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adding a new version of reindex batch job

This commit is contained in:
leif stawnyczy 2024-09-26 16:02:46 -04:00
parent 5b50545a50
commit bb5d91ac37
25 changed files with 941 additions and 911 deletions
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45
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaResourceDaoCodeSystem.java
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@ -27,7 +27,11 @@ import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.context.support.LookupCodeRequest;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -176,6 +180,47 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
}
/**
* If there are more code systems to process
* than {@link JpaStorageSettings#getDeferIndexingForCodesystemsOfSize()},
* then these codes will have their processing deferred (for a later time).
*
* This can result in future reindex steps *skipping* these code systems (if
* they're still deferred) and thus incorrect expansions resulting.
*
* So we override the reindex method for CodeSystems specifically to
* force reindex batch jobs to wait until all code systems are processed before
* moving on.
*/
@SuppressWarnings("rawtypes")
@Override
public ReindexOutcome reindex(
IResourcePersistentId thePid,
ReindexParameters theReindexParameters,
RequestDetails theRequest,
TransactionDetails theTransactionDetails) {
ReindexOutcome outcome = super.reindex(thePid, theReindexParameters, theRequest, theTransactionDetails);
if (outcome.getWarnings().isEmpty()) {
outcome.setHasPendingWork(true);
}
return outcome;
}
@Override
public ReindexJobStatus getReindexJobStatus() {
boolean isQueueEmpty = myTermDeferredStorageSvc.isStorageQueueEmpty(true);
ReindexJobStatus status = new ReindexJobStatus();
status.setHasReindexWorkPending(!isQueueEmpty);
if (status.isHasReindexWorkPending()) {
// force a run
myTermDeferredStorageSvc.saveDeferred();
}
return status;
}
@Override
public ResourceTable updateEntity(
RequestDetails theRequest,

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
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@ -23,6 +23,7 @@ import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.models.JobInstanceFetchRequest;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;

4
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4IndexStorageOptimizedTest.java
View File

@ -23,7 +23,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.model.util.SearchParamHash;
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.jpa.reindex.ReindexStepTest;
import ca.uhn.fhir.jpa.reindex.ReindexStepV1Test;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.param.BaseParam;
@ -321,7 +321,7 @@ public class FhirResourceDaoR4IndexStorageOptimizedTest extends BaseJpaR4Test {
// Additional existing tests with enabled IndexStorageOptimized
@Nested
public class IndexStorageOptimizedReindexStepTest extends ReindexStepTest {
public class IndexStorageOptimizedReindexStepTestV1 extends ReindexStepV1Test {
@BeforeEach
void setUp() {
myStorageSettings.setIndexStorageOptimized(true);

32
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
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@ -2,12 +2,15 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.chunk.TypedPidJson;
import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeStep;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStepV1;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
@ -18,13 +21,13 @@ import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.reindex.ReindexTestHelper;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.interceptor.ForceOffsetSearchModeInterceptor;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.jpa.reindex.ReindexTestHelper;
import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.subscription.triggering.ISubscriptionTriggeringSvc;
@ -146,7 +149,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
@Autowired
private ISubscriptionTriggeringSvc mySubscriptionTriggeringSvc;
@Autowired
private ReindexStep myReindexStep;
private ReindexStepV1 myReindexStepV1;
@Autowired
private DeleteExpungeStep myDeleteExpungeStep;
@Autowired
@ -1018,7 +1021,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
// insert to: HFJ_RESOURCE, HFJ_RES_VER, HFJ_RES_LINK
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
}
@ParameterizedTest
@ -1031,7 +1033,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
})
public void testReindexJob_OptimizeStorage(boolean theOptimisticLock, ReindexParameters.OptimizeStorageModeEnum theOptimizeStorageModeEnum, int theExpectedSelectCount, int theExpectedUpdateCount) {
// Setup
ResourceIdListWorkChunkJson data = new ResourceIdListWorkChunkJson();
IIdType patientId = createPatient(withActiveTrue());
IIdType orgId = createOrganization(withName("MY ORG"));
@ -1056,7 +1057,14 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
// execute
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, mock(IJobDataSink.class), "123", "456", params);
JobInstance instance = new JobInstance();
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
mock(WorkChunk.class)
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, mock(IJobDataSink.class));
// validate
assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(theExpectedSelectCount);
@ -1064,7 +1072,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertThat(myCaptureQueriesListener.getInsertQueriesForCurrentThread()).isEmpty();
assertThat(myCaptureQueriesListener.getDeleteQueriesForCurrentThread()).isEmpty();
assertEquals(10, outcome.getRecordsProcessed());
}
@Test
@ -1095,7 +1102,14 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
// execute
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, mock(IJobDataSink.class), "123", "456", params);
JobInstance instance = new JobInstance();
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
mock(WorkChunk.class)
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, mock(IJobDataSink.class));
assertEquals(20, outcome.getRecordsProcessed());
// validate
@ -1103,10 +1117,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
public void assertNoPartitionSelectors() {
List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
for (SqlQuery next : selectQueries) {

8
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/tx/ReindexStepTest.java → hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/tx/ReindexStepV1Test.java
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@ -6,7 +6,7 @@ import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrl;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStepV1;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@ -26,7 +26,7 @@ import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class ReindexStepTest {
public class ReindexStepV1Test {
@Mock
private HapiTransactionService myHapiTransactionService;
@ -34,7 +34,7 @@ public class ReindexStepTest {
private IJobDataSink<VoidModel> myDataSink;
@InjectMocks
private ReindexStep myReindexStep;
private ReindexStepV1 myReindexStepV1;
@Captor
private ArgumentCaptor<HapiTransactionService.ExecutionBuilder> builderArgumentCaptor;
@ -51,7 +51,7 @@ public class ReindexStepTest {
when(myHapiTransactionService.buildExecutionBuilder(any())).thenCallRealMethod();
// when
myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", reindexJobParameters);
myReindexStepV1.doReindex(data, myDataSink, "index-id", "chunk-id", reindexJobParameters);
// then
assertMethodArgumentRequestPartitionId(expectedPartitionId);

81
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexStepTest.java → hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexStepV1Test.java
View File

