org.obolibrary.obo2owl.OwlStringTools Maven / Gradle / Ivy

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A java library for converting obo format documents to OWL, and for converting (a subset of) OWL to obo format. This version has been slightly modified to be included directly in the OWL API. The upstream code for this module and its authors can be found at https://code.google.com/p/oboformat/.

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package org.obolibrary.obo2owl;

import java.io.StringWriter;
import java.io.Writer;
import java.util.HashSet;
import java.util.Set;
import java.util.concurrent.locks.ReadWriteLock;
import java.util.concurrent.locks.ReentrantReadWriteLock;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat;
import org.semanticweb.owlapi.functional.renderer.OWLFunctionalSyntaxRenderer;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.io.OWLRendererException;
import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyFactory;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.UnloadableImportException;
import org.semanticweb.owlapi.utilities.Injector;

/**
 * Tools to read and write a set of owl axioms to/from a string. Used to preserve untranslatable
 * axioms in an owl2obo conversion.
 */
public class OwlStringTools {

    /**
     * Exception indicating an un-recoverable error during the handling of axiom strings.
     */
    public static class OwlStringException extends Exception {

        // generated
        private static final long serialVersionUID = 40000L;

        /**
         * @param cause cause
         */
        protected OwlStringException(Throwable cause) {
            super(cause);
        }
    }

    private static final Injector injector = injector();

    /**
     * Create a string for the given set of axioms. Return null for empty sets or if the set is
     * null.
     * 
     * @param axioms axioms
     * @param translationManager translationManager
     * @return string or null
     * @throws OwlStringException OwlStringException
     * @see #translate(String, OWLOntologyManager)
     */
    @Nullable
    public static String translate(@Nullable Set axioms,
        @Nonnull OWLOntologyManager translationManager) throws OwlStringException {
        if (axioms == null || axioms.isEmpty()) {
            return null;
        }
        try {

            OWLOntologyManager m =
                injector.inject(injector.getImplementation(OWLOntologyManager.class));
            Set set = new HashSet<>();
            translationManager.getOntologyFactories().forEach(set::add);
            m.setOntologyFactories(set);
            OWLOntology ontology = m.createOntology();
            ontology.getOWLOntologyManager().addAxioms(ontology, axioms);
            OWLFunctionalSyntaxRenderer r = new OWLFunctionalSyntaxRenderer();
            Writer writer = new StringWriter();
            r.render(ontology, writer);
            return writer.toString();
        } catch (OWLRendererException e) {
            throw new OwlStringException(e);
        } catch (OWLOntologyCreationException e) {
            throw new OwlStringException(e);
        }
    }

    private static Injector injector() {
        Injector i = new Injector();
        i.bindToOne(() -> new ReentrantReadWriteLock(), ReadWriteLock.class);
        return i;
    }

    /**
     * Parse the axioms from the given axiom string. Returns null for empty and null strings.
     * 
     * @param axioms axioms
     * @param translationManager translationManager
     * @return set of axioms or null
     * @throws OwlStringException OwlStringException
     * @see #translate(Set,OWLOntologyManager)
     */
    @Nullable
    public static Set translate(@Nullable String axioms,
        @Nonnull OWLOntologyManager translationManager) throws OwlStringException {
        if (axioms == null || axioms.isEmpty()) {
            return null;
        }
        try {
            OWLOntologyDocumentSource documentSource = new StringDocumentSource(axioms,
                IRI.generateDocumentIRI(), new FunctionalSyntaxDocumentFormat(), null);
            OWLOntologyManager m =
                injector.inject(injector.getImplementation(OWLOntologyManager.class));
            Set set = new HashSet<>();
            translationManager.getOntologyFactories().forEach(set::add);
            m.setOntologyFactories(set);
            return m.loadOntologyFromOntologyDocument(documentSource).getAxioms();
        } catch (UnloadableImportException e) {
            throw new OwlStringException(e);
        } catch (OWLOntologyCreationException e) {
            throw new OwlStringException(e);
        } catch (OWLParserException e) {
            throw new OwlStringException(e);
        }
    }
}