Issue 3992 elastic search mapper parsing exception when uploading loinc terminology (#4141)
* Revert TermConceptProperty indexing to not-nested type to avoid hitting elastic default maximums and fix regexp issue which was main reason to change indexing way in the first place. * Add changelog * Document that terminology reindexing is required. * Implement revision suggestions. Fix file name typo. * Adjust and enable test created to reproduce bug Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto
GitHub
parent
1dba9392ef
commit
2830792c4b
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@ -0,0 +1,7 @@
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---
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type: fix
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issue: 3992
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title: "Previously when ValueSets were pre-expanded after loinc terminology upload, expansion was failing with an exception for each ValueSet
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with more than 10,000 properties. This problem has been fixed.
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This fix changed some freetext mappings (definitions about how resources are freetext indexed) for terminology resources, which requires
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reindexing those resources. To do this use the `reindex-terminology` command."
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@ -0,0 +1,4 @@
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This release has breaking changes.
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* Hibernate Search mappings for Terminology entities have been upgraded, which requires terminology freetext reindexing.
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To recreate Terminology freetext indexes use CLI command: `reindex-terminology`
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@ -30,14 +30,14 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.apache.commons.lang3.builder.ToStringBuilder;
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import org.apache.commons.lang3.builder.ToStringStyle;
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import org.hibernate.search.engine.backend.types.ObjectStructure;
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import org.hibernate.search.engine.backend.types.Projectable;
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import org.hibernate.search.engine.backend.types.Searchable;
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import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.PropertyBinderRef;
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import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.RoutingBinderRef;
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import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
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import org.hibernate.search.mapper.pojo.mapping.definition.annotation.GenericField;
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import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
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import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
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import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyBinding;
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import org.hl7.fhir.r4.model.Coding;
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import javax.annotation.Nonnull;
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@ -114,12 +114,8 @@ public class TermConcept implements Serializable {
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@FullTextField(name = "myDisplayPhonetic", searchable= Searchable.YES, projectable= Projectable.NO, analyzer = "autocompletePhoneticAnalyzer")
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private String myDisplay;
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/**
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* IndexedEmbedded uses ObjectStructure.NESTED to be able to use hibernate search nested predicate queries.
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* @see "https://docs.jboss.org/hibernate/search/6.0/reference/en-US/html_single/#search-dsl-predicate-nested"
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*/
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@OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
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@IndexedEmbedded(structure = ObjectStructure.NESTED)
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@PropertyBinding(binder = @PropertyBinderRef(type = TermConceptPropertyBinder.class))
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private Collection<TermConceptProperty> myProperties;
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@OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
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@ -458,7 +454,7 @@ public class TermConcept implements Serializable {
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* Returns a view of {@link #getChildren()} but containing the actual child codes
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*/
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public List<TermConcept> getChildCodes() {
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return getChildren().stream().map(t -> t.getChild()).collect(Collectors.toList());
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return getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList());
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}
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}
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@ -0,0 +1,83 @@
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package ca.uhn.fhir.jpa.entity;
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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 org.hibernate.search.engine.backend.document.DocumentElement;
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import org.hibernate.search.engine.backend.document.model.dsl.IndexSchemaElement;
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import org.hibernate.search.engine.backend.types.dsl.IndexFieldTypeFactory;
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import org.hibernate.search.mapper.pojo.bridge.PropertyBridge;
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import org.hibernate.search.mapper.pojo.bridge.binding.PropertyBindingContext;
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import org.hibernate.search.mapper.pojo.bridge.mapping.programmatic.PropertyBinder;
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import org.hibernate.search.mapper.pojo.bridge.runtime.PropertyBridgeWriteContext;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.Collection;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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/**
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* Allows hibernate search to index individual concepts' properties
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*/
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public class TermConceptPropertyBinder implements PropertyBinder {
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public static final String CONCEPT_PROPERTY_PREFIX_NAME = "P:";
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private static final Logger ourLog = LoggerFactory.getLogger(TermConceptPropertyBinder.class);
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@Override
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public void bind(PropertyBindingContext thePropertyBindingContext) {
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thePropertyBindingContext.dependencies().use("myKey").use("myValue");
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IndexSchemaElement indexSchemaElement = thePropertyBindingContext.indexSchemaElement();
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//In order to support dynamic fields, we have to use field templates. We _must_ define the template at bootstrap time and cannot
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//create them adhoc. https://docs.jboss.org/hibernate/search/6.0/reference/en-US/html_single/#mapper-orm-bridge-index-field-dsl-dynamic
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indexSchemaElement.fieldTemplate("propTemplate", IndexFieldTypeFactory::asString)
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.matchingPathGlob(CONCEPT_PROPERTY_PREFIX_NAME + "*")
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.multiValued();
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thePropertyBindingContext.bridge(Collection.class, new TermConceptPropertyBridge());
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}
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@SuppressWarnings("rawtypes")
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private static class TermConceptPropertyBridge implements PropertyBridge<Collection> {