@ -2,10 +2,13 @@ package ca.uhn.fhir.jpa.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStepV1;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
@ -25,13 +28,14 @@ import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.INDEX_STATUS_INDEXED;
import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
public class ReindexStepTest extends BaseJpaR4Test {
public class ReindexStepV1Test extends BaseJpaR4Test {
@Autowired
private ReindexStep myReindexStep;
private ReindexStepV1 myReindexStepV1;
@Mock
private IJobDataSink<VoidModel> myDataSink;
@ -46,9 +50,7 @@ public class ReindexStepTest extends BaseJpaR4Test {
@Test
public void testReindex_NoActionNeeded() {
// Setup
Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
@ -57,9 +59,19 @@ public class ReindexStepTest extends BaseJpaR4Test {
data.addTypedPid("Patient", id1);
// Execute
ReindexJobParameters params = new ReindexJobParameters();
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
JobInstance instance = new JobInstance();
instance.setInstanceId("index-id");
WorkChunk chunk = new WorkChunk();
chunk.setId("chunk-id");
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
chunk
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
// Verify
assertEquals(2, outcome.getRecordsProcessed());
@ -72,12 +84,9 @@ public class ReindexStepTest extends BaseJpaR4Test {
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Test
public void testReindex_NoActionNeeded_IndexMissingFieldsEnabled() {
// Setup
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.ENABLED);
Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
@ -88,9 +97,16 @@ public class ReindexStepTest extends BaseJpaR4Test {
data.addTypedPid("Patient", id1);
// Execute
ReindexJobParameters params = new ReindexJobParameters();
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
JobInstance instance = new JobInstance();
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
mock(WorkChunk.class)
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
// Verify
assertEquals(2, outcome.getRecordsProcessed());
@ -121,9 +137,16 @@ public class ReindexStepTest extends BaseJpaR4Test {
});
// Execute
ReindexJobParameters params = new ReindexJobParameters();
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
JobInstance instance = new JobInstance();
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
mock(WorkChunk.class)
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
// Verify
assertEquals(2, outcome.getRecordsProcessed());
@ -136,12 +159,9 @@ public class ReindexStepTest extends BaseJpaR4Test {
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Test
public void testReindex_IndexesAddedAndRemoved_IndexMissingFieldsEnabled() {
// Setup
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.ENABLED);
boolean markResourcesForReindexingUponSearchParameterChange = myStorageSettings.isMarkResourcesForReindexingUponSearchParameterChange();
myStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false); // if this were true, it would set up a lot of reindex jobs extraneous to the one we're trying to test
@ -189,9 +209,16 @@ public class ReindexStepTest extends BaseJpaR4Test {
mySearchParamRegistry.forceRefresh();
// Execute
ReindexJobParameters params = new ReindexJobParameters();
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
JobInstance instance = new JobInstance();
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
mock(WorkChunk.class)
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
// Verify
assertEquals(2, outcome.getRecordsProcessed());
@ -207,9 +234,7 @@ public class ReindexStepTest extends BaseJpaR4Test {
@Test
public void testReindex_OneResourceReindexFailedButOthersSucceeded() {
// Setup
Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
Long idPatientToInvalidate = createPatient().getIdPartAsLong();
@ -234,9 +259,19 @@ public class ReindexStepTest extends BaseJpaR4Test {
});
// Execute
ReindexJobParameters params = new ReindexJobParameters();
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id", new ReindexJobParameters());
JobInstance instance = new JobInstance();
instance.setInstanceId("index-id");
WorkChunk workChunk = new WorkChunk();
workChunk.setId("workid");
StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> stepExecutionDetails = new StepExecutionDetails<>(
params,
data,
instance,
workChunk
);
RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, myDataSink);
// Verify
assertEquals(4, outcome.getRecordsProcessed());

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexJobTest.java → hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexTaskTest.java
View File

@ -47,7 +47,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@SuppressWarnings("SqlDialectInspection")
public class ReindexJobTest extends BaseJpaR4Test {
public class ReindexTaskTest extends BaseJpaR4Test {
@Autowired
private IJobCoordinator myJobCoordinator;

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexJobWithPartitioningTest.java → hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexTaskWithPartitioningTest.java
View File

@ -27,7 +27,7 @@ import java.util.stream.Stream;
import static org.assertj.core.api.Assertions.assertThat;
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class ReindexJobWithPartitioningTest extends BaseJpaR4Test {
public class ReindexTaskWithPartitioningTest extends BaseJpaR4Test {
@Autowired
private IJobCoordinator myJobCoordinator;

