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Merge 82075fa3ee into 061390d76b

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TipzCM 2024-11-27 08:24:34 -05:00 committed by GitHub
parent 061390d76b 82075fa3ee
commit 28ce779d6a
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10 changed files with 228 additions and 30 deletions
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8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6478-transaction-bundle-updates-with-multiple-conditional-urls.yaml Normal file
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@ -0,0 +1,8 @@
---
type: perf
issue: 6478
jira: SMILE-8955
title: "Transactions with multiple saved search urls will have the saved search urls
deleted in a batch, instead of 1 at a time.
This is a minor performance update.
"

56
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -2351,13 +2351,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
RequestDetails theRequest,
TransactionDetails theTransactionDetails,
RequestPartitionId theRequestPartitionId) {
DaoMethodOutcome outcome = null;
preProcessResourceForStorage(theResource);
preProcessResourceForStorage(theResource, theRequest, theTransactionDetails, thePerformIndexing);
ResourceTable entity = null;
IIdType resourceId;
IIdType resourceId = null;
RestOperationTypeEnum update = RestOperationTypeEnum.UPDATE;
if (isNotBlank(theMatchUrl)) {
// Validate that the supplied resource matches the conditional.
@ -2399,7 +2399,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
theResource.setId(UUID.randomUUID().toString());
theResource.setUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED, Boolean.TRUE);
}
DaoMethodOutcome outcome = doCreateForPostOrPut(
outcome = doCreateForPostOrPut(
theRequest,
theResource,
theMatchUrl,
@ -2414,8 +2414,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
myMatchResourceUrlService.matchUrlResolved(
theTransactionDetails, getResourceName(), theMatchUrl, (JpaPid) outcome.getPersistentId());
}
return outcome;
}
} else {
/*
@ -2445,7 +2443,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
if (create) {
return doCreateForPostOrPut(
outcome = doCreateForPostOrPut(
theRequest,
theResource,
null,
@ -2458,16 +2456,35 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
// Start
return doUpdateForUpdateOrPatch(
theRequest,
resourceId,
theMatchUrl,
thePerformIndexing,
theForceUpdateVersion,
theResource,
entity,
update,
theTransactionDetails);
if (outcome == null) {
outcome = doUpdateForUpdateOrPatch(
theRequest,
resourceId,
theMatchUrl,
thePerformIndexing,
theForceUpdateVersion,
theResource,
entity,
update,
theTransactionDetails);
}
postUpdateTransaction(theTransactionDetails);
return outcome;
}
@SuppressWarnings("rawtypes")
protected void postUpdateTransaction(TransactionDetails theTransactionDetails) {
// Transactions will delete these at the end of the entire transaction
if (!theTransactionDetails.isFhirTransaction()) {
Set<IResourcePersistentId> resourceIds = theTransactionDetails.getUpdatedResourceIds();
if (resourceIds != null && !resourceIds.isEmpty()) {
List<Long> ids = resourceIds.stream().map(r -> (Long) r.getId()).collect(Collectors.toList());
myResourceSearchUrlSvc.deleteByResIds(ids);
}
}
}
@Override
@ -2489,9 +2506,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
*/
ResourceTable entity = (ResourceTable) theEntity;
if (entity.isSearchUrlPresent()) {
myResourceSearchUrlSvc.deleteByResId(
(Long) theEntity.getPersistentId().getId());
entity.setSearchUrlPresent(false);
JpaPid persistentId = JpaPid.fromId(entity.getResourceId());
theTransactionDetails.addUpdatedResourceId(persistentId);
entity.setSearchUrlPresent(false); // it will be removed at the end
}
return super.doUpdateForUpdateOrPatch(

