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Code Issues Packages Projects Releases Wiki Activity

Transaction create performance improvement (#1899) 

* Work on perf issue

* Improve write performance for large bundles with tags

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Test fix

* Test fixes

* Test fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
This commit is contained in:
James Agnew 2020-06-05 05:26:06 -04:00 committed by GitHub
parent eb7b8e816b
commit 21330a0a22
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20 changed files with 78734 additions and 86 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml Normal file
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@ -0,0 +1,6 @@
---
type: perf
issue: 1899
title: "When submitting a transaction bundle containing a large number of resources being written, where the
resources had tags or profile definitions, a number of redundant database calls have been optimized out. This should
significantly improve performance for these scenarios."

28
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
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@ -193,6 +193,34 @@ public class DaoConfig {
*/
private boolean myDeleteEnabled = true;
/**
* If set to <code>true</code> (default is <code>false</code>) the <code>$lastn</code> operation will be enabled for
* indexing Observation resources. This operation involves creating a special set of tables in ElasticSearch for
* discovering Observation resources. Enabling this setting increases the amount of storage space required, and can
* slow write operations, but can be very useful for searching for collections of Observations for some applications.
*
* @since 5.1.0
*/
public boolean isLastNEnabled() {
return myLastNEnabled;
}
/**
* If set to <code>true</code> (default is <code>false</code>) the <code>$lastn</code> operation will be enabled for
* indexing Observation resources. This operation involves creating a special set of tables in ElasticSearch for
* discovering Observation resources. Enabling this setting increases the amount of storage space required, and can
* slow write operations, but can be very useful for searching for collections of Observations for some applications.
*
* @since 5.1.0
*/
public void setLastNEnabled(boolean theLastNEnabled) {
myLastNEnabled = theLastNEnabled;
}
/**
* @since 5.1.0
*/
private boolean myLastNEnabled = false;
/**
* Constructor

2
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDao.java
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@ -93,8 +93,6 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
/**
* This method does not throw an exception if there are delete conflicts, but populates them
* in the provided list
*
* @param theRequestDetails TODO
*/
DaoMethodOutcome delete(IIdType theResource, DeleteConflictList theDeleteConflictsListToPopulate, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails);

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -47,6 +47,7 @@ import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
import ca.uhn.fhir.jpa.searchparam.config.SearchParamConfig;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
@ -182,6 +183,11 @@ public abstract class BaseConfig {
return new BinaryStorageInterceptor();
}
@Bean
public MemoryCacheService memoryCacheService() {
return new MemoryCacheService();
}
@Bean
@Primary
public IResourceLinkResolver daoResourceLinkResolver() {

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -47,7 +47,6 @@ import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
@ -59,6 +58,7 @@ import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
@ -76,6 +76,7 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@ -91,6 +92,7 @@ import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
@ -233,6 +235,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
private PersistedJpaBundleProviderFactory myPersistedJpaBundleProviderFactory;
@Autowired
private IPartitionLookupSvc myPartitionLookupSvc;
@Autowired
private MemoryCacheService myMemoryCacheService;
@Override
protected IInterceptorBroadcaster getInterceptorBroadcaster() {
@ -393,11 +397,17 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
}
/**
* <code>null</code> will only be returned if the scheme and tag are both blank
*/
protected TagDefinition getTagOrNull(TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
if (isBlank(theScheme) && isBlank(theTerm) && isBlank(theLabel)) {
return null;
}
Pair<String, String> key = Pair.of(theScheme, theTerm);
return myMemoryCacheService.get(MemoryCacheService.CacheEnum.TAG_DEFINITION, key, k -> {
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
Root<TagDefinition> from = cq.from(TagDefinition.class);
@ -424,6 +434,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
myEntityManager.persist(retVal);
return retVal;
}
});
}
protected IBundleProvider history(RequestDetails theRequest, String theResourceType, Long theResourcePid, Date theRangeStartInclusive, Date theRangeEndInclusive) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDaoObservation.java
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@ -54,6 +54,7 @@ public abstract class BaseHapiFhirResourceDaoObservation<T extends IBaseResource
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion,
theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isLastNEnabled()) {
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
// Update indexes here for LastN operation.
@ -62,6 +63,7 @@ public abstract class BaseHapiFhirResourceDaoObservation<T extends IBaseResource
myObservationLastNIndexPersistSvc.deleteObservationIndex(theEntity);
}
}
}
return retVal;
}

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
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@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
@ -105,6 +106,8 @@ class ResourceExpungeService implements IResourceExpungeService {
private IResourceProvenanceDao myResourceHistoryProvenanceTableDao;
@Autowired
private ISearchParamPresentDao mySearchParamPresentDao;
@Autowired
private DaoConfig myDaoConfig;
@Override
@Transactional
@ -238,20 +241,43 @@ class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void deleteAllSearchParams(Long theResourceId) {
ResourceTable resource = myResourceTableDao.findById(theResourceId).orElse(null);
if (resource == null || resource.isParamsUriPopulated()) {
myResourceIndexedSearchParamUriDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsCoordsPopulated()) {
myResourceIndexedSearchParamCoordsDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsDatePopulated()) {
myResourceIndexedSearchParamDateDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsNumberPopulated()) {
myResourceIndexedSearchParamNumberDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsQuantityPopulated()) {
myResourceIndexedSearchParamQuantityDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsStringPopulated()) {
myResourceIndexedSearchParamStringDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsTokenPopulated()) {
myResourceIndexedSearchParamTokenDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isParamsCompositeStringUniquePresent()) {
myResourceIndexedCompositeStringUniqueDao.deleteByResourceId(theResourceId);
}
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
mySearchParamPresentDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isHasLinks()) {
myResourceLinkDao.deleteByResourceId(theResourceId);
}
if (resource == null || resource.isHasTags()) {
myResourceTagDao.deleteByResourceId(theResourceId);
}
}
private void expungeHistoricalVersionsOfId(RequestDetails theRequestDetails, Long myResourceId, AtomicInteger theRemainingCount) {
ResourceTable resource = myResourceTableDao.findById(myResourceId).orElseThrow(IllegalArgumentException::new);

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -30,6 +30,7 @@ import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.cross.ResourceLookup;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -105,17 +106,6 @@ public class IdHelperService {
@Autowired
private FhirContext myFhirCtx;
private Cache<String, Long> myPersistentIdCache;
private Cache<String, IResourceLookup> myResourceLookupCache;
private Cache<Long, Optional<String>> myForcedIdCache;
@PostConstruct
public void start() {
myPersistentIdCache = newCache();
myResourceLookupCache = newCache();
myForcedIdCache = newCache();
}
public void delete(ForcedId forcedId) {
myForcedIdDao.deleteByPid(forcedId.getId());
}
@ -138,6 +128,9 @@ public class IdHelperService {
return matches.iterator().next();
}
@Autowired
private MemoryCacheService myMemoryCacheService;
/**
* Given a resource type and ID, determines the internal persistent ID for the resource.
*
@ -151,7 +144,7 @@ public class IdHelperService {
retVal = resolveResourceIdentity(theRequestPartitionId, theResourceType, theId);
} else {
String key = RequestPartitionId.stringifyForKey(theRequestPartitionId) + "/" + theResourceType + "/" + theId;
retVal = myPersistentIdCache.get(key, t -> resolveResourceIdentity(theRequestPartitionId, theResourceType, theId));
retVal = myMemoryCacheService.get(MemoryCacheService.CacheEnum.PERSISTENT_ID, key, t -> resolveResourceIdentity(theRequestPartitionId, theResourceType, theId));
}
} else {
@ -201,7 +194,7 @@ public class IdHelperService {
for (Iterator<String> idIterator = nextIds.iterator(); idIterator.hasNext(); ) {
String nextId = idIterator.next();
String key = RequestPartitionId.stringifyForKey(theRequestPartitionId) + "/" + nextResourceType + "/" + nextId;
Long nextCachedPid = myPersistentIdCache.getIfPresent(key);
Long nextCachedPid = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.PERSISTENT_ID, key);
if (nextCachedPid != null) {
idIterator.remove();
retVal.add(new ResourcePersistentId(nextCachedPid));
@ -226,7 +219,7 @@ public class IdHelperService {
retVal.add(new ResourcePersistentId(pid));
String key = RequestPartitionId.stringifyForKey(theRequestPartitionId) + "/" + nextResourceType + "/" + forcedId;
myPersistentIdCache.put(key, pid);
myMemoryCacheService.put(MemoryCacheService.CacheEnum.PERSISTENT_ID, key, pid);
}
}
@ -255,7 +248,7 @@ public class IdHelperService {
public Optional<String> translatePidIdToForcedId(ResourcePersistentId theId) {
return myForcedIdCache.get(theId.getIdAsLong(), pid -> myForcedIdDao.findByResourcePid(pid).map(t -> t.getForcedId()));
return myMemoryCacheService.get(MemoryCacheService.CacheEnum.FORCED_ID, theId.getIdAsLong(), pid -> myForcedIdDao.findByResourcePid(pid).map(t -> t.getForcedId()));
}
private ListMultimap<String, String> organizeIdsByResourceType(Collection<IIdType> theIds) {
@ -329,7 +322,7 @@ public class IdHelperService {
for (Iterator<String> forcedIdIterator = nextIds.iterator(); forcedIdIterator.hasNext(); ) {
String nextForcedId = forcedIdIterator.next();
String nextKey = nextResourceType + "/" + nextForcedId;
IResourceLookup cachedLookup = myResourceLookupCache.getIfPresent(nextKey);
IResourceLookup cachedLookup = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
if (cachedLookup != null) {
forcedIdIterator.remove();
retVal.add(cachedLookup);
@ -361,7 +354,7 @@ public class IdHelperService {
if (!myDaoConfig.isDeleteEnabled()) {
String key = resourceType + "/" + forcedId;
myResourceLookupCache.put(key, lookup);
myMemoryCacheService.put(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, key, lookup);
}
}
}
@ -377,7 +370,7 @@ public class IdHelperService {
for (Iterator<Long> forcedIdIterator = thePidsToResolve.iterator(); forcedIdIterator.hasNext(); ) {
Long nextPid = forcedIdIterator.next();
String nextKey = Long.toString(nextPid);
IResourceLookup cachedLookup = myResourceLookupCache.getIfPresent(nextKey);
IResourceLookup cachedLookup = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
if (cachedLookup != null) {
forcedIdIterator.remove();
theTarget.add(cachedLookup);
@ -403,30 +396,16 @@ public class IdHelperService {
theTarget.add(t);
if (!myDaoConfig.isDeleteEnabled()) {
String nextKey = Long.toString(t.getResourceId());
myResourceLookupCache.put(nextKey, t);
myMemoryCacheService.put(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, t);
}
});
}
}
public void clearCache() {
myPersistentIdCache.invalidateAll();
myResourceLookupCache.invalidateAll();
myForcedIdCache.invalidateAll();
}
private <T, V> @NonNull Cache<T, V> newCache() {
return Caffeine
.newBuilder()
.maximumSize(10000)
.expireAfterWrite(10, TimeUnit.MINUTES)
.build();
}
public Map<Long, Optional<String>> translatePidsToForcedIds(Set<Long> thePids) {
Map<Long, Optional<String>> retVal = new HashMap<>(myForcedIdCache.getAllPresent(thePids));
Map<Long, Optional<String>> retVal = new HashMap<>(myMemoryCacheService.getAllPresent(MemoryCacheService.CacheEnum.FORCED_ID, thePids));
List<Long> remainingPids = thePids
.stream()
@ -440,7 +419,7 @@ public class IdHelperService {
Long nextResourcePid = forcedId.getResourceId();
Optional<String> nextForcedId = Optional.of(forcedId.getForcedId());
retVal.put(nextResourcePid, nextForcedId);
myForcedIdCache.put(nextResourcePid, nextForcedId);
myMemoryCacheService.put(MemoryCacheService.CacheEnum.FORCED_ID, nextResourcePid, nextForcedId);
}
});
@ -450,7 +429,7 @@ public class IdHelperService {
.collect(Collectors.toList());
for (Long nextResourcePid : remainingPids) {
retVal.put(nextResourcePid, Optional.empty());
myForcedIdCache.put(nextResourcePid, Optional.empty());
myMemoryCacheService.put(MemoryCacheService.CacheEnum.FORCED_ID, nextResourcePid, Optional.empty());
}
return retVal;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/CascadingDeleteInterceptor.java
View File

@ -117,6 +117,7 @@ public class CascadingDeleteInterceptor {
String nextSourceId = nextSource.toUnqualifiedVersionless().getValue();
if (!cascadedDeletes.contains(nextSourceId)) {
cascadedDeletes.add(nextSourceId);
IFhirResourceDao dao = myDaoRegistry.getResourceDao(nextSource.getResourceType());
@ -132,9 +133,6 @@ public class CascadingDeleteInterceptor {
// Actually perform the delete
ourLog.info("Have delete conflict {} - Cascading delete", next);
dao.delete(nextSource, theConflictList, theRequest, theTransactionDetails);
cascadedDeletes.add(nextSourceId);
}
}

72
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java Normal file
View File

@ -0,0 +1,72 @@
package ca.uhn.fhir.jpa.util;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import javax.annotation.PostConstruct;
import java.util.EnumMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import java.util.function.Function;
/**
* This class acts as a central spot for all of the many Caffeine caches we use in HAPI FHIR.
* <p>
* The API is super simplistic, and caches are all 1-minute, max 10000 entries for starters. We could definitely add nuance to this,
* which will be much easier now that this is being centralized. Some logging/monitoring would be good too.
*/
public class MemoryCacheService {
private EnumMap<CacheEnum, Cache<?, ?>> myCaches;
@PostConstruct
public void start() {
myCaches = new EnumMap<>(CacheEnum.class);
for (CacheEnum next : CacheEnum.values()) {
Cache<Object, Object> nextCache = Caffeine.newBuilder().expireAfterWrite(1, TimeUnit.MINUTES).maximumSize(10000).build();
myCaches.put(next, nextCache);
}
}
public <K, T> T get(CacheEnum theCache, K theKey, Function<K, T> theSupplier) {
Cache<K, T> cache = getCache(theCache);
return cache.get(theKey, theSupplier);
}
public <K, V> V getIfPresent(CacheEnum theCache, K theKey) {
return (V) getCache(theCache).getIfPresent(theKey);
}
public <K, V> void put(CacheEnum theCache, K theKey, V theValue) {
getCache(theCache).put(theKey, theValue);
}
public <K, V> Map<K, V> getAllPresent(CacheEnum theCache, Iterable<K> theKeys) {
return (Map<K, V>) getCache(theCache).getAllPresent(theKeys);
}
public void invalidateAllCaches() {
myCaches.values().forEach(t -> t.invalidateAll());
}
private <K, T> Cache<K, T> getCache(CacheEnum theCache) {
return (Cache<K, T>) myCaches.get(theCache);
}
public enum CacheEnum {
TAG_DEFINITION,
PERSISTENT_ID,
RESOURCE_LOOKUP,
FORCED_ID,
}
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -21,6 +21,7 @@ import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.rest.api.Constants;
@ -122,6 +123,8 @@ public abstract class BaseJpaTest extends BaseTest {
protected IPartitionLookupSvc myPartitionConfigSvc;
@Autowired
private IdHelperService myIdHelperService;
@Autowired
private MemoryCacheService myMemoryCacheService;
@After
public void afterPerformCleanup() {
@ -132,10 +135,9 @@ public abstract class BaseJpaTest extends BaseTest {
if (myPartitionConfigSvc != null) {
myPartitionConfigSvc.clearCaches();
}
if (myIdHelperService != null) {
myIdHelperService.clearCache();
if (myMemoryCacheService != null) {
myMemoryCacheService.invalidateAllCaches();
}
}
@After

57
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -1,9 +1,13 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.GZipUtil;
import ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
@ -21,8 +25,10 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.Maps;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Appointment;
import org.hl7.fhir.dstu3.model.Attachment;
@ -60,6 +66,8 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.mockito.internal.stubbing.answers.CallsRealMethods;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
@ -68,8 +76,11 @@ import java.io.IOException;
import java.io.InputStream;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
@ -90,15 +101,25 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.doAnswer;
import static org.mockito.Mockito.when;
public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu3Test.class);
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private IInterceptorService myInterceptorBroadcaster;
@After
public void after() {
myDaoConfig.setAllowInlineMatchUrlReferences(false);
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myDaoConfig.setMaximumDeleteConflictQueryCount(new DaoConfig().getMaximumDeleteConflictQueryCount());
}
@Before
@ -1826,6 +1847,42 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
}
/**
* There is nothing here that isn't tested elsewhere, but it's useful for testing a large transaction followed
* by a large cascading delete
*/
@Test
@Ignore
public void testTransactionFromBundle_Slow() throws Exception {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
myDaoConfig.setMaximumDeleteConflictQueryCount(10000);
StopWatch sw = new StopWatch();
sw.startTask("Parse Bundle");
Bundle bundle = loadBundle("/dstu3/slow_bundle.xml");
sw.startTask("Process transaction");
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info("Tasks: {}", sw.formatTaskDurations());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
doAnswer(new CallsRealMethods()).when(mySrd).setParameters(any());
when(mySrd.getParameters()).thenCallRealMethod();
when(mySrd.getUserData()).thenReturn(new HashMap<>());
Map<String, String[]> params = Maps.newHashMap();
params.put(Constants.PARAMETER_CASCADE_DELETE, new String[]{Constants.CASCADE_DELETE});
mySrd.setParameters(params);
CascadingDeleteInterceptor deleteInterceptor = new CascadingDeleteInterceptor(myFhirCtx, myDaoRegistry, myInterceptorBroadcaster);
myInterceptorBroadcaster.registerInterceptor(deleteInterceptor);
myPatientDao.deleteByUrl("Patient?identifier=http://fhir.nl/fhir/NamingSystem/bsn|900197341", mySrd);
}
@Test
public void testTransactionOrdering() {
String methodName = "testTransactionOrdering";

