Examples with Options com.b2international.commons.options.Options used on opensource projects

Example 1 with Options

use of com.b2international.commons.options.Options in project snow-owl by b2ihealthcare.

the class ResourceConverter method expandCommits.

private void expandCommits(List<Resource> results) {
    if (expand().containsKey(TerminologyResource.Expand.COMMITS)) {
        Options expandOptions = expand().getOptions(TerminologyResource.Expand.COMMITS);
        // commit searches must be performed individually on each resource to provide correct results
        var commitSearchRequests = results.stream().filter(TerminologyResource.class::isInstance).map(TerminologyResource.class::cast).map(res -> {
            return RepositoryRequests.commitInfos().prepareSearchCommitInfo().filterByBranch(res.getBranchPath()).setLimit(getLimit(expandOptions)).setFields(expandOptions.containsKey("fields") ? expandOptions.getList("fields", String.class) : CommitInfo.Fields.DEAFULT_FIELD_SELECTION).sortBy(expandOptions.containsKey("sort") ? expandOptions.getString("sort") : null).setLocales(locales()).build(res.getToolingId()).execute(context().service(IEventBus.class)).then(commits -> {
                res.setCommits(commits);
                return commits;
            });
        }).collect(Collectors.toList());
        // wait until all search requests resolve, or timeout of 3 minutes reached
        Promise.all(commitSearchRequests).getSync(3, TimeUnit.MINUTES);
    }
}

Example 2 with Options

use of com.b2international.commons.options.Options in project snow-owl by b2ihealthcare.

the class ConceptMapMappingSearchRequest method doExecute.

@Override
protected ConceptMapMappings doExecute(ServiceProvider context) throws IOException {
    final int limit = limit();
    Options options = Options.builder().putAll(options()).put(ConceptMapMappingSearchRequestEvaluator.OptionKey.AFTER, searchAfter()).put(ConceptMapMappingSearchRequestEvaluator.OptionKey.LIMIT, limit()).put(ConceptMapMappingSearchRequestEvaluator.OptionKey.LOCALES, locales()).put(SearchResourceRequest.OptionKey.SORT_BY, sortBy()).build();
    List<ConceptMapMappings> evaluatedMappings = context.service(RepositoryManager.class).repositories().stream().flatMap(repository -> {
        ConceptMapMappingSearchRequestEvaluator evaluator = repository.service(ConceptMapMappingSearchRequestEvaluator.class);
        Set<ResourceURI> targets = evaluator.evaluateSearchTargetResources(context, options);
        return targets.stream().map(uri -> {
            return evaluator.evaluate(uri, context, options);
        });
    }).collect(Collectors.toList());
    // calculate grand total
    int total = 0;
    for (ConceptMapMappings evaluatedMember : evaluatedMappings) {
        total += evaluatedMember.getTotal();
    }
    return new ConceptMapMappings(// TODO add manual sorting here if multiple resources have been fetched
    evaluatedMappings.stream().flatMap(ConceptMapMappings::stream).limit(limit).collect(Collectors.toList()), null, /* not supported across resources, TODO support it when a single Conceptmap is being fetched */
    limit, total);
}

Example 3 with Options

use of com.b2international.commons.options.Options in project snow-owl by b2ihealthcare.

the class ConceptSearchRequest method doExecute.

