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Merge branch 'gg_20201105-remove-person-references' of github.com:jamesagnew/hapi-fhir into gg_20201105-remove-person-references

This commit is contained in:
Tadgh 2020-11-09 21:45:18 -05:00
parent d7974a6f1d 8efafa112a
commit 625744b23d
7 changed files with 265 additions and 206 deletions
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49
hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/dao/EmpiLinkDaoSvc.java
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@ -113,9 +113,8 @@ public class EmpiLinkDaoSvc {
/** /**
* Given a Target Pid, and a match result, return all links that match these criteria. * Given a Target Pid, and a match result, return all links that match these criteria.
* *
* @param theTargetPid the target of the relationship. * @param theTargetPid the target of the relationship.
* @param theMatchResult the Match Result of the relationship * @param theMatchResult the Match Result of the relationship
*
* @return a list of {@link EmpiLink} entities matching these criteria. * @return a list of {@link EmpiLink} entities matching these criteria.
*/ */
public List<EmpiLink> getEmpiLinksByTargetPidAndMatchResult(Long theTargetPid, EmpiMatchResultEnum theMatchResult) { public List<EmpiLink> getEmpiLinksByTargetPidAndMatchResult(Long theTargetPid, EmpiMatchResultEnum theMatchResult) {
@ -164,10 +163,9 @@ public class EmpiLinkDaoSvc {
/** /**
* Given a person a target and a match result, return the matching EmpiLink, if it exists. * Given a person a target and a match result, return the matching EmpiLink, if it exists.
* *
* @param thePersonPid The Pid of the Person in the relationship * @param thePersonPid The Pid of the Person in the relationship
* @param theTargetPid The Pid of the target in the relationship * @param theTargetPid The Pid of the target in the relationship
* @param theMatchResult The MatchResult you are looking for. * @param theMatchResult The MatchResult you are looking for.
*
* @return an Optional {@link EmpiLink} containing the matched link if it exists. * @return an Optional {@link EmpiLink} containing the matched link if it exists.
*/ */
public Optional<EmpiLink> getEmpiLinksByPersonPidTargetPidAndMatchResult(Long thePersonPid, Long theTargetPid, EmpiMatchResultEnum theMatchResult) { public Optional<EmpiLink> getEmpiLinksByPersonPidTargetPidAndMatchResult(Long thePersonPid, Long theTargetPid, EmpiMatchResultEnum theMatchResult) {
@ -216,7 +214,6 @@ public class EmpiLinkDaoSvc {
* Given a Person, return all links in which they are the source Person of the {@link EmpiLink} * Given a Person, return all links in which they are the source Person of the {@link EmpiLink}
* *
* @param thePersonResource The {@link IBaseResource} Person who's links you would like to retrieve. * @param thePersonResource The {@link IBaseResource} Person who's links you would like to retrieve.
*
* @return A list of all {@link EmpiLink} entities in which thePersonResource is the source Person. * @return A list of all {@link EmpiLink} entities in which thePersonResource is the source Person.
*/ */
public List<EmpiLink> findEmpiLinksBySourceResource(IBaseResource thePersonResource) { public List<EmpiLink> findEmpiLinksBySourceResource(IBaseResource thePersonResource) {
@ -254,7 +251,6 @@ public class EmpiLinkDaoSvc {
* for the Person resources which were the sources of the links. * for the Person resources which were the sources of the links.
* *
* @param theTargetType the type of relationship you would like to delete. * @param theTargetType the type of relationship you would like to delete.
*
* @return A list of longs representing the Pids of the Person resources used as the sources of the relationships that were deleted. * @return A list of longs representing the Pids of the Person resources used as the sources of the relationships that were deleted.
*/ */
public List<Long> deleteAllEmpiLinksOfTypeAndReturnPersonPids(String theTargetType) { public List<Long> deleteAllEmpiLinksOfTypeAndReturnPersonPids(String theTargetType) {
@ -269,7 +265,6 @@ public class EmpiLinkDaoSvc {
* Persist an EmpiLink to the database. * Persist an EmpiLink to the database.
* *
* @param theEmpiLink the link to save. * @param theEmpiLink the link to save.
*
* @return the persisted {@link EmpiLink} entity. * @return the persisted {@link EmpiLink} entity.
*/ */
public EmpiLink save(EmpiLink theEmpiLink) { public EmpiLink save(EmpiLink theEmpiLink) {
@ -285,19 +280,17 @@ public class EmpiLinkDaoSvc {
* Given an example {@link EmpiLink}, return all links from the database which match the example. * Given an example {@link EmpiLink}, return all links from the database which match the example.
* *
* @param theExampleLink The EmpiLink containing the data we would like to search for. * @param theExampleLink The EmpiLink containing the data we would like to search for.
*
* @return a list of {@link EmpiLink} entities which match the example. * @return a list of {@link EmpiLink} entities which match the example.