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@Override
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public void write(DocumentElement theDocument, Collection theObject, PropertyBridgeWriteContext thePropertyBridgeWriteContext) {
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@SuppressWarnings("unchecked")
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Collection<TermConceptProperty> properties = (Collection<TermConceptProperty>) theObject;
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if (properties != null) {
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for (TermConceptProperty next : properties) {
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theDocument.addValue(CONCEPT_PROPERTY_PREFIX_NAME + next.getKey(), next.getValue());
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ourLog.trace("Adding Prop: {}{} -- {}", CONCEPT_PROPERTY_PREFIX_NAME, next.getKey(), next.getValue());
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if (next.getType() == TermConceptPropertyTypeEnum.CODING && isNotBlank(next.getDisplay())) {
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theDocument.addValue(CONCEPT_PROPERTY_PREFIX_NAME + next.getKey(), next.getDisplay());
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ourLog.trace("Adding multivalue Prop: {}{} -- {}", CONCEPT_PROPERTY_PREFIX_NAME, next.getKey(), next.getDisplay());
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}
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}
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}
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}
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}
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}
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@ -104,9 +104,6 @@ public class HapiHSearchAnalysisConfigurers {
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theLuceneCtx.analyzer("conceptParentPidsAnalyzer").custom()
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.tokenizer(WhitespaceTokenizerFactory.class);
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theLuceneCtx.analyzer("termConceptPropertyAnalyzer").custom()
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.tokenizer(WhitespaceTokenizerFactory.class);
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theLuceneCtx.normalizer(LOWERCASE_ASCIIFOLDING_NORMALIZER).custom()
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.tokenFilter(LowerCaseFilterFactory.class)
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.tokenFilter(ASCIIFoldingFilterFactory.class);
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@ -178,9 +175,6 @@ public class HapiHSearchAnalysisConfigurers {
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theConfigCtx.analyzer("conceptParentPidsAnalyzer").custom()
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.tokenizer("whitespace");
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theConfigCtx.analyzer("termConceptPropertyAnalyzer").custom()
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.tokenizer("whitespace");
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theConfigCtx.normalizer( LOWERCASE_ASCIIFOLDING_NORMALIZER ).custom()
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.tokenFilters( "lowercase", "asciifolding" );
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@ -65,7 +65,6 @@ import ca.uhn.fhir.jpa.model.sched.HapiJob;
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import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
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import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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import ca.uhn.fhir.jpa.search.ElasticsearchNestedQueryBuilderUtil;
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import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
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@ -91,7 +90,6 @@ import com.github.benmanes.caffeine.cache.Caffeine;
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import com.google.common.annotations.VisibleForTesting;
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import com.google.common.base.Stopwatch;
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import com.google.common.collect.ArrayListMultimap;
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import com.google.gson.JsonObject;
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import org.apache.commons.collections4.ListUtils;
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import org.apache.commons.lang3.ObjectUtils;
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import org.apache.commons.lang3.StringUtils;
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@ -99,12 +97,7 @@ import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.time.DateUtils;
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import org.apache.lucene.index.Term;
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import org.apache.lucene.search.BooleanQuery;
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import org.apache.lucene.search.Query;
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import org.apache.lucene.search.RegexpQuery;
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import org.apache.lucene.search.TermQuery;
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import org.hibernate.CacheMode;
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import org.hibernate.search.backend.elasticsearch.ElasticsearchExtension;
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import org.hibernate.search.backend.lucene.LuceneExtension;
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import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
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import org.hibernate.search.engine.search.predicate.dsl.PredicateFinalStep;
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import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
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@ -193,6 +186,7 @@ import java.util.concurrent.TimeUnit;
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import java.util.function.Consumer;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.jpa.entity.TermConceptPropertyBinder.CONCEPT_PROPERTY_PREFIX_NAME;
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import static ca.uhn.fhir.jpa.term.api.ITermLoaderSvc.LOINC_URI;
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import static java.lang.String.join;
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import static java.util.stream.Collectors.joining;
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@ -284,10 +278,6 @@ public class TermReadSvcImpl implements ITermReadSvc {
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private HibernatePropertiesProvider myHibernatePropertiesProvider;
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private boolean isFullTextSetToUseElastic() {
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return "elasticsearch".equalsIgnoreCase(myHibernatePropertiesProvider.getHibernateSearchBackend());
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}
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@Override
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public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
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TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem);
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@ -509,7 +499,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
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/*
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* ValueSet doesn't exist in pre-expansion database, so perform in-memory expansion
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*/
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if (!optionalTermValueSet.isPresent()) {
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if (optionalTermValueSet.isEmpty()) {
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ourLog.debug("ValueSet is not present in terminology tables. Will perform in-memory expansion without parameters. {}", getValueSetInfo(theValueSetToExpand));
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String msg = myContext.getLocalizer().getMessage(TermReadSvcImpl.class, "valueSetExpandedUsingInMemoryExpansion", getValueSetInfo(theValueSetToExpand));
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theAccumulator.addMessage(msg);
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@ -815,7 +805,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
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}
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/**
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* @return Returns true if there are potentially more results to process.
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* Returns true if there are potentially more results to process.