@Override
protected Concepts doExecute(ServiceProvider context) throws IOException {
    final int limit = limit();
    Options conceptSearchOptions = Options.builder().putAll(options()).put(ConceptSearchRequestEvaluator.OptionKey.ID, componentIds()).put(ConceptSearchRequestEvaluator.OptionKey.AFTER, searchAfter()).put(ConceptSearchRequestEvaluator.OptionKey.LIMIT, limit).put(ConceptSearchRequestEvaluator.OptionKey.LOCALES, locales()).put(ConceptSearchRequestEvaluator.OptionKey.FIELDS, fields()).put(ConceptSearchRequestEvaluator.OptionKey.EXPAND, expand()).put(SearchResourceRequest.OptionKey.SORT_BY, sortBy()).build();
    final CodeSystemSearchRequestBuilder codeSystemSearchReq = CodeSystemRequests.prepareSearchCodeSystem().all();
    final Map<ResourceURI, ResourceURI> codeSystemResourceFiltersByResource;
    if (containsKey(OptionKey.CODESYSTEM)) {
        // remove path so we can use the code resource URI as key
        codeSystemResourceFiltersByResource = Maps.uniqueIndex(getCollection(OptionKey.CODESYSTEM, ResourceURI.class), uri -> uri.withoutPath());
        // for filtering use the keys
        codeSystemSearchReq.filterByIds(codeSystemResourceFiltersByResource.keySet().stream().map(ResourceURI::getResourceId).collect(Collectors.toSet()));
    } else {
        codeSystemResourceFiltersByResource = Collections.emptyMap();
    }
    // .filterByToolingIds(toolingIds) TODO perform TOOLING filtering
    // .filterByUrls(urls) TODO perform URL filtering
    List<Concepts> concepts = codeSystemSearchReq.buildAsync().execute(context).stream().map(codeSystem -> {
        final ResourceURI uriToEvaluateOn = codeSystemResourceFiltersByResource.getOrDefault(codeSystem.getResourceURI(), codeSystem.getResourceURI());
        return context.service(RepositoryManager.class).get(codeSystem.getToolingId()).service(ConceptSearchRequestEvaluator.class).evaluate(uriToEvaluateOn, context, conceptSearchOptions);
    }).collect(Collectors.toList());
    // for single CodeSystem searches, sorting, paging works as it should
    if (concepts.size() == 1) {
        return Iterables.getOnlyElement(concepts);
    }
    // otherwise, check if searchAfter was used, as it would return bogus results; it can not be applied across code systems
    if (searchAfter() != null) {
        throw new BadRequestException("searchAfter is not supported in Concept Search API for multiple code systems.");
    }
    // calculate grand total
    int total = 0;
    for (Concepts conceptsToAdd : concepts) {
        total += conceptsToAdd.getTotal();
    }
    return new Concepts(// TODO add manual sorting here if multiple resources have been fetched
    concepts.stream().flatMap(Concepts::stream).limit(limit).collect(Collectors.toList()), null, /* not supported across codesystems */
    limit, total);
}

Example 4 with Options

use of com.b2international.commons.options.Options in project snow-owl by b2ihealthcare.

the class DescriptionChangeConverter method expand.

@Override
public void expand(final List<DescriptionChange> results) {
    if (!expand().containsKey(DescriptionChange.Expand.DESCRIPTION)) {
        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, DescriptionChange> itemsByBranch = getItemsByBranch(results);
    // Check if we only need to load inferred CD members in their entirety
    final Options expandOptions = expand().getOptions(DescriptionChange.Expand.DESCRIPTION);
    final boolean inferredOnly = expandOptions.getBoolean("inferredOnly");
    final Options descriptionExpandOptions = expandOptions.getOptions("expand");
    final Options conceptOptions = descriptionExpandOptions.getOptions("concept");
    final boolean needsConcept = descriptionExpandOptions.keySet().contains("concept");
    for (final String branch : itemsByBranch.keySet()) {
        final Collection<DescriptionChange> itemsForCurrentBranch = itemsByBranch.get(branch);
        /*
			 * Expand concept on "new" descriptions via a separate search request, they will
			 * be different from the concept on the "origin" description.
			 */
        if (needsConcept) {
            final List<ReasonerDescription> blankDescriptions = itemsForCurrentBranch.stream().filter(c -> ChangeNature.NEW.equals(c.getChangeNature())).map(DescriptionChange::getDescription).collect(Collectors.toList());
            final Multimap<String, ReasonerDescription> descriptionsByConceptId = FluentIterable.from(blankDescriptions).index(ReasonerDescription::getConceptId);
            final Set<String> conceptIds = descriptionsByConceptId.keySet();
            final Request<BranchContext, SnomedConcepts> conceptSearchRequest = SnomedRequests.prepareSearchConcept().filterByIds(conceptIds).setLimit(conceptIds.size()).setExpand(conceptOptions.get("expand", Options.class)).setLocales(locales()).build();
            final SnomedConcepts concepts = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(conceptSearchRequest)).execute(context());
            for (final SnomedConcept concept : concepts) {
                final String conceptId = concept.getId();
                final Collection<ReasonerDescription> descriptionsForConcept = descriptionsByConceptId.get(conceptId);
                for (final ReasonerDescription description : descriptionsForConcept) {
                    description.setConcept(concept);
                }
            }
        }
        /*
			 * Then fetch all the required descriptions. Note that the same "origin"
			 * description might be used for multiple eg. "new" counterparts.
			 */
        final Set<String> descriptionIds = itemsForCurrentBranch.stream().filter(c -> !inferredOnly || ChangeNature.NEW.equals(c.getChangeNature())).map(c -> c.getDescription().getOriginDescriptionId()).collect(Collectors.toSet());
        final Request<BranchContext, SnomedDescriptions> descriptionSearchRequest = SnomedRequests.prepareSearchDescription().filterByIds(descriptionIds).setLimit(descriptionIds.size()).setExpand(descriptionExpandOptions).setLocales(locales()).build();
        final SnomedDescriptions descriptions = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(descriptionSearchRequest)).execute(context());
        final Map<String, SnomedDescription> descriptionsById = Maps.uniqueIndex(descriptions, SnomedDescription::getId);
        for (final DescriptionChange item : itemsForCurrentBranch) {
            final ReasonerDescription reasonerDescription = item.getDescription();
            final String descriptionId = reasonerDescription.getOriginDescriptionId();
            switch(item.getChangeNature()) {
                case NEW:
                    {
                        final SnomedDescription expandedDescription = descriptionsById.get(descriptionId);
                        reasonerDescription.setAcceptabilityMap(expandedDescription.getAcceptabilityMap());
                        reasonerDescription.setCaseSignificanceId(expandedDescription.getCaseSignificanceId());
                        // reasonerDescription.setConcept(...) is already set earlier (or expanded)
                        reasonerDescription.setLanguageCode(expandedDescription.getLanguageCode());
                        // reasonerMember.setReleased(...) is already set
                        reasonerDescription.setTerm(expandedDescription.getTerm());
                        reasonerDescription.setType(expandedDescription.getType());
                    }
                    break;
                case REDUNDANT:
                    if (!inferredOnly) {
                        final SnomedDescription expandedDescription = descriptionsById.get(descriptionId);
                        reasonerDescription.setAcceptabilityMap(expandedDescription.getAcceptabilityMap());
                        reasonerDescription.setCaseSignificanceId(expandedDescription.getCaseSignificanceId());
                        reasonerDescription.setConcept(expandedDescription.getConcept());
                        reasonerDescription.setLanguageCode(expandedDescription.getLanguageCode());
                        // reasonerMember.setReleased(...) is already set
                        reasonerDescription.setTerm(expandedDescription.getTerm());
                        reasonerDescription.setType(expandedDescription.getType());
                    }
                    break;
                default:
                    throw new IllegalStateException(String.format("Unexpected description change '%s' found with SCTID '%s'.", item.getChangeNature(), item.getDescription().getOriginDescriptionId()));
            }
        }
    }
}