805
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeSearchParam;
@ -36,7 +36,6 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.BundleBuilder;
import com.google.common.collect.Lists;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -54,22 +53,19 @@ import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.time.Duration;
import java.time.temporal.ChronoUnit;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.util.HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE;
import static org.assertj.core.api.Assertions.assertThat;
import static org.awaitility.Awaitility.await;
@ -2099,659 +2095,156 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test implements IValueSet
}
@Test
public void expandValuesetAfterReindex() {
public void reindexCodeSystems_withDeferredCodeSystems_reindexesAllCodeSystems() {
// setup
IParser parser = myFhirContext.newJsonParser();
CodeSystem cs;
ValueSet vs;
String csStr;
{
String vsStr = """
int deferredIndexingDefault = myStorageSettings.getDeferIndexingForCodesystemsOfSize();
try {
// deferred count must be less than the number of concepts on the
// CodeSystem we will upload
myStorageSettings.setDeferIndexingForCodesystemsOfSize(3);
ReindexUtils.setRetryDelay(Duration.of(500, ChronoUnit.MILLIS));
IParser parser = myFhirContext.newJsonParser();
RequestDetails rq = new SystemRequestDetails();
CodeSystem cs;
ValueSet vs;
String csStr;
{
String vsStr = """
{
"resourceType": "ValueSet",
"id": "0447bffa-01fa-4405-828a-96192e74a5d8",
"meta": {
"versionId": "2",
"lastUpdated": "2024-04-09T15:06:24.025+00:00",
"source": "#f4491e490a6a2900"
},
"url": "https://health.gov.on.ca/idms/fhir/ValueSet/IDMS-Submission-Types",
"version": "1.0.0",
"name": "IDMS-SUBMISSION-TYPES",
"title": "IDMS Submission Types",
"status": "active",
"experimental": false,
"date": "2023-09-28",
"publisher": "IDMS",
"description": "List of Submission Types",
"compose": {
"include": [
{
"system": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types"
}
]
}
}
""";
vs = parser.parseResource(ValueSet.class, vsStr);
csStr = """
{
"resourceType": "ValueSet",
"id": "0447bffa-01fa-4405-828a-96192e74a5d8",
"meta": {
"versionId": "2",
"lastUpdated": "2024-04-09T15:06:24.025+00:00",
"source": "#f4491e490a6a2900"
},
"url": "https://health.gov.on.ca/idms/fhir/ValueSet/IDMS-Submission-Types",
"version": "1.0.0",
"name": "IDMS-SUBMISSION-TYPES",
"title": "IDMS Submission Types",
"status": "active",
"experimental": false,
"date": "2023-09-28",
"publisher": "IDMS",
"description": "List of Submission Types",
"compose": {
"include": [
{
"system": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types"
}
]
}
}
""";
vs = parser.parseResource(ValueSet.class, vsStr);
csStr = """
{
"resourceType": "CodeSystem",
"id": "d9acd5b8-9533-4fa1-bb70-b4380957a8c3",
"meta": {
"versionId": "14",
"lastUpdated": "2024-06-03T17:49:56.580+00:00",
"source": "#261a82258b0978a8"
},
"url": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types",
"version": "1.0.0",
"name": "IDMS-Internal-Submission-Types",
"status": "active",
"date": "2023-09-07",
"publisher": "IDMS",
"description": "This contains a lists of codes Submission Type Codes.",
"content": "complete",
"concept": [
{
"code": "SUB-BRAND-PRODUCT",
"display": "New Brand Product (Non-New Chemical Entity)"
},
{
"code": "SUB-CLASSIFICATION",
"display": "Classification Change"
},
{
"code": "SUB-CLINICIAN-LED-SUBMISSIONS",
"display": "Clinician-Led Submissions"
},
{
"code": "SUB-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-DIN-CHANGE",
"display": "Drug Identification Number (DIN) Change"
},
{
"code": "SUB-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-DRUG-PRODUCT-NAME",
"display": "Drug Product Name Change"
},
{
"code": "SUB-FORMULATION",
"display": "Formulation Change"
},
{
"code": "SUB-GENERIC-LINE",
"display": "Generic Line Extension"
},
{
"code": "SUB-GENERIC-PRODUCT",
"display": "New Generic Product"
},
{
"code": "SUB-LINE-EXTENSION",
"display": "Line Extension"
},
{
"code": "SUB-NEW-INDICATION",
"display": "New Indication"
},
{
"code": "SUB-NEW-NATURAL",
"display": "New Natural Health Product"
},
{
"code": "SUB-NEW-OVER-COUNTER",
"display": "New Over the Counter (OTC) Product"
},
{
"code": "SUB-NEW-CHEMICAL",
"display": "New Chemical Entity"
},
{
"code": "SUB-NEW-NUTRITIONAL",
"display": "New Nutrition Product"
},
{
"code": "SUB-NUTRITIONAL-LINE",
"display": "Line Extension"
},
{
"code": "SUB-NEW-BIOSIMILAR",
"display": "New Biosimilar"
},
{
"code": "SUB-BIOSIMILAR-LINE",
"display": "Line Extension"
},
{
"code": "SUB-NEW-DIABETIC",
"display": "New Diabetic Testing Agent (DTA)"
},
{
"code": "SUB-NEW-GLUCOUSE",
"display": "New Flash Glucose Monitoring (FGM) Product"
},
{
"code": "SUB-NON-FORMULARY-SINGLE",
"display": "Non-Formulary Single Source"
},
{
"code": "SUB-NON-FORMULARY-MULTIPLE",
"display": "Non-Formulary Multiple Source "
},
{
"code": "SUB-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-PRODUCT-MONOGRAPH",
"display": "Product Monograph Change"
},
{
"code": "SUB-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-PRODUCT-CHANGE",
"display": "Product Change"
},
{
"code": "SUB-SPECIAL-PROJECTS",
"display": "Special Projects"
},
{
"code": "SUB-TEMPORARY-BENEFITS",
"display": "Temporary Benefits"
},
{
"code": "SUB-VALVED",
"display": "New Valved Holding Chamber (VHC)"
},
{
"code": "SUB-REDESIGNATION-BENEFITS",
"display": "Re-Designation of Benefits"
},
{
"code": "SUB-MANUFACTURER-INQUIRIES",
"display": "Manufacturer Inquiries"
},
{
"code": "SUB-CHALLENGES",
"display": "Challenges"
},
{
"code": "SUB-NEW-LINE",
"display": "Line Extension"
},
{
"code": "SUB-MULTI-DIN-CHANGE",
"display": "Drug Identification Number (DIN) Change"
},
{
"code": "SUB-MULTI-DRUG-PRODUCT-NAME",
"display": "Drug Product Name Change"
},
{
"code": "SUB-MULTI-PRODUCT-MONOGRAPH",
"display": "Product Monograph Change"
},
{
"code": "SUB-MULTI-FORMULATION",
"display": "Formulation Change"
},
{
"code": "SUB-MULTI-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-MULTI-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-MULTI-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-MULTI-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-MULTI-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-MULTI-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-MULTI-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-BIO-DIN-CHANGE",
"display": "Drug Identification Number (DIN) Change"
},
{
"code": "SUB-BIO-DRUG-PRODUCT-NAME",
"display": "Drug Product Name Change"
},
{
"code": "SUB-BIO-PRODUCT-MONOGRAPH",
"display": "Product Monograph Change"
},
{
"code": "SUB-BIO-FORMULATION",
"display": "Formulation Change"
},
{
"code": "SUB-BIO-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-BIO-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-BIO-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-BIO-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-BIO-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-BIO-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-BIO-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-OTC-DIN-CHANGE",
"display": "Drug Identification Number (DIN) Change"
},
{
"code": "SUB-OTC-DRUG-PRODUCT-NAME",
"display": "Drug Product Name Change"
},
{
"code": "SUB-OTC-PRODUCT-MONOGRAPH",
"display": "Product Monograph Change"
},
{
"code": "SUB-OTC-FORMULATION",
"display": "Formulation Change"
},
{
"code": "SUB-OTC-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-OTC-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-OTC-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-OTC-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-OTC-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-OTC-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-OTC-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-DIABETIC-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-DIABETIC-PRODUCT-CHANGE",
"display": "Product Change"
},
{
"code": "SUB-DIABETIC-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-DIABETIC-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-DIABETIC-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-DIABETIC-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-DIABETIC-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-DIABETIC-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-DIABETIC-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-GLUCOSE-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-GLUCOSE-PRODUCT-CHANGE",
"display": "Product Change"
},
{
