Issue 3421 pre expansion fails for valuesets with more than 1024 concepts (#3434)
* Build search queries involving many predicates avoiding crashing when number is larger than configured BooleanQuery.maxClauseCount * Add changelog * Restore temp directory config Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto
GitHub
parent
f614eaf6c8
commit
4b5f75c069
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 3421
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title: "ValueSet pre-expansion was failing when number of concepts was larger than configured BooleanQuery.maxClauseCount
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value (default is 1024). This is now fixed."
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@ -88,11 +88,13 @@ 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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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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@ -144,6 +146,7 @@ import org.springframework.transaction.interceptor.NoRollbackRuleAttribute;
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import org.springframework.transaction.interceptor.RuleBasedTransactionAttribute;
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import org.springframework.transaction.support.TransactionSynchronizationManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import org.springframework.util.CollectionUtils;
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import org.springframework.util.comparator.Comparators;
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import javax.annotation.Nonnull;
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@ -928,21 +931,19 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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.filter(StringUtils::isNotBlank)
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.collect(Collectors.toList());
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PredicateFinalStep expansionStep = buildExpansionPredicate(codes, predicate);
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final PredicateFinalStep finishedQuery;
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if (expansionStep == null) {
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finishedQuery = step;
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} else {
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finishedQuery = predicate.bool().must(step).must(expansionStep);
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}
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Optional<PredicateFinalStep> expansionStepOpt = buildExpansionPredicate(codes, predicate);
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final PredicateFinalStep finishedQuery = expansionStepOpt.isPresent()
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? predicate.bool().must(step).must(expansionStepOpt.get()) : step;
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/*
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* DM 2019-08-21 - Processing slows after any ValueSets with many codes explicitly identified. This might
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* be due to the dark arts that is memory management. Will monitor but not do anything about this right now.
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*/
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//BooleanQuery.setMaxClauseCount(SearchBuilder.getMaximumPageSize());
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//TODO GGG HS looks like we can't set max clause count, but it can be set server side.
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//BooleanQuery.setMaxClauseCount(10000);
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// JM 2-22-02-15 - Hopefully increasing maxClauseCount should be not needed anymore
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StopWatch sw = new StopWatch();
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AtomicInteger count = new AtomicInteger(0);
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@ -1003,7 +1004,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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for (TermConcept concept : termConcepts) {
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count.incrementAndGet();
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countForBatch.incrementAndGet();
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if (theAdd && expansionStep != null) {
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if (theAdd && expansionStepOpt.isPresent()) {
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ValueSet.ConceptReferenceComponent theIncludeConcept = getMatchedConceptIncludedInValueSet(theIncludeOrExclude, concept);
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if (theIncludeConcept != null && isNotBlank(theIncludeConcept.getDisplay())) {
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concept.setDisplay(theIncludeConcept.getDisplay());
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@ -1037,29 +1038,30 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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/**
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* Helper method which builds a predicate for the expansion
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*/
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private PredicateFinalStep buildExpansionPredicate(List<String> theCodes, SearchPredicateFactory thePredicate) {
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PredicateFinalStep expansionStep;
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/*
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* Include/Exclude Concepts
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*/
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List<Term> codes = theCodes
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.stream()
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.map(t -> new Term("myCode", t))
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.collect(Collectors.toList());
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private Optional<PredicateFinalStep> buildExpansionPredicate(List<String> theCodes, SearchPredicateFactory thePredicate) {
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if (CollectionUtils.isEmpty(theCodes)) { return Optional.empty(); }
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if (codes.size() > 0) {
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expansionStep = thePredicate.bool(b -> {
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if (theCodes.size() < BooleanQuery.getMaxClauseCount()) {
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return Optional.of(thePredicate.simpleQueryString()
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.field( "myCode" ).matching( String.join(" | ", theCodes)) );
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}
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// Number of codes is larger than maxClauseCount, so we split the query in several clauses
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// partition codes in lists of BooleanQuery.getMaxClauseCount() size
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List<List<String>> listOfLists = ListUtils.partition(theCodes, BooleanQuery.getMaxClauseCount());
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PredicateFinalStep step = thePredicate.bool(b -> {
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b.minimumShouldMatchNumber(1);
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for (Term code : codes) {
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b.should(thePredicate.match().field(code.field()).matching(code.text()));
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for (List<String> codeList : listOfLists) {
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b.should(p -> p.simpleQueryString().field("myCode").matching(String.join(" | ", codeList)));