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*/
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private void expandValueSetHandleIncludeOrExclude(@Nullable ValueSetExpansionOptions theExpansionOptions,
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IValueSetConceptAccumulator theValueSetCodeAccumulator,
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@ -853,9 +843,8 @@ public class TermReadSvcImpl implements ITermReadSvc {
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}
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}
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Consumer<FhirVersionIndependentConcept> consumer = c -> {
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Consumer<FhirVersionIndependentConcept> consumer = c ->
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addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, system, c.getCode(), c.getDisplay(), c.getSystemVersion());
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};
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try {
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ConversionContext40_50.INSTANCE.init(new VersionConvertor_40_50(new BaseAdvisor_40_50()), "ValueSet");
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@ -901,7 +890,6 @@ public class TermReadSvcImpl implements ITermReadSvc {
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return myFulltextSearchSvc != null && !ourForceDisableHibernateSearchForUnitTest;
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}
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@Nonnull
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private void expandValueSetHandleIncludeOrExcludeUsingDatabase(
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ValueSetExpansionOptions theExpansionOptions,
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IValueSetConceptAccumulator theValueSetCodeAccumulator,
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@ -1141,11 +1129,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
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private @Nonnull
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ValueSetExpansionOptions provideExpansionOptions(@Nullable ValueSetExpansionOptions theExpansionOptions) {
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if (theExpansionOptions != null) {
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return theExpansionOptions;
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} else {
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return DEFAULT_EXPANSION_OPTIONS;
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}
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return Objects.requireNonNullElse(theExpansionOptions, DEFAULT_EXPANSION_OPTIONS);
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}
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private void addOrRemoveCode(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, boolean theAdd, String theSystem, String theCode, String theDisplay, String theSystemVersion) {
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@ -1205,7 +1189,9 @@ public class TermReadSvcImpl implements ITermReadSvc {
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private void handleFilterPropertyDefault(SearchPredicateFactory theF,
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BooleanPredicateClausesStep<?> theB, ValueSet.ConceptSetFilterComponent theFilter) {
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theB.must(getPropertyNameValueNestedPredicate(theF, theFilter.getProperty(), theFilter.getValue()));
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String value = theFilter.getValue();
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Term term = new Term(CONCEPT_PROPERTY_PREFIX_NAME + theFilter.getProperty(), value);
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theB.must(theF.match().field(term.field()).matching(term.text()));
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}
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@ -1213,7 +1199,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
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/*
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* We treat the regex filter as a match on the regex
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* anywhere in the property string. The spec does not
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* say whether or not this is the right behaviour, but
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* say whether this is the right behaviour or not, but
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* there are examples that seem to suggest that it is.
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*/
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String value = theFilter.getValue();
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@ -1228,43 +1214,26 @@ public class TermReadSvcImpl implements ITermReadSvc {
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value = value.substring(1);
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}
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if (isFullTextSetToUseElastic()) {
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ElasticsearchNestedQueryBuilderUtil nestedQueryBuildUtil = new ElasticsearchNestedQueryBuilderUtil(
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"myProperties", "myKey", theFilter.getProperty(),
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"myValueString", value);
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JsonObject nestedQueryJO = nestedQueryBuildUtil.toGson();
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ourLog.debug("Build nested Elasticsearch query: {}", nestedQueryJO);
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theB.must(theF.extension(ElasticsearchExtension.get()).fromJson(nestedQueryJO));
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return;
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}
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// native Lucene configured
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Query termPropKeyQuery = new TermQuery(new Term(IDX_PROP_KEY, theFilter.getProperty()));
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Query regexpValueQuery = new RegexpQuery(new Term(IDX_PROP_VALUE_STRING, value));
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theB.must(theF.nested().objectField("myProperties").nest(
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theF.bool()
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.must(theF.extension(LuceneExtension.get()).fromLuceneQuery(termPropKeyQuery))
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.must(theF.extension(LuceneExtension.get()).fromLuceneQuery(regexpValueQuery))
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));
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theB.must(theF.regexp()
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.field(CONCEPT_PROPERTY_PREFIX_NAME + theFilter.getProperty())
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.matching(value) );
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}
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private void handleFilterLoincCopyright(SearchPredicateFactory theF, BooleanPredicateClausesStep<?> theB, ValueSet.ConceptSetFilterComponent theFilter) {
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private void handleFilterLoincCopyright(SearchPredicateFactory theF, BooleanPredicateClausesStep<?> theB,
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ValueSet.ConceptSetFilterComponent theFilter) {
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if (theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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String copyrightFilterValue = defaultString(theFilter.getValue()).toLowerCase();
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switch (copyrightFilterValue) {
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case "3rdparty":
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logFilteringValueOnProperty(theFilter.getValue(), theFilter.getProperty());
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addFilterLoincCopyright3rdParty(theF, theB, theFilter);
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addFilterLoincCopyright3rdParty(theF, theB);
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break;
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case "loinc":
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logFilteringValueOnProperty(theFilter.getValue(), theFilter.getProperty());
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addFilterLoincCopyrightLoinc(theF, theB, theFilter);
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addFilterLoincCopyrightLoinc(theF, theB);
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break;
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default:
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throwInvalidRequestForValueOnProperty(theFilter.getValue(), theFilter.getProperty());
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@ -1275,21 +1244,13 @@ public class TermReadSvcImpl implements ITermReadSvc {
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}
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}
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private void addFilterLoincCopyrightLoinc(SearchPredicateFactory theF,
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BooleanPredicateClausesStep<?> theB, ValueSet.ConceptSetFilterComponent theFilter) {
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theB.mustNot(theF.match().field(IDX_PROP_KEY).matching("EXTERNAL_COPYRIGHT_NOTICE"));
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private void addFilterLoincCopyrightLoinc(SearchPredicateFactory theF, BooleanPredicateClausesStep<?> theB) {
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theB.mustNot(theF.exists().field(CONCEPT_PROPERTY_PREFIX_NAME + "EXTERNAL_COPYRIGHT_NOTICE"));
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}
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private void addFilterLoincCopyright3rdParty(SearchPredicateFactory thePredicateFactory,
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BooleanPredicateClausesStep<?> theBooleanClause, ValueSet.ConceptSetFilterComponent theFilter) {
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//TODO GGG HS These used to be Term term = new Term(TermConceptPropertyBinder.CONCEPT_FIELD_PROPERTY_PREFIX + "EXTERNAL_COPYRIGHT_NOTICE", ".*");, which was lucene-specific.
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//TODO GGG HS ask diederik if this is equivalent.
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//This old .* regex is the same as an existence check on a field, which I've implemented here.
