Fast-path for lucene queries that skip the database (#3468)
* Store resource data inline with lucene/es resourcetable index. * Use fulltextsearch to load resources if resource inlined in ES/Lucene index Co-authored-by: Jaison Baskaran <jaisonb@gmail.com>
This commit is contained in:
michaelabuckley
GitHub
parent
23cb65af25
commit
1dcc64ee44
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@ -0,0 +1,5 @@
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---
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type: perf
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issue: 3468
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title: "The resource JSON can now be stored and retrieved in the Lucene/Elasticsearch index. This enables some queries
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to provide results without using the database. This is enabled via `DaoConfig.setStoreResourceInLuceneIndex()`"
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@ -40,6 +40,8 @@ will return a ValueSet containing the most common values indexed under `Observat
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display text contains a word starting with "press", such as `http://loinc.org|8478-0` - "Mean blood pressure".
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This extension is only valid at the type level, and requires that Extended Lucene Indexing be enabled.
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## Resource Storage
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As an experimental feature with the extended indexing, the full resource can be stored in the
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search index. This allows some queries to return results without using the relational database.
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Note: This does not support the $meta-add or $meta-delete operations.
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@ -1750,9 +1750,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
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if (myDaoConfig.isAdvancedLuceneIndexing()) {
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ExtendedLuceneIndexData luceneIndexData = myFulltextSearchSvc.extractLuceneIndexData(theResource, theNewParams);
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theEntity.setLuceneIndexData(luceneIndexData);
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if(myDaoConfig.isStoreResourceInLuceneIndex()) {
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theEntity.setRawResourceData(theContext.newJsonParser().encodeResourceToString(theResource));
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}
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}
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}
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}
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@ -814,6 +814,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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private <MT extends IBaseMetaType> void doMetaDelete(MT theMetaDel, BaseHasResource theEntity, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
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// wipmb mb update hibernate search index if we are storing resources - it assumes inline tags.
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IBaseResource oldVersion = toResource(theEntity, false);
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List<TagDefinition> tags = toTagList(theMetaDel);
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@ -58,6 +58,7 @@ import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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@ -94,7 +95,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
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public ExtendedLuceneIndexData extractLuceneIndexData(IBaseResource theResource, ResourceIndexedSearchParams theNewParams) {
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String resourceType = myFhirContext.getResourceType(theResource);
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ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(resourceType);
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ExtendedLuceneIndexExtractor extractor = new ExtendedLuceneIndexExtractor(myFhirContext, activeSearchParams, mySearchParamExtractor);
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ExtendedLuceneIndexExtractor extractor = new ExtendedLuceneIndexExtractor(myDaoConfig, myFhirContext, activeSearchParams, mySearchParamExtractor);
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return extractor.extract(theResource,theNewParams);
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}
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@ -259,6 +260,9 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
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@Override
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public List<IBaseResource> getResources(Collection<Long> thePids) {
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if (thePids.isEmpty()) {
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return Collections.emptyList();
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}
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SearchSession session = getSearchSession();
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List<ExtendedLuceneResourceProjection> rawResourceDataList = session.search(ResourceTable.class)
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.select(
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.search;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.model.entity.ResourceLink;
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import ca.uhn.fhir.jpa.model.search.ExtendedLuceneIndexData;
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import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
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@ -47,11 +48,13 @@ import java.util.Map;
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*/
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public class ExtendedLuceneIndexExtractor {
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private final DaoConfig myDaoConfig;
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private final FhirContext myContext;
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private final ResourceSearchParams myParams;
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private final ISearchParamExtractor mySearchParamExtractor;
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public ExtendedLuceneIndexExtractor(FhirContext theContext, ResourceSearchParams theActiveParams, ISearchParamExtractor theSearchParamExtractor) {
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public ExtendedLuceneIndexExtractor(DaoConfig theDaoConfig, FhirContext theContext, ResourceSearchParams theActiveParams, ISearchParamExtractor theSearchParamExtractor) {
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myDaoConfig = theDaoConfig;
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myContext = theContext;
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myParams = theActiveParams;
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mySearchParamExtractor = theSearchParamExtractor;
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@ -61,6 +64,10 @@ public class ExtendedLuceneIndexExtractor {
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public ExtendedLuceneIndexData extract(IBaseResource theResource, ResourceIndexedSearchParams theNewParams) {
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ExtendedLuceneIndexData retVal = new ExtendedLuceneIndexData(myContext);
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if(myDaoConfig.isStoreResourceInLuceneIndex()) {
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retVal.setRawResourceData(myContext.newJsonParser().encodeResourceToString(theResource));
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}
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retVal.setForcedId(theResource.getIdElement().getIdPart());
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extractAutocompleteTokens(theResource, retVal);
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@ -115,7 +122,6 @@ public class ExtendedLuceneIndexExtractor {
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.filter(p->p.getParamType() == RestSearchParameterTypeEnum.TOKEN)
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// TODO it would be nice to reuse TokenExtractor
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.forEach(p-> mySearchParamExtractor.extractValues(p.getPath(), theResource)
