Add ITermConceptClientMappingSvc interface to represent terminology t… (#5410)
* Add ITermConceptClientMappingSvc interface to represent terminology translate functions * Add javadoc --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
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jmarchionatto
GitHub
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commit
c89fc46863
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package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.TranslateConceptResult;
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import ca.uhn.fhir.context.support.TranslateConceptResults;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.api.model.TranslationQuery;
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import ca.uhn.fhir.jpa.api.model.TranslationRequest;
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import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptMapDao;
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import ca.uhn.fhir.jpa.entity.TermConceptMap;
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import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
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import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
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import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
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import ca.uhn.fhir.jpa.model.dao.JpaPid;
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import ca.uhn.fhir.jpa.term.api.ITermConceptClientMappingSvc;
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import ca.uhn.fhir.jpa.util.MemoryCacheService;
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import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import org.apache.commons.lang3.StringUtils;
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import org.hibernate.ScrollMode;
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import org.hibernate.ScrollableResults;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Coding;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.data.domain.PageRequest;
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import org.springframework.data.domain.Pageable;
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import org.springframework.transaction.annotation.Propagation;
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import org.springframework.transaction.annotation.Transactional;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import javax.persistence.TypedQuery;
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import javax.persistence.criteria.CriteriaBuilder;
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import javax.persistence.criteria.CriteriaQuery;
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import javax.persistence.criteria.Join;
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import javax.persistence.criteria.Predicate;
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import javax.persistence.criteria.Root;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class TermConceptClientMappingSvcImpl implements ITermConceptClientMappingSvc {
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private static final Logger ourLog = LoggerFactory.getLogger(TermConceptClientMappingSvcImpl.class);
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private final int myFetchSize = TermReadSvcImpl.DEFAULT_FETCH_SIZE;
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protected static boolean ourLastResultsFromTranslationCache; // For testing.
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protected static boolean ourLastResultsFromTranslationWithReverseCache; // For testing.
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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@Autowired
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protected FhirContext myContext;
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@Autowired
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protected MemoryCacheService myMemoryCacheService;
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@Autowired
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protected IIdHelperService<JpaPid> myIdHelperService;
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@Autowired
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protected ITermConceptMapDao myConceptMapDao;
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@Override
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@Transactional(propagation = Propagation.REQUIRED)
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public TranslateConceptResults translate(TranslationRequest theTranslationRequest) {
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TranslateConceptResults retVal = new TranslateConceptResults();
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CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
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CriteriaQuery<TermConceptMapGroupElementTarget> query =
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criteriaBuilder.createQuery(TermConceptMapGroupElementTarget.class);
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Root<TermConceptMapGroupElementTarget> root = query.from(TermConceptMapGroupElementTarget.class);
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Join<TermConceptMapGroupElementTarget, TermConceptMapGroupElement> elementJoin =
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root.join("myConceptMapGroupElement");
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Join<TermConceptMapGroupElement, TermConceptMapGroup> groupJoin = elementJoin.join("myConceptMapGroup");
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Join<TermConceptMapGroup, TermConceptMap> conceptMapJoin = groupJoin.join("myConceptMap");
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List<TranslationQuery> translationQueries = theTranslationRequest.getTranslationQueries();
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List<TranslateConceptResult> cachedTargets;
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ArrayList<Predicate> predicates;
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Coding coding;
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// -- get the latest ConceptMapVersion if theTranslationRequest has ConceptMap url but no ConceptMap version
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String latestConceptMapVersion = null;
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if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
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latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
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for (TranslationQuery translationQuery : translationQueries) {
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cachedTargets = myMemoryCacheService.getIfPresent(
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MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION, translationQuery);
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if (cachedTargets == null) {
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final List<TranslateConceptResult> targets = new ArrayList<>();
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predicates = new ArrayList<>();
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coding = translationQuery.getCoding();
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if (coding.hasCode()) {
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predicates.add(criteriaBuilder.equal(elementJoin.get("myCode"), coding.getCode()));
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} else {
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throw new InvalidRequestException(
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Msg.code(842) + "A code must be provided for translation to occur.");
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}
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if (coding.hasSystem()) {
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predicates.add(criteriaBuilder.equal(groupJoin.get("mySource"), coding.getSystem()));
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}
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if (coding.hasVersion()) {
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predicates.add(criteriaBuilder.equal(groupJoin.get("mySourceVersion"), coding.getVersion()));
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}
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if (translationQuery.hasTargetSystem()) {
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predicates.add(
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criteriaBuilder.equal(groupJoin.get("myTarget"), translationQuery.getTargetSystem()));
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}
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if (translationQuery.hasUrl()) {
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl()));
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if (translationQuery.hasConceptMapVersion()) {
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// both url and conceptMapVersion
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predicates.add(criteriaBuilder.equal(
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conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion()));
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} else {
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if (StringUtils.isNotBlank(latestConceptMapVersion)) {
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// only url and use latestConceptMapVersion
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predicates.add(
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criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
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} else {
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predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
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}
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}
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}
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if (translationQuery.hasSource()) {
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("mySource"), translationQuery.getSource()));
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}
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if (translationQuery.hasTarget()) {
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myTarget"), translationQuery.getTarget()));
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}
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if (translationQuery.hasResourceId()) {
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IIdType resourceId = translationQuery.getResourceId();
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JpaPid resourcePid =
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myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getId()));
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}
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Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
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query.where(outerPredicate);
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// Use scrollable results.
