owlapi-version5/oboformat/src/main/java/org/obolibrary/macro/ManchesterSyntaxTool.java
package org.obolibrary.macro;

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

import java.util.Collection;
import java.util.Optional;
import java.util.Set;
import java.util.concurrent.atomic.AtomicBoolean;

import javax.annotation.Nullable;

import org.obolibrary.obo2owl.OWLAPIObo2Owl;
import org.obolibrary.oboformat.model.OBODoc;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
import org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl;
import org.semanticweb.owlapi.manchestersyntax.renderer.ParserException;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnnotationValue;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.model.OntologyConfigurator;
import org.semanticweb.owlapi.util.BidirectionalShortFormProviderAdapter;
import org.semanticweb.owlapi.util.IRIShortFormProvider;
import org.semanticweb.owlapi.util.OntologyAxiomPair;
import org.semanticweb.owlapi.util.ShortFormProvider;
import org.semanticweb.owlapi.util.SimpleIRIShortFormProvider;
import org.semanticweb.owlapi.util.mansyntax.ManchesterOWLSyntaxParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * wrapper for parsing Manchester Syntax.
 *
 * @author heiko
 */
public class ManchesterSyntaxTool {

    private static final Logger LOG = LoggerFactory.getLogger(ManchesterSyntaxTool.class);
    protected final IRIShortFormProvider iriShortFormProvider = new SimpleIRIShortFormProvider();
    private final OWLDataFactory dataFactory;
    private final AdvancedEntityChecker entityChecker;
    private final ShortFormProvider shortFormProvider =
        e -> iriShortFormProvider.getShortForm(e.getIRI());
    private final AtomicBoolean disposed = new AtomicBoolean(false);

    /**
     * Create a new parser instance for the given ontology. By default, this parser will also try to
     * resolve {@code OWLObject} instances via their identifier or rdfs:label.
     *
     * @param inputOntology input ontology
     */
    public ManchesterSyntaxTool(OWLOntology inputOntology) {
        this(inputOntology, null);
    }

    /**
     * Create a new parser instance for the given ontologies. By default, this parser will also try
     * to resolve {@code OWLObject} instances via their identifier or rdfs:label.
     *
     * @param inputOntology input ontology
     * @param auxiliaryOntologies set of additional ontologies or null
     */
    public ManchesterSyntaxTool(OWLOntology inputOntology,
        @Nullable Collection<OWLOntology> auxiliaryOntologies) {
        OWLOntologyManager manager = inputOntology.getOWLOntologyManager();
        dataFactory = manager.getOWLDataFactory();
        Set<OWLOntology> ontologies = asUnorderedSet(inputOntology.importsClosure());
        if (auxiliaryOntologies != null) {
            auxiliaryOntologies.forEach(o -> add(ontologies, o.importsClosure()));
        }
        ShortFormEntityChecker defaultInstance = new ShortFormEntityChecker(
            new BidirectionalShortFormProviderAdapter(manager, ontologies, shortFormProvider));
        entityChecker = new AdvancedEntityChecker(defaultInstance, ontologies,
            inputOntology.getOWLOntologyManager());
    }

    /**
     * Parse frame expressions in Manchester syntax.
     *
     * @param expression expression
     * @return set of {@link OntologyAxiomPair}
     * @throws ParserException parser exception
     */
    public Set<OntologyAxiomPair> parseManchesterExpressionFrames(String expression) {
        ManchesterOWLSyntaxParser parser = createParser(expression);
        return parser.parseFrames();
    }

    /**
     * Parse a class expression in Manchester syntax.
     *
     * @param expression expression
     * @return {@link OWLClassExpression}
     * @throws ParserException parser exception
     */
    public OWLClassExpression parseManchesterExpression(String expression) {
        ManchesterOWLSyntaxParser parser = createParser(expression);
        return parser.parseClassExpression();
    }

    private ManchesterOWLSyntaxParser createParser(String expression) {
        if (disposed.get()) {
            throw new OWLRuntimeException("Illegal State: Trying to use an disposed instance.");
        }
        ManchesterOWLSyntaxParser parser =
            new ManchesterOWLSyntaxParserImpl(new OntologyConfigurator(), dataFactory);
        parser.setStringToParse(expression);
        parser.setOWLEntityChecker(entityChecker);
        LOG.info("parsing: {}", expression);
        return parser;
    }

