Search in sources :

Example 1 with ExpressionConstraint

use of com.b2international.snomed.ecl.ecl.ExpressionConstraint in project snow-owl by b2ihealthcare.

the class SnomedEclLabelerRequest method execute.

@Override
public LabeledEclExpressions execute(BranchContext context) {
    final EclSerializer eclSerializer = context.service(EclSerializer.class);
    final EclParser eclParser = context.service(EclParser.class);
    final Set<String> conceptIdsToLabel = Sets.newHashSetWithExpectedSize(expressions.size());
    final Map<String, ExpressionConstraint> queries = Maps.newHashMapWithExpectedSize(expressions.size());
    final LinkedHashMap<String, Object> errors = Maps.newLinkedHashMap();
    for (String expression : expressions) {
        if (Strings.isNullOrEmpty(expression)) {
            continue;
        }
        try {
            ExpressionConstraint query = queries.computeIfAbsent(expression, (key) -> eclParser.parse(key));
            conceptIdsToLabel.addAll(collect(query));
        } catch (ApiException e) {
            if (e instanceof SyntaxException) {
                errors.put(expression, List.copyOf(((SyntaxException) e).getAdditionalInfo().values()));
            } else if (e instanceof BadRequestException) {
                errors.put(expression, e.getMessage());
            } else {
                throw e;
            }
        }
    }
    if (!errors.isEmpty()) {
        BadRequestException badRequestException = new BadRequestException("One or more ECL syntax errors");
        badRequestException.withAdditionalInfo("erroneousExpressions", errors);
        throw badRequestException;
    }
    // fetch all concept labels
    final Map<String, String> labels = SnomedRequests.prepareSearchConcept().filterByIds(conceptIdsToLabel).setLimit(conceptIdsToLabel.size()).setExpand(descriptionType.toLowerCase() + "()").setLocales(locales()).build().execute(context).stream().collect(Collectors.toMap(SnomedConcept::getId, this::extractLabel));
    // expand all queries with labels
    List<String> results = expressions.stream().map(expression -> {
        if (Strings.isNullOrEmpty(expression)) {
            return expression;
        } else {
            ExpressionConstraint query = queries.get(expression);
            expand(query, labels);
            return eclSerializer.serialize(query);
        }
    }).collect(Collectors.toList());
    return new LabeledEclExpressions(results);
}
Also used : ExpressionConstraint(com.b2international.snomed.ecl.ecl.ExpressionConstraint) BadRequestException(com.b2international.commons.exceptions.BadRequestException) SnomedConcept(com.b2international.snowowl.snomed.core.domain.SnomedConcept) JsonProperty(com.fasterxml.jackson.annotation.JsonProperty) java.util(java.util) EObjectWalker(com.b2international.snowowl.core.emf.EObjectWalker) EObjectTreeNode(com.b2international.snowowl.core.emf.EObjectTreeNode) NotNull(javax.validation.constraints.NotNull) Collectors(java.util.stream.Collectors) Maps(com.google.common.collect.Maps) Sets(com.google.common.collect.Sets) Strings(com.google.common.base.Strings) SnomedRequests(com.b2international.snowowl.snomed.datastore.request.SnomedRequests) NotEmpty(org.hibernate.validator.constraints.NotEmpty) AccessControl(com.b2international.snowowl.core.authorization.AccessControl) SyntaxException(com.b2international.commons.exceptions.SyntaxException) Permission(com.b2international.snowowl.core.identity.Permission) EclConceptReference(com.b2international.snomed.ecl.ecl.EclConceptReference) ExpressionConstraint(com.b2international.snomed.ecl.ecl.ExpressionConstraint) BranchContext(com.b2international.snowowl.core.domain.BranchContext) NoopTreeVisitor(com.b2international.commons.tree.NoopTreeVisitor) ApiException(com.b2international.commons.exceptions.ApiException) ResourceRequest(com.b2international.snowowl.core.request.ResourceRequest) SyntaxException(com.b2international.commons.exceptions.SyntaxException) BadRequestException(com.b2international.commons.exceptions.BadRequestException) ApiException(com.b2international.commons.exceptions.ApiException)

Example 2 with ExpressionConstraint

use of com.b2international.snomed.ecl.ecl.ExpressionConstraint in project snow-owl by b2ihealthcare.

the class SnomedQueryOptimizer method optimize.