"code": "SUB-GLUCOSE-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-GLUCOSE-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-GLUCOSE-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-GLUCOSE-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-GLUCOSE-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-GLUCOSE-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-GLUCOSE-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-VALVED-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-VALVED-PRODUCT-CHANGE",
"display": "Product Change"
},
{
"code": "SUB-VALVED-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-VALVED-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-VALVED-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-VALVED-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-VALVED-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-VALVED-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-VALVED-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-NATURAL-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-NATURAL-PRODUCT-CHANGE",
"display": "Product Change"
},
{
"code": "SUB-NATURAL-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-NATURAL-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-NATURAL-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-NATURAL-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-NATURAL-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-NATURAL-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-NATURAL-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-OTHER-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-OTHER-PRODUCT-CHANGE",
"display": "Product Change"
},
{
"code": "SUB-OTHER-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-OTHER-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-OTHER-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-OTHER-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-OTHER-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-OTHER-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-OTHER-OTHER-TYPE-IN",
"display": "Other"
},
{
"code": "SUB-NUTRITIONAL-PRODUCT-NAME",
"display": "Product Name Change"
},
{
"code": "SUB-NUTRITIONAL-FORMULATION",
"display": "Formulation Change"
},
{
"code": "SUB-NUTRITIONAL-DRUG-REGULATION",
"display": "Change in Food and Drug Regulation Classification"
},
{
"code": "SUB-ADVERTISING-POLICY",
"display": "Change in Advertising Policy"
},
{
"code": "SUB-NUTRITIONAL-OWNERSHIP",
"display": "Ownership Change"
},
{
"code": "SUB-NUTRITIONAL-DISTRIBUTOR",
"display": "Distributor Change"
},
{
"code": "SUB-NUTRITIONAL-ORG-NAME",
"display": "Organization Name Change"
},
{
"code": "SUB-NUTRITIONAL-PRODUCT-DISCONTINUE",
"display": "Product Discontinuation"
},
{
"code": "SUB-NUTRITIONAL-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-NUTRITIONAL-PRICE-CHANGE",
"display": "Price Change"
},
{
"code": "SUB-NUTRITIONAL-OTHER-TYPE-IN",
"display": "Other"
}
]
}
""";
cs = parser.parseResource(CodeSystem.class, csStr);
}
RequestDetails rq = new SystemRequestDetails();
int csToCreate = 1;
// create a bunch of code systems
myValueSetDao.update(vs, rq);
String csUrl = cs.getUrl();
BundleBuilder builder = new BundleBuilder(myFhirContext);
// while (cs.getConcept().size() > 90) {
// cs.getConcept().remove(1);
// }
for (int i = 0; i < csToCreate; i++) {
if (i > 0) {
"resourceType": "CodeSystem",
"id": "d9acd5b8-9533-4fa1-bb70-b4380957a8c3",
"meta": {
"versionId": "14",
"lastUpdated": "2024-06-03T17:49:56.580+00:00",
"source": "#261a82258b0978a8"
},
"url": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types",
"version": "1.0.0",
"name": "IDMS-Internal-Submission-Types",
"status": "active",
"date": "2023-09-07",
"publisher": "IDMS",
"description": "This contains a lists of codes Submission Type Codes.",
"content": "complete",
"concept": [
{
"code": "SUB-BRAND-PRODUCT",
"display": "New Brand Product (Non-New Chemical Entity)"
},
{
"code": "SUB-CLASSIFICATION",
"display": "Classification Change"
},
{
"code": "SUB-CLINICIAN-LED-SUBMISSIONS",
"display": "Clinician-Led Submissions"
},
{
"code": "SUB-DELISTING",
"display": "Delisting"
},
{
"code": "SUB-DIN-CHANGE",
"display": "Drug Identification Number (DIN) Change"
},
{
"code": "SUB-DISTRIBUTOR",
"display": "Distributor Change"
}
]
}
""";
cs = parser.parseResource(CodeSystem.class, csStr);
cs.setId("cs" + i);
cs.setUrl(csUrl + "-" + i);
}
builder.addTransactionUpdateEntry(cs);
// myCodeSystemDao.update(cs, rq);
// create our ValueSet
myValueSetDao.update(vs, rq);
// and the code system
myCodeSystemDao.update(cs, rq);
// sanity check to make sure our code system was actually created
SearchParameterMap spMap = new SearchParameterMap();
spMap.setLoadSynchronous(true);
IBundleProvider bp = myCodeSystemDao.search(spMap, rq);
assertEquals(1, bp.getAllResources().size());
IBaseResource baseResource = bp.getAllResources().get(0);
CodeSystem cssaved;
if (baseResource instanceof CodeSystem saved) {
cssaved = saved;
} else {
fail("Should be a code system");
return;
}
assertEquals(cs.getConcept().size(), cssaved.getConcept().size());
// test
// perform the reindex (we'll only target the CodeSystem here)
ReindexJobParameters params = new ReindexJobParameters();
params.addUrl("CodeSystem?");
JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
startRequest.setParameters(params);
// and wait for it to complete
Batch2JobStartResponse response = myJobCoordinator.startInstance(rq, startRequest);
myBatch2JobHelper.awaitJobCompletion(response);
// verify by doing the value expansion
ValueSetExpansionOptions options = new ValueSetExpansionOptions();
options.setCount(200); // this is way more than exist, so it's ok
ValueSet expanded = myValueSetDao.expand(vs, options);
assertNotNull(expanded);
/*
* If the reindex was performed correctly, the expanded ValueSet
* should contain all the CodeSystems that we originally
* uploaded (and nothing else).
*/
HashSet<String> all = new HashSet<>();
for (CodeSystem.ConceptDefinitionComponent set : cs.getConcept()) {
all.add(set.getCode());
}
for (ValueSet.ValueSetExpansionContainsComponent v : expanded.getExpansion().getContains()) {
all.remove(v.getCode());
}
assertTrue(all.isEmpty(), String.join(", ", all));
assertEquals(cs.getConcept().size(), expanded.getExpansion().getTotal());
} finally {
// set back to standard values
myStorageSettings.setDeferIndexingForCodesystemsOfSize(deferredIndexingDefault);
ReindexUtils.setRetryDelay(null);
}
builder.setType("transaction");
Bundle bundle = (Bundle) builder.getBundle();
mySystemDao.transaction(rq, bundle);
System.out.println("XXXX " + myDeferredStorageSvc.isStorageQueueEmpty());
myDeferredStorageSvc.logQueueForUnitTest();
AtomicInteger counter = new AtomicInteger();
await()
.atMost(10, TimeUnit.SECONDS)
.pollDelay(500, TimeUnit.MILLISECONDS)
.until(() -> {
boolean isQueueEmpty = myDeferredStorageSvc.isStorageQueueEmpty(false);
if (!isQueueEmpty) {
myDeferredStorageSvc.saveAllDeferred();
}
return isQueueEmpty;
});
if (myDeferredStorageSvc.isJobsExecuting()) {
System.out.println("running jobs");
myDeferredStorageSvc.saveAllDeferred();
myBatch2JobHelper.awaitJobCompletion(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
myBatch2JobHelper.awaitJobCompletion(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
}
System.out.println("XXX " + myDeferredStorageSvc.isStorageQueueEmpty() + " " + counter.get());
myDeferredStorageSvc.logQueueForUnitTest();
myDeferredStorageSvc.toString();
// myDeferredStorageSvc.saveAllDeferred();
// perform the reindex
ReindexJobParameters params = new ReindexJobParameters();
params.addUrl("CodeSystem?");
JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
startRequest.setParameters(params);
System.out.println("xxxx starting reindex");
Batch2JobStartResponse response = myJobCoordinator.startInstance(rq, startRequest);
myBatch2JobHelper.awaitJobCompletion(response);
System.out.println("XXXX reindex done " + myDeferredStorageSvc.isStorageQueueEmpty());
// get the codes
SearchParameterMap spMap = new SearchParameterMap();
spMap.setLoadSynchronous(true);
IBundleProvider bp = myCodeSystemDao.search(spMap, rq);
// do value expansion
ValueSetExpansionOptions options = new ValueSetExpansionOptions();
options.setCount(200);
ValueSet expanded = myValueSetDao.expand(vs, options);
assertNotNull(expanded);
HashSet<String> all = new HashSet<>();
for (CodeSystem.ConceptDefinitionComponent set : cs.getConcept()) {
all.add(set.getCode());
}
for (ValueSet.ValueSetExpansionContainsComponent v : expanded.getExpansion().getContains()) {
all.remove(v.getCode());
}
assertTrue(all.isEmpty(), String.join(", ", all));
assertEquals(cs.getConcept().size(), expanded.getExpansion().getTotal());
}
@Autowired
private IJobCoordinator myJobCoordinator;
@Autowired
private ITermDeferredStorageSvc myDeferredStorageSvc;
}

