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Renamed sourceResource to goldenResource

This commit is contained in:
Nick Goupinets 2020-11-27 16:53:21 -05:00
parent 8a7dc4e80b
commit 36ce84335a
4 changed files with 49 additions and 48 deletions
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0
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MatchedSourceResourceCandidate.java → hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MatchedGoldenResourceCandidate.java
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0
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/matcher/BaseSourceResourceMatcher.java → hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/matcher/BaseGoldenResourceMatcher.java
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0
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/matcher/IsSameSourceResourceAs.java → hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/matcher/IsSameGoldenResourceAs.java
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97
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java
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@ -92,35 +92,35 @@ public class GoldenResourceHelper {
// get a ref to the actual ID Field
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(theIncomingResource);
IBaseResource newSourceResource = resourceDefinition.newInstance();
IBaseResource newGoldenResource = resourceDefinition.newInstance();
// hapi has 2 metamodels: for children and types
BaseRuntimeChildDefinition sourceResourceIdentifier = resourceDefinition.getChildByName(FIELD_NAME_IDENTIFIER);
BaseRuntimeChildDefinition goldenResourceIdentifier = resourceDefinition.getChildByName(FIELD_NAME_IDENTIFIER);
cloneAllExternalEidsIntoNewSourceResource(sourceResourceIdentifier, theIncomingResource, newSourceResource);
cloneAllExternalEidsIntoNewGoldenResource(goldenResourceIdentifier, theIncomingResource, newGoldenResource);
addHapiEidIfNoExternalEidIsPresent(newSourceResource, sourceResourceIdentifier, theIncomingResource);
addHapiEidIfNoExternalEidIsPresent(newGoldenResource, goldenResourceIdentifier, theIncomingResource);
MdmUtil.setMdmManaged(newSourceResource);
MdmUtil.setGoldenResource(newSourceResource);
MdmUtil.setMdmManaged(newGoldenResource);
MdmUtil.setGoldenResource(newGoldenResource);
return (T) newSourceResource;
return (T) newGoldenResource;
}
/**
* If there are no external EIDs on the incoming resource, create a new HAPI EID on the new SourceResource.
* If there are no external EIDs on the incoming resource, create a new HAPI EID on the new Golden Resource.
*/
//TODO GGG ask james if there is any way we can convert this canonical EID into a generic STU-agnostic IBase.
private <T extends IAnyResource> void addHapiEidIfNoExternalEidIsPresent(
IBaseResource theNewSourceResource, BaseRuntimeChildDefinition theSourceResourceIdentifier, IAnyResource theTargetResource) {
IBaseResource theNewGoldenResource, BaseRuntimeChildDefinition theGoldenResourceIdentifier, IAnyResource theTargetResource) {
List<CanonicalEID> eidsToApply = myEIDHelper.getExternalEid(theNewSourceResource);
List<CanonicalEID> eidsToApply = myEIDHelper.getExternalEid(theNewGoldenResource);
if (!eidsToApply.isEmpty()) {
return;
}
CanonicalEID hapiEid = myEIDHelper.createHapiEid();
theSourceResourceIdentifier.getMutator().addValue(theNewSourceResource, toId(hapiEid));
theGoldenResourceIdentifier.getMutator().addValue(theNewGoldenResource, toId(hapiEid));
// set identifier on the target resource
cloneEidIntoResource(theTargetResource, hapiEid);
@ -185,18 +185,19 @@ public class GoldenResourceHelper {
}).findFirst().isPresent();
}
private void cloneAllExternalEidsIntoNewSourceResource(BaseRuntimeChildDefinition theSourceResourceIdentifier, IBase theSourceResource, IBase theNewSourceResource) {
private void cloneAllExternalEidsIntoNewGoldenResource(BaseRuntimeChildDefinition theGoldenResourceIdentifier,
IBase theGoldenResource, IBase theNewGoldenResource) {
// FHIR choice types - fields within fhir where we have a choice of ids
IFhirPath fhirPath = myFhirContext.newFhirPath();
List<IBase> sourceResourceIdentifiers = theSourceResourceIdentifier.getAccessor().getValues(theSourceResource);
List<IBase> goldenResourceIdentifiers = theGoldenResourceIdentifier.getAccessor().getValues(theGoldenResource);
for (IBase base : sourceResourceIdentifiers) {
for (IBase base : goldenResourceIdentifiers) {
Optional<IPrimitiveType> system = fhirPath.evaluateFirst(base, "system", IPrimitiveType.class);
if (system.isPresent()) {
String mdmSystem = myMdmSettings.getMdmRules().getEnterpriseEIDSystem();
String baseSystem = system.get().getValueAsString();
if (Objects.equals(baseSystem, mdmSystem)) {
cloneEidIntoResource(theSourceResourceIdentifier, base, theNewSourceResource);
cloneEidIntoResource(theGoldenResourceIdentifier, base, theNewGoldenResource);
ourLog.debug("System {} differs from system in the MDM rules {}", baseSystem, mdmSystem);
}
} else {
@ -214,47 +215,47 @@ public class GoldenResourceHelper {
}
/**
* Update a Person's EID based on the incoming target resource. If the incoming resource has an external EID, it is applied
* to the Person, unless that person already has an external EID which does not match, in which case throw {@link IllegalArgumentException}
* Updates EID on Golden Resource, based on the incoming target resource. If the incoming resource has an external EID, it is applied
* to the Golden Resource, unless that person already has an external EID which does not match, in which case throw {@link IllegalArgumentException}
* <p>
* If running in multiple EID mode, then incoming EIDs are simply added to the Person without checking for matches.
