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 java.io.IOException;
import java.io.Writer;
import java.util.Map;
import java.util.Set;

import javax.annotation.Nonnull;

import org.semanticweb.owlapi.formats.LabelFunctionalDocumentFormat;
import org.semanticweb.owlapi.functional.renderer.FunctionalSyntaxObjectRenderer;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
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.PrefixManager;
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 {

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

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

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

    static class LabelPrefixManager implements PrefixManager {

        private static final long serialVersionUID = 40000L;
        @Nonnull
        private final OWLOntology ontology;
        @Nonnull
        private final PrefixManager delegate;

        LabelPrefixManager(@Nonnull OWLOntology ontology) {
            this.ontology = ontology;
            OWLDocumentFormat ontologyFormat =
                ontology.getOWLOntologyManager().getOntologyFormat(ontology);
            if (ontologyFormat instanceof PrefixManager) {
                delegate = (PrefixManager) ontologyFormat;
            } else {
                delegate = new DefaultPrefixManager();
            }
        }

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

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

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

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

        @Override
        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 Set getPrefixNames() {
            return delegate.getPrefixNames();
        }

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

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

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

        @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
        }
    }
}