Examples with SnomedCoreConfiguration com.b2international.snowowl.snomed.datastore.config.SnomedCoreConfiguration used on opensource projects

Example 1 with SnomedCoreConfiguration

use of com.b2international.snowowl.snomed.datastore.config.SnomedCoreConfiguration in project snow-owl by b2ihealthcare.

the class SnomedStatedEclEvaluationTest method setup.

@Before
public void setup() {
    SnomedCoreConfiguration config = new SnomedCoreConfiguration();
    config.setConcreteDomainSupported(true);
    RepositoryConfiguration repositoryConfig = new RepositoryConfiguration();
    IndexConfiguration indexConfiguration = new IndexConfiguration();
    indexConfiguration.setResultWindow(IndexClientFactory.DEFAULT_RESULT_WINDOW);
    repositoryConfig.setIndexConfiguration(indexConfiguration);
    context = TestBranchContext.on(MAIN).with(EclParser.class, new DefaultEclParser(INJECTOR.getInstance(IParser.class), INJECTOR.getInstance(IResourceValidator.class))).with(EclSerializer.class, new DefaultEclSerializer(INJECTOR.getInstance(ISerializer.class))).with(Index.class, rawIndex()).with(RevisionIndex.class, index()).with(SnomedCoreConfiguration.class, config).with(RepositoryConfiguration.class, repositoryConfig).with(ResourceURI.class, CodeSystem.uri("SNOMEDCT")).build();
}

Example 2 with SnomedCoreConfiguration

use of com.b2international.snowowl.snomed.datastore.config.SnomedCoreConfiguration in project snow-owl by b2ihealthcare.

the class SnomedConcreteDomainImportPostProcessor method postProcess.

@Override
public void postProcess(final BranchContext context, String userId, Logger logger) {
    final SnomedCoreConfiguration config = context.service(SnomedCoreConfiguration.class);
    if (!config.isConcreteDomainSupported()) {
        return;
    }
    List<RequestBuilder<TransactionContext, ?>> requests = newArrayList();
    if (!conceptExists(config.getConcreteDomainTypeRefsetIdentifier(), context)) {
        // create module
        createConcept(context, logger, MODULE_B2I_EXTENSION, B2I_MODULE_FSN, B2I_MODULE_PT, MODULE_ROOT, requests);
        // create defining type refset concept
        createConcept(context, logger, REFSET_DEFINING_TYPE, DEFINING_TYPE_REFSET_FSN, DEFINING_TYPE_REFSET_PT, REFSET_ROOT_CONCEPT, requests);
        // create concrete domain type refset concept
        createConcept(context, logger, config.getConcreteDomainTypeRefsetIdentifier(), CONCRETE_DOMAIN_TYPE_REFSET_FSN, CONCRETE_DOMAIN_TYPE_REFSET_PT, REFSET_DEFINING_TYPE, requests);
        // create measurement type concrete domain refset concept
        createConcept(context, logger, REFSET_MEASUREMENT_TYPE, MEASUREMENT_TYPE_REFSET_FSN, MEASUREMENT_TYPE_REFSET_PT, config.getConcreteDomainTypeRefsetIdentifier(), requests);
    }
    // create boolean concrete domain refset identifier concept and refset
    createRefsetAndConcept(context, logger, config.getBooleanDatatypeRefsetIdentifier(), BOOLEAN_DATATYPE_REFSET_FSN, BOOLEAN_DATATYPE_REFSET_PT, config.getConcreteDomainTypeRefsetIdentifier(), requests);
    // create string concrete domain refset identifier concept and refset
    createRefsetAndConcept(context, logger, config.getStringDatatypeRefsetIdentifier(), STRING_DATATYPE_REFSET_FSN, STRING_DATATYPE_REFSET_PT, config.getConcreteDomainTypeRefsetIdentifier(), requests);
    // create date-time concrete domain refset identifier concept and refset
    createRefsetAndConcept(context, logger, config.getDatetimeDatatypeRefsetIdentifier(), DATETIME_DATATYPE_REFSET_FSN, DATETIME_DATATYPE_REFSET_PT, config.getConcreteDomainTypeRefsetIdentifier(), requests);
    // create integer concrete domain refset identifier concept and refset
    createRefsetAndConcept(context, logger, config.getIntegerDatatypeRefsetIdentifier(), INTEGER_DATATYPE_REFSET_FSN, INTEGER_DATATYPE_REFSET_PT, REFSET_MEASUREMENT_TYPE, requests);
    // create float concrete domain refset identifier concept and refset
    createRefsetAndConcept(context, logger, config.getFloatDatatypeRefsetIdentifier(), FLOAT_DATATYPE_REFSET_FSN, FLOAT_DATATYPE_REFSET_PT, REFSET_MEASUREMENT_TYPE, requests);
    if (!requests.isEmpty()) {
        try {
            final BulkRequestBuilder<TransactionContext> bulkRequest = BulkRequest.create();
            requests.forEach(bulkRequest::add);
            SnomedRequests.prepareCommit().setBody(bulkRequest).setAuthor(userId).setCommitComment("Import post processor created concrete domain reference sets").setParentContextDescription(DatastoreLockContextDescriptions.IMPORT).build().execute(context);
        } catch (final Exception e) {
            logger.error("Caught exception while creating concrete domain reference sets in {}", getClass().getSimpleName(), e);
        }
    }
}

Example 3 with SnomedCoreConfiguration

use of com.b2international.snowowl.snomed.datastore.config.SnomedCoreConfiguration in project snow-owl by b2ihealthcare.

the class BaseSnomedEclEvaluationRequestTest method setup.