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View File

@ -33,10 +33,12 @@ import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.search.ResourceSearchUrlSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
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.param.TokenParam;
import ca.uhn.fhir.util.FhirTerser;
@ -114,6 +116,9 @@ public class TransactionProcessor extends BaseTransactionProcessor {
@Autowired
private MatchUrlService myMatchUrlService;
@Autowired
private ResourceSearchUrlSvc myResourceSearchUrlSvc;
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionSvc;
@ -224,6 +229,16 @@ public class TransactionProcessor extends BaseTransactionProcessor {
systemDao.preFetchResources(JpaPid.fromLongList(idsToPreFetch), true);
}
@SuppressWarnings("rawtypes")
protected void postTransactionProcess(TransactionDetails theTransactionDetails) {
Set<IResourcePersistentId> resourceIds = theTransactionDetails.getUpdatedResourceIds();
if (resourceIds != null && !resourceIds.isEmpty()) {
List<Long> ids = resourceIds.stream().map(r -> (Long) r.getId()).collect(Collectors.toList());
myResourceSearchUrlSvc.deleteByResIds(ids);
}
}
private void preFetchResourcesById(
TransactionDetails theTransactionDetails,
List<IBase> theEntries,

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceSearchUrlDao.java
View File

@ -26,6 +26,7 @@ import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Date;
import java.util.List;
public interface IResourceSearchUrlDao extends JpaRepository<ResourceSearchUrlEntity, Long>, IHapiFhirJpaRepository {
@ -36,4 +37,8 @@ public interface IResourceSearchUrlDao extends JpaRepository<ResourceSearchUrlEn
@Modifying
@Query("DELETE FROM ResourceSearchUrlEntity s WHERE (s.myResourcePid = :resID)")
int deleteByResId(@Param("resID") long resId);
@Modifying
@Query("DELETE FROM ResourceSearchUrlEntity s WHERE s.myResourcePid IN (:resIDS)")
int deleteByResIds(@Param("resIDS") List<Long> theIds);
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/ResourceSearchUrlSvc.java
View File

@ -34,6 +34,7 @@ import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import java.util.Date;
import java.util.List;
/**
* This service ensures uniqueness of resources during create or create-on-update
@ -84,6 +85,10 @@ public class ResourceSearchUrlSvc {
myResourceSearchUrlDao.deleteByResId(theResId);
}
public void deleteByResIds(List<Long> theResIds) {
myResourceSearchUrlDao.deleteByResIds(theResIds);
}
/**
* We store a record of match urls with res_id so a db constraint can catch simultaneous creates that slip through.
*/

9
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
View File

@ -556,7 +556,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(1L, id.getVersionIdPartAsLong());
// Update 1 - Should delete search URL
p.setActive(true);
myCaptureQueriesListener.clear();
id = myPatientDao.update(p, "Patient?identifier=http://foo|123", mySrd).getId();
@ -564,13 +563,11 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(2L, id.getVersionIdPartAsLong());
// Update 2 - Should not try to delete search URL
p.setActive(false);
myCaptureQueriesListener.clear();
id = myPatientDao.update(p, "Patient?identifier=http://foo|123", mySrd).getId();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(3L, id.getVersionIdPartAsLong());
}
/**
@ -2500,7 +2497,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.logUpdateQueries();
assertEquals(8, myCaptureQueriesListener.countUpdateQueries());
assertEquals(4, myCaptureQueriesListener.countDeleteQueries());
assertEquals(1, myCaptureQueriesListener.countDeleteQueries());
/*
* Third time with mass ingestion mode enabled
@ -3699,7 +3696,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myCaptureQueriesListener.logInsertQueries();
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(7, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(2, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(1, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
IdType patientId = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
@ -3782,7 +3779,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(2, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(6, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(2, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(1, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
}

2
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirSystemDaoTransactionR5Test.java
View File

@ -162,7 +162,7 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
assertEquals(theMatchUrlCacheEnabled ? 3 : 4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(4, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(4, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(1, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
assertEquals(1, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());

115
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ServerR5Test.java
View File