3
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java
View File

@ -19,6 +19,7 @@
*/
package ca.uhn.fhir.jpa.test;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
import ca.uhn.fhir.context.FhirContext;
@ -559,6 +560,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Autowired
protected IJobMaintenanceService myJobMaintenanceService;
@Autowired
protected IJobCoordinator myJobCoordinator;
@RegisterExtension
private final PreventDanglingInterceptorsExtension myPreventDanglingInterceptorsExtension = new PreventDanglingInterceptorsExtension(()-> myInterceptorRegistry);

69
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/BaseReindexStep.java Normal file
View File

@ -0,0 +1,69 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
public class BaseReindexStep {
public static final int REINDEX_MAX_RETRIES = 10;
protected final HapiTransactionService myHapiTransactionService;
protected IFhirSystemDao<?, ?> mySystemDao;
protected DaoRegistry myDaoRegistry;
protected IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
public BaseReindexStep(
HapiTransactionService theHapiTransactionService,
IFhirSystemDao<?, ?> theSystemDao,
DaoRegistry theRegistry,
IIdHelperService<IResourcePersistentId<?>> theIdHelperService
) {
myHapiTransactionService = theHapiTransactionService;
mySystemDao = theSystemDao;
myDaoRegistry = theRegistry;
myIdHelperService = theIdHelperService;
}
public ReindexResults doReindex(
ResourceIdListWorkChunkJson data,
IJobDataSink<?> theDataSink,
String theInstanceId,
String theChunkId,
ReindexJobParameters theJobParameters) {
RequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setRetry(true);
requestDetails.setMaxRetries(REINDEX_MAX_RETRIES);
TransactionDetails transactionDetails = new TransactionDetails();
ReindexTask.JobParameters jp = new ReindexTask.JobParameters();
jp.setData(data)
.setRequestDetails(requestDetails)
.setTransactionDetails(transactionDetails)
.setDataSink(theDataSink)
.setInstanceId(theInstanceId)
.setChunkId(theChunkId)
.setJobParameters(theJobParameters);
ReindexTask reindexJob = new ReindexTask(
jp, myDaoRegistry, mySystemDao, myIdHelperService
);
return myHapiTransactionService
.withRequest(requestDetails)
.withTransactionDetails(transactionDetails)
.withRequestPartitionId(data.getRequestPartitionId())
.execute(reindexJob);
}
}

42
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/CheckPendingReindexWorkStep.java Normal file
View File

@ -0,0 +1,42 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.api.RetryChunkLaterException;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import jakarta.annotation.Nonnull;
import org.springframework.beans.factory.annotation.Autowired;
public class CheckPendingReindexWorkStep implements IJobStepWorker<ReindexJobParameters, ReindexResults, VoidModel> {
@Autowired
private ReindexJobService myReindexJobService;
@Nonnull
@Override
public RunOutcome run(
@Nonnull StepExecutionDetails<ReindexJobParameters, ReindexResults> theStepExecutionDetails,
@Nonnull IJobDataSink<VoidModel> theDataSink) throws JobExecutionFailedException {
ReindexResults results = theStepExecutionDetails.getData();
if (!results.getResourceToHasWorkToComplete().isEmpty()) {
if (myReindexJobService.anyResourceHasPendingReindexWork(results.getResourceToHasWorkToComplete())) {
// give time for reindex work to complete
throw new RetryChunkLaterException(ReindexUtils.getRetryLaterDelay());
}
}
return RunOutcome.SUCCESS;
}
}

81
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexAppCtx.java
View File

@ -26,12 +26,20 @@ import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ChunkRangeJson;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
import ca.uhn.fhir.batch2.jobs.step.GenerateRangeChunksStep;
import ca.uhn.fhir.batch2.jobs.step.LoadIdsStep;
import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -40,12 +48,22 @@ public class ReindexAppCtx {
public static final String JOB_REINDEX = "REINDEX";
@Autowired
private HapiTransactionService myHapiTransactionService;
@Autowired
private IFhirSystemDao<?, ?> mySystemDao;
@Autowired
private DaoRegistry myRegistry;
@Autowired
private IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
// Version 2
@Bean
public JobDefinition<ReindexJobParameters> reindexJobDefinition(IBatch2DaoSvc theBatch2DaoSvc) {
public JobDefinition<ReindexJobParameters> reindexJobDefinitionV2(IBatch2DaoSvc theBatch2DaoSvc) {
return JobDefinition.newBuilder()
.setJobDefinitionId(JOB_REINDEX)
.setJobDescription("Reindex resources")
.setJobDefinitionVersion(1)
.setJobDefinitionVersion(2)
.setParametersType(ReindexJobParameters.class)
.setParametersValidator(reindexJobParametersValidator(theBatch2DaoSvc))
.gatedExecution()
@ -59,12 +77,42 @@ public class ReindexAppCtx {
"Load IDs of resources to reindex",
ResourceIdListWorkChunkJson.class,
reindexLoadIdsStep(theBatch2DaoSvc))
.addLastStep("reindex",
.addIntermediateStep("reindex-start",
"Perform the resource reindex",
reindexStep())
ReindexResults.class,
reindexStepV2())
.addLastStep("reindex-pending-work",
"Waits for reindex work to complete.",
pendingWorkStep())
.build();
}
// Version 1
@Bean
public JobDefinition<ReindexJobParameters> reindexJobDefinitionV1(IBatch2DaoSvc theBatch2DaoSvc) {
return JobDefinition.newBuilder()
.setJobDefinitionId(JOB_REINDEX)
.setJobDescription("Reindex resources")
.setJobDefinitionVersion(1)
.setParametersType(ReindexJobParameters.class)
.setParametersValidator(reindexJobParametersValidator(theBatch2DaoSvc))
.gatedExecution()
.addFirstStep(
"generate-ranges",
"Generate data ranges to reindex",
ChunkRangeJson.class,
reindexGenerateRangeChunksStep())
.addIntermediateStep(
"load-ids",
"Load IDs of resources to reindex",
ResourceIdListWorkChunkJson.class,
reindexLoadIdsStep(theBatch2DaoSvc))
.addLastStep("reindex-start",
"Start the resource reindex",
reindexStepV1())
.build();
}
@Bean
public IJobStepWorker<ReindexJobParameters, VoidModel, ChunkRangeJson> reindexGenerateRangeChunksStep() {
return new GenerateRangeChunksStep<>();
@ -83,15 +131,30 @@ public class ReindexAppCtx {
}
@Bean
public ReindexStep reindexStep() {
return new ReindexStep();
public ReindexStepV1 reindexStepV1() {
return new ReindexStepV1(myHapiTransactionService, mySystemDao, myRegistry, myIdHelperService);
}
@Bean
public ReindexStepV2 reindexStepV2() {
return new ReindexStepV2(jobService(), myHapiTransactionService, mySystemDao, myRegistry, myIdHelperService);
}
@Bean
public CheckPendingReindexWorkStep pendingWorkStep() {
return new CheckPendingReindexWorkStep();
}
@Bean
public ReindexProvider reindexProvider(
FhirContext theFhirContext,
IJobCoordinator theJobCoordinator,
IJobPartitionProvider theJobPartitionHandler) {
FhirContext theFhirContext,
IJobCoordinator theJobCoordinator,
IJobPartitionProvider theJobPartitionHandler) {
return new ReindexProvider(theFhirContext, theJobCoordinator, theJobPartitionHandler);
}
@Bean
public ReindexJobService jobService() {
return new ReindexJobService(myRegistry);
}
}