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final TypedQuery<TermConceptMapGroupElementTarget> typedQuery =
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myEntityManager.createQuery(query.select(root));
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org.hibernate.query.Query<TermConceptMapGroupElementTarget> hibernateQuery =
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(org.hibernate.query.Query<TermConceptMapGroupElementTarget>) typedQuery;
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hibernateQuery.setFetchSize(myFetchSize);
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ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
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try (ScrollableResultsIterator<TermConceptMapGroupElementTarget> scrollableResultsIterator =
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new ScrollableResultsIterator<>(scrollableResults)) {
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Set<TermConceptMapGroupElementTarget> matches = new HashSet<>();
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while (scrollableResultsIterator.hasNext()) {
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TermConceptMapGroupElementTarget next = scrollableResultsIterator.next();
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if (matches.add(next)) {
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TranslateConceptResult translationMatch = new TranslateConceptResult();
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if (next.getEquivalence() != null) {
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translationMatch.setEquivalence(
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next.getEquivalence().toCode());
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}
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translationMatch.setCode(next.getCode());
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translationMatch.setSystem(next.getSystem());
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translationMatch.setSystemVersion(next.getSystemVersion());
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translationMatch.setDisplay(next.getDisplay());
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translationMatch.setValueSet(next.getValueSet());
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translationMatch.setSystemVersion(next.getSystemVersion());
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translationMatch.setConceptMapUrl(next.getConceptMapUrl());
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targets.add(translationMatch);
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}
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}
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}
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ourLastResultsFromTranslationCache = false; // For testing.
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myMemoryCacheService.put(MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION, translationQuery, targets);
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retVal.getResults().addAll(targets);
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} else {
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ourLastResultsFromTranslationCache = true; // For testing.
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retVal.getResults().addAll(cachedTargets);
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}
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}
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buildTranslationResult(retVal);
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return retVal;
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}
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@Override
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@Transactional(propagation = Propagation.REQUIRED)
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public TranslateConceptResults translateWithReverse(TranslationRequest theTranslationRequest) {
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TranslateConceptResults retVal = new TranslateConceptResults();
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CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
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CriteriaQuery<TermConceptMapGroupElement> query = criteriaBuilder.createQuery(TermConceptMapGroupElement.class);
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Root<TermConceptMapGroupElement> root = query.from(TermConceptMapGroupElement.class);
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Join<TermConceptMapGroupElement, TermConceptMapGroupElementTarget> targetJoin =
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root.join("myConceptMapGroupElementTargets");
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Join<TermConceptMapGroupElement, TermConceptMapGroup> groupJoin = root.join("myConceptMapGroup");
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Join<TermConceptMapGroup, TermConceptMap> conceptMapJoin = groupJoin.join("myConceptMap");
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List<TranslationQuery> translationQueries = theTranslationRequest.getTranslationQueries();
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List<TranslateConceptResult> cachedElements;
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ArrayList<Predicate> predicates;
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Coding coding;
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// -- get the latest ConceptMapVersion if theTranslationRequest has ConceptMap url but no ConceptMap version
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String latestConceptMapVersion = null;
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if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
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latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
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for (TranslationQuery translationQuery : translationQueries) {
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cachedElements = myMemoryCacheService.getIfPresent(
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MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION_REVERSE, translationQuery);
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if (cachedElements == null) {
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final List<TranslateConceptResult> elements = new ArrayList<>();
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predicates = new ArrayList<>();
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coding = translationQuery.getCoding();
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String targetCode;
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String targetCodeSystem = null;
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if (coding.hasCode()) {
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predicates.add(criteriaBuilder.equal(targetJoin.get("myCode"), coding.getCode()));
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targetCode = coding.getCode();
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} else {
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throw new InvalidRequestException(
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Msg.code(843) + "A code must be provided for translation to occur.");
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}
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if (coding.hasSystem()) {
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predicates.add(criteriaBuilder.equal(groupJoin.get("myTarget"), coding.getSystem()));
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targetCodeSystem = coding.getSystem();
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}
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if (coding.hasVersion()) {
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predicates.add(criteriaBuilder.equal(groupJoin.get("myTargetVersion"), coding.getVersion()));
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}
