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Disallow matching a resource to more than one golden record (#4344) 

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto 2022-12-08 12:26:05 -05:00 committed by GitHub
parent f4ce765122
commit c7d991c345
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7 changed files with 266 additions and 8 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4156-mdm-one-source-resource-can-be-matched-to-multimple-golden-resources.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 4156
title: "Before multiple MDM `POSSIBLE_MATCH` links pointing to different Golden Resources could be accepted (updated to `MATCH`).
This has now been fixed, allowing only one MATCH."

42
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImpl.java
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@ -21,14 +21,13 @@ package ca.uhn.fhir.jpa.mdm.svc;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
import ca.uhn.fhir.jpa.mdm.util.MdmPartitionHelper;
import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
@ -47,6 +46,7 @@ import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
@ -61,8 +61,6 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
@Autowired
MdmLinkDaoSvc myMdmLinkDaoSvc;
@Autowired
IMdmLinkSvc myMdmLinkSvc;
@Autowired
MdmResourceDaoSvc myMdmResourceDaoSvc;
@Autowired
MdmMatchLinkSvc myMdmMatchLinkSvc;
@ -83,17 +81,20 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
validateUpdateLinkRequest(theGoldenResource, theSourceResource, theMatchResult, sourceType);
ResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
ResourcePersistentId targetId = myIdHelperService.getPidOrThrowException(theSourceResource);
ResourcePersistentId sourceResourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
// check if the golden resource and the source resource are in the same partition, throw error if not
myMdmPartitionHelper.validateResourcesInSamePartition(theGoldenResource, theSourceResource);
Optional<? extends IMdmLink> optionalMdmLink = myMdmLinkDaoSvc.getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourceId, targetId);
if (!optionalMdmLink.isPresent()) {
Optional<? extends IMdmLink> optionalMdmLink = myMdmLinkDaoSvc.getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourceId, sourceResourceId);
if (optionalMdmLink.isEmpty()) {
throw new InvalidRequestException(Msg.code(738) + myMessageHelper.getMessageForNoLink(theGoldenResource, theSourceResource));
}
IMdmLink mdmLink = optionalMdmLink.get();
validateNoMatchPresentWhenAcceptingPossibleMatch(theSourceResource, goldenResourceId, theMatchResult);
if (mdmLink.getMatchResult() == theMatchResult) {
ourLog.warn("MDM Link for " + theGoldenResource.getIdElement().toVersionless() + ", " + theSourceResource.getIdElement().toVersionless() + " already has value " + theMatchResult + ". Nothing to do.");
return theGoldenResource;
@ -124,6 +125,31 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
return theGoldenResource;
}
/**
* When updating POSSIBLE_MATCH link to a MATCH we need to validate that a MATCH to a different golden resource
* doesn't exist, because a resource mustn't be a MATCH to more than one golden resource
*/
private void validateNoMatchPresentWhenAcceptingPossibleMatch(IAnyResource theSourceResource,
ResourcePersistentId theGoldenResourceId, MdmMatchResultEnum theMatchResult) {
// if theMatchResult != MATCH, we are not accepting POSSIBLE_MATCH so there is nothing to validate
if (theMatchResult != MdmMatchResultEnum.MATCH) { return; }
ResourcePersistentId sourceResourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
List<? extends IMdmLink> mdmLinks = myMdmLinkDaoSvc
.getMdmLinksBySourcePidAndMatchResult(sourceResourceId, MdmMatchResultEnum.MATCH);
// if a link for a different golden resource exists, throw an exception
for (IMdmLink mdmLink : mdmLinks) {
if (mdmLink.getGoldenResourcePersistenceId() != theGoldenResourceId) {
IAnyResource existingGolden = myMdmResourceDaoSvc.readGoldenResourceByPid(mdmLink.getGoldenResourcePersistenceId(), mdmLink.getMdmSourceType());
throw new InvalidRequestException(Msg.code(2218) +
myMessageHelper.getMessageForAlreadyAcceptedLink(existingGolden, theSourceResource));
}
}
}
private void validateUpdateLinkRequest(IAnyResource theGoldenRecord, IAnyResource theSourceResource, MdmMatchResultEnum theMatchResult, String theSourceType) {
String goldenRecordType = myFhirContext.getResourceType(theGoldenRecord);
@ -162,7 +188,7 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
ResourcePersistentId targetId = myIdHelperService.getPidOrThrowException(theTargetGoldenResource);
Optional<? extends IMdmLink> oMdmLink = myMdmLinkDaoSvc.getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourceId, targetId);
if (!oMdmLink.isPresent()) {
if (oMdmLink.isEmpty()) {
throw new InvalidRequestException(Msg.code(745) + "No link exists between " + theGoldenResource.getIdElement().toVersionless() + " and " + theTargetGoldenResource.getIdElement().toVersionless());
}

119
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImplIT.java Normal file
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@ -0,0 +1,119 @@
package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.MessageHelper;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.util.ResourceUtils;
import java.io.File;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.List;
import java.util.Optional;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
class MdmLinkUpdaterSvcImplIT extends BaseMdmR4Test {
public static final String TEST_RSC_PATH = "mdm/mdm-link-update/";
public static final String Patient_A_JSON_PATH = TEST_RSC_PATH + "patient-A.json/";
public static final String Patient_B_JSON_PATH = TEST_RSC_PATH + "patient-B.json/";
public static final String Patient_C_JSON_PATH = TEST_RSC_PATH + "patient-C.json/";
@Autowired
private IMdmLinkUpdaterSvc myMdmLinkUpdaterSvc;
@Autowired
private MdmResourceDaoSvc myMdmResourceDaoSvc;
@Autowired
private MessageHelper myMessageHelper;
@Test
void testUpdateLinkToMatchWhenAnotherLinkToDifferentGoldenExistsMustFail() throws Exception {
// create Patient A -> MATCH GR A
Patient patientA = createPatientFromJsonInputFile(Patient_A_JSON_PATH);
// create Patient B -> MATCH GR B
Patient patientB = createPatientFromJsonInputFile(Patient_B_JSON_PATH);
Patient goldenA = getGoldenFor(patientA);
Patient goldenB = getGoldenFor(patientB);
// create Patient C -> no MATCH link. Only POSSIBLE_MATCH GR A and POSSIBLE_MATCH GR B and
Patient patientC = createPatientFromJsonInputFileWithPossibleMatches( List.of(goldenA, goldenB) );
MdmTransactionContext mdmTransactionContext = getPatientUpdateLinkContext();
// update POSSIBLE_MATCH Patient C -> GR A to MATCH (should work OK)
myMdmLinkUpdaterSvc.updateLink(goldenA, patientC, MdmMatchResultEnum.MATCH, mdmTransactionContext);
// update POSSIBLE_MATCH Patient C -> GR B to MATCH (should throw exception)
InvalidRequestException thrown = assertThrows(InvalidRequestException.class,
() -> myMdmLinkUpdaterSvc.updateLink(goldenB, patientC, MdmMatchResultEnum.MATCH, mdmTransactionContext));
String expectedExceptionMessage = Msg.code(2218) + myMessageHelper.getMessageForAlreadyAcceptedLink(goldenA, patientC);
assertEquals(expectedExceptionMessage, thrown.getMessage());
}
private Patient createPatientFromJsonInputFileWithPossibleMatches(List<Patient> theGoldens) throws Exception {
Patient patient = createPatientFromJsonInputFile(Patient_C_JSON_PATH, false);
for (Patient golden : theGoldens) {
myMdmLinkDaoSvc.createOrUpdateLinkEntity(golden, patient, MdmMatchOutcome.POSSIBLE_MATCH, MdmLinkSourceEnum.AUTO, new MdmTransactionContext());
}
return patient;
}
private MdmTransactionContext getPatientUpdateLinkContext() {
MdmTransactionContext ctx = new MdmTransactionContext();
ctx.setRestOperation(MdmTransactionContext.OperationType.UPDATE_LINK);
ctx.setResourceType("Patient");
return ctx;
}
private Patient getGoldenFor(Patient thePatient) {
Optional<? extends IMdmLink> patientALink = myMdmLinkDaoSvc.findMdmLinkBySource(thePatient);
assertTrue(patientALink.isPresent());
Patient golden = (Patient) myMdmResourceDaoSvc.readGoldenResourceByPid(patientALink.get().getGoldenResourcePersistenceId(), "Patient");
assertNotNull(golden);
return golden;
}
private Patient createPatientFromJsonInputFile(String thePath) throws Exception {
return createPatientFromJsonInputFile(thePath, true);
}
private Patient createPatientFromJsonInputFile(String thePath, boolean theCreateGolden) throws Exception {
File jsonInputUrl = ResourceUtils.getFile(ResourceUtils.CLASSPATH_URL_PREFIX + thePath);
String jsonPatient = Files.readString(Paths.get(jsonInputUrl.toURI()), StandardCharsets.UTF_8);
Patient patient = (Patient) myFhirContext.newJsonParser().parseResource(jsonPatient);
DaoMethodOutcome daoOutcome = myPatientDao.create(patient, new SystemRequestDetails());
if (theCreateGolden) {
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient, createContextForCreate("Patient"));
}
return (Patient) daoOutcome.getResource();
}
}