203
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexStep.java
View File

@ -1,203 +0,0 @@
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.StopWatch;
import jakarta.annotation.Nonnull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import java.util.List;
import java.util.concurrent.TimeUnit;
public class ReindexStep implements IJobStepWorker<ReindexJobParameters, ResourceIdListWorkChunkJson, VoidModel> {
public static final int REINDEX_MAX_RETRIES = 10;
private static final Logger ourLog = LoggerFactory.getLogger(ReindexStep.class);
@Autowired
private HapiTransactionService myHapiTransactionService;
@Autowired
private IFhirSystemDao<?, ?> mySystemDao;
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private IIdHelperService<IResourcePersistentId> myIdHelperService;
@Nonnull
@Override
public RunOutcome run(
@Nonnull StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails,
@Nonnull IJobDataSink<VoidModel> theDataSink)
throws JobExecutionFailedException {
ResourceIdListWorkChunkJson data = theStepExecutionDetails.getData();
ReindexJobParameters jobParameters = theStepExecutionDetails.getParameters();
return doReindex(
data,
theDataSink,
theStepExecutionDetails.getInstance().getInstanceId(),
theStepExecutionDetails.getChunkId(),
jobParameters);
}
@Nonnull
public RunOutcome doReindex(
ResourceIdListWorkChunkJson data,
IJobDataSink<VoidModel> theDataSink,
String theInstanceId,
String theChunkId,
ReindexJobParameters theJobParameters) {
RequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setRetry(true);
requestDetails.setMaxRetries(REINDEX_MAX_RETRIES);
TransactionDetails transactionDetails = new TransactionDetails();
ReindexJob reindexJob = new ReindexJob(
data, requestDetails, transactionDetails, theDataSink, theInstanceId, theChunkId, theJobParameters);
myHapiTransactionService
.withRequest(requestDetails)
.withTransactionDetails(transactionDetails)
.withRequestPartitionId(data.getRequestPartitionId())
.execute(reindexJob);
return new RunOutcome(data.size());
}
private class ReindexJob implements TransactionCallback<Void> {
private final ResourceIdListWorkChunkJson myData;
private final RequestDetails myRequestDetails;
private final TransactionDetails myTransactionDetails;
private final IJobDataSink<VoidModel> myDataSink;
private final String myChunkId;
private final String myInstanceId;
private final ReindexJobParameters myJobParameters;
public ReindexJob(
ResourceIdListWorkChunkJson theData,
RequestDetails theRequestDetails,
TransactionDetails theTransactionDetails,
IJobDataSink<VoidModel> theDataSink,
String theInstanceId,
String theChunkId,
ReindexJobParameters theJobParameters) {
myData = theData;
myRequestDetails = theRequestDetails;
myTransactionDetails = theTransactionDetails;
myDataSink = theDataSink;
myInstanceId = theInstanceId;
myChunkId = theChunkId;
myJobParameters = theJobParameters;
myDataSink.setWarningProcessor(new ReindexWarningProcessor());
}
@Override
public Void doInTransaction(@Nonnull TransactionStatus theStatus) {
List<IResourcePersistentId> persistentIds = myData.getResourcePersistentIds(myIdHelperService);
ourLog.info(
"Starting reindex work chunk with {} resources - Instance[{}] Chunk[{}]",
persistentIds.size(),
myInstanceId,
myChunkId);
StopWatch sw = new StopWatch();
// Prefetch Resources from DB
boolean reindexSearchParameters =
myJobParameters.getReindexSearchParameters() != ReindexParameters.ReindexSearchParametersEnum.NONE;
mySystemDao.preFetchResources(persistentIds, reindexSearchParameters);
ourLog.info(
"Prefetched {} resources in {} - Instance[{}] Chunk[{}]",
persistentIds.size(),
sw,
myInstanceId,
myChunkId);
ReindexParameters parameters = new ReindexParameters()
.setReindexSearchParameters(myJobParameters.getReindexSearchParameters())
.setOptimizeStorage(myJobParameters.getOptimizeStorage())
.setOptimisticLock(myJobParameters.getOptimisticLock());
// Reindex
sw.restart();
for (int i = 0; i < myData.size(); i++) {
String nextResourceType = myData.getResourceType(i);
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextResourceType);
IResourcePersistentId<?> resourcePersistentId = persistentIds.get(i);
try {
ReindexOutcome outcome =
dao.reindex(resourcePersistentId, parameters, myRequestDetails, myTransactionDetails);
outcome.getWarnings().forEach(myDataSink::recoveredError);
} catch (BaseServerResponseException | DataFormatException e) {
String resourceForcedId = myIdHelperService
.translatePidIdToForcedIdWithCache(resourcePersistentId)
.orElse(resourcePersistentId.toString());
String resourceId = nextResourceType + "/" + resourceForcedId;
ourLog.debug("Failure during reindexing {}", resourceId, e);
myDataSink.recoveredError("Failure reindexing " + resourceId + ": " + e.getMessage());
}
}
ourLog.info(
"Finished reindexing {} resources in {} - {}/sec - Instance[{}] Chunk[{}]",
persistentIds.size(),
sw,
sw.formatThroughput(persistentIds.size(), TimeUnit.SECONDS),
myInstanceId,
myChunkId);
return null;
}
}
}

66
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexStepV1.java Normal file
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@ -0,0 +1,66 @@
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import jakarta.annotation.Nonnull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ReindexStepV1 extends BaseReindexStep implements IJobStepWorker<ReindexJobParameters, ResourceIdListWorkChunkJson, VoidModel> {
private static final Logger ourLog = LoggerFactory.getLogger(ReindexStepV1.class);
public ReindexStepV1(HapiTransactionService theHapiTransactionService, IFhirSystemDao<?, ?> theSystemDao, DaoRegistry theRegistry, IIdHelperService<IResourcePersistentId<?>> theIdHelperService) {
super(theHapiTransactionService, theSystemDao, theRegistry, theIdHelperService);
}
@Nonnull
@Override
public RunOutcome run(
@Nonnull StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails,
@Nonnull IJobDataSink<VoidModel> theDataSink)
throws JobExecutionFailedException {
ResourceIdListWorkChunkJson data = theStepExecutionDetails.getData();
ReindexJobParameters jobParameters = theStepExecutionDetails.getParameters();
doReindex(
data,
theDataSink,
theStepExecutionDetails.getInstance().getInstanceId(),
theStepExecutionDetails.getChunkId(),
jobParameters);
return new RunOutcome(data.size());
}
}