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}
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});
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return expansionStep;
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} else {
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return null;
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}
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return Optional.of(step);
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}
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private String buildCodeSystemUrlAndVersion(String theSystem, String theIncludeOrExcludeVersion) {
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String codeSystemUrlAndVersion;
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if (theIncludeOrExcludeVersion != null) {
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@ -62,6 +62,7 @@ public class TestHibernateSearchAddInConfig {
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Path tempDirPath = Files.createTempDirectory(null);
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String dirPath = tempDirPath.toString();
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Map<String, String> luceneProperties = new HashMap<>();
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luceneProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "lucene");
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luceneProperties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
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@ -78,8 +79,7 @@ public class TestHibernateSearchAddInConfig {
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}
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@Bean(name={"searchDao", "searchDaoDstu2", "searchDaoDstu3", "searchDaoR4", "searchDaoR5"})
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public IFulltextSearchSvc searchDao() {
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public IFulltextSearchSvc fullTextSearchSvc() {
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ourLog.info("Hibernate Search: FulltextSearchSvcImpl present");
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return new FulltextSearchSvcImpl();
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}
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@ -123,9 +123,7 @@ public class TestHibernateSearchAddInConfig {
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@Bean
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IHibernateSearchConfigurer hibernateSearchConfigurer() {
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ourLog.info("Hibernate Search is disabled");
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return (theProperties) -> {
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theProperties.put("hibernate.search.enabled", "false");
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};
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return (theProperties) -> theProperties.put("hibernate.search.enabled", "false");
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}
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@Primary
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@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
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import ca.uhn.fhir.jpa.dao.BaseJpaTest;
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import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
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@ -26,6 +27,14 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
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import org.apache.commons.collections4.ListUtils;
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import org.apache.lucene.search.BooleanQuery;
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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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import org.hibernate.search.engine.search.query.SearchQuery;
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import org.hibernate.search.mapper.orm.Search;
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import org.hibernate.search.mapper.orm.common.EntityReference;
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import org.hibernate.search.mapper.orm.session.SearchSession;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeableConcept;
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@ -42,12 +51,17 @@ import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.test.util.AopTestUtils;
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import org.springframework.test.util.ReflectionTestUtils;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.annotation.Transactional;
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import javax.persistence.EntityManager;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.IntStream;
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import static ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc.MAKE_LOADING_VERSION_CURRENT;
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import static ca.uhn.fhir.jpa.term.api.ITermLoaderSvc.LOINC_URI;
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@ -56,6 +70,8 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.hamcrest.Matchers.empty;
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import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.ArgumentMatchers.anyCollection;
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import static org.mockito.ArgumentMatchers.anyString;
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@ -72,8 +88,8 @@ import static org.mockito.Mockito.when;
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//@ExtendWith(SpringExtension.class)
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//@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
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//@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
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public abstract class AbstractValeSetFreeTextExpansionR4Test extends BaseJpaTest {
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private static final Logger ourLog = LoggerFactory.getLogger(AbstractValeSetFreeTextExpansionR4Test.class);
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public abstract class AbstractValueSetFreeTextExpansionR4Test extends BaseJpaTest {
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private static final Logger ourLog = LoggerFactory.getLogger(AbstractValueSetFreeTextExpansionR4Test.class);
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private static final String CS_URL = "http://example.com/my_code_system";
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private static final String CS_URL_2 = "http://example.com/my_code_system2";
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@ -129,6 +145,9 @@ public abstract class AbstractValeSetFreeTextExpansionR4Test extends BaseJpaTest
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@Autowired
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private IBulkDataExportSvc myBulkDataExportSvc;
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@Autowired
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protected ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
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@Mock
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private IValueSetConceptAccumulator myValueSetCodeAccumulator;
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@ -1669,6 +1688,187 @@ public abstract class AbstractValeSetFreeTextExpansionR4Test extends BaseJpaTest
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}
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/**
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* Test associated to searching with a number of terms larger than BooleanQuery.getMaxClauseCount()
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*/
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@Nested