*/ */
public List<EmpiLink> findEmpiLinkByExample(Example<EmpiLink> theExampleLink) { public List<EmpiLink> findEmpiLinkByExample(Example<EmpiLink> theExampleLink) {
return myEmpiLinkDao.findAll(theExampleLink); return myEmpiLinkDao.findAll(theExampleLink);
} }
/** /**
* Given a target {@link IBaseResource}, return all {@link EmpiLink} entities in which this target is the target * Given a target {@link IBaseResource}, return all {@link EmpiLink} entities in which this target is the target
* of the relationship. This will show you all links for a given Patient/Practitioner. * of the relationship. This will show you all links for a given Patient/Practitioner.
* *
* @param theTargetResource the target resource to find links for. * @param theTargetResource the target resource to find links for.
*
* @return all links for the target. * @return all links for the target.
*/ */
public List<EmpiLink> findEmpiLinksByTarget(IBaseResource theTargetResource) { public List<EmpiLink> findEmpiLinksByTarget(IBaseResource theTargetResource) {
@ -316,7 +309,6 @@ public class EmpiLinkDaoSvc {
* of the relationship. * of the relationship.
* *
* @param theSourceResource the source resource to find links for. * @param theSourceResource the source resource to find links for.
*
* @return all links for the source. * @return all links for the source.
*/ */
public List<EmpiLink> findEmpiMatchLinksBySource(IBaseResource theSourceResource) { public List<EmpiLink> findEmpiMatchLinksBySource(IBaseResource theSourceResource) {
@ -333,9 +325,40 @@ public class EmpiLinkDaoSvc {
/** /**
* Factory delegation method, whenever you need a new EmpiLink, use this factory method. * Factory delegation method, whenever you need a new EmpiLink, use this factory method.
* //TODO Should we make the constructor private for EmpiLink? or work out some way to ensure they can only be instantiated via factory. * //TODO Should we make the constructor private for EmpiLink? or work out some way to ensure they can only be instantiated via factory.
*
* @return A new {@link EmpiLink}. * @return A new {@link EmpiLink}.
*/ */
public EmpiLink newEmpiLink() { public EmpiLink newEmpiLink() {
return myEmpiLinkFactory.newEmpiLink(); return myEmpiLinkFactory.newEmpiLink();
} }
// @Transactional
// public List<EmpiLink> deleteEmpiLinks(IAnyResource theSourceResource, IAnyResource theTargetResource) {
// Long sourceResourcePid = myIdHelperService.getPidOrNull(theSourceResource);
// if (sourceResourcePid == null) {
// if (ourLog.isDebugEnabled()) {
// ourLog.debug(String.format("Unable to find source resource for ID %s, no links deleted", sourceResourcePid));
// }
// return new ArrayList<>();
// }
//
// Long targetResourcePid = myIdHelperService.getPidOrNull(theSourceResource);
// if (targetResourcePid == null) {
// if (ourLog.isDebugEnabled()) {
// ourLog.debug(String.format("Unable to find target resource for ID %s, no links deleted", targetResourcePid));
// }
//
// return new ArrayList<>();
// }
//
// EmpiLink exampleLink = myEmpiLinkFactory
// .newEmpiLink()
// .setSourceResourcePid(sourceResourcePid)
// .setTargetPid(targetResourcePid);
//
// Example<EmpiLink> example = Example.of(exampleLink);
// List<EmpiLink> linksToDelete = myEmpiLinkDao.findAll(example);
// myEmpiLinkDao.deleteAll(linksToDelete);
// return linksToDelete;
// }
} }

10
hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/svc/EmpiLinkSvcImpl.java
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@ -124,12 +124,14 @@ public class EmpiLinkSvcImpl implements IEmpiLinkSvc {
} }
@Override @Override
public void deleteLink(IAnyResource theExistingPerson, IAnyResource theResource, EmpiTransactionContext theEmpiTransactionContext) { public void deleteLink(IAnyResource theSourceResource, IAnyResource theTargetResource, EmpiTransactionContext theEmpiTransactionContext) {
myPersonHelper.removeLink(theExistingPerson, theResource.getIdElement(), theEmpiTransactionContext); // myPersonHelper.removeLink(theExistingPerson, theResource.getIdElement(), theEmpiTransactionContext);
Optional<EmpiLink> oEmpiLink = getEmpiLinkForPersonTargetPair(theExistingPerson, theResource); // myEmpiLinkDaoSvc.deleteEmpiLinks(theSourceResource, theTargetResource);
Optional<EmpiLink> oEmpiLink = getEmpiLinkForPersonTargetPair(theSourceResource, theTargetResource);
if (oEmpiLink.isPresent()) { if (oEmpiLink.isPresent()) {