65
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexStepV2.java Normal file
View File

@ -0,0 +1,65 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.api.RetryChunkLaterException;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.chunk.TypedPidJson;
import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
import ca.uhn.fhir.batch2.jobs.reindex.svcs.ReindexJobService;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import jakarta.annotation.Nonnull;
import java.util.HashMap;
import java.util.Map;
import java.util.stream.Collectors;
public class ReindexStepV2 extends BaseReindexStep implements IJobStepWorker<ReindexJobParameters, ResourceIdListWorkChunkJson, ReindexResults> {
private ReindexJobService myReindexJobService;
public ReindexStepV2(ReindexJobService theJobService,
HapiTransactionService theHapiTransactionService, IFhirSystemDao<?, ?> theSystemDao, DaoRegistry theRegistry, IIdHelperService<IResourcePersistentId<?>> theIdHelperService) {
super(theHapiTransactionService, theSystemDao, theRegistry, theIdHelperService);
myReindexJobService = theJobService;
}
@Nonnull
@Override
public RunOutcome run(@Nonnull StepExecutionDetails<ReindexJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails, @Nonnull IJobDataSink<ReindexResults> theDataSink) throws JobExecutionFailedException {
ResourceIdListWorkChunkJson data = theStepExecutionDetails.getData();
ReindexJobParameters jobParameters = theStepExecutionDetails.getParameters();
// This is not strictly necessary;
// but we'll ensure that no outstanding "reindex work"
// is waiting to be completed, so that when we do
// our reindex, it won't skip over data
Map<String, Boolean> resourceTypesToCheckFlag = new HashMap<>();
data.getTypedPids().forEach(id -> {
// we don't really care about duplicates
resourceTypesToCheckFlag.put(id.getResourceType(), true);
});
if (myReindexJobService.anyResourceHasPendingReindexWork(resourceTypesToCheckFlag)) {
throw new RetryChunkLaterException(ReindexUtils.getRetryLaterDelay());
}
ReindexResults results = doReindex(
data,
theDataSink,
theStepExecutionDetails.getInstance().getInstanceId(),
theStepExecutionDetails.getChunkId(),
jobParameters);
theDataSink.accept(results);
return new RunOutcome(data.size());
}
}

201
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexTask.java Normal file
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@ -0,0 +1,201 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
import ca.uhn.fhir.batch2.jobs.reindex.models.ReindexResults;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.StopWatch;
import jakarta.annotation.Nonnull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import java.util.List;
import java.util.concurrent.TimeUnit;
public class ReindexTask implements TransactionCallback<ReindexResults> {
private static final Logger ourLog = LoggerFactory.getLogger(ReindexTask.class);
public static class JobParameters {
private ResourceIdListWorkChunkJson myData;
private RequestDetails myRequestDetails;
private TransactionDetails myTransactionDetails;
private IJobDataSink<?> myDataSink;
private String myChunkId;
private String myInstanceId;
private ReindexJobParameters myJobParameters;
public ResourceIdListWorkChunkJson getData() {
return myData;
}
public JobParameters setData(ResourceIdListWorkChunkJson theData) {
myData = theData;
return this;
}
public RequestDetails getRequestDetails() {
return myRequestDetails;
}
public JobParameters setRequestDetails(RequestDetails theRequestDetails) {
myRequestDetails = theRequestDetails;
return this;
}
public TransactionDetails getTransactionDetails() {
return myTransactionDetails;
}
public JobParameters setTransactionDetails(TransactionDetails theTransactionDetails) {
myTransactionDetails = theTransactionDetails;
return this;
}
public IJobDataSink<?> getDataSink() {
return myDataSink;
}
public JobParameters setDataSink(IJobDataSink<?> theDataSink) {
myDataSink = theDataSink;
return this;
}
public String getChunkId() {
return myChunkId;
}
public JobParameters setChunkId(String theChunkId) {
myChunkId = theChunkId;
return this;
}
public String getInstanceId() {
return myInstanceId;
}
public JobParameters setInstanceId(String theInstanceId) {
myInstanceId = theInstanceId;
return this;
}
public ReindexJobParameters getJobParameters() {
return myJobParameters;
}
public JobParameters setJobParameters(ReindexJobParameters theJobParameters) {
myJobParameters = theJobParameters;
return this;
}
}
private final DaoRegistry myDaoRegistry;
private final IFhirSystemDao<?, ?> mySystemDao;
private final IIdHelperService<IResourcePersistentId<?>> myIdHelperService;
private final ResourceIdListWorkChunkJson myData;
private final RequestDetails myRequestDetails;
private final TransactionDetails myTransactionDetails;
private final IJobDataSink<?> myDataSink;
private final String myChunkId;
private final String myInstanceId;
private final ReindexJobParameters myJobParameters;
public ReindexTask(
JobParameters theJobParameters,
DaoRegistry theRegistry,
IFhirSystemDao<?, ?> theSystemDao,
IIdHelperService<IResourcePersistentId<?>> theIdHelperService
) {
myDaoRegistry = theRegistry;
mySystemDao = theSystemDao;
myIdHelperService = theIdHelperService;
myData = theJobParameters.getData();
myRequestDetails = theJobParameters.getRequestDetails();
myTransactionDetails = theJobParameters.getTransactionDetails();
myDataSink = theJobParameters.getDataSink();
myInstanceId = theJobParameters.getInstanceId();
myChunkId = theJobParameters.getChunkId();
myJobParameters = theJobParameters.getJobParameters();
myDataSink.setWarningProcessor(new ReindexWarningProcessor());
}
@Override
public ReindexResults doInTransaction(@Nonnull TransactionStatus theStatus) {
List<IResourcePersistentId<?>> persistentIds = myData.getResourcePersistentIds(myIdHelperService);
ourLog.info(
"Starting reindex work chunk with {} resources - Instance[{}] Chunk[{}]",
persistentIds.size(),
myInstanceId,
myChunkId);
StopWatch sw = new StopWatch();
ReindexResults reindexResults = new ReindexResults();
// Prefetch Resources from DB
boolean reindexSearchParameters =
myJobParameters.getReindexSearchParameters() != ReindexParameters.ReindexSearchParametersEnum.NONE;
mySystemDao.preFetchResources(persistentIds, reindexSearchParameters);
ourLog.info(
"Prefetched {} resources in {} - Instance[{}] Chunk[{}]",
persistentIds.size(),
sw,
myInstanceId,
myChunkId);
ReindexParameters parameters = new ReindexParameters()
.setReindexSearchParameters(myJobParameters.getReindexSearchParameters())
.setOptimizeStorage(myJobParameters.getOptimizeStorage())
.setOptimisticLock(myJobParameters.getOptimisticLock());
// Reindex
sw.restart();
for (int i = 0; i < myData.size(); i++) {
String nextResourceType = myData.getResourceType(i);
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextResourceType);
IResourcePersistentId<?> resourcePersistentId = persistentIds.get(i);
try {
ReindexOutcome outcome =
dao.reindex(resourcePersistentId, parameters, myRequestDetails, myTransactionDetails);
outcome.getWarnings().forEach(myDataSink::recoveredError);
reindexResults.addResourceTypeToCompletionStatus(nextResourceType,
outcome.isHasPendingWork());
} catch (BaseServerResponseException | DataFormatException e) {
String resourceForcedId = myIdHelperService
.translatePidIdToForcedIdWithCache(resourcePersistentId)
.orElse(resourcePersistentId.toString());
String resourceId = nextResourceType + "/" + resourceForcedId;
ourLog.error("Failure during reindexing {}", resourceId, e);
myDataSink.recoveredError("Failure reindexing " + resourceId + ": " + e.getMessage());
}
}
ourLog.info(
"Finished reindexing {} resources in {} - {}/sec - Instance[{}] Chunk[{}]",
persistentIds.size(),
sw,
sw.formatThroughput(persistentIds.size(), TimeUnit.SECONDS),
myInstanceId,
myChunkId);
return reindexResults;
}
}