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// theBooleanClause.must(thePredicateFactory.exists().field("EXTERNAL_COPYRIGHT_NOTICE"));
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theBooleanClause.must(thePredicateFactory.match().field(IDX_PROP_KEY).matching("EXTERNAL_COPYRIGHT_NOTICE"));
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private void addFilterLoincCopyright3rdParty(SearchPredicateFactory theF, BooleanPredicateClausesStep<?> theB) {
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theB.must(theF.exists().field(CONCEPT_PROPERTY_PREFIX_NAME + "EXTERNAL_COPYRIGHT_NOTICE"));
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}
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@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
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@ -1308,21 +1269,21 @@ public class TermReadSvcImpl implements ITermReadSvc {
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}
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private void addLoincFilterAncestorEqual(String theSystem, SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
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long parentPid = getAncestorCodePid(theSystem, theFilter.getProperty(), theFilter.getValue());
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b.must(f.match().field("myParentPids").matching(String.valueOf(parentPid)));
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addLoincFilterAncestorEqual(theSystem, f, b, theFilter.getProperty(), theFilter.getValue());
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}
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|
||||
private void addLoincFilterAncestorEqual(String theSystem, SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, String theProperty, String theValue) {
|
||||
List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
|
||||
b.must(f.bool(innerB -> terms.forEach(term -> innerB.should(f.match().field(term.field()).matching(term.text())))));
|
||||
}
|
||||
|
||||
private void addLoincFilterAncestorIn(String theSystem, SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
String[] values = theFilter.getValue().split(",");
|
||||
List<Long> ancestorCodePidList = new ArrayList<>();
|
||||
List<Term> terms = new ArrayList<>();
|
||||
for (String value : values) {
|
||||
ancestorCodePidList.add(getAncestorCodePid(theSystem, theFilter.getProperty(), value));
|
||||
terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value));
|
||||
}
|
||||
|
||||
b.must(f.bool(innerB -> ancestorCodePidList.forEach(
|
||||
ancestorPid -> innerB.should(f.match().field("myParentPids").matching(String.valueOf(ancestorPid)))
|
||||
)));
|
||||
b.must(f.bool(innerB -> terms.forEach(term -> innerB.should(f.match().field(term.field()).matching(term.text())))));
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -1342,32 +1303,20 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
private void addLoincFilterParentChildIn(SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
String[] values = theFilter.getValue().split(",");
|
||||
b.minimumShouldMatchNumber(1);
|
||||
List<Term> terms = new ArrayList<>();
|
||||
for (String value : values) {
|
||||
logFilteringValueOnProperty(value, theFilter.getProperty());
|
||||
b.should(getPropertyNameValueNestedPredicate(f, theFilter.getProperty(), value));
|
||||
terms.add(getPropertyTerm(theFilter.getProperty(), value));
|
||||
}
|
||||
|
||||
b.must(f.bool(innerB -> terms.forEach(term -> innerB.should(f.match().field(term.field()).matching(term.text())))));
|
||||
}
|
||||
|
||||
private void addLoincFilterParentChildEqual(SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, String theProperty, String theValue) {
|
||||
logFilteringValueOnProperty(theValue, theProperty);
|
||||
b.must(getPropertyNameValueNestedPredicate(f, theProperty, theValue));
|
||||
b.must(f.match().field(CONCEPT_PROPERTY_PREFIX_NAME + theProperty).matching(theValue));
|
||||
}
|
||||
|
||||
/**
|
||||
* A nested predicate is required for both predicates to be applied to same property, otherwise if properties
|
||||
* propAA:valueAA and propBB:valueBB are defined, a search for propAA:valueBB would be a match
|
||||
* @see "https://docs.jboss.org/hibernate/search/6.0/reference/en-US/html_single/#search-dsl-predicate-nested"
|
||||
*/
|
||||
private PredicateFinalStep getPropertyNameValueNestedPredicate(SearchPredicateFactory f, String theProperty, String theValue) {
|
||||
return f.nested().objectField(IDX_PROPERTIES).nest(
|
||||
f.bool()
|
||||
.must(f.match().field(IDX_PROP_KEY).matching(theProperty))
|
||||
.must(f.match().field(IDX_PROP_VALUE_STRING).field(IDX_PROP_DISPLAY_STRING).matching(theValue))
|
||||
);
|
||||
}
|
||||
|
||||
|
||||
private void handleFilterConceptAndCode(String theSystem, SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
TermConcept code = findCodeForFilterCriteria(theSystem, theFilter);
|
||||
|
||||
|
|
@ -1427,14 +1376,24 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
);
|
||||
}
|
||||
|
||||
private long getAncestorCodePid(String theSystem, String theProperty, String theValue) {
|
||||
private Term getPropertyTerm(String theProperty, String theValue) {
|
||||
return new Term(CONCEPT_PROPERTY_PREFIX_NAME + theProperty, theValue);
|
||||
}
|
||||
|
||||
|
||||
private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue) {
|
||||
