Examples with ResourceURI com.b2international.snowowl.core.ResourceURI used on opensource projects

Example 1 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI 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 2 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI 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 3 with ResourceURI

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

the class SnomedRf2ImportRequest method updateCodeSystemSettings.

private void updateCodeSystemSettings(final BranchContext context, final ResourceURI codeSystemUri) throws Exception {
    SnomedReferenceSets languageReferenceSets = SnomedRequests.prepareSearchRefSet().all().filterByType(SnomedRefSetType.LANGUAGE).filterByActive(true).setFields(SnomedConceptDocument.Fields.ID).sortBy(Sort.fieldAsc(SnomedConceptDocument.Fields.ID)).build().execute(context);
    /*
		 * XXX: The default language in locales is always "en", as there is no
		 * machine-readable information about what language code each language type
		 * reference set is associated with.
		 */
    final List<ExtendedLocale> locales = languageReferenceSets.stream().map(refSet -> new ExtendedLocale("en", "", refSet.getId())).collect(Collectors.toList());
    // fetch codesystem again to get the latest settings
    CodeSystem currentSnomedCodeSystem = CodeSystemRequests.prepareGetCodeSystem(codeSystemUri.getResourceId()).buildAsync().get(context);
    Map<String, SnomedLanguageConfig> mergedLanguagesConfiguration = Maps.newLinkedHashMap();
    SnomedDescriptionUtils.getLanguagesConfiguration(context.service(ObjectMapper.class), currentSnomedCodeSystem).forEach(config -> {
        mergedLanguagesConfiguration.put(config.getLanguageTag(), config);
    });
    languageReferenceSets.stream().map(SnomedReferenceSet::getId).filter(SnomedTerminologyComponentConstants.LANG_REFSET_DIALECT_ALIASES::containsKey).forEach(langRefsetId -> {
        final String dialect = SnomedTerminologyComponentConstants.LANG_REFSET_DIALECT_ALIASES.get(langRefsetId);
        // ignore any aliases that are already defined by using computeIfAbsent
        mergedLanguagesConfiguration.computeIfAbsent(dialect, languageTag -> new SnomedLanguageConfig(languageTag, langRefsetId));
    });
    CodeSystemRequests.prepareUpdateCodeSystem(codeSystemUri.getResourceId()).setSettings(Map.of(CodeSystem.CommonSettings.LOCALES, locales, SnomedTerminologyComponentConstants.CODESYSTEM_LANGUAGE_CONFIG_KEY, mergedLanguagesConfiguration.values())).build(context.service(User.class).getUsername(), String.format("Update '%s' settings based on RF2 import", codeSystemUri.getResourceId())).execute(context.service(IEventBus.class)).getSync(2, TimeUnit.MINUTES);
}

Example 4 with ResourceURI

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

the class SnomedExtensionUpgradeTest method upgrade18UpgradeFromCodeSystemVersionWithUnpublishedChanges.

@Test
public void upgrade18UpgradeFromCodeSystemVersionWithUnpublishedChanges() {
    // create extension on the latest SI VERSION
    CodeSystem extension = createExtension(latestInternationalVersion, branchPath.lastSegment());
    // new SI concept
    String newConceptId = createConcept(SnomedContentRule.SNOMEDCT, createConceptRequestBody(Concepts.ROOT_CONCEPT, Concepts.MODULE_SCT_CORE));
    // create a new INT version
    LocalDate effectiveDate = getNextAvailableEffectiveDate(SNOMEDCT);
    createVersion(SNOMEDCT, effectiveDate).statusCode(201);
    ResourceURI upgradeVersion = CodeSystem.uri(SNOMEDCT, effectiveDate.toString());
    // version extension
    LocalDate effectiveDate2 = LocalDate.now();
    createVersion(extension.getId(), effectiveDate2).statusCode(201);
    ResourceURI extensionVersion = CodeSystem.uri(extension.getId(), effectiveDate2.toString());
    // new SE concept
    String extensionModuleId = createModule(extension);
    String newConceptId2 = createConcept(extension.getResourceURI(), createConceptRequestBody(Concepts.ROOT_CONCEPT, extensionModuleId));
    // start upgrade to the new available upgrade version
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extensionVersion, upgradeVersion);
    assertEquals(upgradeVersion, upgradeCodeSystem.getExtensionOf());
    getComponent(upgradeCodeSystem.getResourceURI(), SnomedComponentType.CONCEPT, newConceptId).statusCode(200);
    getComponent(upgradeCodeSystem.getResourceURI(), SnomedComponentType.CONCEPT, newConceptId2).statusCode(404);
}

Example 5 with ResourceURI

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

the class SnomedExtensionUpgradeTest method upgrade02NewExtensionConceptOnly.

@Test
public void upgrade02NewExtensionConceptOnly() {
    // create extension on the latest SI VERSION
    CodeSystem extension = createExtension(latestInternationalVersion, branchPath.lastSegment());
    // create a new INT version without any changes
    LocalDate effectiveTime = getNextAvailableEffectiveDate(SNOMEDCT);
    createVersion(SNOMEDCT, effectiveTime).statusCode(201);
    ResourceURI upgradeVersion = CodeSystem.uri(SNOMEDCT, effectiveTime.toString());
    // create new extension version with one new concept, module in this case
    String moduleId = createModule(extension);
    createVersion(extension.getId(), "v1", LocalDate.now()).statusCode(201);
    // start upgrade to the new available upgrade version
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extension.getResourceURI(), upgradeVersion);
    assertEquals(upgradeVersion, upgradeCodeSystem.getExtensionOf());
    getComponent(upgradeCodeSystem.getResourceURI(), SnomedComponentType.CONCEPT, moduleId).statusCode(200);
}