EmpiLink empiLink = oEmpiLink.get(); EmpiLink empiLink = oEmpiLink.get();
log(theEmpiTransactionContext, "Deleting EmpiLink [" + theExistingPerson.getIdElement().toVersionless() + " -> " + theResource.getIdElement().toVersionless() + "] with result: " + empiLink.getMatchResult()); log(theEmpiTransactionContext, "Deleting EmpiLink [" + theSourceResource.getIdElement().toVersionless() + " -> " + theTargetResource.getIdElement().toVersionless() + "] with result: " + empiLink.getMatchResult());
myEmpiLinkDaoSvc.deleteLink(empiLink); myEmpiLinkDaoSvc.deleteLink(empiLink);
} }
} }

25
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiMatchLinkSvcTest.java
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@ -7,6 +7,7 @@ import ca.uhn.fhir.empi.api.IEmpiLinkSvc;
import ca.uhn.fhir.empi.model.CanonicalEID; import ca.uhn.fhir.empi.model.CanonicalEID;
import ca.uhn.fhir.empi.util.EIDHelper; import ca.uhn.fhir.empi.util.EIDHelper;
import ca.uhn.fhir.empi.util.PersonHelper; import ca.uhn.fhir.empi.util.PersonHelper;
import ca.uhn.fhir.jpa.dao.data.IEmpiLinkDao;
import ca.uhn.fhir.jpa.empi.BaseEmpiR4Test; import ca.uhn.fhir.jpa.empi.BaseEmpiR4Test;
import ca.uhn.fhir.jpa.empi.dao.EmpiLinkDaoSvc; import ca.uhn.fhir.jpa.empi.dao.EmpiLinkDaoSvc;
import ca.uhn.fhir.jpa.entity.EmpiLink; import ca.uhn.fhir.jpa.entity.EmpiLink;
@ -52,6 +53,8 @@ public class EmpiMatchLinkSvcTest extends BaseEmpiR4Test {
private PersonHelper myPersonHelper; private PersonHelper myPersonHelper;
@Autowired @Autowired
private EmpiResourceDaoSvc myEmpiResourceDaoSvc; // TODO NG - remove? private EmpiResourceDaoSvc myEmpiResourceDaoSvc; // TODO NG - remove?
@Autowired
private IEmpiLinkDao myEmpiLinkDao;
@BeforeEach @BeforeEach
public void before() { public void before() {
@ -374,7 +377,7 @@ public class EmpiMatchLinkSvcTest extends BaseEmpiR4Test {
} }
@Test @Test
public void testWhenAllMatchResultsArePOSSIBLE_MATCHThattheyAreLinkedAndNoPersonIsCreated() { public void testWhenAllMatchResultsArePOSSIBLE_MATCHThattheyAreLinkedAndNoSourceREsourceIsCreated() {
/** /**
* CASE 4: Only POSSIBLE_MATCH outcomes -> In this case, empi-link records are created with POSSIBLE_MATCH * CASE 4: Only POSSIBLE_MATCH outcomes -> In this case, empi-link records are created with POSSIBLE_MATCH
* outcome and await manual assignment to either NO_MATCH or MATCHED. Person link is added. * outcome and await manual assignment to either NO_MATCH or MATCHED. Person link is added.
@ -384,15 +387,30 @@ public class EmpiMatchLinkSvcTest extends BaseEmpiR4Test {
patient = createPatientAndUpdateLinks(patient); patient = createPatientAndUpdateLinks(patient);
assertThat(patient, is(sameSourceResourceAs(patient))); assertThat(patient, is(sameSourceResourceAs(patient)));
System.out.println("Created patient");
print(patient);
Patient patient2 = buildJanePatient(); Patient patient2 = buildJanePatient();
patient2.getNameFirstRep().setFamily("pleasedonotmatchatall"); patient2.getNameFirstRep().setFamily("pleasedonotmatchatall");
patient2 = createPatientAndUpdateLinks(patient2); patient2 = createPatientAndUpdateLinks(patient2);
assertThat(patient2, is(possibleMatchWith(patient))); assertThat(patient2, is(possibleMatchWith(patient)));
System.out.println("Created patient2");
print(patient2);
myEmpiLinkDao.findAll().forEach(empiLink -> {
System.out.println(empiLink);
});
Patient patient3 = buildJanePatient(); Patient patient3 = buildJanePatient();
patient3.getNameFirstRep().setFamily("pleasedonotmatchatall"); patient3.getNameFirstRep().setFamily("pleasedonotmatchatall");
patient3 = createPatientAndUpdateLinks(patient3); patient3 = createPatientAndUpdateLinks(patient3);
System.out.println("Created patient3");
print(patient3);
myEmpiLinkDao.findAll().forEach(empiLink -> {
System.out.println(empiLink);
});
assertThat(patient3, is(possibleMatchWith(patient2))); assertThat(patient3, is(possibleMatchWith(patient2)));
assertThat(patient3, is(possibleMatchWith(patient))); assertThat(patient3, is(possibleMatchWith(patient)));
@ -552,10 +570,9 @@ public class EmpiMatchLinkSvcTest extends BaseEmpiR4Test {
System.out.println("Paul Before"); System.out.println("Paul Before");
print(paul); print(paul);
Patient pailTemp = paul;
paul = updatePatientAndUpdateLinks(paul); paul = updatePatientAndUpdateLinks(paul);
System.out.println("Paul After"); System.out.println("Paul After");
print(pailTemp); print(paul); // TODO NG - Paul after still has the EID - is it ok?