List<Term> retVal = new ArrayList<>();
|
||||
|
||||
TermConcept code = findCode(theSystem, theValue)
|
||||
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
|
||||
|
||||
retVal.add(new Term("myParentPids", "" + code.getId()));
|
||||
logFilteringValueOnProperty(theValue, theProperty);
|
||||
return code.getId();
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
|
||||
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
|
||||
private void handleFilterLoincDescendant(String theSystem, SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
switch (theFilter.getOp()) {
|
||||
|
|
@ -1640,7 +1599,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
IBaseResource valueSet = myDaoRegistry.getResourceDao("ValueSet").read(theValueSetId, theRequestDetails);
|
||||
ValueSet canonicalValueSet = myVersionCanonicalizer.valueSetToCanonical(valueSet);
|
||||
Optional<TermValueSet> optionalTermValueSet = fetchValueSetEntity(canonicalValueSet);
|
||||
if (!optionalTermValueSet.isPresent()) {
|
||||
if (optionalTermValueSet.isEmpty()) {
|
||||
return myContext.getLocalizer().getMessage(TermReadSvcImpl.class, "valueSetNotFoundInTerminologyDatabase", theValueSetId);
|
||||
}
|
||||
|
||||
|
|
@ -1666,7 +1625,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
public boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet) {
|
||||
Optional<TermValueSet> optionalTermValueSet = fetchValueSetEntity(theValueSet);
|
||||
|
||||
if (!optionalTermValueSet.isPresent()) {
|
||||
if (optionalTermValueSet.isEmpty()) {
|
||||
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory code validation. {}", getValueSetInfo(theValueSet));
|
||||
return false;
|
||||
}
|
||||
|
|
@ -1684,13 +1643,11 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
private Optional<TermValueSet> fetchValueSetEntity(ValueSet theValueSet) {
|
||||
ResourcePersistentId valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
|
||||
return optionalTermValueSet;
|
||||
return myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
|
||||
}
|
||||
|
||||
private ResourcePersistentId getValueSetResourcePersistentId(ValueSet theValueSet) {
|
||||
ResourcePersistentId valueSetResourcePid = myIdHelperService.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), theValueSet.getIdElement().getResourceType(), theValueSet.getIdElement().getIdPart());
|
||||
return valueSetResourcePid;
|
||||
return myIdHelperService.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), theValueSet.getIdElement().getResourceType(), theValueSet.getIdElement().getIdPart());
|
||||
}
|
||||
|
||||
protected IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(
|
||||
|
|
@ -1726,7 +1683,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
return null;
|
||||
}
|
||||
|
||||
TermValueSet valueSetEntity = myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong()).orElseThrow(() -> new IllegalStateException());
|
||||
TermValueSet valueSetEntity = myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong()).orElseThrow(IllegalStateException::new);
|
||||
String timingDescription = toHumanReadableExpansionTimestamp(valueSetEntity);
|
||||
String msg = myContext.getLocalizer().getMessage(TermReadSvcImpl.class, "validationPerformedAgainstPreExpansion", timingDescription);
|
||||
|
||||
|
|
@ -1813,18 +1770,6 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
}
|
||||
|
||||
private CodeSystem.ConceptDefinitionComponent findCode(List<CodeSystem.ConceptDefinitionComponent> theConcepts, String theCode) {
|
||||
for (CodeSystem.ConceptDefinitionComponent next : theConcepts) {
|
||||
if (theCode.equals(next.getCode())) {
|
||||
return next;
|
||||
}
|
||||
CodeSystem.ConceptDefinitionComponent val = findCode(next.getConcept(), theCode);
|
||||
if (val != null) {
|
||||
return val;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<TermConcept> findCode(String theCodeSystem, String theCode) {
|
||||
|
|
@ -1909,7 +1854,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
StopWatch stopwatch = new StopWatch();
|
||||
|
||||
Optional<TermConcept> concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
|
||||
if (!concept.isPresent()) {
|
||||
if (concept.isEmpty()) {
|
||||
return Collections.emptySet();
|
||||
}
|
||||
|
||||
|
|
@ -1941,7 +1886,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
Stopwatch stopwatch = Stopwatch.createStarted();
|
||||
|
||||
Optional<TermConcept> concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
|
||||
if (!concept.isPresent()) {
|
||||
if (concept.isEmpty()) {
|
||||
return Collections.emptySet();
|
||||
}
|
||||
|
||||
|
|
@ -2003,7 +1948,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
StopWatch sw = new StopWatch();
|
||||
TermValueSet valueSetToExpand = txTemplate.execute(t -> {
|
||||
Optional<TermValueSet> optionalTermValueSet = getNextTermValueSetNotExpanded();
|
||||
if (!optionalTermValueSet.isPresent()) {
|
||||
if (optionalTermValueSet.isEmpty()) {
|
||||
return null;
|
||||
}
|
||||
|
||||
|
|
@ -2071,9 +2016,9 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
boolean haveCodeableConcept = codeableConcept != null && codeableConcept.getCoding().size() > 0;
|
||||
|
||||
Coding canonicalCodingToValidate = myVersionCanonicalizer.codingToCanonical((IBaseCoding) theCodingToValidate);
|
||||
boolean haveCoding = canonicalCodingToValidate != null && canonicalCodingToValidate.isEmpty() == false;
|
||||