* If running in multiple EID mode, then incoming EIDs are simply added to the Golden Resource without checking for matches.
*
* @param theSourceResource The person to update the external EID on.
* @param theGoldenResource The golden resource to update the external EID on.
* @param theTargetResource The target we will retrieve the external EID from.
* @return the modified {@link IBaseResource} representing the person.
* @return the modified {@link IBaseResource} representing the Golden Resource.
*/
public IAnyResource updateSourceResourceExternalEidFromTargetResource(IAnyResource theSourceResource, IAnyResource
public IAnyResource updateGoldenResourceExternalEidFromTargetResource(IAnyResource theGoldenResource, IAnyResource
theTargetResource, MdmTransactionContext theMdmTransactionContext) {
//This handles overwriting an automatically assigned EID if a patient that links is coming in with an official EID.
List<CanonicalEID> incomingTargetEid = myEIDHelper.getExternalEid(theTargetResource);
List<CanonicalEID> personOfficialEid = myEIDHelper.getExternalEid(theSourceResource);
List<CanonicalEID> personOfficialEid = myEIDHelper.getExternalEid(theGoldenResource);
if (!incomingTargetEid.isEmpty()) {
if (personOfficialEid.isEmpty() || !myMdmSettings.isPreventMultipleEids()) {
log(theMdmTransactionContext, "Incoming resource:" + theTargetResource.getIdElement().toUnqualifiedVersionless() + " + with EID " + incomingTargetEid.stream().map(CanonicalEID::toString).collect(Collectors.joining(",")) + " is applying this EIDs to its related Source Resource, as this Source Resource does not yet have an external EID");
addCanonicalEidsToSourceResourceIfAbsent(theSourceResource, incomingTargetEid);
addCanonicalEidsToGoldenResourceIfAbsent(theGoldenResource, incomingTargetEid);
} else if (!personOfficialEid.isEmpty() && myEIDHelper.eidMatchExists(personOfficialEid, incomingTargetEid)) {
log(theMdmTransactionContext, "incoming resource:" + theTargetResource.getIdElement().toVersionless() + " with EIDs " + incomingTargetEid.stream().map(CanonicalEID::toString).collect(Collectors.joining(",")) + " does not need to overwrite person, as this EID is already present");
} else {
throw new IllegalArgumentException("This would create a duplicate person!");
}
}
return theSourceResource;
return theGoldenResource;
}
public IBaseResource overwriteExternalEids(IBaseResource theSourceResource, List<CanonicalEID> theNewEid) {
clearExternalEids(theSourceResource);
addCanonicalEidsToSourceResourceIfAbsent(theSourceResource, theNewEid);
return theSourceResource;
public IBaseResource overwriteExternalEids(IBaseResource theGoldenResource, List<CanonicalEID> theNewEid) {
clearExternalEids(theGoldenResource);
addCanonicalEidsToGoldenResourceIfAbsent(theGoldenResource, theNewEid);
return theGoldenResource;
}
private void clearExternalEidsFromTheSourceResource(BaseRuntimeChildDefinition theSourceResourceIdentifier, IBase theSourceResource) {
private void clearExternalEidsFromTheGoldenResource(BaseRuntimeChildDefinition theGoldenResourceIdentifier, IBase theGoldenResource) {
IFhirPath fhirPath = myFhirContext.newFhirPath();
List<IBase> sourceResourceIdentifiers = theSourceResourceIdentifier.getAccessor().getValues(theSourceResource);
List<IBase> goldenResourceIdentifiers = theGoldenResourceIdentifier.getAccessor().getValues(theGoldenResource);
List<IBase> clonedIdentifiers = new ArrayList<>();
FhirTerser terser = myFhirContext.newTerser();
for (IBase base : sourceResourceIdentifiers) {
for (IBase base : goldenResourceIdentifiers) {
Optional<IPrimitiveType> system = fhirPath.evaluateFirst(base, "system", IPrimitiveType.class);
