Examples with ReasonerTaxonomy com.b2international.snowowl.snomed.datastore.index.taxonomy.ReasonerTaxonomy used on opensource projects

Example 1 with ReasonerTaxonomy

use of com.b2international.snowowl.snomed.datastore.index.taxonomy.ReasonerTaxonomy 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);
    }
}

Example 2 with ReasonerTaxonomy

use of com.b2international.snowowl.snomed.datastore.index.taxonomy.ReasonerTaxonomy in project snow-owl by b2ihealthcare.

the class OntologyExportRequest method execute.

@Override
public String execute(final BranchContext context) {
    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 concreteDomainSupportEnabled = configuration.isConcreteDomainSupported();
    final ReasonerTaxonomyBuilder taxonomyBuilder = new ReasonerTaxonomyBuilder(reasonerExcludedModuleIds);
    taxonomyBuilder.addActiveConceptIds(revisionSearcher);
    taxonomyBuilder.finishConcepts();
    taxonomyBuilder.addFullySpecifiedNames(revisionSearcher);
    taxonomyBuilder.addConceptFlags(revisionSearcher);
    taxonomyBuilder.addActiveStatedEdges(revisionSearcher);
    taxonomyBuilder.addActiveStatedRelationships(revisionSearcher);
    taxonomyBuilder.addNeverGroupedTypeIds(revisionSearcher);
    taxonomyBuilder.addActiveAxioms(revisionSearcher);
    if (concreteDomainSupportEnabled) {
        taxonomyBuilder.addActiveConcreteDomainMembers(revisionSearcher);
    }
    final ReasonerTaxonomy taxonomy = taxonomyBuilder.build();
    final OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
    ontologyManager.getOntologyFactories().add(new DelegateOntologyFactory(taxonomy));
    final IRI ontologyIRI = IRI.create(DelegateOntology.NAMESPACE_SCTM + ontologyModuleId);
    try {
        final OWLOntology ontology = ontologyManager.createOntology(ontologyIRI);
        OWLOntology ontologyToExport = ontologyManager.createOntology();
        ontology.getAxioms().forEach(axiom -> {
            ontologyManager.addAxiom(ontologyToExport, axiom);
        });
        final OWLDocumentFormat documentFormat = getOWLDocumentFormat();
        final AttachmentRegistry fileRegistry = context.service(AttachmentRegistry.class);
        final UUID id = UUID.randomUUID();
        final PipedOutputStream os = new PipedOutputStream();
        final PipedInputStream is = new PipedInputStream(os, PIPE_SIZE);
        final ForkJoinTask<?> uploadTask = ForkJoinTask.adapt(() -> fileRegistry.upload(id, is));
        final ForkJoinTask<?> saveTask = ForkJoinTask.adapt(() -> {
            try {
                ontologyManager.saveOntology(ontologyToExport, documentFormat, os);
            } catch (final OWLOntologyStorageException e) {
                throw createExportFailedException(context, e);
            } finally {
                try {
                    os.close();
                } catch (final IOException e) {
                    throw createExportFailedException(context, e);
                }
            }
        });
        ForkJoinTask.invokeAll(saveTask, uploadTask);
        return id.toString();
    } catch (final OWLOntologyCreationException e) {
        throw createExportFailedException(context, e);
    } catch (final IOException e) {
        throw createExportFailedException(context, e);
    } finally {
        // invalidate static cache entries :'(
        ontologyManager.getOntologies().forEach(o -> {
            ontologyManager.applyChange(new SetOntologyID(o, new OWLOntologyID()));
        });
    }
}