    /**
     * Translate the {@link IRI} into the short form as expected by the parser.
     *
     * @param iri iri
     * @return short form
     */
    public String getId(IRI iri) {
        if (disposed.get()) {
            throw new OWLRuntimeException("Illegal State: Trying to use an disposed instance.");
        }
        return iriShortFormProvider.getShortForm(iri);
    }

    /**
     * Translate the {@link OWLEntity} identifier into the short form as expected by the parser.
     *
     * @param entity entity
     * @return short form
     */
    public String getId(OWLEntity entity) {
        if (disposed.get()) {
            throw new OWLRuntimeException("Illegal State: Trying to use an disposed instance.");
        }
        return shortFormProvider.getShortForm(entity);
    }

    /**
     * Call this method to dispose the internal data structures. This will remove also the listeners
     * registered with the ontology manager.
     */
    public void dispose() {
        if (!disposed.getAndSet(true)) {
            shortFormProvider.dispose();
        }
    }

    /**
     * {@link OWLEntityChecker} which additionally checks for corresponding identifiers and labels
     * to retrieve entities. The intended behavior is specified as follows:
     * <ul>
     * <li>If the string is enclosed with matching single quotes, try to resolve as label</li>
     * <li>Otherwise, try to resolve as identifier</li>
     * </ul>
     */
    static class AdvancedEntityChecker implements OWLEntityChecker {

        private final OWLEntityChecker defaultInstance;
        private final Set<OWLOntology> ontologies;
        private final OWLOntologyManager manager;

        /**
         * @param defaultInstance default instance
         * @param ontologies ontologies
         * @param manager manager
         */
        AdvancedEntityChecker(OWLEntityChecker defaultInstance, Set<OWLOntology> ontologies,
            OWLOntologyManager manager) {
            this.defaultInstance = defaultInstance;
            this.ontologies = ontologies;
            this.manager = manager;
        }

        private static boolean isQuoted(String s) {
            int length = s.length();
            if (length >= 2) {
                return s.charAt(0) == '\'' && s.charAt(length - 1) == '\'';
            }
            return false;
        }

        @Override
        @Nullable
        public OWLClass getOWLClass(String name) {
            OWLClass owlClass = defaultInstance.getOWLClass(name);
            if (owlClass == null) {
                IRI iri = getIRI(name);
                if (iri != null) {
                    owlClass = getOWLClass(iri);
                }
            }
            return owlClass;
        }

        @Override
        @Nullable
        public OWLObjectProperty getOWLObjectProperty(String name) {
            OWLObjectProperty owlObjectProperty = defaultInstance.getOWLObjectProperty(name);
            if (owlObjectProperty == null) {
                IRI iri = getIRI(name);
                if (iri != null) {
                    owlObjectProperty = getOWLObjectProperty(iri);
                }
            }
            return owlObjectProperty;
        }

        @Override
        @Nullable
        public OWLDataProperty getOWLDataProperty(String name) {
            return defaultInstance.getOWLDataProperty(name);
        }

        @Override
        @Nullable
        public OWLNamedIndividual getOWLIndividual(String name) {
            OWLNamedIndividual owlIndividual = defaultInstance.getOWLIndividual(name);
            if (owlIndividual == null) {
                IRI iri = getIRI(name);
                if (iri != null) {
                    owlIndividual = getOWLIndividual(iri);
                }
            }
            return owlIndividual;
        }

        @Override
        @Nullable
        public OWLDatatype getOWLDatatype(String name) {
            return defaultInstance.getOWLDatatype(name);
        }

        @Override
        @Nullable
        public OWLAnnotationProperty getOWLAnnotationProperty(String name) {
            return defaultInstance.getOWLAnnotationProperty(name);
        }