if (system.isPresent()) {
String mdmSystem = myMdmSettings.getMdmRules().getEnterpriseEIDSystem();
@ -266,38 +267,38 @@ public class GoldenResourceHelper {
}
BaseRuntimeElementCompositeDefinition<?> childIdentifier = (BaseRuntimeElementCompositeDefinition<?>)
theSourceResourceIdentifier.getChildByName(FIELD_NAME_IDENTIFIER);
IBase sourceResourceNewIdentifier = childIdentifier.newInstance();
terser.cloneInto(base, sourceResourceNewIdentifier, true);
theGoldenResourceIdentifier.getChildByName(FIELD_NAME_IDENTIFIER);
IBase goldenResourceNewIdentifier = childIdentifier.newInstance();
terser.cloneInto(base, goldenResourceNewIdentifier, true);
clonedIdentifiers.add(sourceResourceNewIdentifier);
clonedIdentifiers.add(goldenResourceNewIdentifier);
}
sourceResourceIdentifiers.clear();
sourceResourceIdentifiers.addAll(clonedIdentifiers);
goldenResourceIdentifiers.clear();
goldenResourceIdentifiers.addAll(clonedIdentifiers);
}
private void clearExternalEids(IBaseResource theSourceResource) {
private void clearExternalEids(IBaseResource theGoldenResource) {
// validate the system - if it's set to EID system - then clear it - type and STU version
validateContextSupported();
// get a ref to the actual ID Field
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(theSourceResource);
BaseRuntimeChildDefinition sourceResourceIdentifier = resourceDefinition.getChildByName(FIELD_NAME_IDENTIFIER);
clearExternalEidsFromTheSourceResource(sourceResourceIdentifier, theSourceResource);
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(theGoldenResource);
BaseRuntimeChildDefinition goldenResourceIdentifier = resourceDefinition.getChildByName(FIELD_NAME_IDENTIFIER);
clearExternalEidsFromTheGoldenResource(goldenResourceIdentifier, theGoldenResource);
}
/**
* Given a list of incoming External EIDs, and a Source Resource, apply all the EIDs to this resource, which did not already exist on it.
* Given a list of incoming External EIDs, and a Golden Resource, apply all the EIDs to this resource, which did not already exist on it.
*/
private void addCanonicalEidsToSourceResourceIfAbsent(IBaseResource theSourceResource, List<CanonicalEID> theIncomingTargetExternalEids) {
List<CanonicalEID> sourceResourceExternalEids = myEIDHelper.getExternalEid(theSourceResource);
private void addCanonicalEidsToGoldenResourceIfAbsent(IBaseResource theGoldenResource, List<CanonicalEID> theIncomingTargetExternalEids) {
List<CanonicalEID> goldenResourceExternalEids = myEIDHelper.getExternalEid(theGoldenResource);
for (CanonicalEID incomingExternalEid : theIncomingTargetExternalEids) {
if (sourceResourceExternalEids.contains(incomingExternalEid)) {
if (goldenResourceExternalEids.contains(incomingExternalEid)) {
continue;
} else {
cloneEidIntoResource(theSourceResource, incomingExternalEid);
cloneEidIntoResource(theGoldenResource, incomingExternalEid);
}
}
}
@ -489,11 +490,11 @@ public class GoldenResourceHelper {
ourLog.debug(theMessage);
}
public void handleExternalEidAddition(IAnyResource theSourceResource, IAnyResource theTargetResource, MdmTransactionContext
public void handleExternalEidAddition(IAnyResource theGoldenResource, IAnyResource theTargetResource, MdmTransactionContext
theMdmTransactionContext) {
List<CanonicalEID> eidFromResource = myEIDHelper.getExternalEid(theTargetResource);
if (!eidFromResource.isEmpty()) {
updateSourceResourceExternalEidFromTargetResource(theSourceResource, theTargetResource, theMdmTransactionContext);
updateGoldenResourceExternalEidFromTargetResource(theGoldenResource, theTargetResource, theMdmTransactionContext);
}
}