@Before
public void setup() {
    SnomedCoreConfiguration config = new SnomedCoreConfiguration();
    config.setConcreteDomainSupported(true);
    RepositoryConfiguration repositoryConfig = new RepositoryConfiguration();
    IndexConfiguration indexConfiguration = new IndexConfiguration();
    indexConfiguration.setResultWindow(IndexClientFactory.DEFAULT_RESULT_WINDOW);
    repositoryConfig.setIndexConfiguration(indexConfiguration);
    context = TestBranchContext.on(MAIN).with(EclParser.class, new DefaultEclParser(INJECTOR.getInstance(IParser.class), INJECTOR.getInstance(IResourceValidator.class))).with(EclSerializer.class, new DefaultEclSerializer(INJECTOR.getInstance(ISerializer.class))).with(Index.class, rawIndex()).with(RevisionIndex.class, index()).with(SnomedCoreConfiguration.class, config).with(ObjectMapper.class, getMapper()).with(TerminologyResource.class, createCodeSystem(MAIN)).with(ResourceURI.class, CodeSystem.uri("SNOMEDCT")).with(RepositoryConfiguration.class, repositoryConfig).build();
}

Example 4 with SnomedCoreConfiguration

use of com.b2international.snowowl.snomed.datastore.config.SnomedCoreConfiguration in project snow-owl by b2ihealthcare.

the class SnomedPlugin method init.

@Override
public void init(SnowOwlConfiguration configuration, Environment env) throws Exception {
    final SnomedCoreConfiguration coreConfig = configuration.getModuleConfig(SnomedCoreConfiguration.class);
    env.services().registerService(SnomedCoreConfiguration.class, coreConfig);
    final Injector injector = new EclStandaloneSetup().createInjectorAndDoEMFRegistration();
    env.services().registerService(EclParser.class, new DefaultEclParser(injector.getInstance(IParser.class), injector.getInstance(IResourceValidator.class)));
    env.services().registerService(EclSerializer.class, new DefaultEclSerializer(injector.getInstance(ISerializer.class)));
    // register SNOMED CT Query based validation rule evaluator
    ValidationRuleEvaluator.Registry.register(new SnomedQueryValidationRuleEvaluator());
}

Example 5 with SnomedCoreConfiguration

use of com.b2international.snowowl.snomed.datastore.config.SnomedCoreConfiguration in project snow-owl by b2ihealthcare.

the class ClassificationJobRequest method executeClassification.

private void executeClassification(final BranchContext context, final String classificationId, final ClassificationTracker tracker) {
    final RevisionSearcher revisionSearcher = context.service(RevisionSearcher.class);
    TerminologyResource resource = context.service(TerminologyResource.class);
    @SuppressWarnings("unchecked") final Set<String> reasonerExcludedModuleIds = Collections3.toImmutableSet((Iterable) resource.getSettings().getOrDefault(REASONER_EXCLUDE_MODULE_IDS, Collections.emptySet()));
    final SnomedCoreConfiguration configuration = context.service(SnomedCoreConfiguration.class);
    final boolean concreteDomainSupported = configuration.isConcreteDomainSupported();
    final ReasonerTaxonomy taxonomy;
    try (Locks locks = Locks.on(context).lock(DatastoreLockContextDescriptions.CLASSIFY, parentLockContext)) {
        taxonomy = buildTaxonomy(revisionSearcher, reasonerExcludedModuleIds, concreteDomainSupported);
    } catch (final LockedException e) {
        throw new ReasonerApiException("Couldn't acquire exclusive access to terminology store for classification; %s", e.getMessage(), e);
    }
    final OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
    ontologyManager.getOntologyFactories().add(new DelegateOntologyFactory(taxonomy));
    // TODO: custom moduleId in ontology IRI?
    final IRI ontologyIRI = IRI.create(DelegateOntology.NAMESPACE_SCTM + Concepts.MODULE_SCT_CORE);
    try {
        final DelegateOntology ontology = (DelegateOntology) ontologyManager.createOntology(ontologyIRI);
        final ReasonerTaxonomyInferrer inferrer = new ReasonerTaxonomyInferrer(reasonerId, ontology, context);
        final ReasonerTaxonomy inferredTaxonomy = inferrer.addInferences(taxonomy);
        final NormalFormGenerator normalFormGenerator = new NormalFormGenerator(inferredTaxonomy);
        tracker.classificationCompleted(classificationId, inferredTaxonomy, normalFormGenerator);
    } catch (final OWLOntologyCreationException e) {
        throw new ReasonerApiException("Exception caught while creating ontology instance.", e);
    } catch (final ReasonerInterruptedException | OWLReasonerRuntimeException e) {
        throw new ReasonerApiException("Exception caught while classifying the ontology.", e);
    }
}