Example 5 with Options

use of com.b2international.commons.options.Options in project snow-owl by b2ihealthcare.

the class EquivalentConceptSetConverter method expand.

@Override
public void expand(final List<EquivalentConceptSet> results) {
    if (!expand().containsKey(EquivalentConceptSet.Expand.EQUIVALENT_CONCEPTS)) {
        return;
    }
    final Set<String> classificationTaskIds = results.stream().map(EquivalentConceptSet::getClassificationId).collect(Collectors.toSet());
    final Map<String, String> branchesByClassificationIdMap = ClassificationRequests.prepareSearchClassification().filterByIds(classificationTaskIds).all().build().execute(context()).stream().collect(Collectors.toMap(ClassificationTask::getId, ClassificationTask::getBranch));
    final Multimap<String, EquivalentConceptSet> itemsByBranch = Multimaps.index(results, r -> branchesByClassificationIdMap.get(r.getClassificationId()));
    final Options expandOptions = expand().get(EquivalentConceptSet.Expand.EQUIVALENT_CONCEPTS, Options.class);
    for (final String branch : itemsByBranch.keySet()) {
        final Collection<EquivalentConceptSet> itemsForCurrentBranch = itemsByBranch.get(branch);
        final Set<String> conceptIds = itemsForCurrentBranch.stream().flatMap(c -> c.getEquivalentConcepts().stream()).map(SnomedConcept::getId).collect(Collectors.toSet());
        final SnomedConcepts concepts = SnomedRequests.prepareSearchConcept().filterByIds(conceptIds).all().setExpand(expandOptions.get("expand", Options.class)).setLocales(locales()).build(branch).getRequest().execute(context());
        final Map<String, SnomedConcept> conceptsById = Maps.uniqueIndex(concepts, SnomedConcept::getId);
        for (final EquivalentConceptSet item : itemsForCurrentBranch) {
            final List<SnomedConcept> equivalentConcepts = item.getEquivalentConcepts().getItems();
            for (int i = 0; i < equivalentConcepts.size(); i++) {
                final SnomedConcept placeholderConcept = equivalentConcepts.get(i);
                final SnomedConcept expandedConcept = conceptsById.get(placeholderConcept.getId());
                equivalentConcepts.set(i, expandedConcept);
            }
        }
    }
}