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Code Issues Packages Projects Releases Wiki Activity

Reindex batch job fails when processing deleted resources. (#4482)

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* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
This commit is contained in:
Etienne Poirier 2023-02-01 08:15:33 -05:00 committed by GitHub
parent 67ace43492
commit dd8c8a3b24
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3 changed files with 49 additions and 2 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4481-reindex-batch-job-fails-when-processing-deleted-resources.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 4481
jira: SMILE-4961
title: "Previously, a reindex batch job would fail when executing on deleted resources. This issue has been fixed."

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/Batch2DaoSvcImpl.java
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@ -51,6 +51,7 @@ import javax.annotation.Nullable;
import java.util.Date;
import java.util.List;
import java.util.stream.Collectors;
import static org.apache.commons.collections4.CollectionUtils.isNotEmpty;
public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
@ -99,8 +100,9 @@ public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
List<IResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
Date lastDate = null;
if (ids.size() > 0) {
lastDate = dao.readByPid(ids.get(ids.size() - 1)).getMeta().getLastUpdated();
if (isNotEmpty(ids)) {
IResourcePersistentId lastResourcePersistentId = ids.get(ids.size() - 1);
lastDate = dao.readByPid(lastResourcePersistentId, true).getMeta().getLastUpdated();
}
return new HomogeneousResourcePidList(resourceType, ids, lastDate);

40
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
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@ -9,6 +9,7 @@ import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.jpa.test.PatientReindexTestHelper;
@ -23,15 +24,19 @@ import org.junit.jupiter.params.provider.MethodSource;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
import java.util.Date;
import java.util.List;
import java.util.stream.Stream;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class ReindexJobTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ReindexJobTest.class);
@Autowired
private IJobCoordinator myJobCoordinator;
@ -89,6 +94,41 @@ public class ReindexJobTest extends BaseJpaR4Test {
myDaoConfig.setMarkResourcesForReindexingUponSearchParameterChange(reindexPropertyCache);
}
@Test
public void testReindexDeletedResources_byUrl_willRemoveDeletedResourceEntriesFromIndexTables(){
IIdType obsId = myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.FINAL);
runInTransaction(() -> {
int entriesInSpIndexTokenTable = myResourceIndexedSearchParamTokenDao.countForResourceId(obsId.getIdPartAsLong());
assertThat(entriesInSpIndexTokenTable, equalTo(1));
// simulate resource deletion
ResourceTable resource = myResourceTableDao.findById(obsId.getIdPartAsLong()).get();
Date currentDate = new Date();
resource.setDeleted(currentDate);
resource.setUpdated(currentDate);
resource.setHashSha256(null);
resource.setVersion(2L);
myResourceTableDao.save(resource);
});
// execute reindexing
ReindexJobParameters parameters = new ReindexJobParameters();
parameters.addUrl("Observation?status=final");
JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
startRequest.setParameters(parameters);
Batch2JobStartResponse res = myJobCoordinator.startInstance(startRequest);
myBatch2JobHelper.awaitJobCompletion(res);
// then
runInTransaction(() -> {
int entriesInSpIndexTokenTablePostReindexing = myResourceIndexedSearchParamTokenDao.countForResourceId(obsId.getIdPartAsLong());
assertThat(entriesInSpIndexTokenTablePostReindexing, equalTo(0));
});
}
@Test
public void testReindex_Everything() {
// setup