33
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/mdm-link-update/patient-A.json Normal file
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@ -0,0 +1,33 @@
{
"resourceType": "Patient",
"meta": {
"tag": [{
"system" : "http://acme.org/codes",
"code" : "tagA02"
}]
},
"identifier": [ {
"system": "urn:oid:1.2.36.146.595.217.0.1",
"value": "Pabc"
} ],
"name": [ {
"family": "Conde",
"given": [ "Carlos" ]
} ],
"gender": "male",
"birthDate": "1974-01-01",
"address": [ {
"line": [ "534 Erewhon St" ],
"city": "PleasantVille",
"state": "Vic",
"postalCode": "3999"
} ],
"telecom": [
{
"system": "phone",
"value": "(416) 555 1234",
"use": "home",
"rank": 1
}
]
}

33
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/mdm-link-update/patient-B.json Normal file
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@ -0,0 +1,33 @@
{
"resourceType": "Patient",
"meta": {
"tag": [{
"system" : "http://acme.org/codes",
"code" : "tagA02"
}]
},
"identifier": [ {
"system": "urn:oid:1.2.36.146.595.217.0.1",
"value": "Pabc"
} ],
"name": [ {
"family": "Conde",
"given": [ "Carlos" ]
} ],
"gender": "male",
"birthDate": "1974-02-10",
"address": [ {
"line": [ "534 Erewhon St" ],
"city": "PleasantVille",
"state": "Vic",
"postalCode": "3999"
} ],
"telecom": [
{
"system": "phone",
"value": "(416) 666 5678",
"use": "home",
"rank": 1
}
]
}

33
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/mdm-link-update/patient-C.json Normal file
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@ -0,0 +1,33 @@
{
"resourceType": "Patient",
"meta": {
"tag": [{
"system" : "http://acme.org/codes",
"code" : "tagA02"
}]
},
"identifier": [ {
"system": "urn:oid:1.2.36.146.595.217.0.1",
"value": "Pabc"
} ],
"name": [ {
"family": "Conde",
"given": [ "Carlos" ]
} ],
"gender": "male",
"birthDate": "1974-02-10",
"address": [ {
"line": [ "534 Erewhon St" ],
"city": "PleasantVille",
"state": "Vic",
"postalCode": "3999"
} ],
"telecom": [
{
"system": "phone",
"value": "(416) 555 1234",
"use": "home",
"rank": 1
}
]
}

9
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/MessageHelper.java
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@ -91,6 +91,15 @@ public class MessageHelper {
return "No link exists between " + theGoldenRecord + " and " + theSourceResource;
}
public String getMessageForAlreadyAcceptedLink(IAnyResource theGoldenRecord, IAnyResource theSourceResource) {
return getMessageForAlreadyAcceptedLink(theGoldenRecord.getIdElement().toVersionless().toString(),
theSourceResource.getIdElement().toVersionless().toString());
}
public String getMessageForAlreadyAcceptedLink(String theGoldenId, String theSourceId) {
return "A match with a different golden resource (" + theGoldenId + ") exists for resource " + theSourceId;
}
public String getMessageForPresentLink(IAnyResource theGoldenRecord, IAnyResource theSourceResource) {
return getMessageForPresentLink(theGoldenRecord.getIdElement().toVersionless().toString(),
theSourceResource.getIdElement().toVersionless().toString());