@ -1,31 +1,45 @@
package ca.uhn.fhir.jpa.provider.r5;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.SqlQuery;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.ExtensionConstants;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.Identifier;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Quantity;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.fail;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -145,6 +159,99 @@ public class ServerR5Test extends BaseResourceProviderR5Test {
}
@Test
public void updateOrCreate_batchesSearchUrlDelete() {
int numOfObs = 10;
int txSize = 5;
List<SqlQuery> deleteQueries;
myCaptureQueriesListener.clear();
String prefix = "p1";
// initial insert
doUpdateOrCreate(prefix, numOfObs, txSize);
// verify we have created the observations (sanity check)
@SuppressWarnings("unchecked")
IFhirResourceDao<Observation> obsDao = myDaoRegistry.getResourceDao("Observation");
IBundleProvider result = obsDao.search(new SearchParameterMap().setLoadSynchronous(true), new SystemRequestDetails());
assertFalse(result.isEmpty());
// creates create the initial search urls, so we expect no deletes
deleteQueries = myCaptureQueriesListener.getDeleteQueries();
assertTrue(deleteQueries.isEmpty());
myCaptureQueriesListener.clear();
// update
doUpdateOrCreate(prefix, numOfObs, txSize);
// the searchURLs should be deleted now, so we expect some deletes
// specifically, as many deletes as there were "transaction bundles" to process
deleteQueries = myCaptureQueriesListener.getDeleteQueries();
assertFalse(deleteQueries.isEmpty());
assertEquals(numOfObs / txSize, deleteQueries.size());
myCaptureQueriesListener.clear();
}
private void doUpdateOrCreate(String prefix, int numOfObs, int txSize) {
for (int i = 0; i < numOfObs / txSize; i++) {
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
List<Bundle.BundleEntryComponent> bundleEntryComponents = createObservations(prefix, 10000 + i * txSize, txSize);
bundle.setEntry(bundleEntryComponents);
mySystemDao.transaction(new SystemRequestDetails(),
bundle);
}
}
private List<Bundle.BundleEntryComponent> createObservations(String prefix, int observationId, int num) {
List<Bundle.BundleEntryComponent> list = new ArrayList<>();
for (int i = 0; i < num; i++) {
Bundle.BundleEntryComponent bundleEntryComponent = new Bundle.BundleEntryComponent();
Observation obs = new Observation();
List<Identifier> identifierList = new ArrayList<>();
identifierList.add(new Identifier().setValue(prefix + observationId + i));
obs.setIdentifier(identifierList);
obs.setStatus(Enumerations.ObservationStatus.FINAL);
Coding code = new Coding("http://loinc.org", "85354-9", "Blood pressure");
obs.setCode(new CodeableConcept().addCoding(code));
obs.setEffective(createDateTime("2020-01-01T12:00:00-05:00"));
Coding code1 = new Coding("http://loinc.org", "8480-6", "Systolic blood pressure");
List<Observation.ObservationComponentComponent> obsccList = new ArrayList<>();
Observation.ObservationComponentComponent obsvC = new Observation.ObservationComponentComponent();
CodeableConcept cc = new CodeableConcept().addCoding(code1);
obsvC.setValue(cc);
Quantity quantity = new Quantity();
quantity.setUnit("mmHg");
quantity.setValue(170);
quantity.setSystem("http://unitsofmeasure.org");
quantity.setCode("mm[Hg]");
obsvC.setValue(quantity);
obsccList.add(obsvC);
Observation.ObservationComponentComponent obsvC1 = new Observation.ObservationComponentComponent();
CodeableConcept cc1 = new CodeableConcept(new Coding("http://loinc.org", "8462-4", "Diastolic blood pressure"));
Quantity quantity1 = new Quantity();
quantity1.setValue(110);
quantity1.setUnit("mmHg");
quantity1.setSystem("http://unitsofmeasure.org");
quantity1.setCode("mm[Hg]");
obsvC1.setCode(cc1);
obsvC1.setValue(quantity1);
obsccList.add(obsvC1);
bundleEntryComponent.setResource(obs);
Bundle.BundleEntryRequestComponent bundleEntryRequestComponent = new Bundle.BundleEntryRequestComponent();
bundleEntryRequestComponent.setMethod(Bundle.HTTPVerb.PUT);
bundleEntryRequestComponent.setUrl("Observation?identifier=" + prefix + observationId + i);
bundleEntryComponent.setRequest(bundleEntryRequestComponent);
list.add(bundleEntryComponent);
}
return list;
}
private DateTimeType createDateTime(String theDateString) {
return new DateTimeType(theDateString);
}
}