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public class TestSearchWithManyCodes {
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private List<String> allCodesNotIncludingSearched;
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private List<String> existingCodes = Arrays.asList("50015-7", "43343-3", "43343-4", "47239-9");
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private Long termCsId;
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@BeforeEach
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void generateLongSearchedCodesList() {
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int codesQueriedCount = (int) (BooleanQuery.getMaxClauseCount() * 1.5);
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allCodesNotIncludingSearched = generateCodes(codesQueriedCount);
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termCsId = createLoincSystemWithSomeCodes();
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}
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@Test
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public void testShouldNotFindAny() {
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List<EntityReference> hits = search(allCodesNotIncludingSearched);
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assertNotNull(hits);
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assertTrue(hits.isEmpty());
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}
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@Test
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public void testHitsInFirstSublist() {
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int insertIndex = BooleanQuery.getMaxClauseCount() / 2;
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// insert existing codes into list of codes searched
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allCodesNotIncludingSearched.addAll(insertIndex, existingCodes);
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List<EntityReference> hits = search(allCodesNotIncludingSearched);
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assertEquals(existingCodes.size(), hits.size());
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}
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@Test
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public void testHitsInLastSublist() {
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// insert existing codes into list of codes searched
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allCodesNotIncludingSearched.addAll(allCodesNotIncludingSearched.size(), existingCodes);
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List<EntityReference> hits = search(allCodesNotIncludingSearched);
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assertEquals(existingCodes.size(), hits.size());
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}
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@Test
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public void testHitsInBothSublists() {
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// insert half of existing codes in first sublist and half in last
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List<List<String>> partitionedExistingCodes = ListUtils.partition(existingCodes, existingCodes.size() / 2);
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assertEquals(2, partitionedExistingCodes.size());
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// insert first partition of existing codes into first sublist of searched codes
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allCodesNotIncludingSearched.addAll(0, partitionedExistingCodes.get(0));
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// insert last partition of existing codes into last sublist of searched codes
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allCodesNotIncludingSearched.addAll(allCodesNotIncludingSearched.size(), partitionedExistingCodes.get(1));
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List<EntityReference> hits = search(allCodesNotIncludingSearched);
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assertEquals(existingCodes.size(), hits.size());
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}
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private List<EntityReference> search(List<String> theSearchedCodes) {
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return runInTransaction(() -> {
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TermCodeSystemVersion termCsVersion = myTermCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(termCsId);
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Long termCsvPid = termCsVersion.getPid();
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SearchSession searchSession = Search.session(myEntityManager);
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SearchPredicateFactory predicate = searchSession.scope(TermConcept.class).predicate();
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Optional<PredicateFinalStep> lastStepOpt = ReflectionTestUtils.invokeMethod(
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new TermReadSvcR4(), "buildExpansionPredicate", theSearchedCodes, predicate);
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assertNotNull(lastStepOpt);
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assertTrue(lastStepOpt.isPresent());
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PredicateFinalStep step = predicate.bool(b -> {
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b.must(predicate.match().field("myCodeSystemVersionPid").matching(termCsvPid));
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b.must(lastStepOpt.get());
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});
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int maxResultsPerBatch = 800;
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SearchQuery<EntityReference> termConceptsQuery = searchSession
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.search(TermConcept.class)
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.selectEntityReference()
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.where(f -> step)
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.toQuery();
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ourLog.trace("About to query: {}", termConceptsQuery.queryString());
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return termConceptsQuery.fetchHits(0, maxResultsPerBatch);
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});
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}
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}
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private List<String> generateCodes(int theCodesQueriedCount) {
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return IntStream.range(0, theCodesQueriedCount)
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.mapToObj(i -> "generated-code-" + i).collect(Collectors.toList());
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}
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public long createLoincSystemWithSomeCodes() {
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CodeSystem codeSystem = new CodeSystem();
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codeSystem.setUrl(LOINC_URI);
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codeSystem.setId("test-loinc");
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codeSystem.setVersion("SYSTEM VERSION");
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codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
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IIdType csId = myCodeSystemDao.create(codeSystem).getId().toUnqualified();
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ResourceTable table = myResourceTableDao.findById(csId.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
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TermCodeSystemVersion termCodeSystemVersion = new TermCodeSystemVersion();