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if (translationQuery.hasUrl()) {
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl()));
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if (translationQuery.hasConceptMapVersion()) {
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// both url and conceptMapVersion
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predicates.add(criteriaBuilder.equal(
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conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion()));
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} else {
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if (StringUtils.isNotBlank(latestConceptMapVersion)) {
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// only url and use latestConceptMapVersion
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predicates.add(
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criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
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} else {
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predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
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}
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}
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}
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if (translationQuery.hasTargetSystem()) {
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predicates.add(
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criteriaBuilder.equal(groupJoin.get("mySource"), translationQuery.getTargetSystem()));
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}
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if (translationQuery.hasSource()) {
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myTarget"), translationQuery.getSource()));
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}
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if (translationQuery.hasTarget()) {
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("mySource"), translationQuery.getTarget()));
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}
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if (translationQuery.hasResourceId()) {
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IIdType resourceId = translationQuery.getResourceId();
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JpaPid resourcePid =
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myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
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predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getId()));
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}
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Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
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query.where(outerPredicate);
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// Use scrollable results.
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final TypedQuery<TermConceptMapGroupElement> typedQuery =
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myEntityManager.createQuery(query.select(root));
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org.hibernate.query.Query<TermConceptMapGroupElement> hibernateQuery =
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(org.hibernate.query.Query<TermConceptMapGroupElement>) typedQuery;
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hibernateQuery.setFetchSize(myFetchSize);
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ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
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try (ScrollableResultsIterator<TermConceptMapGroupElement> scrollableResultsIterator =
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new ScrollableResultsIterator<>(scrollableResults)) {
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Set<TermConceptMapGroupElementTarget> matches = new HashSet<>();
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while (scrollableResultsIterator.hasNext()) {
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TermConceptMapGroupElement nextElement = scrollableResultsIterator.next();
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/* TODO: The invocation of the size() below does not seem to be necessary but for some reason,
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* but removing it causes tests in TerminologySvcImplR4Test to fail. We use the outcome
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* in a trace log to avoid ErrorProne flagging an unused return value.
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*/
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int size =
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nextElement.getConceptMapGroupElementTargets().size();
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ourLog.trace("Have {} targets", size);
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myEntityManager.detach(nextElement);
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if (isNotBlank(targetCode)) {
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for (TermConceptMapGroupElementTarget next :
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nextElement.getConceptMapGroupElementTargets()) {
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if (matches.add(next)) {
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if (isBlank(targetCodeSystem)
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|| StringUtils.equals(targetCodeSystem, next.getSystem())) {
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if (StringUtils.equals(targetCode, next.getCode())) {
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TranslateConceptResult translationMatch = new TranslateConceptResult();
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translationMatch.setCode(nextElement.getCode());
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translationMatch.setSystem(nextElement.getSystem());
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translationMatch.setSystemVersion(nextElement.getSystemVersion());
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translationMatch.setDisplay(nextElement.getDisplay());
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translationMatch.setValueSet(nextElement.getValueSet());
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translationMatch.setSystemVersion(nextElement.getSystemVersion());
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translationMatch.setConceptMapUrl(nextElement.getConceptMapUrl());
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if (next.getEquivalence() != null) {
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translationMatch.setEquivalence(
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next.getEquivalence().toCode());
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}
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if (alreadyContainsMapping(elements, translationMatch)
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|| alreadyContainsMapping(retVal.getResults(), translationMatch)) {
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continue;
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}
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elements.add(translationMatch);
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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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}
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ourLastResultsFromTranslationWithReverseCache = false; // For testing.
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myMemoryCacheService.put(
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MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION_REVERSE, translationQuery, elements);
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retVal.getResults().addAll(elements);
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} else {
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ourLastResultsFromTranslationWithReverseCache = true; // For testing.