boolean haveCoding = canonicalCodingToValidate != null && !canonicalCodingToValidate.isEmpty();
|
||||
|
||||
boolean haveCode = theCodeToValidate != null && theCodeToValidate.isEmpty() == false;
|
||||
boolean haveCode = theCodeToValidate != null && !theCodeToValidate.isEmpty();
|
||||
|
||||
if (!haveCodeableConcept && !haveCoding && !haveCode) {
|
||||
throw new InvalidRequestException(Msg.code(899) + "No code, coding, or codeableConcept provided to validate");
|
||||
|
|
@ -2183,7 +2128,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
} else {
|
||||
optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
|
||||
}
|
||||
if (!optionalExistingTermValueSetByUrl.isPresent()) {
|
||||
if (optionalExistingTermValueSetByUrl.isEmpty()) {
|
||||
|
||||
myTermValueSetDao.save(termValueSet);
|
||||
|
||||
|
|
@ -2557,9 +2502,9 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
boolean haveCodeableConcept = codeableConcept != null && codeableConcept.getCoding().size() > 0;
|
||||
|
||||
Coding coding = myVersionCanonicalizer.codingToCanonical((IBaseCoding) theCoding);
|
||||
boolean haveCoding = coding != null && coding.isEmpty() == false;
|
||||
boolean haveCoding = coding != null && !coding.isEmpty();
|
||||
|
||||
boolean haveCode = theCode != null && theCode.isEmpty() == false;
|
||||
boolean haveCode = theCode != null && !theCode.isEmpty();
|
||||
|
||||
if (!haveCodeableConcept && !haveCoding && !haveCode) {
|
||||
throw new InvalidRequestException(Msg.code(906) + "No code, coding, or codeableConcept provided to validate.");
|
||||
|
|
@ -2622,7 +2567,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
public Optional<TermValueSet> findCurrentTermValueSet(String theUrl) {
|
||||
if (TermReadSvcUtil.isLoincUnversionedValueSet(theUrl)) {
|
||||
Optional<String> vsIdOpt = TermReadSvcUtil.getValueSetId(theUrl);
|
||||
if (!vsIdOpt.isPresent()) {
|
||||
if (vsIdOpt.isEmpty()) {
|
||||
return Optional.empty();
|
||||
}
|
||||
|
||||
|
|
@ -2763,7 +2708,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
IConnectionPoolInfoProvider connectionPoolInfoProvider =
|
||||
new ConnectionPoolInfoProvider(myHibernatePropertiesProvider.getDataSource());
|
||||
Optional<Integer> maxConnectionsOpt = connectionPoolInfoProvider.getTotalConnectionSize();
|
||||
if ( ! maxConnectionsOpt.isPresent() ) {
|
||||
if (maxConnectionsOpt.isEmpty()) {
|
||||
return DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS;
|
||||
}
|
||||
|
||||
|
|
@ -2894,7 +2839,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
|
|||
/**
|
||||
* Properties returned from method buildSearchScroll
|
||||
*/
|
||||
private final class SearchProperties {
|
||||
private static final class SearchProperties {
|
||||
private SearchScroll<EntityReference> mySearchScroll;
|
||||
private Optional<PredicateFinalStep> myExpansionStepOpt;
|
||||
private List<String> myIncludeOrExcludeCodes;
|
||||
|
|
|
|||
|
|
@ -0,0 +1,56 @@
|
|||
package ca.uhn.fhir.jpa.util;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR Storage api
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2022 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%
|
||||
*/
|
||||
|
||||
import com.google.gson.JsonArray;
|
||||
import com.google.gson.JsonObject;
|
||||
import com.google.gson.JsonPrimitive;
|
||||
|
||||
/**
|
||||
* The whole purpose of his class is to ease construction of a non-trivial gson.JsonObject,
|
||||
* which can't be done the easy way in this case (using a JSON string), because there are
|
||||
* valid regex strings which break gson, as this: ".*\\^Donor$"
|
||||
*/
|
||||
public class RegexpGsonBuilderUtil {
|
||||
|
||||
|
||||
private RegexpGsonBuilderUtil() { }
|
||||
|
||||
/**
|
||||
* Builds a json object as this sample:
|
||||
* {"regexp":{" + thePropName + ":{"value":" + theValue + "}}}
|
||||
*/
|
||||
public static JsonObject toGson(String thePropName, String theValue) {
|
||||
JsonObject valueJO = new JsonObject();
|
||||
valueJO.add("value", new JsonPrimitive(theValue));
|
||||
|
||||
JsonObject systemValueJO = new JsonObject();
|
||||
systemValueJO.add(thePropName, valueJO);
|
||||
|
||||
JsonObject regexpJO = new JsonObject();
|
||||
regexpJO.add("regexp", systemValueJO);
|
||||
|
||||
JsonArray a = new JsonArray();
|
||||
return regexpJO;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
package ca.uhn.fhir.jpa.util;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
import com.google.gson.JsonObject;
|
||||
import com.google.gson.JsonSyntaxException;
|
||||
import com.google.gson.stream.MalformedJsonException;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import static ca.uhn.fhir.jpa.entity.TermConceptPropertyBinder.CONCEPT_PROPERTY_PREFIX_NAME;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
class RegexpGsonBuilderUtilTest {
|
||||
|
||||
private static final String PROP_NAME = "myValueString";
|
||||
|
||||
// a valid regex string which breaks gson
|
||||
private static final String GSON_FAILING_REGEX = ".*\\^Donor$";
|
||||
|
||||
|
||||
@Test
|
||||
void testBuildUsingTestedClass() {
|
||||
String propertyValue = "propAAA";
|
||||
String expectedGson = "{\"regexp\":{\"P:" + PROP_NAME + "\":{\"value\":\"" + propertyValue + "\"}}}";
|
||||
|
||||
assertEquals(expectedGson, RegexpGsonBuilderUtil.toGson(
|
||||
CONCEPT_PROPERTY_PREFIX_NAME + PROP_NAME, propertyValue).toString());
|
||||
}
|
||||
|
||||
/**
|
||||
* This test demonstrates that valid regex strings break gson library.