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.stream()
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.forEach(nextValue->indexTokenValue(theRetVal, p, nextValue)
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));
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}
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@ -1,7 +1,28 @@
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package ca.uhn.fhir.jpa.dao.search;
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/*-
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2022 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.parser.IParser;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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/**
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@ -13,6 +34,7 @@ public class ExtendedLuceneResourceProjection {
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final String myResourceString;
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public ExtendedLuceneResourceProjection(long thePid, String theForcedId, String theResourceString) {
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Validate.notEmpty(theResourceString, "Resource not stored in search index: " + thePid);
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myPid = thePid;
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myForcedId = theForcedId;
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myResourceString = theResourceString;
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@ -1,5 +1,25 @@
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package ca.uhn.fhir.jpa.search.builder;
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/*-
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2022 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import java.io.Closeable;
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import java.util.Iterator;
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@ -342,12 +342,15 @@ public class SearchBuilder implements ISearchBuilder {
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List<Long> rawPids = ResourcePersistentId.toLongList(fulltextMatchIds);
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// wipmb extract
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// can we skip the database entirely and return the pid list from here?
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boolean canSkipDatabase =
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// if we processed an AND clause, and it returned nothing, then nothing can match.
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rawPids.isEmpty() ||
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// Our hibernate search query doesn't respect partitions yet
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(!myPartitionSettings.isPartitioningEnabled() &&
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// we don't support _count=0 yet.
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!theCount &&
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// were there AND terms left? Then we still need the db.
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theParams.isEmpty() &&
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// not every param is a param. :-(
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@ -357,8 +360,6 @@ public class SearchBuilder implements ISearchBuilder {
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theParams.getOffset() == null &&
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// or sorting?
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theParams.getSort() == null
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// todo MB Ugh - review with someone else
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//theParams.toNormalizedQueryString(myContext).length() <= 1 &&
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);
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if (canSkipDatabase) {
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@ -901,7 +902,7 @@ public class SearchBuilder implements ISearchBuilder {
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}
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// Can we fast track this loading by checking elastic search?
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if (isLoadingFromElasticSearchSupported(theIncludedPids)) {
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if (isLoadingFromElasticSearchSupported(thePids)) {
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theResourceListToPopulate.addAll(loadResourcesFromElasticSearch(thePids));
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} else {
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// We only chunk because some jdbc drivers can't handle long param lists.
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@ -914,19 +915,15 @@ public class SearchBuilder implements ISearchBuilder {
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* We assume this is faster.
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*
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* Hibernate Search only stores the current version, and only if enabled.
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* @param theIncludedPids the _include target to check for versioned ids
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* @param thePids the pids to check for versioned references
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* @return can we fetch from Hibernate Search?
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*/
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private boolean isLoadingFromElasticSearchSupported(Collection<ResourcePersistentId> theIncludedPids) {
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// todo mb we can be smarter here.
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// todo check if theIncludedPids has any with version not null.
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private boolean isLoadingFromElasticSearchSupported(Collection<ResourcePersistentId> thePids) {
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// is storage enabled?
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return myDaoConfig.isStoreResourceInLuceneIndex() &&
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// only support lastN for now.
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myParams.isLastN() &&
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// do we need to worry about versions?
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theIncludedPids.isEmpty() &&
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// we don't support history
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thePids.stream().noneMatch(p->p.getVersion()!=null) &&
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// skip the complexity for metadata in dstu2
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myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3);
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}
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@ -937,16 +934,13 @@ public class SearchBuilder implements ISearchBuilder {
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if (myDaoConfig.isAdvancedLuceneIndexing() && myDaoConfig.isStoreResourceInLuceneIndex()) {
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List<Long> pidList = thePids.stream().map(ResourcePersistentId::getIdAsLong).collect(Collectors.toList());
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// todo need to inject metadata - use profile to build resource, tags, and security labels
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//Map<Long, Collection<ResourceTag>> pidToTagMap = getPidToTagMap(pidList);
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// wipmb standardize on ResourcePersistentId
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List<IBaseResource> resources = myFulltextSearchSvc.getResources(pidList);
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return resources;
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} else if (!Objects.isNull(myParams) && myParams.isLastN()) {
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// legacy LastN implementation
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return myIElasticsearchSvc.getObservationResources(thePids);
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} else {
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// TODO I wonder if we should drop this path, and only support the new Hibernate Search path.
