum.MATCH, 3);
final List<MdmLink> mdmLinksWithLinkedPatients2 = createMdmLinksWithLinkedPatients(MdmMatchResultEnum.MATCH, 4);
MdmHistorySearchParameters mdmHistorySearchParameters = null;
final JpaPid goldenResourceId1 = mdmLinksWithLinkedPatients1.get(0).getGoldenResourcePersistenceId();
final JpaPid goldenResourceId2 = mdmLinksWithLinkedPatients2.get(0).getGoldenResourcePersistenceId();
final JpaPid sourceId1_1 = mdmLinksWithLinkedPatients1.get(0).getSourcePersistenceId();
final JpaPid sourceId2_1 = mdmLinksWithLinkedPatients2.get(0).getSourcePersistenceId();
List<MdmLinkWithRevision<MdmLink>> expectedMdLinkRevisions = List.of(
buildMdmLinkWithRevision(1, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId1, sourceId1_1),
buildMdmLinkWithRevision(4, RevisionType.ADD, MdmMatchResultEnum.MATCH, goldenResourceId2, sourceId2_1)
);
switch (mode) {
// $mdm-link-history?resourceId=Patient/unknown&goldenResourceId=Patient/1,Patient/2
case "allUnknownSourceId" -> {
mdmHistorySearchParameters = new MdmHistorySearchParameters()
.setSourceIds(List.of("unknown"))
.setGoldenResourceIds(new ArrayList<>(getIdsFromMdmLinks(MdmLink::getGoldenResourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0))));
expectedMdLinkRevisions = new ArrayList<>();
}
// $mdm-link-history?resourceId=Patient/1,Patient/2&goldenResourceId=Patient/unknown
case "allUnknownGoldenId" -> {
mdmHistorySearchParameters = new MdmHistorySearchParameters()
.setSourceIds(new ArrayList<>(getIdsFromMdmLinks(MdmLink::getSourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0))))
.setGoldenResourceIds(List.of("unknown"));
expectedMdLinkRevisions = new ArrayList<>();
}
// $mdm-link-history?resourceId=Patient/unknown&goldenResourceId=Patient/unknownGolden
case "allUnknownBoth" -> {
mdmHistorySearchParameters = new MdmHistorySearchParameters()
.setSourceIds(List.of("unknown"))
.setGoldenResourceIds(List.of("unknownGolden"));
expectedMdLinkRevisions = new ArrayList<>();
}
// $mdm-link-history?resourceId=Patient/1,Patient/2,Patient/unknown&goldenResourceId=Patient/3,Patient/4
case "someUnknownSourceId" -> {
List<String> sourceIdsWithSomeUnknown = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getSourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
sourceIdsWithSomeUnknown.add("unknown");
List<String> goldenResourceIds = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getGoldenResourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
mdmHistorySearchParameters = new MdmHistorySearchParameters()
.setSourceIds(sourceIdsWithSomeUnknown)
.setGoldenResourceIds(goldenResourceIds);
}
// $mdm-link-history?resourceId=Patient/1,Patient/2&goldenResourceId=Patient/3,Patient/4,Patient/unknown
case "someUnknownGoldenId" -> {
List<String> sourceIds = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getSourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
List<String> goldenResourceIdsSomeUnknown = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getGoldenResourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
goldenResourceIdsSomeUnknown.add("unknown");
mdmHistorySearchParameters = new MdmHistorySearchParameters()
.setSourceIds(sourceIds)
.setGoldenResourceIds(goldenResourceIdsSomeUnknown);
}
// $mdm-link-history?resourceId=Patient/1,Patient/2,Patient/unknown&goldenResourceId=Patient/3,Patient/4,Patient/unknownGolden
case "someUnknownBoth" -> {
List<String> sourceIdsSomeUnknown = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getSourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
sourceIdsSomeUnknown.add("unknown");
List<String> goldenResourceIdsSomeUnknown = new ArrayList<>(getIdsFromMdmLinks(MdmLink::getGoldenResourcePersistenceId, mdmLinksWithLinkedPatients1.get(0), mdmLinksWithLinkedPatients2.get(0)));
goldenResourceIdsSomeUnknown.add("unknownGolden");
mdmHistorySearchParameters = new MdmHistorySearchParameters()
.setSourceIds(sourceIdsSomeUnknown)
.setGoldenResourceIds(goldenResourceIdsSomeUnknown);
}
}
// execute
final List<MdmLinkWithRevision<MdmLink>> actualMdmLinkRevisions = myMdmLinkDaoSvc.findMdmLinkHistory(mdmHistorySearchParameters);
// verify
assert expectedMdLinkRevisions != null;
assertMdmRevisionsEqual(expectedMdLinkRevisions, actualMdmLinkRevisions);
}
@Nonnull
private static List<String> getIdsFromMdmLinks(Function<MdmLink, JpaPid> getIdFunction, MdmLink... mdmLinks) {
return Arrays.stream(mdmLinks)