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

This commit is contained in:
Tadgh 2020-07-27 17:29:27 -07:00
parent 82dcc395ec
commit 606b642b1e
5 changed files with 47 additions and 39 deletions
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2
hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/dao/EmpiLinkDaoSvc.java
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@ -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;
}

69
hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/svc/EmpiResetSvcImpl.java
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@ -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()
.distinct().collect(Collectors.toList());
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()));
deleteResourcesAndHandleConflicts(longs);
expungeHistoricalAndCurrentVersiondsOfIds(longs);
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);
}
}

4
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/provider/EmpiProviderBatchR4Test.java
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@ -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();
}

8
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/provider/EmpiProviderClearLinkR4Test.java
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@ -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")));
}
}

3
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiBatchSvcImplTest.java
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@ -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();