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retVal.getResults().addAll(cachedElements);
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}
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}
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buildTranslationResult(retVal);
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return retVal;
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}
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@Override
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public FhirContext getFhirContext() {
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return myContext;
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}
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// Special case for the translate operation with url and without
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// conceptMapVersion, find the latest conecptMapVersion
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private String getLatestConceptMapVersion(TranslationRequest theTranslationRequest) {
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Pageable page = PageRequest.of(0, 1);
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List<TermConceptMap> theConceptMapList = myConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(
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page, theTranslationRequest.getUrl());
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if (!theConceptMapList.isEmpty()) {
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return theConceptMapList.get(0).getVersion();
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}
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return null;
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}
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private void buildTranslationResult(TranslateConceptResults theTranslationResult) {
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String msg;
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if (theTranslationResult.getResults().isEmpty()) {
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theTranslationResult.setResult(false);
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msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "noMatchesFound");
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theTranslationResult.setMessage(msg);
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} else {
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theTranslationResult.setResult(true);
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msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "matchesFound");
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theTranslationResult.setMessage(msg);
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}
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}
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private boolean alreadyContainsMapping(
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List<TranslateConceptResult> elements, TranslateConceptResult translationMatch) {
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for (TranslateConceptResult nextExistingElement : elements) {
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if (StringUtils.equals(nextExistingElement.getSystem(), translationMatch.getSystem())) {
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if (StringUtils.equals(nextExistingElement.getSystemVersion(), translationMatch.getSystemVersion())) {
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if (StringUtils.equals(nextExistingElement.getCode(), translationMatch.getCode())) {
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return true;
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}
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}
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}
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}
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return false;
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}
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}
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@ -19,15 +19,10 @@
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*/
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package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.TranslateConceptResult;
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import ca.uhn.fhir.context.support.TranslateConceptResults;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.api.model.TranslationQuery;
|
||||
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
|
||||
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementTargetDao;
|
||||
|
|
@ -35,21 +30,13 @@ import ca.uhn.fhir.jpa.entity.TermConceptMap;
|
|||
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
|
||||
import ca.uhn.fhir.jpa.model.dao.JpaPid;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
|
||||
import ca.uhn.fhir.jpa.util.MemoryCacheService;
|
||||
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.util.ValidateUtil;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hibernate.ScrollMode;
|
||||
import org.hibernate.ScrollableResults;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
|
|
@ -61,39 +48,17 @@ import org.hl7.fhir.r4.model.UriType;
|
|||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
import org.springframework.data.domain.Pageable;
|
||||
import org.springframework.transaction.annotation.Propagation;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import javax.persistence.EntityManager;
|
||||
import javax.persistence.PersistenceContext;
|
||||
import javax.persistence.PersistenceContextType;
|
||||
import javax.persistence.TypedQuery;
|
||||
import javax.persistence.criteria.CriteriaBuilder;
|
||||
import javax.persistence.criteria.CriteriaQuery;
|
||||
import javax.persistence.criteria.Join;
|
||||
import javax.persistence.criteria.Predicate;
|
||||
import javax.persistence.criteria.Root;
|
||||
|
||||
import static ca.uhn.fhir.jpa.term.TermReadSvcImpl.isPlaceholder;
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
|
||||
public class TermConceptMappingSvcImpl extends TermConceptClientMappingSvcImpl implements ITermConceptMappingSvc {
|
||||
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(TermConceptMappingSvcImpl.class);
|
||||
private static boolean ourLastResultsFromTranslationCache; // For testing.
|
||||
private static boolean ourLastResultsFromTranslationWithReverseCache; // For testing.