28
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexUtils.java Normal file
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@ -0,0 +1,28 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import com.google.common.annotations.VisibleForTesting;
import java.time.Duration;
import java.time.temporal.ChronoUnit;
public class ReindexUtils {
private static final Duration RETRY_DELAY = Duration.of(30, ChronoUnit.SECONDS);
private static Duration myDelay;
/**
* Returns the retry delay for reindex jobs that require polling.
*/
public static Duration getRetryLaterDelay() {
if (myDelay != null) {
return myDelay;
}
return RETRY_DELAY;
}
@VisibleForTesting
public static void setRetryDelay(Duration theDuration) {
myDelay = theDuration;
}
}

30
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/models/ReindexResults.java Normal file
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@ -0,0 +1,30 @@
package ca.uhn.fhir.batch2.jobs.reindex.models;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.HashMap;
public class ReindexResults implements IModelJson {
/**
* A map of resource type : whether or not the reindex is completed;
* true = more work needed. false (or omitted) = reindex is done
*/
@JsonProperty("resource2NeedsWork")
private HashMap<String, Boolean> myResourceToHasWorkToComplete;
public ReindexResults() {}
public HashMap<String, Boolean> getResourceToHasWorkToComplete() {
if (myResourceToHasWorkToComplete == null) {
myResourceToHasWorkToComplete = new HashMap<>();
}
return myResourceToHasWorkToComplete;
}
public void addResourceTypeToCompletionStatus(String theResourceType, boolean theRequiresMoreWork) {
getResourceToHasWorkToComplete()
.put(theResourceType, theRequiresMoreWork);
}
}

38
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/svcs/ReindexJobService.java Normal file
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@ -0,0 +1,38 @@
package ca.uhn.fhir.batch2.jobs.reindex.svcs;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
import java.util.Map;
public class ReindexJobService {
private final DaoRegistry myDaoRegistry;
public ReindexJobService(DaoRegistry theRegistry) {
myDaoRegistry = theRegistry;
}
/**
* Checks if any of the resource types in the map have any pending reindex work waiting.
* This will return true after the first such encounter, and only return false if no
* reindex work is required for any resource.
* @param theResourceTypesToCheckFlag map of resourceType:whether or not to check
* @return true if there's reindex work pending, false otherwise
*/
public boolean anyResourceHasPendingReindexWork(Map<String, Boolean> theResourceTypesToCheckFlag) {
for (String resourceType : theResourceTypesToCheckFlag.keySet()) {
boolean toCheck = theResourceTypesToCheckFlag.get(resourceType);
if (toCheck) {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
ReindexJobStatus status = dao.getReindexJobStatus();
if (status.isHasReindexWorkPending()) {
return true;
}
}
}
return false;
}
}

2
hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexJobParametersValidatorTest.java → hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexTaskParametersValidatorTest.java
View File

@ -13,7 +13,7 @@ import java.util.List;
import static org.assertj.core.api.Assertions.assertThat;
@ExtendWith(MockitoExtension.class)
public class ReindexJobParametersValidatorTest {
public class ReindexTaskParametersValidatorTest {
@Mock
private UrlListValidator myListValidator;

2
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/chunk/ResourceIdListWorkChunkJson.java
View File

@ -62,7 +62,7 @@ public class ResourceIdListWorkChunkJson implements IModelJson {
return myRequestPartitionId;
}
private List<TypedPidJson> getTypedPids() {
public List<TypedPidJson> getTypedPids() {
if (myTypedPids == null) {
myTypedPids = new ArrayList<>();
}

13
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDao.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -315,12 +316,24 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
* @param theResourcePersistentId The ID
* @return
*/
@SuppressWarnings("rawtypes")
ReindexOutcome reindex(
IResourcePersistentId theResourcePersistentId,
ReindexParameters theReindexParameters,
RequestDetails theRequest,
TransactionDetails theTransactionDetails);
/**
* Returns ReindexJobStatus information object that tells the caller
* if a reindex job is still in progress or not.
*
* If the implementing DAO requires additional work during reindexing,
* this is the method to override.
*/
default ReindexJobStatus getReindexJobStatus() {
return ReindexJobStatus.NO_WORK_NEEDED;
}
void removeTag(
IIdType theId, TagTypeEnum theTagType, String theSystem, String theCode, RequestDetails theRequestDetails);

13
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/dao/ReindexOutcome.java
View File

@ -29,6 +29,11 @@ public class ReindexOutcome {
private List<String> myWarnings;
/**
* True if there is additional (async) work to wait on.
*/
private boolean myHasPendingWork;
public List<String> getWarnings() {
return defaultIfNull(myWarnings, Collections.emptyList());
}
@ -39,4 +44,12 @@ public class ReindexOutcome {
}
myWarnings.add(theWarning);
}
public boolean isHasPendingWork() {
return myHasPendingWork;
}
public void setHasPendingWork(boolean theHasPendingWork) {
myHasPendingWork = theHasPendingWork;
}
}

16
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/model/ReindexJobStatus.java Normal file
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@ -0,0 +1,16 @@
package ca.uhn.fhir.jpa.api.model;
public class ReindexJobStatus {
public static ReindexJobStatus NO_WORK_NEEDED = new ReindexJobStatus();
private boolean myHasReindexWorkPending;
public boolean isHasReindexWorkPending() {
return myHasReindexWorkPending;
}
public void setHasReindexWorkPending(boolean theHasReindexWorkPending) {
myHasReindexWorkPending = theHasReindexWorkPending;
}
}