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Enabling massIngestionMode causes incomplete resource deletion (#4476) 

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
This commit is contained in:
Etienne Poirier 2023-01-30 07:34:50 -05:00 committed by GitHub
parent 078dcd9c0d
commit 1a9b749b5a
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4 changed files with 68 additions and 12 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4475-fix-incomplete-resource-deletion-with-massinjectionmode-enabled.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 4475
jira: SMILE-4961
title: "Enabling mass ingestion mode alters the resource deletion process leaving resources partially deleted. The problem has been fixed."

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -143,7 +143,7 @@ import java.util.Set;
import java.util.StringTokenizer;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.ALL_PARTITIONS_NAME;
import static java.util.Objects.nonNull;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -601,7 +601,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
} else {
theEntity.setHashSha256(null);
if(nonNull(theEntity.getHashSha256())){
theEntity.setHashSha256(null);
changed = true;
}
resourceBinary = null;
resourceText = null;
encoding = ResourceEncodingEnum.DEL;
@ -939,7 +943,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
entity.setUpdated(theDeletedTimestampOrNull);
entity.setNarrativeText(null);
entity.setContentText(null);
entity.setHashSha256(null);
entity.setIndexStatus(INDEX_STATUS_INDEXED);
changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);

36
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
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@ -2895,9 +2895,28 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
}
private void printQueryCount(String theMessage){
ourLog.info("QueryCount {} is: ", theMessage);
@Test
public void testDeleteResource_WithMassIngestionMode_enabled(){
myDaoConfig.setMassIngestionMode(true);
// given
Observation observation = new Observation()
.setStatus(Observation.ObservationStatus.FINAL)
.addCategory(new CodeableConcept().addCoding(new Coding("http://category-type", "12345", null)))
.setCode(new CodeableConcept().addCoding(new Coding("http://coverage-type", "12345", null)));
IIdType idDt = myObservationDao.create(observation, mySrd).getEntity().getIdDt();
// when
myCaptureQueriesListener.clear();
myObservationDao.delete(idDt, mySrd);
// then
assertQueryCount(3,1,1, 1);
}
private void printQueryCount(){
ourLog.info("\tselect: {}", myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
ourLog.info("\tupdate: {}", myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
ourLog.info("\tinsert: {}", myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
@ -2905,16 +2924,15 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
}
private void assertQueryCount(int theExpectedSelect, int theExpectedUpdate, int theExpectedInsert, int theExpectedDelete){
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
private void assertQueryCount(int theExpectedSelectCount, int theExpectedUpdateCount, int theExpectedInsertCount, int theExpectedDeleteCount){
assertEquals(theExpectedSelect, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
assertEquals(theExpectedSelectCount, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(theExpectedUpdate, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertEquals(theExpectedUpdateCount, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(theExpectedInsert, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
assertEquals(theExpectedInsertCount, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(theExpectedDelete, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
assertEquals(theExpectedDeleteCount, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
private Group createGroup(List<IIdType> theIIdTypeList) {

30
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
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@ -175,6 +175,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
myDaoConfig.setInternalSynchronousSearchSize(new DaoConfig().getInternalSynchronousSearchSize());
myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
myDaoConfig.setHistoryCountMode(DaoConfig.DEFAULT_HISTORY_COUNT_MODE);
myDaoConfig.setMassIngestionMode(false);
}
private void assertGone(IIdType theId) {
@ -2498,6 +2499,35 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
}
@Test
public void testDeleteWithMassInjectionModeEnabled(){
myDaoConfig.setMassIngestionMode(true);
// given
Observation observation = new Observation()
.setStatus(ObservationStatus.FINAL)
.addCategory(newCodeableConcept("http://somesystem","somecode"))
.setCode(newCodeableConcept("http://loinc.org", "15074-8"));
// when
IIdType idDt = myObservationDao.create(observation, mySrd).getEntity().getIdDt();
myObservationDao.delete(idDt, mySrd);
// then
runInTransaction(() -> {
Long obsertionId = idDt.getIdPartAsLong();
Long resourceCurrentVersion = myResourceTableDao.findCurrentVersionByPid(obsertionId);
int resourceVersionCount = myResourceHistoryTableDao.findAllVersionsForResourceIdInOrder(obsertionId).size();
int indexedTokenCount = myResourceIndexedSearchParamTokenDao.countForResourceId(obsertionId);
assertThat(resourceCurrentVersion, equalTo(2L));
assertThat(resourceVersionCount, equalTo(2));
assertThat(indexedTokenCount, equalTo(0));
});
}
@Test
public void testPersistContactPoint() {
List<IAnyResource> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_TELECOM, new TokenParam(null, "555-123-4567")).setLoadSynchronous(true)));