|
||||
* If one day this test fails would mean the library added support for this kind of strings
|
||||
* so the tested class could be removed and the code using it just build a gson.JsonObject from a JSON string
|
||||
*/
|
||||
@Test
|
||||
void testShowGsonLibFailing() {
|
||||
String workingRegex = ".*[abc]?jk";
|
||||
String workingRegexQuery = "{'regexp':{'P:SYSTEM':{'value':'" + workingRegex + "'}}}";
|
||||
|
||||
JsonObject jsonObj = new Gson().fromJson(workingRegexQuery, JsonObject.class);
|
||||
assertFalse(jsonObj.isJsonNull());
|
||||
|
||||
// same json structure fails with some valid regex strings
|
||||
String failingRegexQuery = "{'regexp':{'P:SYSTEM':{'value':'" + GSON_FAILING_REGEX + "'}}}";
|
||||
|
||||
JsonSyntaxException thrown = assertThrows(
|
||||
JsonSyntaxException.class,
|
||||
() -> new Gson().fromJson(failingRegexQuery, JsonObject.class));
|
||||
|
||||
assertTrue(thrown.getCause() instanceof MalformedJsonException);
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -36,7 +36,6 @@ import org.hl7.fhir.r4.model.Enumerations;
|
|||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Disabled;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Answers;
|
||||
|
|
@ -287,7 +286,6 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
|
|||
* Reproduced: https://github.com/hapifhir/hapi-fhir/issues/3992
|
||||
*/
|
||||
@Test
|
||||
@Disabled("until bug gets fixed")
|
||||
public void testExpandValueSetWithMoreThanElasticDefaultNestedObjectCount() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL);
|
||||
|
|
@ -301,8 +299,13 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
|
|||
codeSystemVersion.setResource(csResource);
|
||||
|
||||
TermConcept tc = new TermConcept(codeSystemVersion, "test-code-1");
|
||||
|
||||
// need to be more than elastic [index.mapping.nested_objects.limit] index level setting (default = 10_000)
|
||||
addTerConceptProperties(tc, 10_100);
|
||||
// however, the new mapping (not nested, multivalued) groups properties by key, and there can't be more than 1000
|
||||
// properties (keys), so we test here with a number of properties > 10_000 but grouped in max 200 property keys
|
||||
// (current loinc version (2.73) has 82 property keys maximum in a TermConcept)
|
||||
addTermConceptProperties(tc, 10_100, 200);
|
||||
|
||||
codeSystemVersion.getConcepts().add(tc);
|
||||
|
||||
ValueSet valueSet = new ValueSet();
|
||||
|
|
@ -320,10 +323,21 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
|
|||
|
||||
}
|
||||
|
||||
private void addTerConceptProperties(TermConcept theTermConcept, int theCount) {
|
||||
for (int i = 0; i < theCount; i++) {
|
||||
String suff = String.format("%05d", i);
|
||||
theTermConcept.addPropertyString("prop-" + suff, "value-" + suff);
|
||||
private void addTermConceptProperties(TermConcept theTermConcept, int thePropertiesCount, int thePropertyKeysCount) {
|
||||
int valuesPerPropKey = thePropertiesCount / thePropertyKeysCount;
|
||||
|
||||
int propsCreated = 0;
|
||||
while(propsCreated < thePropertiesCount) {
|
||||
|
||||
int propKeysCreated = 0;
|
||||
while(propKeysCreated < thePropertyKeysCount && propsCreated < thePropertiesCount) {
|
||||
String propKey = String.format("%05d", propKeysCreated);
|
||||
String propSeq = String.format("%05d", propsCreated);
|
||||
theTermConcept.addPropertyString("prop-key-" + propKey, "value-" + propSeq);
|
||||
|
||||
propKeysCreated++;
|
||||
propsCreated++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -108,7 +108,7 @@ import static org.mockito.Mockito.when;
|
|||
*/
|
||||
//@ExtendWith(SpringExtension.class)
|
||||
//@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.DefaultLuceneHeap.class})
|
||||
//@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.DefaultLuceneHeap.class})
|
||||
//@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.Elasticsearch.class})
|
||||
public abstract class AbstractValueSetHSearchExpansionR4Test extends BaseJpaTest {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(AbstractValueSetHSearchExpansionR4Test.class);
|
||||
|
||||
|
|
|
|||
|
|
@ -1,94 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.search;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR Storage api
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2022 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%
|
||||
*/
|
||||
|
||||
import com.google.gson.JsonArray;
|
||||
import com.google.gson.JsonObject;
|
||||
|
||||
/**
|
||||
* The whole purpose of his class is to ease construction of a non-trivial gson.JsonObject,
|
||||
* which can't be done the easy way in this case (using a JSON string), because there are
|
||||
* valid regex strings which break gson, as this: ".*\\^Donor$"
|
||||
*/
|
||||
public class ElasticsearchNestedQueryBuilderUtil {
|
||||
|
||||
private final String myNestedObjName;
|
||||
private final String myNestedKeyPropName;
|
||||
private final String myNestedKeyPropValue;
|
||||
private final String myNestedValuePropName;
|
||||
private final String myNestedValuePropValue;
|
||||
|
||||
private final String myNestedPropertyKeyPath;
|
||||
private final String myNestedPropertyValuePath;
|
||||
|
||||
private JsonObject builtJsonObj = new JsonObject();
|
||||
|
||||
public ElasticsearchNestedQueryBuilderUtil(String theNestedObjName, String theNestedKeyPropName,
|
||||
String theNestedKeyPropValue, String theNestedValuePropName, String theNestedValuePropValue) {
