comment fixes and removing dead code

hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/svc/EmpiMatchLinkSvc.java

@@ -76,6 +76,7 @@ public class EmpiMatchLinkSvc {
 
 	private EmpiTransactionContext doEmpiUpdate(IAnyResource theResource, EmpiTransactionContext theEmpiTransactionContext) {
 		CandidateList candidateList = myEmpiPersonFindingSvc.findPersonCandidates(theResource);
+
 		if (candidateList.isEmpty()) {
 			handleEmpiWithNoCandidates(theResource, theEmpiTransactionContext);
 		} else if (candidateList.exactlyOneMatch()) {
@@ -121,6 +122,7 @@ public class EmpiMatchLinkSvc {
 	private void handleEmpiWithNoCandidates(IAnyResource theResource, EmpiTransactionContext theEmpiTransactionContext) {
 		log(theEmpiTransactionContext, "There were no matched candidates for EMPI, creating a new Person.");
 		IAnyResource newPerson = myPersonHelper.createPersonFromEmpiTarget(theResource);
+
 		myEmpiLinkSvc.updateLink(newPerson, theResource, EmpiMatchOutcome.NEW_PERSON_MATCH, EmpiLinkSourceEnum.AUTO, theEmpiTransactionContext);
 	}
 

hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/svc/candidate/EmpiPersonFindingSvc.java

@@ -38,8 +38,10 @@ public class EmpiPersonFindingSvc {
 
 	@Autowired
 	private FindCandidateByEidSvc myFindCandidateByEidSvc;
+
 	@Autowired
 	private FindCandidateByLinkSvc myFindCandidateByLinkSvc;
+
 	@Autowired
 	private FindCandidateByScoreSvc myFindCandidateByScoreSvc;
 
@@ -63,12 +65,14 @@ public class EmpiPersonFindingSvc {
 		if (matchedPersonCandidates.isEmpty()) {
 			matchedPersonCandidates = myFindCandidateByLinkSvc.findCandidates(theResource);
 		}
+
 		if (matchedPersonCandidates.isEmpty()) {
 			//OK, so we have not found any links in the EmpiLink table with us as a target. Next, let's find possible Patient/Practitioner
 			//matches by following EMPI rules.
 
 			matchedPersonCandidates = myFindCandidateByScoreSvc.findCandidates(theResource);
 		}
+
 		return matchedPersonCandidates;
 	}
 

hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/svc/candidate/FindCandidateByScoreSvc.java

@@ -66,6 +66,8 @@ public class FindCandidateByScoreSvc extends BaseCandidateFinder {
 		List<MatchedPersonCandidate> retval = new ArrayList<>();
 
 		List<Long> personPidsToExclude = getNoMatchPersonPids(theTarget);
+
+
 		List<MatchedTarget> matchedCandidates = myEmpiMatchFinderSvc.getMatchedTargets(myFhirContext.getResourceType(theTarget), theTarget);
 
 		//Convert all possible match targets to their equivalent Persons by looking up in the EmpiLink table,

hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/api/IEmpiMatchFinderSvc.java

@@ -21,14 +21,13 @@ package ca.uhn.fhir.empi.api;
  */
 
 import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import javax.annotation.Nonnull;
 import java.util.List;
 
 public interface IEmpiMatchFinderSvc {
 	/**
-	 * Retrieve a list of possible Patient/Practitioner candidates for matching, based on the given {@link IBaseResource}
+	 * Retrieve a list of possible Patient/Practitioner candidates for matching, based on the given {@link IAnyResource}
 	 * Internally, performs all EMPI matching rules on the type of the resource.
 	 *
 	 * @param theResourceType the type of the resource.

hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/util/PersonHelper.java

@@ -214,7 +214,6 @@ public class PersonHelper {
 	 * @return the Person that is created.
 	 */
 	public IAnyResource createPersonFromEmpiTarget(IAnyResource theSourceResource) {
-		String eidSystem = myEmpiConfig.getEmpiRules().getEnterpriseEIDSystem();
 		List<CanonicalEID> eidsToApply = myEIDHelper.getExternalEid(theSourceResource);
 		if (eidsToApply.isEmpty()) {
 			eidsToApply.add(myEIDHelper.createHapiEid());
@@ -222,6 +221,7 @@ public class PersonHelper {
 		switch (myFhirContext.getVersion().getVersion()) {
 			case R4:
 				Person personR4 = new Person();
+
 				personR4.setActive(true);
 				eidsToApply.forEach(eid -> personR4.addIdentifier(eid.toR4()));
 				personR4.getMeta().addTag((Coding) buildEmpiManagedTag());
@@ -396,7 +396,6 @@ public class PersonHelper {
 		List<CanonicalEID> incomingTargetEid = myEIDHelper.getExternalEid(theEmpiTarget);
 		List<CanonicalEID> personOfficialEid = myEIDHelper.getExternalEid(thePerson);
 
-
 		if (!incomingTargetEid.isEmpty()) {
 			if (personOfficialEid.isEmpty() || !myEmpiConfig.isPreventMultipleEids()) {
 				log(theEmpiTransactionContext, "Incoming resource:" + theEmpiTarget.getIdElement().toUnqualifiedVersionless() + " + with EID " + incomingTargetEid.stream().map(CanonicalEID::toString).collect(Collectors.joining(",")) + " is applying this EIDs to its related Person, as this person does not yet have an external EID");

lgtm.yml

@@ -5,5 +5,3 @@ extraction:
         - exclude: "**/jquery*.js"
         - exclude: "**/bootstrap*.js"
         - exclude: "**/webapp/fa/*.js"
-
-