|
||||
private final int myFetchSize = TermReadSvcImpl.DEFAULT_FETCH_SIZE;
|
||||
|
||||
@Autowired
|
||||
protected ITermConceptMapDao myConceptMapDao;
|
||||
|
||||
@Autowired
|
||||
protected ITermConceptMapGroupDao myConceptMapGroupDao;
|
||||
|
|
@ -104,29 +69,12 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
|
|||
@Autowired
|
||||
protected ITermConceptMapGroupElementTargetDao myConceptMapGroupElementTargetDao;
|
||||
|
||||
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
|
||||
protected EntityManager myEntityManager;
|
||||
|
||||
@Autowired
|
||||
private FhirContext myContext;
|
||||
|
||||
@Autowired
|
||||
private MemoryCacheService myMemoryCacheService;
|
||||
|
||||
@Autowired
|
||||
private IIdHelperService<JpaPid> myIdHelperService;
|
||||
|
||||
@Override
|
||||
@Transactional
|
||||
public void deleteConceptMapAndChildren(ResourceTable theResourceTable) {
|
||||
deleteConceptMap(theResourceTable);
|
||||
}
|
||||
|
||||
@Override
|
||||
public FhirContext getFhirContext() {
|
||||
return myContext;
|
||||
}
|
||||
|
||||
@Override
|
||||
@Transactional
|
||||
public TranslateConceptResults translateConcept(TranslateCodeRequest theRequest) {
|
||||
|
|
@ -205,7 +153,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
|
|||
optionalExistingTermConceptMapByUrl =
|
||||
myConceptMapDao.findTermConceptMapByUrlAndVersion(conceptMapUrl, conceptMapVersion);
|
||||
}
|
||||
if (!optionalExistingTermConceptMapByUrl.isPresent()) {
|
||||
if (optionalExistingTermConceptMapByUrl.isEmpty()) {
|
||||
try {
|
||||
if (isNotBlank(source)) {
|
||||
termConceptMap.setSource(source);
|
||||
|
|
@ -328,320 +276,6 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
|
|||
theConceptMap.getIdElement().toVersionless().getValueAsString());
|
||||
}
|
||||
|
||||
@Override
|
||||
@Transactional(propagation = Propagation.REQUIRED)
|
||||
public TranslateConceptResults translate(TranslationRequest theTranslationRequest) {
|
||||
TranslateConceptResults retVal = new TranslateConceptResults();
|
||||
|
||||
CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
|
||||
CriteriaQuery<TermConceptMapGroupElementTarget> query =
|
||||
criteriaBuilder.createQuery(TermConceptMapGroupElementTarget.class);
|
||||
Root<TermConceptMapGroupElementTarget> root = query.from(TermConceptMapGroupElementTarget.class);
|
||||
|
||||
Join<TermConceptMapGroupElementTarget, TermConceptMapGroupElement> elementJoin =
|
||||
root.join("myConceptMapGroupElement");
|
||||
Join<TermConceptMapGroupElement, TermConceptMapGroup> groupJoin = elementJoin.join("myConceptMapGroup");
|
||||
Join<TermConceptMapGroup, TermConceptMap> conceptMapJoin = groupJoin.join("myConceptMap");
|
||||
|
||||
List<TranslationQuery> translationQueries = theTranslationRequest.getTranslationQueries();
|
||||
List<TranslateConceptResult> cachedTargets;
|
||||
ArrayList<Predicate> predicates;
|
||||
Coding coding;
|
||||
|
||||
// -- get the latest ConceptMapVersion if theTranslationRequest has ConceptMap url but no ConceptMap version
|
||||
String latestConceptMapVersion = null;
|
||||
if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
|
||||
latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
|
||||
|
||||
for (TranslationQuery translationQuery : translationQueries) {
|
||||
cachedTargets = myMemoryCacheService.getIfPresent(
|
||||
MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION, translationQuery);
|
||||
if (cachedTargets == null) {
|
||||
final List<TranslateConceptResult> targets = new ArrayList<>();
|
||||
|
||||
predicates = new ArrayList<>();
|
||||
|
||||
coding = translationQuery.getCoding();
|
||||
if (coding.hasCode()) {
|
||||
predicates.add(criteriaBuilder.equal(elementJoin.get("myCode"), coding.getCode()));
|
||||
} else {
|
||||
throw new InvalidRequestException(
|
||||
Msg.code(842) + "A code must be provided for translation to occur.");
|
||||
}
|
||||
|
||||
if (coding.hasSystem()) {
|
||||
predicates.add(criteriaBuilder.equal(groupJoin.get("mySource"), coding.getSystem()));
|
||||
}
|
||||
|
||||
if (coding.hasVersion()) {
|
||||
predicates.add(criteriaBuilder.equal(groupJoin.get("mySourceVersion"), coding.getVersion()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasTargetSystem()) {
|
||||
predicates.add(
|
||||
criteriaBuilder.equal(groupJoin.get("myTarget"), translationQuery.getTargetSystem()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasUrl()) {
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl()));
|
||||
if (translationQuery.hasConceptMapVersion()) {
|
||||
// both url and conceptMapVersion
|
||||
predicates.add(criteriaBuilder.equal(
|
||||
conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion()));
|
||||
} else {
|
||||
if (StringUtils.isNotBlank(latestConceptMapVersion)) {
|
||||
// only url and use latestConceptMapVersion
|
||||
predicates.add(
|
||||
criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
|
||||
} else {
|
||||
predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (translationQuery.hasSource()) {
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("mySource"), translationQuery.getSource()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasTarget()) {
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myTarget"), translationQuery.getTarget()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasResourceId()) {
|
||||
IIdType resourceId = translationQuery.getResourceId();
|
||||
JpaPid resourcePid =
|
||||
myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getId()));
|
||||
}
|
||||
|
||||
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
|
||||
query.where(outerPredicate);
|
||||
|
||||
// Use scrollable results.