|
||||
|
||||
myNestedObjName = theNestedObjName ;
|
||||
myNestedKeyPropName = theNestedKeyPropName;
|
||||
myNestedKeyPropValue = theNestedKeyPropValue;
|
||||
myNestedValuePropName = theNestedValuePropName;
|
||||
myNestedValuePropValue = theNestedValuePropValue;
|
||||
|
||||
myNestedPropertyKeyPath = myNestedObjName + "." + myNestedKeyPropName;
|
||||
myNestedPropertyValuePath = myNestedObjName + "." + myNestedValuePropName;
|
||||
|
||||
buildJsonObj();
|
||||
}
|
||||
|
||||
|
||||
private void buildJsonObj() {
|
||||
JsonObject matchPropJO = new JsonObject();
|
||||
matchPropJO.addProperty(myNestedObjName + "." + myNestedKeyPropName, myNestedKeyPropValue);
|
||||
JsonObject matchJO = new JsonObject();
|
||||
matchJO.add("match", matchPropJO);
|
||||
|
||||
JsonObject regexpPropJO = new JsonObject();
|
||||
regexpPropJO.addProperty(myNestedObjName + "." + myNestedValuePropName, myNestedValuePropValue);
|
||||
JsonObject regexpJO = new JsonObject();
|
||||
regexpJO.add("regexp", regexpPropJO);
|
||||
|
||||
JsonArray mustPropJA = new JsonArray();
|
||||
mustPropJA.add(matchJO);
|
||||
mustPropJA.add(regexpJO);
|
||||
|
||||
JsonObject mustPropJO = new JsonObject();
|
||||
mustPropJO.add("must", mustPropJA);
|
||||
|
||||
JsonObject boolJO = new JsonObject();
|
||||
boolJO.add("bool", mustPropJO);
|
||||
|
||||
JsonObject nestedJO = new JsonObject();
|
||||
nestedJO.addProperty("path", myNestedObjName);
|
||||
nestedJO.add("query", boolJO);
|
||||
|
||||
builtJsonObj.add("nested", nestedJO);
|
||||
}
|
||||
|
||||
public JsonObject toGson() { return builtJsonObj; }
|
||||
|
||||
public String getNestedPropertyKeyPath() { return myNestedPropertyKeyPath; }
|
||||
|
||||
public String getNestedPropertyValuePath() { return myNestedPropertyValuePath; }
|
||||
|
||||
}
|
||||
|
|
@ -1,87 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.search;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
import com.google.gson.JsonArray;
|
||||
import com.google.gson.JsonObject;
|
||||
import com.google.gson.JsonSyntaxException;
|
||||
import com.google.gson.stream.MalformedJsonException;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
class ElasticsearchNestedQueryBuilderUtilTest {
|
||||
|
||||
private static final String NESTED_KEY_PROP_NAME = "myKey";
|
||||
private static final String NESTED_VALUE_PROP_NAME = "myValueString";
|
||||
private static final String NESTED_OBJECT_NAME = "myProperties";
|
||||
|
||||
// a valid regex string which breaks gson
|
||||
private static final String GSON_FAILING_REGEX = ".*\\^Donor$";
|
||||
|
||||
|
||||
private ElasticsearchNestedQueryBuilderUtil testedUtil;
|
||||
|
||||
|
||||
@Test
|
||||
void testBuildUsingTestedClass() {
|
||||
String propertyValue = "propAAA";
|
||||
|
||||
testedUtil = new ElasticsearchNestedQueryBuilderUtil(
|
||||
NESTED_OBJECT_NAME, NESTED_KEY_PROP_NAME, propertyValue, NESTED_VALUE_PROP_NAME, GSON_FAILING_REGEX);
|
||||
|
||||
assertFalse(testedUtil.toGson().isJsonNull());
|
||||
|
||||
JsonObject generatedJson = testedUtil.toGson();
|
||||
JsonObject nestedJO = generatedJson.getAsJsonObject("nested");
|
||||
assertEquals(NESTED_OBJECT_NAME, nestedJO.get("path").getAsString());
|
||||
|
||||
JsonObject queryJO = nestedJO.getAsJsonObject("query");
|
||||
JsonObject boolJO = queryJO.getAsJsonObject("bool");
|
||||
JsonArray mustJA = boolJO.getAsJsonArray("must");
|
||||
|
||||
JsonObject matchPropKeyJE = (JsonObject) mustJA.get(0);
|
||||
JsonObject propKeyJO = matchPropKeyJE.getAsJsonObject("match");
|
||||
assertEquals(propertyValue, propKeyJO.get(testedUtil.getNestedPropertyKeyPath()).getAsString());
|
||||
|
||||
JsonObject regexpPropValueJE = (JsonObject) mustJA.get(1);
|
||||
JsonObject propValueJO = regexpPropValueJE.getAsJsonObject("regexp");
|
||||
assertEquals(GSON_FAILING_REGEX, propValueJO.get(testedUtil.getNestedPropertyValuePath()).getAsString());
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* This test demonstrates that valid regex strings break gson library.
|
||||
* If one day this test fails would mean the library added support for this kind of strings
|
||||
* so the tested class could be removed and the code using it just build a gson.JsonObject from a JSON string
|
||||
*/
|
||||
@Test
|
||||
void testShowGsonLibFailing() {
|
||||
String workingRegex = ".*[abc]?jk";
|
||||
String workingNestedQuery =
|
||||
"{'nested': { 'path': 'myProperties', 'query': { 'bool': { 'must': [" +
|
||||
"{'match': {'myProperties.myKey': 'propAAA' }}," +
|
||||
"{'regexp': {'myProperties.myValueString': '" + workingRegex + "'}}" +
|
||||
"]}}}}";
|
||||
|
||||
JsonObject jsonObj = new Gson().fromJson(workingNestedQuery, JsonObject.class);
|
||||
assertFalse(jsonObj.isJsonNull());
|
||||
|
||||
// same json structure fails with some valid regex strings
|
||||
String nestedQuery =
|
||||
"{'nested': { 'path': 'myProperties', 'query': { 'bool': { 'must': [" +
|
||||
"{'match': {'myProperties.myKey': 'propAAA' }}," +
|
||||
"{'regexp': {'myProperties.myValueString': '" + GSON_FAILING_REGEX + "'}}" +
|
||||
"]}}}}";
|
||||
|
||||
// MalformedJsonException thrown = assertThrows(
|
||||
JsonSyntaxException thrown = assertThrows(
|
||||
JsonSyntaxException.class,
|
||||
() -> new Gson().fromJson(nestedQuery, JsonObject.class));
|
||||
|
||||
assertTrue(thrown.getCause() instanceof MalformedJsonException);
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue