org.obolibrary.owl.LabelFunctionalSyntaxStorer 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.owl;

import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;

import java.io.PrintWriter;
import java.util.Map;
import java.util.Optional;
import java.util.stream.Stream;

import javax.annotation.Nullable;

import org.semanticweb.owlapi.formats.LabelFunctionalDocumentFormat;
import org.semanticweb.owlapi.functional.renderer.FunctionalSyntaxObjectRenderer;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnnotationValue;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.model.PrefixManager;
import org.semanticweb.owlapi.search.Searcher;
import org.semanticweb.owlapi.util.AbstractOWLStorer;
import org.semanticweb.owlapi.util.DefaultPrefixManager;
import org.semanticweb.owlapi.util.StringComparator;

/**
 * Implement the writer for {@link LabelFunctionalDocumentFormat}.
 */
public class LabelFunctionalSyntaxStorer extends AbstractOWLStorer {

    @Override
    public boolean canStoreOntology(OWLDocumentFormat ontologyFormat) {
        return ontologyFormat instanceof LabelFunctionalDocumentFormat;
    }

    @Override
    protected void storeOntology(OWLOntology ontology, PrintWriter writer, OWLDocumentFormat format)
        throws OWLOntologyStorageException {
        try {
            FunctionalSyntaxObjectRenderer renderer =
                new FunctionalSyntaxObjectRenderer(ontology, format, writer);
            renderer.setPrefixManager(new LabelPrefixManager(ontology));
            ontology.accept(renderer);
            writer.flush();
        } catch (OWLRuntimeException e) {
            throw new OWLOntologyStorageException(e);
        }
    }

    static class LabelPrefixManager implements PrefixManager {

        private final OWLOntology ontology;
        private final PrefixManager delegate;
        private final OWLAnnotationProperty rdfsLabel;

        LabelPrefixManager(OWLOntology ontology) {
            this.ontology = ontology;
            OWLDocumentFormat ontologyFormat = ontology.getFormat();
            if (ontologyFormat instanceof PrefixManager) {
                delegate = (PrefixManager) ontologyFormat;
            } else {
                delegate = new DefaultPrefixManager();
            }
            rdfsLabel = ontology.getOWLOntologyManager().getOWLDataFactory().getRDFSLabel();
        }

        @Override
        @Nullable
        public String getPrefixIRI(IRI iri) {
            for (OWLAnnotationAssertionAxiom annotation : asList(
                ontology.annotationAssertionAxioms(iri))) {
                if (annotation.getProperty().isLabel()) {
                    OWLAnnotationValue value = annotation.getValue();
                    if (value instanceof OWLLiteral) {
                        return '<' + ((OWLLiteral) value).getLiteral() + '>';
                    }
                }
            }
            return delegate.getPrefixIRI(iri);
        }

        @Override
        @Nullable
        public String getDefaultPrefix() {
            return delegate.getDefaultPrefix();
        }

        @Override
        public void setDefaultPrefix(@Nullable String defaultPrefix) {
            // do not propagate changes to the original manager
            // there should be no changes during rendering anyway
        }

        @Override
        public String getPrefixIRIIgnoreQName(IRI iri) {
            Optional lit = labels(iri).map(OWLAnnotation::getValue)
                .filter(OWLAnnotationValue::isLiteral).findFirst();
            return lit.map(x -> "<" + x.asLiteral().get().getLiteral() + ">")
                .orElse(delegate.getPrefixIRIIgnoreQName(iri));
        }

        protected Stream labels(IRI iri) {
            return Searcher.annotationObjects(ontology.annotationAssertionAxioms(iri), rdfsLabel);
        }

        @Override
        public boolean containsPrefixMapping(String prefixName) {
            return delegate.containsPrefixMapping(prefixName);
        }

        @Override
        @Nullable
        public String getPrefix(String prefixName) {
            return delegate.getPrefix(prefixName);
        }

        @Override
        public Map getPrefixName2PrefixMap() {
            return delegate.getPrefixName2PrefixMap();
        }

        @Override
        public IRI getIRI(String prefixIRI) {
            return delegate.getIRI(prefixIRI);
        }

        @Override
        public Stream prefixNames() {
            return delegate.prefixNames();
        }

        @Override
        public StringComparator getPrefixComparator() {
            return delegate.getPrefixComparator();
        }

        @Override
        public void setPrefixComparator(StringComparator comparator) {
            delegate.setPrefixComparator(comparator);
        }

        @Override
        public void setPrefix(String prefixName, String prefix) {
            // do not propagate changes to the original manager
            // there should be no changes during rendering anyway
        }

        @Override
        public void copyPrefixesFrom(PrefixManager from) {
            // do not propagate changes to the original manager
            // there should be no changes during rendering anyway
        }

        @Override
        public void copyPrefixesFrom(Map from) {
            // do not propagate changes to the original manager
            // there should be no changes during rendering anyway
        }

        @Override
        public void unregisterNamespace(String namespace) {
            // do not propagate changes to the original manager
            // there should be no changes during rendering anyway
        }

        @Override
        public void clear() {
            // do not propagate changes to the original manager
            // there should be no changes during rendering anyway
        }
    }
}