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termCodeSystemVersion.setResource(table);
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TermConcept code1 = new TermConcept(termCodeSystemVersion, "50015-7"); // has -3 as a child
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TermConcept code2 = new TermConcept(termCodeSystemVersion, "43343-3"); // has -4 as a child
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TermConcept code3 = new TermConcept(termCodeSystemVersion, "43343-4"); //has no children
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TermConcept code4 = new TermConcept(termCodeSystemVersion, "47239-9"); //has no children
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code1.addPropertyString("SYSTEM", "Bld/Bone mar^Donor");
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code1.addPropertyCoding(
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"child",
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LOINC_URI,
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code2.getCode(),
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code2.getDisplay());
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code1.addChild(code2, RelationshipTypeEnum.ISA);
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termCodeSystemVersion.getConcepts().add(code1);
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code2.addPropertyString("SYSTEM", "Ser");
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code2.addPropertyString("HELLO", "12345-1");
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code2.addPropertyCoding(
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"parent",
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LOINC_URI,
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code1.getCode(),
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code1.getDisplay());
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code2.addPropertyCoding(
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"child",
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LOINC_URI,
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code3.getCode(),
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code3.getDisplay());
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code2.addChild(code3, RelationshipTypeEnum.ISA);
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code2.addPropertyCoding(
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"child",
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LOINC_URI,
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code4.getCode(),
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code4.getDisplay());
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code2.addChild(code4, RelationshipTypeEnum.ISA);
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termCodeSystemVersion.getConcepts().add(code2);
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code3.addPropertyString("SYSTEM", "Ser");
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code3.addPropertyString("HELLO", "12345-2");
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code3.addPropertyCoding(
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"parent",
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LOINC_URI,
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code2.getCode(),
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code2.getDisplay());
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termCodeSystemVersion.getConcepts().add(code3);
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code4.addPropertyString("SYSTEM", "^Patient");
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code4.addPropertyString("EXTERNAL_COPYRIGHT_NOTICE", "Copyright © 2006 World Health Organization...");
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code4.addPropertyCoding(
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"parent",
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LOINC_URI,
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code2.getCode(),
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code2.getDisplay());
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termCodeSystemVersion.getConcepts().add(code4);
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myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), LOINC_URI, "SYSTEM NAME", "SYSTEM VERSION", termCodeSystemVersion, table);
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return csId.getIdPartAsLong();
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}
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@ -1819,77 +2019,6 @@ public abstract class AbstractValeSetFreeTextExpansionR4Test extends BaseJpaTest
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}
|
||||
|
||||
|
||||
public void createLoincSystemWithSomeCodes() {
|
||||
runInTransaction(() -> {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(LOINC_URI);
|
||||
codeSystem.setId("test-loinc");
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem).getId().toUnqualified();
|
||||
|
||||
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
|
||||
|
||||
TermCodeSystemVersion cs = new TermCodeSystemVersion();
|
||||
cs.setResource(table);
|
||||
|
||||
TermConcept code1 = new TermConcept(cs, "50015-7"); // has -3 as a child
|
||||
TermConcept code2 = new TermConcept(cs, "43343-3"); // has -4 as a child
|
||||
TermConcept code3 = new TermConcept(cs, "43343-4"); //has no children
|
||||
TermConcept code4 = new TermConcept(cs, "47239-9"); //has no children
|
||||
|
||||
code1.addPropertyString("SYSTEM", "Bld/Bone mar^Donor");
|
||||
code1.addPropertyCoding(
|
||||
"child",
|
||||
LOINC_URI,
|
||||
code2.getCode(),
|
||||
code2.getDisplay());
|
||||
code1.addChild(code2, RelationshipTypeEnum.ISA);
|
||||
cs.getConcepts().add(code1);
|
||||
|
||||
code2.addPropertyString("SYSTEM", "Ser");
|
||||
code2.addPropertyString("HELLO", "12345-1");
|
||||
code2.addPropertyCoding(
|
||||
"parent",
|
||||
LOINC_URI,
|
||||
code1.getCode(),
|
||||
code1.getDisplay());
|
||||
code2.addPropertyCoding(
|
||||
"child",
|
||||
LOINC_URI,
|
||||
code3.getCode(),
|
||||
code3.getDisplay());
|
||||
code2.addChild(code3, RelationshipTypeEnum.ISA);
|
||||
code2.addPropertyCoding(
|
||||
"child",
|
||||
LOINC_URI,
|
||||
code4.getCode(),
|
||||
code4.getDisplay());
|
||||
code2.addChild(code4, RelationshipTypeEnum.ISA);
|
||||
cs.getConcepts().add(code2);
|
||||
|
||||
code3.addPropertyString("SYSTEM", "Ser");
|
||||
code3.addPropertyString("HELLO", "12345-2");
|
||||
code3.addPropertyCoding(
|
||||
"parent",
|
||||
LOINC_URI,
|
||||
code2.getCode(),
|
||||
code2.getDisplay());
|
||||
cs.getConcepts().add(code3);
|
||||
|
||||
code4.addPropertyString("SYSTEM", "^Patient");
|
||||
code4.addPropertyString("EXTERNAL_COPYRIGHT_NOTICE", "Copyright © 2006 World Health Organization...");
|
||||
code4.addPropertyCoding(
|
||||
"parent",
|
||||
LOINC_URI,
|
||||
code2.getCode(),
|
||||
code2.getDisplay());
|
||||
cs.getConcepts().add(code4);
|
||||
|
||||
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), LOINC_URI, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
|
||||
});
|
||||
}
|
||||
|
||||
private List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
|
||||
List<String> retVal = new ArrayList<>();
|
||||
|
||||
|
|
@ -11,6 +11,6 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
|
|||
*/
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.Elasticsearch.class})
|
||||
public class ValeSetFreeTextExpansionR4ElasticIT extends AbstractValeSetFreeTextExpansionR4Test {
|
||||
public class ValueSetFreeTextExpansionR4ElasticIT extends AbstractValueSetFreeTextExpansionR4Test {
|
||||
|
||||
}
|
||||
|
|
@ -12,6 +12,6 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
|
|||
*/
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
|
||||
public class ValeSetFreeTextExpansionR4LuceneIT extends AbstractValeSetFreeTextExpansionR4Test {
|
||||
public class ValueSetFreeTextExpansionR4LuceneIT extends AbstractValueSetFreeTextExpansionR4Test {
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue