Turns out expunge atomic integer didn't do what I expected for historical versions...

hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/dao/EmpiLinkDaoSvc.java

@@ -238,7 +238,7 @@ public class EmpiLinkDaoSvc {
 	}
 
 	private List<Long> deleteEmpiLinksAndReturnPersonPids(List<EmpiLink> theLinks) {
-		List<Long> collect = theLinks.stream().map(EmpiLink::getPersonPid).collect(Collectors.toList());
+		List<Long> collect = theLinks.stream().map(EmpiLink::getPersonPid).distinct().collect(Collectors.toList());
 		theLinks.forEach(empiLink -> myEmpiLinkDao.delete(empiLink));
 		return collect;
 	}

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

@@ -26,7 +26,6 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DeleteConflict;
 import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
-import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.expunge.IResourceExpungeService;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.empi.dao.EmpiLinkDaoSvc;
@@ -41,7 +40,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
-import java.util.stream.Collectors;
 
 /**
  * This class is in charge of Clearing out existing EMPI links, as well as deleting all persons related to those EMPI Links.
@@ -52,13 +50,8 @@ public class EmpiResetSvcImpl implements IEmpiResetSvc {
 
 	@Autowired
 	EmpiLinkDaoSvc myEmpiLinkDaoSvc;
-
 	@Autowired
 	private IResourceExpungeService myResourceExpungeService;
-
-	@Autowired
-	private IResourceTableDao myResourceTable;
-
 	@Autowired
 	private DaoRegistry myDaoRegistry;
 	@Autowired
@@ -67,12 +60,35 @@ public class EmpiResetSvcImpl implements IEmpiResetSvc {
 	@Override
 	public long expungeAllEmpiLinksOfTargetType(String theResourceType) {
 		throwExceptionIfInvalidTargetType(theResourceType);
-
 		List<Long> longs = myEmpiLinkDaoSvc.deleteAllEmpiLinksOfTypeAndReturnPersonPids(theResourceType);
-		myResourceExpungeService.expungeCurrentVersionOfResources(null, longs, new AtomicInteger(longs.size()));
+		deleteResourcesAndHandleConflicts(longs);
+		expungeHistoricalAndCurrentVersiondsOfIds(longs);
 		return longs.size();
 	}
 
+	/**
+	 * Function which will delete all resources by their PIDs, and also delete any resources that were undeletable due to
+	 * VersionConflictException
+	 * @param theLongs
+	 */
+	private void deleteResourcesAndHandleConflicts(List<Long> theLongs) {
+		DeleteConflictList
+			deleteConflictList = new DeleteConflictList();
+		myTransactionService.execute(null, tx -> {
+			theLongs.stream().forEach(pid -> deleteCascade(pid, deleteConflictList));
+			return null;
+		});
+
+		IFhirResourceDao personDao = myDaoRegistry.getResourceDao("Person");
+		while (!deleteConflictList.isEmpty()) {
+			myTransactionService.execute(null, tx -> {
+				deleteConflictBatch(deleteConflictList, personDao);
+				return null;
+			});
+
+		}
+	}
+
 	private void throwExceptionIfInvalidTargetType(String theResourceType) {
 		if (!EmpiUtil.supportedTargetType(theResourceType)) {
 			throw new InvalidRequestException(ProviderConstants.EMPI_CLEAR + " does not support resource type: " + theResourceType);
@@ -85,30 +101,19 @@ public class EmpiResetSvcImpl implements IEmpiResetSvc {
 	@Override
 	public long expungeAllEmpiLinks() {
 		List<Long> longs = myEmpiLinkDaoSvc.deleteAllEmpiLinksAndReturnPersonPids();
-		longs = longs.stream()
+		deleteResourcesAndHandleConflicts(longs);
-			.distinct().collect(Collectors.toList());
+		expungeHistoricalAndCurrentVersiondsOfIds(longs);
-
-		DeleteConflictList dlc = new DeleteConflictList();
-		List<Long> finalLongs = longs;
-		myTransactionService.execute(null, tx -> {
-			finalLongs.stream().forEach(pid -> {
-				deleteCascade(pid, dlc);
-			});
-			return null;
-		});
-
-		IFhirResourceDao personDao = myDaoRegistry.getResourceDao("Person");
-		while (!dlc.isEmpty()) {
-			myTransactionService.execute(null, tx -> {
-				deleteConflictBatch(dlc, personDao);
-				return null;
-			});
-		}
-		myResourceExpungeService.expungeHistoricalVersionsOfIds(null, longs, new AtomicInteger(longs.size()));
-		//myResourceExpungeService.expungeCurrentVersionOfResources(null, longs, new AtomicInteger(longs.size()));
 		return longs.size();
 	}
 