        @Nullable
        protected IRI getIRI(String name) {
            if (isQuoted(name)) {
                // anything in '....' quotes is a label
                return getIRIByLabel(name.substring(1, name.length() - 1));
            }
            if (name.length() > 2 && name.charAt(0) == '<'
                && name.charAt(name.length() - 1) == '>') {
                // anything between <...> brackets is a complete IRI
                return IRI.create(name.substring(1, name.length() - 1));
            }
            return getIRIByIdentifier(name);
        }

        @Nullable
        protected IRI getIRIByIdentifier(String id) {
            OWLAPIObo2Owl b = new OWLAPIObo2Owl(manager);
            b.setObodoc(new OBODoc());
            return b.oboIdToIRI(id);
        }

        /**
         * Retrieve an {@link IRI} by rdfs:label.
         *
         * @param label label
         * @return {@link IRI} or null
         */
        @Nullable
        protected IRI getIRIByLabel(String label) {
            for (OWLOntology o : ontologies) {
                Optional<OWLAnnotationAssertionAxiom> anyMatch =
                    o.axioms(AxiomType.ANNOTATION_ASSERTION)
                        .filter(aa -> isMatchingLabel(label, aa.getValue(), aa.getProperty())
                            && aa.getSubject().isIRI())
                        .findAny();
                if (anyMatch.isPresent()) {
                    return (IRI) anyMatch.get().getSubject();
                }
            }
            return null;
        }

        /**
         * @param label label to match
         * @param v annotation value
         * @param property property to check
         * @return true if property is a label, v is a literal and v matches label
         */
        protected boolean isMatchingLabel(String label, OWLAnnotationValue v,
            OWLAnnotationProperty property) {
            return property.isLabel() && v instanceof OWLLiteral
                && label.equals(((OWLLiteral) v).getLiteral());
        }

        /**
         * Retrieve the {@link OWLClass} for a given {@link IRI}, if it has at least one
         * {@link OWLDeclarationAxiom}.
         *
         * @param iri iri
         * @return {@link OWLClass} or null
         */
        @Nullable
        protected OWLClass getOWLClass(IRI iri) {
            for (OWLOntology o : ontologies) {
                OWLClass c = o.getOWLOntologyManager().getOWLDataFactory().getOWLClass(iri);
                if (!asList(o.declarationAxioms(c)).isEmpty()) {
                    return c;
                }
                if (o.getOWLOntologyManager().getOWLDataFactory().getOWLNothing().equals(c)) {
                    return c;
                }
            }
            return null;
        }

        /**
         * Retrieve the {@link OWLNamedIndividual} for a given {@link IRI}, if it has at least one
         * corresponding {@link OWLDeclarationAxiom}.
         *
         * @param iri iri
         * @return {@link OWLNamedIndividual} or null
         */
        @Nullable
        protected OWLNamedIndividual getOWLIndividual(IRI iri) {
            for (OWLOntology o : ontologies) {
                OWLNamedIndividual c =
                    o.getOWLOntologyManager().getOWLDataFactory().getOWLNamedIndividual(iri);
                Optional<OWLDeclarationAxiom> found = o.declarationAxioms(c)
                    .filter(da -> da.getEntity().isOWLNamedIndividual()).findAny();
                if (found.isPresent()) {
                    return found.get().getEntity().asOWLNamedIndividual();
                }
            }
            return null;
        }

        /**
         * Retrieve the {@link OWLObjectProperty} for a given {@link IRI}, if it has at least one
         * {@link OWLDeclarationAxiom}.
         *
         * @param iri iri
         * @return {@link OWLObjectProperty} or null
         */
        @Nullable
        protected OWLObjectProperty getOWLObjectProperty(IRI iri) {
            for (OWLOntology o : ontologies) {
                OWLObjectProperty p =
                    o.getOWLOntologyManager().getOWLDataFactory().getOWLObjectProperty(iri);
                if (!asList(o.declarationAxioms(p)).isEmpty()) {
                    return p;
                }
            }
            return null;
        }
    }
}