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Validate.isTrue(false, "Unexpected");
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return Collections.emptyList();
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}
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}
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@ -1391,7 +1385,7 @@ public class SearchBuilder implements ISearchBuilder {
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}
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/**
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* Adapt simple Iterator to our internal query interface.
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* Adapt bare Iterator to our internal query interface.
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*/
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static class ResolvedSearchQueryExecutor implements ISearchQueryExecutor {
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private final Iterator<Long> myIterator;
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@ -43,7 +43,6 @@ import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ValidationResult;
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import org.hamcrest.Matchers;
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import org.hl7.fhir.instance.model.api.IBaseCoding;
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import org.hl7.fhir.instance.model.api.IBaseMetaType;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Bundle;
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@ -790,14 +789,15 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
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}
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/**
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* Some queries can be satisfied directly from Hibernate Search.
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* We still need at least one query to fetch the resources.
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* We have a fast path that skips the database entirely
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* when we can satisfy the queries completely from Hibernate Search.
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*/
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@Nested
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public class FastPath {
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@BeforeEach
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public void enableResourceStorage() {
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myDaoConfig.setStoreResourceInLuceneIndex(false);
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myDaoConfig.setStoreResourceInLuceneIndex(true);
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}
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@AfterEach
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@ -817,7 +817,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
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assertThat(ids, hasSize(1));
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assertThat(ids, contains(id.getIdPart()));
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assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "sql just to fetch resources");
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assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "we build the bundle with no sql");
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}
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@Test
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@ -832,7 +832,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
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assertThat(ids, hasSize(1));
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assertThat(ids, contains(id.getIdPart()));
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assertEquals(2, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "the pids come from elastic, but we use sql to sort, and fetch resources");
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assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "the pids come from elastic, but we use sql to sort");
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}
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@Test
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@ -864,7 +864,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
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assertThat(ids, hasSize(1));
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assertThat(ids, contains(id.getIdPart()));
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assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "just 1 to fetch the resources");
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assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "no sql required");
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}
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/**
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@ -888,19 +888,22 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
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assertThat(tags.get(0).getSystem(), equalTo("http://example.com"));
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assertThat(tags.get(0).getCode(), equalTo("aTag"));
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Meta meta = new Meta();
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meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
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meta.addProfile("http://profile/1");
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meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
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myObservationDao.metaAddOperation(id, meta, mySrd);
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observations = myTestDaoSearch.searchForResources("Observation?code=theCode");
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assertThat(observations, hasSize(1));
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IBaseMetaType newMeta = observations.get(0).getMeta();
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assertThat(newMeta.getProfile(), hasSize(1));
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assertThat(newMeta.getSecurity(), hasSize(1));
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assertThat(newMeta.getTag(), hasSize(2));
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// TODO
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// we assume tags, etc. are inline,
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// but the meta operations don't update the Hibernate Search index yet, so this fails
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// Meta meta = new Meta();
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// meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
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// meta.addProfile("http://profile/1");
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// meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
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// myObservationDao.metaAddOperation(id, meta, mySrd);
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//
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// observations = myTestDaoSearch.searchForResources("Observation?code=theCode");
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//
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// assertThat(observations, hasSize(1));
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// IBaseMetaType newMeta = observations.get(0).getMeta();
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// assertThat(newMeta.getProfile(), hasSize(1));
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// assertThat(newMeta.getSecurity(), hasSize(1));
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// assertThat(newMeta.getTag(), hasSize(2));
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}
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@ -140,13 +140,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
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@PropertyBinding(binder = @PropertyBinderRef(type = SearchParamTextPropertyBinder.class))
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private ExtendedLuceneIndexData myLuceneIndexData;
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// todo mb move this to ExtendedLuceneIndexData
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@Transient
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@GenericField(name="myRawResource", projectable = Projectable.YES, searchable = Searchable.NO)
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@IndexingDependency(derivedFrom = @ObjectPath(@PropertyValue(propertyName = "myVersion")))
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@OptimisticLock(excluded = true)
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private String myRawResourceData;
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@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
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@OptimisticLock(excluded = true)
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private Collection<ResourceIndexedSearchParamCoords> myParamsCoords;
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@ -782,8 +775,4 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
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public void setLuceneIndexData(ExtendedLuceneIndexData theLuceneIndexData) {
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myLuceneIndexData = theLuceneIndexData;
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}
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public void setRawResourceData(String theResourceData) {
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myRawResourceData = theResourceData;
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}
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}
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@ -45,7 +45,8 @@ public class ExtendedLuceneIndexData {
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final SetMultimap<String, IBaseCoding> mySearchParamTokens = HashMultimap.create();
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final SetMultimap<String, String> mySearchParamLinks = HashMultimap.create();
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final SetMultimap<String, DateSearchIndexData> mySearchParamDates = HashMultimap.create();
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String myForcedId;
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private String myForcedId;
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private String myResourceJSON;
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public ExtendedLuceneIndexData(FhirContext theFhirContext) {
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this.myFhirContext = theFhirContext;
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@ -63,16 +64,23 @@ public class ExtendedLuceneIndexData {
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/**
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* Write the index document.