assertNoDuplicates(); assertNoDuplicates();

4
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiPersonMergerSvcTest.java
View File

@ -168,7 +168,7 @@ public class EmpiPersonMergerSvcTest extends BaseEmpiR4Test {
List<EmpiLink> links = getNonRedirectLinksByPerson(mergedSourcePatient); List<EmpiLink> links = getNonRedirectLinksByPerson(mergedSourcePatient);
assertEquals(1, links.size()); assertEquals(1, links.size());
assertThat(mergedSourcePatient, is(possibleLinkedTo(myTargetPatient1))); assertThat(mergedSourcePatient, is(possibleLinkedTo(myTargetPatient1)));
assertEquals(1, myToSourcePatient.getLink().size()); fail("FIXME");
} }
@Test @Test
@ -179,7 +179,7 @@ public class EmpiPersonMergerSvcTest extends BaseEmpiR4Test {
List<EmpiLink> links = getNonRedirectLinksByPerson(mergedSourcePatient); List<EmpiLink> links = getNonRedirectLinksByPerson(mergedSourcePatient);
assertEquals(1, links.size()); assertEquals(1, links.size());
assertThat(mergedSourcePatient, is(possibleLinkedTo(myTargetPatient1))); assertThat(mergedSourcePatient, is(possibleLinkedTo(myTargetPatient1)));
assertEquals(1, myToSourcePatient.getLink().size()); fail("FIXME");
} }
@Test @Test

253
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/util/PersonHelper.java
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@ -26,6 +26,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum; import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition; import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.empi.api.EmpiConstants; import ca.uhn.fhir.empi.api.EmpiConstants;
import ca.uhn.fhir.empi.api.IEmpiLinkQuerySvc;
import ca.uhn.fhir.empi.api.IEmpiSettings; import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.log.Logs; import ca.uhn.fhir.empi.log.Logs;
import ca.uhn.fhir.empi.model.CanonicalEID; import ca.uhn.fhir.empi.model.CanonicalEID;
@ -76,6 +77,8 @@ public class PersonHelper {
@Autowired @Autowired
private EIDHelper myEIDHelper; private EIDHelper myEIDHelper;
private IEmpiLinkQuerySvc queyr;
private final FhirContext myFhirContext; private final FhirContext myFhirContext;
@Autowired @Autowired
@ -83,87 +86,87 @@ public class PersonHelper {
myFhirContext = theFhirContext; myFhirContext = theFhirContext;
} }
/** // /**
* Given a Person, extract all {@link IIdType}s for the linked targets. // * Given a source resource, extract all {@link IIdType}s for the linked targets.
* // *
* @param thePerson the Person to extract link IDs from. // * @param theSourceResource the source resource to extract link IDs from.
* @return a Stream of {@link IIdType}. // * @return a Stream of {@link IIdType}.
*/ // */
public Stream<IIdType> getLinkIds(IBaseResource thePerson) { // public Stream<IIdType> getLinkIds(IBaseResource theSourceResource) {
// TODO we can't rely on links anymore, as the provided resource is likely not to have thoem // // TODO we can't rely on links anymore, as the provided resource is likely not to have thoem
// need a way to pull those from the underlying MDM functionality // // need a way to pull those from the underlying MDM functionality
// how do we pull link IDs now??? // // how do we pull link IDs now???
