org.obolibrary.macro.MacroExpansionGCIVisitor 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.macro;

import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
import java.util.concurrent.atomic.AtomicBoolean;
import javax.annotation.Nullable;
import org.semanticweb.owlapi.model.AxiomType;
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.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLObjectHasValue;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Macro expansion gci visitor.
 */
public class MacroExpansionGCIVisitor {

    protected static final Logger LOG = LoggerFactory.getLogger(MacroExpansionGCIVisitor.class);
    protected final OWLOntology inputOntology;
    protected final OWLOntology outputOntology;
    protected final AbstractDataVisitorEx dataVisitor;
    protected final boolean shouldAddExpansionMarker;
    protected boolean preserveAnnotationsWhenExpanding = false;

    /**
     * @param inputOntology ontology to use
     * @param outputManager manager for ontology creation
     * @param preserveAnnotationsWhenExpanding true if annotations should be preserved when
     * expanding
     */
    public MacroExpansionGCIVisitor(OWLOntology inputOntology, OWLOntologyManager outputManager,
        boolean preserveAnnotationsWhenExpanding) {
        this(outputManager, inputOntology, false);
        this.preserveAnnotationsWhenExpanding = preserveAnnotationsWhenExpanding;
    }

    /**
     * @param outputManager outputManager
     * @param inputOntology inputOntology
     * @param shouldAddExpansionMarker should expansionMarker be added
     */
    public MacroExpansionGCIVisitor(OWLOntologyManager outputManager, OWLOntology inputOntology,
        boolean shouldAddExpansionMarker) {
        this.inputOntology = inputOntology;
        this.shouldAddExpansionMarker = shouldAddExpansionMarker;
        try {
            outputOntology = outputManager.createOntology(inputOntology.getOntologyID());
        } catch (Exception ex) {
            throw new OWLRuntimeException(ex);
        }
        dataVisitor = new AbstractDataVisitorEx(
            inputOntology.getOWLOntologyManager().getOWLDataFactory());
    }

    /**
     * @return ontology for gci
     */
    public OWLOntology createGCIOntology() {
        MacroExpansions expansions = new MacroExpansions();
        outputOntology.add(expansions.getNewAxioms());
        outputOntology.remove(expansions.getRmAxioms());
        return outputOntology;
    }

    /**
     * @return true if annotations should be preserved
     */
    public boolean shouldPreserveAnnotationsWhenExpanding() {
        return preserveAnnotationsWhenExpanding;
    }

    /**
     * @param preserveAnnotationsWhenExpanding new value
     */
    public void setPreserveAnnotationsWhenExpanding(boolean preserveAnnotationsWhenExpanding) {
        this.preserveAnnotationsWhenExpanding = preserveAnnotationsWhenExpanding;
    }

    private class MacroExpansions {

        private final Set newAxioms = new HashSet<>();
        private final Set rmAxioms = new HashSet<>();
        GCIVisitor visitor;

        public MacroExpansions() {
            visitor = new GCIVisitor(inputOntology, newAxioms);
            inputOntology.axioms(AxiomType.SUBCLASS_OF).forEach(axiom -> axiom.accept(visitor));
            inputOntology.axioms(AxiomType.EQUIVALENT_CLASSES)
                .forEach(axiom -> axiom.accept(visitor));
            inputOntology.axioms(AxiomType.CLASS_ASSERTION).forEach(axiom -> axiom.accept(visitor));
            inputOntology.axioms(AxiomType.ANNOTATION_ASSERTION).forEach(this::expand);
        }

        public Set getNewAxioms() {
            return newAxioms;
        }

        public Set getRmAxioms() {
            return rmAxioms;
        }

        private boolean expand(OWLAnnotationAssertionAxiom ax) {
            OWLAnnotationProperty prop = ax.getProperty();
            AtomicBoolean didExpansion = new AtomicBoolean(false);
            String expandTo = visitor.expandAssertionToMap.get(prop.getIRI());
            if (expandTo != null) {
                LOG.info("Template to Expand{}", expandTo);
                expandTo = expandTo
                    .replaceAll("\\?X", visitor.getTool().getId((IRI) ax.getSubject()));
                expandTo = expandTo
                    .replaceAll("\\?Y", visitor.getTool().getId((IRI) ax.getValue()));
                LOG.info("Expanding {}", expandTo);
                try {
                    visitor.getTool().parseManchesterExpressionFrames(expandTo).forEach(axp -> {
                        OWLAxiom axiom = axp.getAxiom();
                        if (shouldPreserveAnnotationsWhenExpanding()) {
                            axiom = axiom.getAnnotatedAxiom(
                                visitor.getAnnotationsWithOptionalExpansionMarker(ax));
                        }
                        newAxioms.add(axiom);
                        didExpansion.set(true);
                    });
                } catch (Exception ex) {
                    LOG.error(ex.getMessage(), ex);
                }
            }
            return didExpansion.get();
        }
    }

    private class GCIVisitor extends AbstractMacroExpansionVisitor {

        final Set expansionMarkingAnnotations;

        GCIVisitor(OWLOntology inputOntology, Set newAxioms) {
            super(inputOntology, shouldAddExpansionMarker);
            if (shouldAddExpansionMarker) {
                expansionMarkingAnnotations = Collections.singleton(expansionMarkerAnnotation);
            } else {
                expansionMarkingAnnotations = EMPTY_ANNOTATIONS;
            }
            rangeVisitor = dataVisitor;
            classVisitor = new ClassVisitor(newAxioms);
            rebuild(inputOntology);
        }

        class ClassVisitor extends AbstractMacroExpansionVisitor.AbstractClassExpressionVisitorEx {

            private Set newAxioms;

            public ClassVisitor(Set newAxioms) {
                this.newAxioms = newAxioms;
            }

            @Override
            @Nullable
            protected OWLClassExpression expandOWLObjSomeVal(OWLClassExpression filler,
                OWLObjectPropertyExpression p) {
                OWLClassExpression gciRHS = expandObject(filler, p);
                if (gciRHS != null) {
                    OWLClassExpression gciLHS = df.getOWLObjectSomeValuesFrom(p, filler);
                    OWLEquivalentClassesAxiom ax = df.getOWLEquivalentClassesAxiom(gciLHS, gciRHS,
                        expansionMarkingAnnotations);
                    newAxioms.add(ax);
                }
                return gciRHS;
            }

            @Override
            @Nullable
            protected OWLClassExpression expandOWLObjHasVal(OWLObjectHasValue desc,
                OWLIndividual filler,
                OWLObjectPropertyExpression p) {
                OWLClassExpression gciRHS = expandObject(filler, p);
                if (gciRHS != null) {
                    OWLClassExpression gciLHS = df.getOWLObjectHasValue(p, filler);
                    OWLEquivalentClassesAxiom ax = df.getOWLEquivalentClassesAxiom(gciLHS, gciRHS,
                        expansionMarkingAnnotations);
                    newAxioms.add(ax);
                }
                return gciRHS;
            }
        }
    }
}