@Override
public QueryExpressionDiffs optimize(BranchContext context, Options params) {
    final Collection<QueryExpression> inclusions = params.getCollection(QueryOptimizer.OptionKey.INCLUSIONS, QueryExpression.class);
    final List<ExtendedLocale> locales = params.getList(QueryOptimizer.OptionKey.LOCALES, ExtendedLocale.class);
    final EclParser eclParser = context.service(EclParser.class);
    final LoadingCache<String, ExpressionConstraint> eclCache = CacheBuilder.newBuilder().build(CacheLoader.from(eclParser::parse));
    final Multimap<String, QueryExpression> singleConceptInclusions = FluentIterable.from(inclusions).filter(ex -> isSingleConceptExpression(eclCache, ex.getQuery())).index(ex -> toSingleConceptId(eclCache, ex.getQuery()));
    // if there are no single concept inclusions to optimize, exit early
    if (singleConceptInclusions.isEmpty()) {
        return new QueryExpressionDiffs(Collections.emptyList());
    }
    // Record the ancestors (both direct and indirect) of each single concept inclusion
    final Multimap<String, QueryExpression> membersByAncestor = HashMultimap.create();
    SnomedRequests.prepareSearchConcept().filterByIds(singleConceptInclusions.keySet()).setLimit(singleConceptInclusions.keySet().size()).stream(context).flatMap(SnomedConcepts::stream).forEach(child -> {
        final Collection<QueryExpression> childExpressions = singleConceptInclusions.get(child.getId());
        final List<String> parentIds = child.getParentIdsAsString();
        final List<String> ancestorIds = child.getAncestorIdsAsString();
        parentIds.forEach(parentId -> {
            if (!IComponent.ROOT_ID.equals(parentId) && !Concepts.ROOT_CONCEPT.equals(parentId)) {
                membersByAncestor.putAll(parentId, childExpressions);
            }
        });
        ancestorIds.forEach(ancestorId -> {
            if (!IComponent.ROOT_ID.equals(ancestorId) && !Concepts.ROOT_CONCEPT.equals(ancestorId)) {
                membersByAncestor.putAll(ancestorId, childExpressions);
            }
        });
    });
    // Get number of referenced descendants (taking possible duplicates into account)
    final Map<String, Long> uniqueDescendantsByParent = ImmutableMap.copyOf(Maps.transformValues(membersByAncestor.asMap(), descendants -> descendants.stream().map(QueryExpression::getQuery).distinct().count()));
    final ImmutableList.Builder<QueryExpressionDiff> diffs = ImmutableList.builder();
    // references can be replaced with a single << expression.
    for (Entry<String, Long> uniqueDescendantsByParentEntry : uniqueDescendantsByParent.entrySet()) {
        SnomedConcept parent = SnomedRequests.prepareGetConcept(uniqueDescendantsByParentEntry.getKey()).setLocales(locales).setExpand("pt(),descendants(direct:false,limit:0)").build().execute(context);
        final String parentId = parent.getId();
        final int referencedDescendants = Ints.checkedCast(uniqueDescendantsByParent.get(parentId));
        final int totalDescendants = parent.getDescendants().getTotal();
        if (totalDescendants == referencedDescendants) {
            final List<QueryExpression> remove = List.copyOf(membersByAncestor.get(parentId).stream().filter(ex -> !ex.isPinned()).collect(Collectors.toList()));
            // The optimization is a "net win" if we can remove at least two clauses from the original
            if (remove.size() > 1) {
                final QueryExpression replacement = new QueryExpression(IDs.base64UUID(), String.format("<%s%s", parent.getId(), getTerm(parent)), false);
                final List<QueryExpression> addToInclusion = List.of(replacement);
                final List<QueryExpression> addToExclusion = List.of();
                final QueryExpressionDiff diff = new QueryExpressionDiff(addToInclusion, addToExclusion, remove);
                diffs.add(diff);
            }
        }
    }
    return new QueryExpressionDiffs(diffs.build());
}
Also used : ExpressionConstraint(com.b2international.snomed.ecl.ecl.ExpressionConstraint) SnomedConcept(com.b2international.snowowl.snomed.core.domain.SnomedConcept) LoadingCache(com.google.common.cache.LoadingCache) Concepts(com.b2international.snowowl.snomed.common.SnomedConstants.Concepts) ExtendedLocale(com.b2international.commons.http.ExtendedLocale) SnomedRequests(com.b2international.snowowl.snomed.datastore.request.SnomedRequests) Options(com.b2international.commons.options.Options) UncheckedExecutionException(com.google.common.util.concurrent.UncheckedExecutionException) Map(java.util.Map) QueryOptimizer(com.b2international.snowowl.core.request.QueryOptimizer) com.google.common.collect(com.google.common.collect) BadRequestException(com.b2international.commons.exceptions.BadRequestException) Collection(java.util.Collection) SnomedConcepts(com.b2international.snowowl.snomed.core.domain.SnomedConcepts) Collectors(java.util.stream.Collectors) Ints(com.google.common.primitives.Ints) IDs(com.b2international.snowowl.core.id.IDs) CacheLoader(com.google.common.cache.CacheLoader) EclParser(com.b2international.snowowl.snomed.core.ecl.EclParser) List(java.util.List) Entry(java.util.Map.Entry) CacheBuilder(com.google.common.cache.CacheBuilder) EclConceptReference(com.b2international.snomed.ecl.ecl.EclConceptReference) ExpressionConstraint(com.b2international.snomed.ecl.ecl.ExpressionConstraint) com.b2international.snowowl.core.domain(com.b2international.snowowl.core.domain) Collections(java.util.Collections) ExtendedLocale(com.b2international.commons.http.ExtendedLocale) SnomedConcept(com.b2international.snowowl.snomed.core.domain.SnomedConcept) ExpressionConstraint(com.b2international.snomed.ecl.ecl.ExpressionConstraint) EclParser(com.b2international.snowowl.snomed.core.ecl.EclParser)

Aggregations

BadRequestException (com.b2international.commons.exceptions.BadRequestException)2 EclConceptReference (com.b2international.snomed.ecl.ecl.EclConceptReference)2 ExpressionConstraint (com.b2international.snomed.ecl.ecl.ExpressionConstraint)2 SnomedConcept (com.b2international.snowowl.snomed.core.domain.SnomedConcept)2 SnomedRequests (com.b2international.snowowl.snomed.datastore.request.SnomedRequests)2 Collectors (java.util.stream.Collectors)2 ApiException (com.b2international.commons.exceptions.ApiException)1 SyntaxException (com.b2international.commons.exceptions.SyntaxException)1 ExtendedLocale (com.b2international.commons.http.ExtendedLocale)1 Options (com.b2international.commons.options.Options)1 NoopTreeVisitor (com.b2international.commons.tree.NoopTreeVisitor)1 AccessControl (com.b2international.snowowl.core.authorization.AccessControl)1 com.b2international.snowowl.core.domain (com.b2international.snowowl.core.domain)1 BranchContext (com.b2international.snowowl.core.domain.BranchContext)1 EObjectTreeNode (com.b2international.snowowl.core.emf.EObjectTreeNode)1 EObjectWalker (com.b2international.snowowl.core.emf.EObjectWalker)1 IDs (com.b2international.snowowl.core.id.IDs)1 Permission (com.b2international.snowowl.core.identity.Permission)1 QueryOptimizer (com.b2international.snowowl.core.request.QueryOptimizer)1 ResourceRequest (com.b2international.snowowl.core.request.ResourceRequest)1