switch (myFhirContext.getVersion().getVersion()) { // switch (myFhirContext.getVersion().getVersion()) {
case R4: // case R4:
Person personR4 = (Person) thePerson; // Person personR4 = (Person) theSourceResource;
return personR4.getLink().stream() // return personR4.getLink().stream()
.map(Person.PersonLinkComponent::getTarget) // .map(Person.PersonLinkComponent::getTarget)
.map(IBaseReference::getReferenceElement) // .map(IBaseReference::getReferenceElement)
.map(IIdType::toUnqualifiedVersionless); // .map(IIdType::toUnqualifiedVersionless);
case DSTU3: // case DSTU3:
org.hl7.fhir.dstu3.model.Person personStu3 = (org.hl7.fhir.dstu3.model.Person) thePerson; // org.hl7.fhir.dstu3.model.Person personStu3 = (org.hl7.fhir.dstu3.model.Person) theSourceResource;
return personStu3.getLink().stream() // return personStu3.getLink().stream()
.map(org.hl7.fhir.dstu3.model.Person.PersonLinkComponent::getTarget) // .map(org.hl7.fhir.dstu3.model.Person.PersonLinkComponent::getTarget)
.map(IBaseReference::getReferenceElement) // .map(IBaseReference::getReferenceElement)
.map(IIdType::toUnqualifiedVersionless); // .map(IIdType::toUnqualifiedVersionless);
default: // default:
throw new UnsupportedOperationException("Version not supported: " + myFhirContext.getVersion().getVersion()); // throw new UnsupportedOperationException("Version not supported: " + myFhirContext.getVersion().getVersion());
} // }
} // }
//
// /**
// * Determine whether or not the given {@link IBaseResource} person contains a link to a particular {@link IIdType}
// *
// * @param thePerson The person to check
// * @param theResourceId The ID to check.
// * @return A boolean indicating whether or not there was a contained link.
// */
// public boolean containsLinkTo(IBaseResource thePerson, IIdType theResourceId) {
// Stream<IIdType> links = getLinkIds(thePerson);
// return links.anyMatch(link -> link.getValue().equals(theResourceId.getValue()));
// }
/** // /**
* Determine whether or not the given {@link IBaseResource} person contains a link to a particular {@link IIdType} // * Create or update a link from source {@link IBaseResource} to the target {@link IIdType}, with the given {@link CanonicalIdentityAssuranceLevel}.
* // *
* @param thePerson The person to check // * @param thePerson The person who's link needs to be updated.
* @param theResourceId The ID to check. // * @param theResourceId The target of the link
* @return A boolean indicating whether or not there was a contained link. // * @param canonicalAssuranceLevel The level of certainty of this link.
*/ // * @param theEmpiTransactionContext
public boolean containsLinkTo(IBaseResource thePerson, IIdType theResourceId) { // */
Stream<IIdType> links = getLinkIds(thePerson); // public void addOrUpdateLink(IBaseResource thePerson, IIdType theResourceId, @Nonnull CanonicalIdentityAssuranceLevel canonicalAssuranceLevel, EmpiTransactionContext theEmpiTransactionContext) {
return links.anyMatch(link -> link.getValue().equals(theResourceId.getValue())); // switch (myFhirContext.getVersion().getVersion()) {
} // case R4:
// handleLinkUpdateR4(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext);
// break;
// case DSTU3:
// handleLinkUpdateDSTU3(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext);
// break;
// default:
// throw new UnsupportedOperationException("Version not supported: " + myFhirContext.getVersion().getVersion());
// }
// }
/** // private void handleLinkUpdateDSTU3(IBaseResource thePerson, IIdType theResourceId, CanonicalIdentityAssuranceLevel theCanonicalAssuranceLevel, EmpiTransactionContext theTransactionLogMessages) {
* Create or update a link from source {@link IBaseResource} to the target {@link IIdType}, with the given {@link CanonicalIdentityAssuranceLevel}. // if (theCanonicalAssuranceLevel == null) {
* // ourLog.warn("Refusing to update or add a link without an Assurance Level.");
* @param thePerson The person who's link needs to be updated. // return;
* @param theResourceId The target of the link // }
* @param canonicalAssuranceLevel The level of certainty of this link. //
* @param theEmpiTransactionContext // org.hl7.fhir.dstu3.model.Person person = (org.hl7.fhir.dstu3.model.Person) thePerson;
*/ // if (!containsLinkTo(thePerson, theResourceId)) {
public void addOrUpdateLink(IBaseResource thePerson, IIdType theResourceId, @Nonnull CanonicalIdentityAssuranceLevel canonicalAssuranceLevel, EmpiTransactionContext theEmpiTransactionContext) { // person.addLink().setTarget(new org.hl7.fhir.dstu3.model.Reference(theResourceId)).setAssurance(theCanonicalAssuranceLevel.toDstu3());
switch (myFhirContext.getVersion().getVersion()) { // logLinkAddMessage(thePerson, theResourceId, theCanonicalAssuranceLevel, theTransactionLogMessages);
case R4: // } else {
handleLinkUpdateR4(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext); // person.getLink().stream()
break; // .filter(link -> link.getTarget().getReference().equalsIgnoreCase(theResourceId.getValue()))
case DSTU3: // .findFirst()
handleLinkUpdateDSTU3(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext); // .ifPresent(link -> {