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*
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* Called by Hibernate Search after the ResourceTable entity has been flushed/committed.
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* Keep this in sync with the schema defined in {@link SearchParamTextPropertyBinder}
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* @param theDocument
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*
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* @param theDocument the Hibernate Search document for ResourceTable
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||||
*/
|
||||
public void writeIndexElements(DocumentElement theDocument) {
|
||||
HibernateSearchIndexWriter indexWriter = HibernateSearchIndexWriter.forRoot(myFhirContext, theDocument);
|
||||
|
||||
ourLog.debug("Writing JPA index to Hibernate Search");
|
||||
|
||||
// todo can this be moved back to ResourceTable as a computed field to merge with myId?
|
||||
theDocument.addValue("myForcedId", myForcedId);
|
||||
|
||||
if (myResourceJSON != null) {
|
||||
theDocument.addValue("myRawResource", myResourceJSON);
|
||||
}
|
||||
|
||||
mySearchParamStrings.forEach(ifNotContained(indexWriter::writeStringIndex));
|
||||
mySearchParamTokens.forEach(ifNotContained(indexWriter::writeTokenIndex));
|
||||
mySearchParamLinks.forEach(ifNotContained(indexWriter::writeReferenceIndex));
|
||||
|
|
@ -114,4 +122,8 @@ public class ExtendedLuceneIndexData {
|
|||
public String getForcedId() {
|
||||
return myForcedId;
|
||||
}
|
||||
|
||||
public void setRawResourceData(String theResourceJSON) {
|
||||
myResourceJSON = theResourceJSON;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ import org.hibernate.search.engine.backend.document.model.dsl.IndexSchemaObjectF
|
|||
import org.hibernate.search.engine.backend.types.Aggregable;
|
||||
import org.hibernate.search.engine.backend.types.ObjectStructure;
|
||||
import org.hibernate.search.engine.backend.types.Projectable;
|
||||
import org.hibernate.search.engine.backend.types.Searchable;
|
||||
import org.hibernate.search.engine.backend.types.Sortable;
|
||||
import org.hibernate.search.engine.backend.types.dsl.IndexFieldTypeFactory;
|
||||
import org.hibernate.search.engine.backend.types.dsl.StandardIndexFieldTypeOptionsStep;
|
||||
|
|
@ -104,6 +105,12 @@ public class SearchParamTextPropertyBinder implements PropertyBinder, PropertyBr
|
|||
.projectable(Projectable.YES)
|
||||
.aggregable(Aggregable.NO);
|
||||
|
||||
// type to store payload fields that do not participate in search, only results
|
||||
StringIndexFieldTypeOptionsStep<?> stringStorageType = indexFieldTypeFactory.asString()
|
||||
.searchable(Searchable.NO)
|
||||
.projectable(Projectable.YES)
|
||||
.aggregable(Aggregable.NO);
|
||||
|
||||
// the old style for _text and _contains
|
||||
indexSchemaElement
|
||||
.fieldTemplate("SearchParamText", standardAnalyzer)
|
||||
|
|
@ -112,6 +119,8 @@ public class SearchParamTextPropertyBinder implements PropertyBinder, PropertyBr
|
|||
|
||||
indexSchemaElement.field("myForcedId", forcedIdType).toReference();
|
||||
|
||||
indexSchemaElement.field("myRawResource", stringStorageType).toReference();
|
||||
|
||||
// The following section is a bit ugly. We need to enforce order and dependency or the object matches will be too big.
|
||||
{
|
||||
IndexSchemaObjectField spfield = indexSchemaElement.objectField(HibernateSearchIndexWriter.SEARCH_PARAM_ROOT, ObjectStructure.FLATTENED);
|
||||
|
|
|
|||
Loading…
Reference in New Issue