|
||||
final TypedQuery<TermConceptMapGroupElementTarget> typedQuery =
|
||||
myEntityManager.createQuery(query.select(root));
|
||||
org.hibernate.query.Query<TermConceptMapGroupElementTarget> hibernateQuery =
|
||||
(org.hibernate.query.Query<TermConceptMapGroupElementTarget>) typedQuery;
|
||||
hibernateQuery.setFetchSize(myFetchSize);
|
||||
ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
|
||||
try (ScrollableResultsIterator<TermConceptMapGroupElementTarget> scrollableResultsIterator =
|
||||
new ScrollableResultsIterator<>(scrollableResults)) {
|
||||
|
||||
Set<TermConceptMapGroupElementTarget> matches = new HashSet<>();
|
||||
while (scrollableResultsIterator.hasNext()) {
|
||||
TermConceptMapGroupElementTarget next = scrollableResultsIterator.next();
|
||||
if (matches.add(next)) {
|
||||
|
||||
TranslateConceptResult translationMatch = new TranslateConceptResult();
|
||||
if (next.getEquivalence() != null) {
|
||||
translationMatch.setEquivalence(
|
||||
next.getEquivalence().toCode());
|
||||
}
|
||||
|
||||
translationMatch.setCode(next.getCode());
|
||||
translationMatch.setSystem(next.getSystem());
|
||||
translationMatch.setSystemVersion(next.getSystemVersion());
|
||||
translationMatch.setDisplay(next.getDisplay());
|
||||
translationMatch.setValueSet(next.getValueSet());
|
||||
translationMatch.setSystemVersion(next.getSystemVersion());
|
||||
translationMatch.setConceptMapUrl(next.getConceptMapUrl());
|
||||
|
||||
targets.add(translationMatch);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
ourLastResultsFromTranslationCache = false; // For testing.
|
||||
myMemoryCacheService.put(MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION, translationQuery, targets);
|
||||
retVal.getResults().addAll(targets);
|
||||
} else {
|
||||
ourLastResultsFromTranslationCache = true; // For testing.
|
||||
retVal.getResults().addAll(cachedTargets);
|
||||
}
|
||||
}
|
||||
|
||||
buildTranslationResult(retVal);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
@Transactional(propagation = Propagation.REQUIRED)
|
||||
public TranslateConceptResults translateWithReverse(TranslationRequest theTranslationRequest) {
|
||||
TranslateConceptResults retVal = new TranslateConceptResults();
|
||||
|
||||
CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
|
||||
CriteriaQuery<TermConceptMapGroupElement> query = criteriaBuilder.createQuery(TermConceptMapGroupElement.class);
|
||||
Root<TermConceptMapGroupElement> root = query.from(TermConceptMapGroupElement.class);
|
||||
|
||||
Join<TermConceptMapGroupElement, TermConceptMapGroupElementTarget> targetJoin =
|
||||
root.join("myConceptMapGroupElementTargets");
|
||||
Join<TermConceptMapGroupElement, TermConceptMapGroup> groupJoin = root.join("myConceptMapGroup");
|
||||
Join<TermConceptMapGroup, TermConceptMap> conceptMapJoin = groupJoin.join("myConceptMap");
|
||||
|
||||
List<TranslationQuery> translationQueries = theTranslationRequest.getTranslationQueries();
|
||||
List<TranslateConceptResult> cachedElements;
|
||||
ArrayList<Predicate> predicates;
|
||||
Coding coding;
|
||||
|
||||
// -- get the latest ConceptMapVersion if theTranslationRequest has ConceptMap url but no ConceptMap version
|
||||
String latestConceptMapVersion = null;
|
||||
if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
|
||||
latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
|
||||
|
||||
for (TranslationQuery translationQuery : translationQueries) {
|
||||
cachedElements = myMemoryCacheService.getIfPresent(
|
||||
MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION_REVERSE, translationQuery);
|
||||
if (cachedElements == null) {
|
||||
final List<TranslateConceptResult> elements = new ArrayList<>();
|
||||
|
||||
predicates = new ArrayList<>();
|
||||
|
||||
coding = translationQuery.getCoding();
|
||||
String targetCode;
|
||||
String targetCodeSystem = null;
|
||||
if (coding.hasCode()) {
|
||||
predicates.add(criteriaBuilder.equal(targetJoin.get("myCode"), coding.getCode()));
|
||||
targetCode = coding.getCode();
|
||||
} else {
|
||||
throw new InvalidRequestException(
|
||||
Msg.code(843) + "A code must be provided for translation to occur.");
|
||||
}
|
||||
|
||||
if (coding.hasSystem()) {
|
||||
predicates.add(criteriaBuilder.equal(groupJoin.get("myTarget"), coding.getSystem()));
|
||||
targetCodeSystem = coding.getSystem();
|
||||
}
|
||||
|
||||
if (coding.hasVersion()) {
|
||||
predicates.add(criteriaBuilder.equal(groupJoin.get("myTargetVersion"), coding.getVersion()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasUrl()) {
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl()));
|
||||
if (translationQuery.hasConceptMapVersion()) {
|
||||
// both url and conceptMapVersion
|
||||
predicates.add(criteriaBuilder.equal(
|
||||
conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion()));
|
||||
} else {
|
||||
if (StringUtils.isNotBlank(latestConceptMapVersion)) {
|
||||
// only url and use latestConceptMapVersion
|
||||
predicates.add(
|
||||
criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
|
||||
} else {
|
||||
predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (translationQuery.hasTargetSystem()) {
|
||||
predicates.add(
|
||||
criteriaBuilder.equal(groupJoin.get("mySource"), translationQuery.getTargetSystem()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasSource()) {
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myTarget"), translationQuery.getSource()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasTarget()) {
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("mySource"), translationQuery.getTarget()));
|
||||
}
|
||||
|
||||
if (translationQuery.hasResourceId()) {
|
||||
IIdType resourceId = translationQuery.getResourceId();
|
||||
JpaPid resourcePid =
|
||||
myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
|
||||
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getId()));
|
||||
}
|
||||
|
||||
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
|
||||
query.where(outerPredicate);
|
||||
|
||||
// Use scrollable results.
|
||||
final TypedQuery<TermConceptMapGroupElement> typedQuery =
|
||||
myEntityManager.createQuery(query.select(root));
|
||||
org.hibernate.query.Query<TermConceptMapGroupElement> hibernateQuery =
|
||||
(org.hibernate.query.Query<TermConceptMapGroupElement>) typedQuery;
|
||||
hibernateQuery.setFetchSize(myFetchSize);
|
||||
ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
|
||||
try (ScrollableResultsIterator<TermConceptMapGroupElement> scrollableResultsIterator =
|
||||
new ScrollableResultsIterator<>(scrollableResults)) {
|
||||
|
||||
Set<TermConceptMapGroupElementTarget> matches = new HashSet<>();
|
||||
while (scrollableResultsIterator.hasNext()) {
|
||||
TermConceptMapGroupElement nextElement = scrollableResultsIterator.next();
|
||||
|
||||
/* TODO: The invocation of the size() below does not seem to be necessary but for some reason,
|
||||
* but removing it causes tests in TerminologySvcImplR4Test to fail. We use the outcome
|
||||
* in a trace log to avoid ErrorProne flagging an unused return value.
|
||||
*/
|
||||
int size =
|
||||
nextElement.getConceptMapGroupElementTargets().size();
|
||||
ourLog.trace("Have {} targets", size);
|
||||
|
||||
myEntityManager.detach(nextElement);
|
||||
|
||||
if (isNotBlank(targetCode)) {
|
||||
for (TermConceptMapGroupElementTarget next :
|
||||
nextElement.getConceptMapGroupElementTargets()) {
|
||||
if (matches.add(next)) {
|
||||
if (isBlank(targetCodeSystem)
|
||||
|| StringUtils.equals(targetCodeSystem, next.getSystem())) {
|
||||
if (StringUtils.equals(targetCode, next.getCode())) {
|
||||
TranslateConceptResult translationMatch = new TranslateConceptResult();
|
||||
translationMatch.setCode(nextElement.getCode());
|
||||
translationMatch.setSystem(nextElement.getSystem());
|
||||
translationMatch.setSystemVersion(nextElement.getSystemVersion());
|
||||
translationMatch.setDisplay(nextElement.getDisplay());
|
||||
translationMatch.setValueSet(nextElement.getValueSet());
|
||||
translationMatch.setSystemVersion(nextElement.getSystemVersion());
|
||||
translationMatch.setConceptMapUrl(nextElement.getConceptMapUrl());
|
||||
if (next.getEquivalence() != null) {
|
||||
translationMatch.setEquivalence(
|
||||
next.getEquivalence().toCode());
|
||||
}
|
||||
|
||||
if (alreadyContainsMapping(elements, translationMatch)
|
||||
|| alreadyContainsMapping(retVal.getResults(), translationMatch)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
elements.add(translationMatch);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
ourLastResultsFromTranslationWithReverseCache = false; // For testing.
|
||||
myMemoryCacheService.put(
|
||||
MemoryCacheService.CacheEnum.CONCEPT_TRANSLATION_REVERSE, translationQuery, elements);
|
||||
retVal.getResults().addAll(elements);
|
||||
} else {
|
||||
ourLastResultsFromTranslationWithReverseCache = true; // For testing.
|
||||
retVal.getResults().addAll(cachedElements);
|
||||
}
|
||||
}
|
||||
|
||||
buildTranslationResult(retVal);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
private boolean alreadyContainsMapping(
|
||||
List<TranslateConceptResult> elements, TranslateConceptResult translationMatch) {
|
||||
for (TranslateConceptResult nextExistingElement : elements) {
|
||||
if (StringUtils.equals(nextExistingElement.getSystem(), translationMatch.getSystem())) {
|
||||
if (StringUtils.equals(nextExistingElement.getSystemVersion(), translationMatch.getSystemVersion())) {
|
||||
if (StringUtils.equals(nextExistingElement.getCode(), translationMatch.getCode())) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
public void deleteConceptMap(ResourceTable theResourceTable) {
|
||||
// Get existing entity so it can be deleted.
|
||||
Optional<TermConceptMap> optionalExistingTermConceptMapById =
|
||||
|
|
@ -671,34 +305,6 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
|
|||
}
|
||||
}
|
||||
|
||||
// Special case for the translate operation with url and without
|
||||
// conceptMapVersion, find the latest conecptMapVersion
|
||||
private String getLatestConceptMapVersion(TranslationRequest theTranslationRequest) {
|
||||
|
||||
Pageable page = PageRequest.of(0, 1);
|
||||
List<TermConceptMap> theConceptMapList = myConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(
|
||||
page, theTranslationRequest.getUrl());
|
||||
if (!theConceptMapList.isEmpty()) {
|
||||
return theConceptMapList.get(0).getVersion();
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
private void buildTranslationResult(TranslateConceptResults theTranslationResult) {
|
||||
|
||||
String msg;
|
||||
if (theTranslationResult.getResults().isEmpty()) {
|
||||
theTranslationResult.setResult(false);
|
||||
msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "noMatchesFound");
|
||||
theTranslationResult.setMessage(msg);
|
||||
} else {
|
||||
theTranslationResult.setResult(true);
|
||||
msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "matchesFound");
|
||||
theTranslationResult.setMessage(msg);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* This method is present only for unit tests, do not call from client code
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -0,0 +1,34 @@
|
|||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR JPA Server
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2023 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%
|
||||
*/
|
||||
package ca.uhn.fhir.jpa.term.api;
|
||||
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
import ca.uhn.fhir.context.support.TranslateConceptResults;
|
||||
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
|
||||
|
||||
/**
|
||||
* Represents the terminology translate functions
|
||||
*/
|
||||
public interface ITermConceptClientMappingSvc extends IValidationSupport {
|
||||
|
||||
TranslateConceptResults translate(TranslationRequest theTranslationRequest);
|
||||
|
||||
TranslateConceptResults translateWithReverse(TranslationRequest theTranslationRequest);
|
||||
}
|
||||
|
|
@ -19,17 +19,13 @@
|
|||
*/
|
||||
package ca.uhn.fhir.jpa.term.api;
|
||||
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
import ca.uhn.fhir.context.support.TranslateConceptResults;
|
||||
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import org.hl7.fhir.r4.model.ConceptMap;
|
||||
|
||||
public interface ITermConceptMappingSvc extends IValidationSupport {
|
||||
|
||||
TranslateConceptResults translate(TranslationRequest theTranslationRequest);
|
||||
|
||||
TranslateConceptResults translateWithReverse(TranslationRequest theTranslationRequest);
|
||||
/**
|
||||
* Represents ConceptMap translation and persistence operations
|
||||
*/
|
||||
public interface ITermConceptMappingSvc extends ITermConceptClientMappingSvc {
|
||||
|
||||
void deleteConceptMapAndChildren(ResourceTable theResourceTable);
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue