Examples with BranchContext com.b2international.snowowl.core.domain.BranchContext used on opensource projects

Example 21 with BranchContext

use of com.b2international.snowowl.core.domain.BranchContext in project snow-owl by b2ihealthcare.

the class SnomedEclRefinementEvaluator method evalMembers.

private Promise<Collection<Property>> evalMembers(BranchContext context, Set<String> focusConceptIds, Collection<String> typeIds, DataTypeComparison comparison) {
    final Object value;
    final DataType type;
    if (comparison instanceof BooleanValueComparison) {
        value = ((BooleanValueComparison) comparison).isValue();
        type = DataType.BOOLEAN;
    } else if (comparison instanceof StringValueComparison) {
        value = ((StringValueComparison) comparison).getValue();
        type = DataType.STRING;
    } else if (comparison instanceof IntegerValueComparison) {
        value = ((IntegerValueComparison) comparison).getValue();
        type = DataType.INTEGER;
    } else if (comparison instanceof DecimalValueComparison) {
        value = ((DecimalValueComparison) comparison).getValue();
        type = DataType.DECIMAL;
    } else {
        return SnomedEclEvaluationRequest.throwUnsupported(comparison);
    }
    final SearchResourceRequest.Operator operator = toSearchOperator(comparison.getOp());
    final Options propFilter = Options.builder().put(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID, getCharacteristicTypes(expressionForm)).put(SnomedRf2Headers.FIELD_TYPE_ID, typeIds).put(SnomedRefSetMemberIndexEntry.Fields.DATA_TYPE, type).put(SnomedRf2Headers.FIELD_VALUE, value).put(SearchResourceRequest.operator(SnomedRf2Headers.FIELD_VALUE), operator).build();
    return SnomedRequests.prepareSearchMember().filterByActive(true).filterByRefSetType(SnomedRefSetType.CONCRETE_DATA_TYPE).filterByReferencedComponent(focusConceptIds).filterByProps(propFilter).setEclExpressionForm(expressionForm).setLimit(context.service(RepositoryConfiguration.class).getIndexConfiguration().getResultWindow()).<Property>transformAsync(context, req -> req.build(context.path()), members -> members.stream().map(input -> {
        return new Property(input.getReferencedComponent().getId(), (String) input.getProperties().get(SnomedRf2Headers.FIELD_TYPE_ID), input.getProperties().get(SnomedRf2Headers.FIELD_VALUE), (Integer) input.getProperties().get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP));
    }));
}

Example 22 with BranchContext

use of com.b2international.snowowl.core.domain.BranchContext in project snow-owl by b2ihealthcare.

the class ConceptSuggestionRequest method doExecute.

@Override
protected Suggestions doExecute(BranchContext context) throws IOException {
    TermFilter termFilter;
    if (containsKey(TERM)) {
        if (containsKey(MIN_OCCURENCE_COUNT)) {
            termFilter = TermFilter.minTermMatch(getString(TERM), (Integer) get(MIN_OCCURENCE_COUNT)).withIgnoreStopwords();
        } else {
            termFilter = TermFilter.defaultTermMatch(getString(TERM)).withIgnoreStopwords();
        }
    } else {
        // Gather tokens
        final Multiset<String> tokenOccurrences = HashMultiset.create();
        final EnglishStemmer stemmer = new EnglishStemmer();
        // Get the suggestion base set of concepts
        final ConceptSearchRequestBuilder baseRequestBuilder = new ConceptSearchRequestBuilder().filterByCodeSystemUri(context.service(ResourceURI.class)).setLimit(SCROLL_LIMIT).setLocales(locales());
        if (containsKey(QUERY)) {
            baseRequestBuilder.filterByInclusions(getCollection(QUERY, String.class));
        }
        if (containsKey(MUST_NOT_QUERY)) {
            baseRequestBuilder.filterByExclusions(getCollection(MUST_NOT_QUERY, String.class));
        }
        baseRequestBuilder.stream(context).flatMap(Concepts::stream).flatMap(concept -> getAllTerms(concept).stream()).map(term -> term.toLowerCase(Locale.US)).flatMap(lowerCaseTerm -> TOKEN_SPLITTER.splitToList(lowerCaseTerm).stream()).map(token -> stemToken(stemmer, token)).forEach(tokenOccurrences::add);
        topTokens = Multisets.copyHighestCountFirst(tokenOccurrences).elementSet().stream().filter(// skip short tokens
        token -> token.length() > 2).limit(topTokenCount).collect(Collectors.toList());
        int minShouldMatch = containsKey(MIN_OCCURENCE_COUNT) ? (Integer) get(MIN_OCCURENCE_COUNT) : DEFAULT_MIN_OCCURENCE_COUNT;
        termFilter = TermFilter.minTermMatch(topTokens.stream().collect(Collectors.joining(" ")), minShouldMatch);
    }
    /* 
		 * Run a search with the top tokens and minimum number of matches, excluding everything
		 * that was included previously.
		 */
    final Set<String> exclusions = newHashSet();
    exclusions.addAll(getCollection(QUERY, String.class));
    exclusions.addAll(getCollection(MUST_NOT_QUERY, String.class));
    final ConceptSearchRequestBuilder resultRequestBuilder = new ConceptSearchRequestBuilder().filterByCodeSystemUri(context.service(ResourceURI.class)).filterByActive(true).filterByTerm(termFilter).setPreferredDisplay(getString(DISPLAY)).setLimit(limit()).setLocales(locales()).setSearchAfter(searchAfter()).sortBy(sortBy());
    if (!exclusions.isEmpty()) {
        resultRequestBuilder.filterByExclusions(exclusions);
    }
    final Concepts conceptSuggestions = resultRequestBuilder.build().execute(context);
    return new Suggestions(topTokens, conceptSuggestions.getItems(), conceptSuggestions.getSearchAfter(), limit(), conceptSuggestions.getTotal());
}

Example 23 with BranchContext

use of com.b2international.snowowl.core.domain.BranchContext in project snow-owl by b2ihealthcare.

the class ConcreteDomainChangeConverter method expandComponentCategory.

// Copied from SnomedReferenceSetMemberConverter
private void expandComponentCategory(final String branch, final ComponentCategory category, final Collection<String> componentIds, final Options componentOptions, final Multimap<String, ReasonerConcreteDomainMember> membersByReferencedComponent) {
    final SearchResourceRequestBuilder<?, BranchContext, ? extends CollectionResource<? extends SnomedCoreComponent>> searchRequestBuilder = createSearchRequestBuilder(category);
    searchRequestBuilder.filterByIds(componentIds).setLimit(componentIds.size()).setLocales(locales()).setExpand(componentOptions.get("expand", Options.class));
    final CollectionResource<? extends SnomedCoreComponent> referencedComponents = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(searchRequestBuilder.build())).execute(context());
    for (final SnomedCoreComponent referencedComponent : referencedComponents) {
        for (final ReasonerConcreteDomainMember member : membersByReferencedComponent.get(referencedComponent.getId())) {
            member.setReferencedComponent(referencedComponent);
        }
    }
}

Example 24 with BranchContext

use of com.b2international.snowowl.core.domain.BranchContext in project snow-owl by b2ihealthcare.

the class ConcreteDomainChangeConverter method expand.

@Override
public void expand(final List<ConcreteDomainChange> results) {
    if (!expand().containsKey(ConcreteDomainChange.Expand.CONCRETE_DOMAIN_MEMBER)) {
        return;
    }
    /*
		 * Depending on the CD member change search request, we might need to issue
		 * SNOMED CT searches against multiple branches; find out which ones we have.
		 */
    final Multimap<String, ConcreteDomainChange> itemsByBranch = getItemsByBranch(results);
    // Check if we only need to load inferred CD members in their entirety
    final Options expandOptions = expand().getOptions(ConcreteDomainChange.Expand.CONCRETE_DOMAIN_MEMBER);
    final boolean inferredOnly = expandOptions.getBoolean("inferredOnly");
    final Options cdMemberExpandOptions = expandOptions.getOptions("expand");
    final Options referencedComponentOptions = cdMemberExpandOptions.getOptions(SnomedReferenceSetMember.Expand.REFERENCED_COMPONENT);
    /*
		 * Remove this option from the member expand options map, so that member search
		 * does not expand the referenced component again
		 */
    final boolean needsReferencedComponent = cdMemberExpandOptions.keySet().remove(SnomedReferenceSetMember.Expand.REFERENCED_COMPONENT);
    for (final String branch : itemsByBranch.keySet()) {
        final Collection<ConcreteDomainChange> itemsForCurrentBranch = itemsByBranch.get(branch);
        /*
			 * Expand referenced component on members via a separate search request, as they
			 * can be different from the referenced component on the "origin" member
			 */
        if (needsReferencedComponent) {
            final List<ReasonerConcreteDomainMember> blankMembers = itemsForCurrentBranch.stream().filter(c -> !inferredOnly || ChangeNature.NEW.equals(c.getChangeNature())).map(ConcreteDomainChange::getConcreteDomainMember).collect(Collectors.toList());
            final Multimap<String, ReasonerConcreteDomainMember> membersByReferencedComponent = Multimaps.index(blankMembers, ReasonerConcreteDomainMember::getReferencedComponentId);
            final Multimap<ComponentCategory, String> referencedComponentsByCategory = Multimaps.index(membersByReferencedComponent.keySet(), SnomedIdentifiers::getComponentCategory);
            for (final Entry<ComponentCategory, Collection<String>> categoryEntry : referencedComponentsByCategory.asMap().entrySet()) {
                expandComponentCategory(branch, categoryEntry.getKey(), categoryEntry.getValue(), referencedComponentOptions, membersByReferencedComponent);
            }
        }
        /*
			 * Then fetch all the required members (these will have a referenced component
			 * ID that should no longer be copied on inferred members). Note that the same "origin"
			 * member might be used for multiple eg. "new" counterparts.
			 */
        final Set<String> cdMemberUuids = itemsForCurrentBranch.stream().filter(c -> !inferredOnly || ChangeNature.NEW.equals(c.getChangeNature())).map(c -> c.getConcreteDomainMember().getOriginMemberId()).collect(Collectors.toSet());
        final Request<BranchContext, SnomedReferenceSetMembers> cdMemberSearchRequest = SnomedRequests.prepareSearchMember().filterByIds(cdMemberUuids).setLimit(cdMemberUuids.size()).setExpand(cdMemberExpandOptions).setLocales(locales()).build();
        final SnomedReferenceSetMembers cdMembers = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(cdMemberSearchRequest)).execute(context());
        final Map<String, SnomedReferenceSetMember> cdMembersByUuid = Maps.uniqueIndex(cdMembers, SnomedReferenceSetMember::getId);
        /*
			 * Finally, set the member on the change item, but preserve the properties that
			 * were already set in "toResource"
			 */
        for (final ConcreteDomainChange item : itemsForCurrentBranch) {
            final ReasonerConcreteDomainMember reasonerMember = item.getConcreteDomainMember();
            final String memberUuid = reasonerMember.getOriginMemberId();
            switch(item.getChangeNature()) {
                case NEW:
                    {
                        final SnomedReferenceSetMember expandedMember = cdMembersByUuid.get(memberUuid);
                        final Map<String, Object> expandedProperties = expandedMember.getProperties();
                        // reasonerMember.setCharacteristicTypeId(...) is already set
                        // reasonerMember.setGroup(...) is already set
                        // reasonerMember.setReferencedComponent(...) is already set (or expanded)
                        reasonerMember.setReferenceSetId(expandedMember.getRefsetId());
                        // reasonerMember.setReleased(...) is already set
                        reasonerMember.setSerializedValue((String) expandedProperties.get(SnomedRf2Headers.FIELD_VALUE));
                        reasonerMember.setTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_TYPE_ID));
                    }
                    break;
                case UPDATED:
                    if (!inferredOnly) {
                        final SnomedReferenceSetMember expandedMember = cdMembersByUuid.get(memberUuid);
                        final Map<String, Object> expandedProperties = expandedMember.getProperties();
                        reasonerMember.setCharacteristicTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID));
                        reasonerMember.setGroup((Integer) expandedProperties.get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP));
                        // reasonerMember.setReferencedComponent(...) is already set (or expanded)
                        reasonerMember.setReferenceSetId(expandedMember.getRefsetId());
                        // reasonerMember.setReleased(...) is already set
                        // reasonerMember.setSerializedValue(...) is already set
                        reasonerMember.setTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_TYPE_ID));
                    }
                    break;
                case REDUNDANT:
                    if (!inferredOnly) {
                        final SnomedReferenceSetMember expandedMember = cdMembersByUuid.get(memberUuid);
                        final Map<String, Object> expandedProperties = expandedMember.getProperties();
                        reasonerMember.setCharacteristicTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID));
                        reasonerMember.setGroup((Integer) expandedProperties.get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP));
                        // reasonerMember.setReferencedComponent(...) is already set (or expanded)
                        reasonerMember.setReferenceSetId(expandedMember.getRefsetId());
                        // reasonerMember.setReleased(...) is already set
                        reasonerMember.setSerializedValue((String) expandedProperties.get(SnomedRf2Headers.FIELD_VALUE));
                        reasonerMember.setTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_TYPE_ID));
                    }
                    break;
                default:
                    throw new IllegalStateException(String.format("Unexpected CD member change '%s' found with UUID '%s'.", item.getChangeNature(), item.getConcreteDomainMember().getOriginMemberId()));
            }
        }
    }
}

Example 25 with BranchContext

use of com.b2international.snowowl.core.domain.BranchContext in project snow-owl by b2ihealthcare.

the class SnomedValidationIssueDetailExtension method extendConceptIssueLabels.

private void extendConceptIssueLabels(BranchContext context, Collection<ValidationIssue> issues, Map<String, Object> ruleParameters) {
    final RevisionSearcher searcher = context.service(RevisionSearcher.class);
    final List<ValidationIssue> conceptIssues = issues.stream().filter(issue -> SnomedConcept.TYPE == issue.getAffectedComponent().getComponentType()).collect(Collectors.toList());
    final Map<String, ValidationIssue> memberIssues = issues.stream().filter(issue -> SnomedReferenceSetMember.TYPE == issue.getAffectedComponent().getComponentType()).collect(Collectors.toMap(issue -> issue.getAffectedComponent().getComponentId(), issue -> issue, (issue1, issue2) -> issue1));
    if (conceptIssues.isEmpty() && memberIssues.isEmpty()) {
        return;
    }
    final Builder<String, ValidationIssue> issuesByConceptId = ImmutableMultimap.builder();
    conceptIssues.forEach(issue -> issuesByConceptId.put(issue.getAffectedComponent().getComponentId(), issue));
    searcher.stream(Query.select(String[].class).from(SnomedRefSetMemberIndexEntry.class).fields(SnomedRefSetMemberIndexEntry.Fields.ID, SnomedRefSetMemberIndexEntry.Fields.REFERENCED_COMPONENT_ID).where(Expressions.builder().filter(SnomedRefSetMemberIndexEntry.Expressions.active()).filter(SnomedRefSetMemberIndexEntry.Expressions.ids(memberIssues.keySet())).build()).limit(SCROLL_SIZE).build()).forEach(hits -> {
        for (String[] hit : hits) {
            final String memberId = hit[0];
            final String containerConcpetId = hit[1];
            issuesByConceptId.put(containerConcpetId, memberIssues.get(memberId));
        }
    });
    final Multimap<String, ValidationIssue> issuesByConceptMap = issuesByConceptId.build();
    final Map<String, String> affectedComponentLabelsByConcept = getAffectedComponentLabels(context, ruleParameters, issuesByConceptMap.keySet());
    if (!affectedComponentLabelsByConcept.isEmpty()) {
        issuesByConceptMap.keySet().forEach(conceptId -> {
            issuesByConceptMap.get(conceptId).forEach(issue -> {
                issue.setAffectedComponentLabels(ImmutableList.of(affectedComponentLabelsByConcept.get(conceptId)));
            });
        });
    }
}