break; // logLinkUpdateMessage(thePerson, theResourceId, theCanonicalAssuranceLevel, theTransactionLogMessages, link.getAssurance().toCode());
default: // link.setAssurance(theCanonicalAssuranceLevel.toDstu3());
throw new UnsupportedOperationException("Version not supported: " + myFhirContext.getVersion().getVersion()); // });
} // }
} // }
private void handleLinkUpdateDSTU3(IBaseResource thePerson, IIdType theResourceId, CanonicalIdentityAssuranceLevel theCanonicalAssuranceLevel, EmpiTransactionContext theTransactionLogMessages) {
if (theCanonicalAssuranceLevel == null) {
ourLog.warn("Refusing to update or add a link without an Assurance Level.");
return;
}
org.hl7.fhir.dstu3.model.Person person = (org.hl7.fhir.dstu3.model.Person) thePerson;
if (!containsLinkTo(thePerson, theResourceId)) {
person.addLink().setTarget(new org.hl7.fhir.dstu3.model.Reference(theResourceId)).setAssurance(theCanonicalAssuranceLevel.toDstu3());
logLinkAddMessage(thePerson, theResourceId, theCanonicalAssuranceLevel, theTransactionLogMessages);
} else {
person.getLink().stream()
.filter(link -> link.getTarget().getReference().equalsIgnoreCase(theResourceId.getValue()))
.findFirst()
.ifPresent(link -> {
logLinkUpdateMessage(thePerson, theResourceId, theCanonicalAssuranceLevel, theTransactionLogMessages, link.getAssurance().toCode());
link.setAssurance(theCanonicalAssuranceLevel.toDstu3());
});
}
}
private void logLinkAddMessage(IBaseResource thePerson, IIdType theResourceId, CanonicalIdentityAssuranceLevel theCanonicalAssuranceLevel, EmpiTransactionContext theEmpiTransactionContext) { private void logLinkAddMessage(IBaseResource thePerson, IIdType theResourceId, CanonicalIdentityAssuranceLevel theCanonicalAssuranceLevel, EmpiTransactionContext theEmpiTransactionContext) {
theEmpiTransactionContext.addTransactionLogMessage("Creating new link from " + (StringUtils.isBlank(thePerson.getIdElement().toUnqualifiedVersionless().getValue()) ? "new Person" : thePerson.getIdElement().toUnqualifiedVersionless()) + " -> " + theResourceId.toUnqualifiedVersionless() + " with IdentityAssuranceLevel: " + theCanonicalAssuranceLevel.name()); theEmpiTransactionContext.addTransactionLogMessage("Creating new link from " + (StringUtils.isBlank(thePerson.getIdElement().toUnqualifiedVersionless().getValue()) ? "new Person" : thePerson.getIdElement().toUnqualifiedVersionless()) + " -> " + theResourceId.toUnqualifiedVersionless() + " with IdentityAssuranceLevel: " + theCanonicalAssuranceLevel.name());
@ -173,54 +176,54 @@ public class PersonHelper {
theEmpiTransactionContext.addTransactionLogMessage("Updating link from " + thePerson.getIdElement().toUnqualifiedVersionless() + " -> " + theResourceId.toUnqualifiedVersionless() + ". Changing IdentityAssuranceLevel: " + theOriginalAssuranceLevel + " -> " + canonicalAssuranceLevel.name()); theEmpiTransactionContext.addTransactionLogMessage("Updating link from " + thePerson.getIdElement().toUnqualifiedVersionless() + " -> " + theResourceId.toUnqualifiedVersionless() + ". Changing IdentityAssuranceLevel: " + theOriginalAssuranceLevel + " -> " + canonicalAssuranceLevel.name());
} }
private void handleLinkUpdateR4(IBaseResource thePerson, IIdType theResourceId, CanonicalIdentityAssuranceLevel canonicalAssuranceLevel, EmpiTransactionContext theEmpiTransactionContext) { // private void handleLinkUpdateR4(IBaseResource thePerson, IIdType theResourceId, CanonicalIdentityAssuranceLevel canonicalAssuranceLevel, EmpiTransactionContext theEmpiTransactionContext) {
if (canonicalAssuranceLevel == null) { // if (canonicalAssuranceLevel == null) {
ourLog.warn("Refusing to update or add a link without an Assurance Level."); // ourLog.warn("Refusing to update or add a link without an Assurance Level.");
return; // return;
} // }
//
Person person = (Person) thePerson; // Person person = (Person) thePerson;
if (!containsLinkTo(thePerson, theResourceId)) { // if (!containsLinkTo(thePerson, theResourceId)) {
person.addLink().setTarget(new Reference(theResourceId)).setAssurance(canonicalAssuranceLevel.toR4()); // person.addLink().setTarget(new Reference(theResourceId)).setAssurance(canonicalAssuranceLevel.toR4());
logLinkAddMessage(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext); // logLinkAddMessage(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext);
} else { // } else {
person.getLink().stream() // person.getLink().stream()
.filter(link -> link.getTarget().getReference().equalsIgnoreCase(theResourceId.getValue())) // .filter(link -> link.getTarget().getReference().equalsIgnoreCase(theResourceId.getValue()))
.findFirst() // .findFirst()
.ifPresent(link -> { // .ifPresent(link -> {
logLinkUpdateMessage(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext, link.getAssurance().toCode()); // logLinkUpdateMessage(thePerson, theResourceId, canonicalAssuranceLevel, theEmpiTransactionContext, link.getAssurance().toCode());
link.setAssurance(canonicalAssuranceLevel.toR4()); // link.setAssurance(canonicalAssuranceLevel.toR4());
}); // });
} // }
} // }
/** // /**
* Removes a link from the given {@link IBaseResource} to the target {@link IIdType}. // * Removes a link from the given {@link IBaseResource} to the target {@link IIdType}.
* // *
* @param thePerson The person to remove the link from. // * @param thePerson The person to remove the link from.
* @param theResourceId The target ID to remove. // * @param theResourceId The target ID to remove.
* @param theEmpiTransactionContext // * @param theEmpiTransactionContext
*/ // */
public void removeLink(IBaseResource thePerson, IIdType theResourceId, EmpiTransactionContext theEmpiTransactionContext) { // public void removeLink(IBaseResource thePerson, IIdType theResourceId, EmpiTransactionContext theEmpiTransactionContext) {
if (!containsLinkTo(thePerson, theResourceId)) { // if (!containsLinkTo(thePerson, theResourceId)) {
return; // return;
} // }
theEmpiTransactionContext.addTransactionLogMessage("Removing PersonLinkComponent from " + thePerson.getIdElement().toUnqualifiedVersionless() + " -> " + theResourceId.toUnqualifiedVersionless()); // theEmpiTransactionContext.addTransactionLogMessage("Removing PersonLinkComponent from " + thePerson.getIdElement().toUnqualifiedVersionless() + " -> " + theResourceId.toUnqualifiedVersionless());
switch (myFhirContext.getVersion().getVersion()) { // switch (myFhirContext.getVersion().getVersion()) {
case R4: // case R4:
Person person = (Person) thePerson; // Person person = (Person) thePerson;
List<Person.PersonLinkComponent> links = person.getLink(); // List<Person.PersonLinkComponent> links = person.getLink();
links.removeIf(component -> component.hasTarget() && component.getTarget().getReference().equals(theResourceId.getValue())); // links.removeIf(component -> component.hasTarget() && component.getTarget().getReference().equals(theResourceId.getValue()));
break; // break;
case DSTU3: // case DSTU3:
org.hl7.fhir.dstu3.model.Person personDstu3 = (org.hl7.fhir.dstu3.model.Person) thePerson; // org.hl7.fhir.dstu3.model.Person personDstu3 = (org.hl7.fhir.dstu3.model.Person) thePerson;
personDstu3.getLink().removeIf(component -> component.hasTarget() && component.getTarget().getReference().equalsIgnoreCase(theResourceId.getValue())); // personDstu3.getLink().removeIf(component -> component.hasTarget() && component.getTarget().getReference().equalsIgnoreCase(theResourceId.getValue()));
break; // break;
default: // default:
throw new UnsupportedOperationException("Version not supported: " + myFhirContext.getVersion().getVersion()); // throw new UnsupportedOperationException("Version not supported: " + myFhirContext.getVersion().getVersion());
} // }
} // }
/** /**
* Creates a copy of the specified resource. This method will carry over resource EID if it exists. If it does not exist, * Creates a copy of the specified resource. This method will carry over resource EID if it exists. If it does not exist,

89
hapi-fhir-server-empi/src/test/java/ca/uhn/fhir/empi/svc/PersonHelperDSTU3Test.java
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@ -9,6 +9,7 @@ import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -21,6 +22,7 @@ import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
public class PersonHelperDSTU3Test { public class PersonHelperDSTU3Test {
public static final FhirContext ourFhirContext = FhirContext.forDstu3(); public static final FhirContext ourFhirContext = FhirContext.forDstu3();
public static final String PATIENT_1 = "Patient/1"; public static final String PATIENT_1 = "Patient/1";
public static final String PATIENT_2 = "Patient/2"; public static final String PATIENT_2 = "Patient/2";
@ -33,52 +35,55 @@ public class PersonHelperDSTU3Test {
person.addLink().setTarget(new Reference(PATIENT_1)); person.addLink().setTarget(new Reference(PATIENT_1));
person.addLink().setTarget(new Reference(PATIENT_2)); person.addLink().setTarget(new Reference(PATIENT_2));
{ // TODO NG - check if we need similar functionality in JPA DAO
List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList()); if (true) {
assertEquals(2, links.size()); return;
assertEquals(PATIENT_1, links.get(0).getValue());
assertEquals(PATIENT_2, links.get(1).getValue());
assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_1)));
assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_2)));
assertFalse(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_BAD)));
} }
{ List<IIdType> links = new ArrayList<>();
MY_PERSON_HELPER.removeLink(person, new IdDt(PATIENT_1), createDummyContext()); // links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList());
List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList()); assertEquals(2, links.size());
assertEquals(1, links.size()); assertEquals(PATIENT_1, links.get(0).getValue());
assertEquals(PATIENT_2, links.get(0).getValue()); assertEquals(PATIENT_2, links.get(1).getValue());
} // assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_1)));
// assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_2)));
// assertFalse(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_BAD)));
} }
@Test {
public void testAddOrUpdateLinks() { // MY_PERSON_HELPER.removeLink(person, new IdDt(PATIENT_1), createDummyContext());
Person person = new Person(); // List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList());
// assertEquals(1, links.size());
//Links with no assurance level are rejected // assertEquals(PATIENT_2, links.get(0).getValue());
{
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), null, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(0)));
}
//Original link addition
{
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL3, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(1)));
}
//Link update
{
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(1)));
}
//New link
{
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_2), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(2)));
}
} }
// @Test
// public void testAddOrUpdateLinks() {
// Person person = new Person();
//
// //Links with no assurance level are rejected
// {
// MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), null, createDummyContext());
// assertThat(person.getLink().size(), is(equalTo(0)));
// }
// //Original link addition
// {
// MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL3, createDummyContext());
// assertThat(person.getLink().size(), is(equalTo(1)));
// }
//
// //Link update
// {
// MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext());
// assertThat(person.getLink().size(), is(equalTo(1)));
// }
//
// //New link
// {
// MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_2), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext());
// assertThat(person.getLink().size(), is(equalTo(2)));
// }
// }
} }

41
hapi-fhir-server-empi/src/test/java/ca/uhn/fhir/empi/svc/PersonHelperR4Test.java
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@ -30,52 +30,61 @@ public class PersonHelperR4Test {
@Test @Test
public void testGetLinks() { public void testGetLinks() {
// TODO NG - Revisit this code checking if we need to keep it - if yes - push to the JPA level, delete otherwise
Person person = new Person(); Person person = new Person();
person.addLink().setTarget(new Reference(PATIENT_1)); person.addLink().setTarget(new Reference(PATIENT_1));
person.addLink().setTarget(new Reference(PATIENT_2)); person.addLink().setTarget(new Reference(PATIENT_2));
{ if (true) {
List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList()); return;
assertEquals(2, links.size());
assertEquals(PATIENT_1, links.get(0).getValue());
assertEquals(PATIENT_2, links.get(1).getValue());
assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_1)));
assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_2)));
assertFalse(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_BAD)));
} }
{ {
MY_PERSON_HELPER.removeLink(person, new IdDt(PATIENT_1), createDummyContext()); // List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList());
List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList()); // assertEquals(2, links.size());
assertEquals(1, links.size()); // assertEquals(PATIENT_1, links.get(0).getValue());
assertEquals(PATIENT_2, links.get(0).getValue()); // assertEquals(PATIENT_2, links.get(1).getValue());
// assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_1)));
// assertTrue(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_2)));
// assertFalse(MY_PERSON_HELPER.containsLinkTo(person, new IdDt(PATIENT_BAD)));
}
{
// MY_PERSON_HELPER.removeLink(person, new IdDt(PATIENT_1), createDummyContext());
// List<IIdType> links = MY_PERSON_HELPER.getLinkIds(person).collect(Collectors.toList());
// assertEquals(1, links.size());
// assertEquals(PATIENT_2, links.get(0).getValue());
} }
} }
@Test @Test
public void testAddOrUpdateLinks() { public void testAddOrUpdateLinks() {
Person person = new Person(); Person person = new Person();
if (true) {
return;
}
//Link addition without assurance level should NOOP //Link addition without assurance level should NOOP
// TODO NG - Revisit this code checking if we need to keep it - if yes - push to the JPA level, delete otherwise
{ {
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), null, null); // MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), null, null);
assertThat(person.getLink().size(), is(equalTo(0))); assertThat(person.getLink().size(), is(equalTo(0)));
} }
//Original link addition //Original link addition
{ {
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL3, createDummyContext()); // MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL3, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(1))); assertThat(person.getLink().size(), is(equalTo(1)));
} }
//Link update //Link update
{ {
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext()); // MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_1), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(1))); assertThat(person.getLink().size(), is(equalTo(1)));
} }
//New link //New link
{ {
MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_2), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext()); // MY_PERSON_HELPER.addOrUpdateLink(person, new IdDt(PATIENT_2), CanonicalIdentityAssuranceLevel.LEVEL4, createDummyContext());
assertThat(person.getLink().size(), is(equalTo(2))); assertThat(person.getLink().size(), is(equalTo(2)));
} }
} }