+	/**
+	 * Use the expunge service to expunge all historical and current versions of the resources associated to the PIDs.
+	 */
+	private void expungeHistoricalAndCurrentVersiondsOfIds(List<Long> theLongs) {
+		myResourceExpungeService.expungeHistoricalVersionsOfIds(null, theLongs, new AtomicInteger(Integer.MAX_VALUE - 1));
+		myResourceExpungeService.expungeCurrentVersionOfResources(null, theLongs, new AtomicInteger(Integer.MAX_VALUE - 1));
+	}
+
 	private void deleteConflictBatch(DeleteConflictList theDcl, IFhirResourceDao<IBaseResource> theDao) {
 		DeleteConflictList newBatch = new DeleteConflictList();
 		for (DeleteConflict next: theDcl) {
@@ -120,10 +125,10 @@ public class EmpiResetSvcImpl implements IEmpiResetSvc {
 		theDcl.addAll(newBatch);
 	}
 
-	private void deleteCascade(Long pid, DeleteConflictList theDcl) {
+	private void deleteCascade(Long pid, DeleteConflictList theDeleteConflictList) {
 		ourLog.debug("About to cascade delete: " + pid);
 		IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao("Person");
-			resourceDao.delete(new IdType("Person/" + pid), theDcl, null, null);
+			resourceDao.delete(new IdType("Person/" + pid), theDeleteConflictList, null, null);
 	}
 }
 

hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/provider/EmpiProviderBatchR4Test.java

@@ -14,6 +14,8 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.io.IOException;
+
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.is;
@@ -42,7 +44,7 @@ public class EmpiProviderBatchR4Test extends BaseLinkR4Test {
 	}
 
 	@AfterEach
-	public void after() {
+	public void after() throws IOException {
 		myInterceptorService.unregisterInterceptor(afterEmpiLatch);
 		super.after();
 	}

hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/provider/EmpiProviderClearLinkR4Test.java

@@ -66,7 +66,7 @@ public class EmpiProviderClearLinkR4Test extends BaseLinkR4Test {
 		assertLinkCount(2);
 		Person read = myPersonDao.read(new IdDt(myPersonId.getValueAsString()).toVersionless());
 		assertThat(read, is(notNullValue()));
-		myEmpiProviderR4.clearEmpiLinks(new StringType("patient"));
+		myEmpiProviderR4.clearEmpiLinks(new StringType("Patient"));
 		assertNoPatientLinksExist();
 		try {
 			myPersonDao.read(new IdDt(myPersonId.getValueAsString()).toVersionless());
@@ -141,7 +141,7 @@ public class EmpiProviderClearLinkR4Test extends BaseLinkR4Test {
 		assertLinkCount(2);
 		Person read = myPersonDao.read(new IdDt(myPractitionerPersonId.getValueAsString()).toVersionless());
 		assertThat(read, is(notNullValue()));
-		myEmpiProviderR4.clearEmpiLinks(new StringType("practitioner"));
+		myEmpiProviderR4.clearEmpiLinks(new StringType("Practitioner"));
 		assertNoPractitionerLinksExist();
 		try {
 			myPersonDao.read(new IdDt(myPractitionerPersonId.getValueAsString()).toVersionless());
@@ -152,10 +152,10 @@ public class EmpiProviderClearLinkR4Test extends BaseLinkR4Test {
 	@Test
 	public void testClearInvalidTargetType() {
 		try {
-			myEmpiProviderR4.clearEmpiLinks(new StringType("observation"));
+			myEmpiProviderR4.clearEmpiLinks(new StringType("Observation"));
 			fail();
 		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), is(equalTo("$empi-clear does not support resource type: observation")));
+			assertThat(e.getMessage(), is(equalTo("$empi-clear does not support resource type: Observation")));
 		}
 	}
 

hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiBatchSvcImplTest.java

@@ -11,6 +11,7 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.io.IOException;
 import java.util.Date;
 
 class EmpiBatchSvcImplTest extends BaseEmpiR4Test {
@@ -28,7 +29,7 @@ class EmpiBatchSvcImplTest extends BaseEmpiR4Test {
 		myInterceptorService.registerAnonymousInterceptor(Pointcut.EMPI_AFTER_PERSISTED_RESOURCE_CHECKED, afterEmpiLatch);
 	}
 	@AfterEach
-	public void after() {
+	public void after() throws IOException {
 		myInterceptorService.unregisterInterceptor(afterEmpiLatch);
 		afterEmpiLatch.clear();
 		super.after();