34
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/TransactionDetails.java
View File

@ -66,6 +66,7 @@ public class TransactionDetails {
private Map<String, IResourcePersistentId> myResolvedMatchUrls = Collections.emptyMap();
private Map<String, Supplier<IBaseResource>> myResolvedResources = Collections.emptyMap();
private Set<IResourcePersistentId> myDeletedResourceIds = Collections.emptySet();
private Set<IResourcePersistentId> myUpdatedResourceIds = Collections.emptySet();
private Map<String, Object> myUserData;
private ListMultimap<Pointcut, HookParams> myDeferredInterceptorBroadcasts;
private EnumSet<Pointcut> myDeferredInterceptorBroadcastPointcuts;
@ -118,9 +119,40 @@ public class TransactionDetails {
}
}
/**
* @since 7.6.0
*/
@SuppressWarnings("rawtypes")
public void addUpdatedResourceId(@Nonnull IResourcePersistentId theResourceId) {
Validate.notNull(theResourceId, "theResourceId must not be null");
if (myUpdatedResourceIds.isEmpty()) {
myUpdatedResourceIds = new HashSet<>();
}
myUpdatedResourceIds.add(theResourceId);
}
/**
* @since 7.6.0
*/
@SuppressWarnings("rawtypes")
public void addUpdatedResourceIds(Collection<? extends IResourcePersistentId> theResourceIds) {
for (IResourcePersistentId id : theResourceIds) {
addUpdatedResourceId(id);
}
}
/**
* @since 7.6.0
*/
@SuppressWarnings("rawtypes")
public Set<IResourcePersistentId> getUpdatedResourceIds() {
return myUpdatedResourceIds;
}
/**
* @since 6.8.0
*/
@SuppressWarnings("rawtypes")
public void addDeletedResourceId(@Nonnull IResourcePersistentId theResourceId) {
Validate.notNull(theResourceId, "theResourceId must not be null");
if (myDeletedResourceIds.isEmpty()) {
@ -132,6 +164,7 @@ public class TransactionDetails {
/**
* @since 6.8.0
*/
@SuppressWarnings("rawtypes")
public void addDeletedResourceIds(Collection<? extends IResourcePersistentId> theResourceIds) {
for (IResourcePersistentId<?> next : theResourceIds) {
addDeletedResourceId(next);
@ -141,6 +174,7 @@ public class TransactionDetails {
/**
* @since 6.8.0
*/
@SuppressWarnings("rawtypes")
@Nonnull
public Set<IResourcePersistentId> getDeletedResourceIds() {
return Collections.unmodifiableSet(myDeletedResourceIds);

9
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -1408,6 +1408,8 @@ public abstract class BaseTransactionProcessor {
theTransactionStopWatch.endCurrentTask();
}
postTransactionProcess(theTransactionDetails);
/*
* Make sure that there are no conflicts from deletions. E.g. we can't delete something
* if something else has a reference to it.. Unless the thing that has a reference to it
@ -1517,6 +1519,13 @@ public abstract class BaseTransactionProcessor {
// nothing
}
/**
* Implement to handle post transaction processing
*/
protected void postTransactionProcess(TransactionDetails theTransactionDetails) {
// nothing
}
/**
* Check for if a resource id should be matched in a conditional update
* If the FHIR version is older than R4, it follows the old specifications and does not match