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
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@ -21,6 +21,7 @@ import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
@ -78,6 +79,16 @@ public class BaseR4SearchLastN extends BaseJpaTest {
return myPlatformTransactionManager;
}
@Before
public void beforeEnableLastN() {
myDaoConfig.setLastNEnabled(true);
}
@After
public void afterDisableLastN() {
myDaoConfig.setLastNEnabled(new DaoConfig().isLastNEnabled());
}
protected final String observationCd0 = "code0";
protected final String observationCd1 = "code1";
protected final String observationCd2 = "code2";

43
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
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@ -1055,6 +1055,49 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
}
@Test
public void testTransactionWithMultipleProfiles() {
myDaoConfig.setDeleteEnabled(true);
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
// Create transaction
Bundle input = new Bundle();
for (int i = 0; i < 5; i++) {
Patient patient = new Patient();
patient.getMeta().addProfile("http://example.com/profile");
patient.getMeta().addTag().setSystem("http://example.com/tags").setCode("tag-1");
patient.getMeta().addTag().setSystem("http://example.com/tags").setCode("tag-2");
input.addEntry()
.setResource(patient)
.getRequest()
.setMethod(Bundle.HTTPVerb.POST)
.setUrl("Patient");
}
myCaptureQueriesListener.clear();
mySystemDao.transaction(mySrd, input);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(8, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
// Do the same a second time
myCaptureQueriesListener.clear();
mySystemDao.transaction(mySrd, input);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(5, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PersistObservationIndexedSearchParamLastNR4IT.java
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@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticsearchClient;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
@ -15,6 +16,7 @@ import ca.uhn.fhir.rest.param.*;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.r4.model.*;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
@ -56,6 +58,9 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
@Autowired
protected FhirContext myFhirCtx;
@Autowired
private DaoConfig myDaoConfig;
@Before
public void before() throws IOException {
@ -63,8 +68,20 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
elasticsearchSvc.deleteAllDocumentsForTest(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
}
@Before
public void beforeEnableLastN() {
myDaoConfig.setLastNEnabled(true);
}
@After
public void afterDisableLastN() {
myDaoConfig.setLastNEnabled(new DaoConfig().isLastNEnabled());
}
private final String SINGLE_SUBJECT_ID = "4567";
private final String SINGLE_OBSERVATION_PID = "123";
private final Date SINGLE_EFFECTIVEDTM = new Date();

78383
hapi-fhir-jpaserver-base/src/test/resources/dstu3/slow_bundle.xml Normal file
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File diff suppressed because one or more lines are too long

1
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/BaseEmpiR4Test.java
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@ -102,6 +102,7 @@ abstract public class BaseEmpiR4Test extends BaseJpaR4Test {
protected ServletRequestDetails myRequestDetails = new ServletRequestDetails(null);
@Override
@After
public void after() {
myEmpiLinkDao.deleteAll();

1
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiLinkSvcTest.java
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@ -24,6 +24,7 @@ public class EmpiLinkSvcTest extends BaseEmpiR4Test {
@Autowired
IEmpiLinkSvc myEmpiLinkSvc;
@Override
@After
public void after() {
myExpungeEverythingService.expungeEverythingByType(EmpiLink.class);

1
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiPersonMergerSvcTest.java
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@ -78,6 +78,7 @@ public class EmpiPersonMergerSvcTest extends BaseEmpiR4Test {
myInterceptorService.registerInterceptor(myEmpiStorageInterceptor);
}
@Override
@After
public void after() {
myInterceptorService.unregisterInterceptor(myEmpiStorageInterceptor);

5
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaTest.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.test;
*/
import ca.uhn.fhir.jpa.dao.expunge.ExpungeEverythingService;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
@ -66,10 +67,14 @@ public abstract class BaseJpaTest {
@Autowired
ApplicationContext myApplicationContext;
@Autowired
MemoryCacheService myMemoryCacheService;
@After
public void after() {
ourLog.info("\n --- @After ---");
myExpungeEverythingService.expungeEverything(null);
myMemoryCacheService.invalidateAllCaches();
}
public TransactionTemplate newTxTemplate() {