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package org.obolibrary.obo2owl;

import static org.obolibrary.obo2owl.Obo2OWLConstants.DEFAULT_IRI_PREFIX;
import static org.obolibrary.obo2owl.Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.emptyOptional;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.optional;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;

import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;

import javax.annotation.Nullable;

import org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary;
import org.obolibrary.oboformat.model.Clause;
import org.obolibrary.oboformat.model.Frame;
import org.obolibrary.oboformat.model.OBODoc;
import org.obolibrary.oboformat.model.QualifierValue;
import org.obolibrary.oboformat.model.Xref;
import org.obolibrary.oboformat.parser.OBOFormatConstants;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
import org.obolibrary.oboformat.parser.OBOFormatException;
import org.obolibrary.oboformat.parser.OBOFormatParser;
import org.obolibrary.oboformat.parser.OBOFormatParserException;
import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.model.AddImport;
import org.semanticweb.owlapi.model.AddOntologyAnnotation;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnnotationSubject;
import org.semanticweb.owlapi.model.OWLAnnotationValue;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLImportsDeclaration;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLNamedObject;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLProperty;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.model.SetOntologyID;
import org.semanticweb.owlapi.model.parameters.ConfigurationOptions;
import org.semanticweb.owlapi.util.CollectionFactory;
import org.semanticweb.owlapi.vocab.Namespaces;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.semanticweb.owlapi.vocab.OWLXMLVocabulary;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.google.common.collect.Sets;

/**
 * The Class OWLAPIObo2Owl.
 */
public class OWLAPIObo2Owl {

    private class IDCache extends LinkedHashMap {
        private final int cacheSize;

        IDCache(int cacheSize) {
            this.cacheSize = cacheSize;
        }

        @Override
        protected boolean removeEldestEntry(@Nullable Map.Entry eldest) {
            return size() > cacheSize;
        }
    }

    private static final String TRUE = "true";
    /**
     * The Constant IRI_PROP_isReversiblePropertyChain.
     */
    public static final String IRI_PROP_ISREVERSIBLEPROPERTYCHAIN =
        DEFAULT_IRI_PREFIX + "IAO_isReversiblePropertyChain";
    protected static final Map ANNOTATIONPROPERTYMAP = initAnnotationPropertyMap();
    private static final Logger LOG = LoggerFactory.getLogger(OWLAPIObo2Owl.class);
    private static final Set SKIPPED_QUALIFIERS = Sets.newHashSet("gci_relation",
        "gci_filler", "cardinality", "minCardinality", "maxCardinality", "all_some", "all_only");
    protected final Map idSpaceMap;
    protected final Set apToDeclare;
    protected final Map clsToDeclare;
    protected final Map typedefToAnnotationProperty;
    protected String defaultIDSpace = "";
    protected OWLOntologyManager manager;
    protected OWLOntology owlOntology;
    protected OWLDataFactory fac;
    protected OBODoc obodoc;
    /**
     * Cache for the id to IRI conversion. This cannot be replaced with a Caffeine cache - the
     * loading of keys is recursive, and a bug in ConcurrentHashMap implementation causes livelocks
     * for this particular situation.
     */
    private Map idToIRICache;

    /**
     * @param manager the manager
     */
    public OWLAPIObo2Owl(OWLOntologyManager manager) {
        idSpaceMap = new HashMap<>();
        apToDeclare = new HashSet<>();
        clsToDeclare = new HashMap<>();
        typedefToAnnotationProperty = new HashMap<>();
        init(manager);
    }

    /**
     * Static convenience method which: (1) creates an Obo2Owl bridge object (2) parses an obo file
     * from a URL (3) converts that to an OWL ontology (4) saves the OWL ontology as RDF/XML.
     *
     * @param iri the iri
     * @param outFile the out file
     * @param manager manager to use
     * @throws IOException Signals that an I/O exception has occurred.
     * @throws OWLOntologyCreationException ontology creation exception
     * @throws OWLOntologyStorageException ontology storage exception
     * @throws OBOFormatParserException OBO format parser exception
     */
    public static void convertURL(String iri, String outFile, OWLOntologyManager manager)
        throws IOException, OWLOntologyCreationException, OWLOntologyStorageException {
        OWLAPIObo2Owl bridge = new OWLAPIObo2Owl(manager);
        OBOFormatParser p = new OBOFormatParser();
        OBODoc obodoc = p.parse(new URL(iri));
        OWLOntology ontology = bridge.convert(obodoc);
        IRI outputStream = IRI.create(outFile);
        OWLDocumentFormat format = new RDFXMLDocumentFormat();
        LOG.info("saving to {} fmt={}", outputStream, format);
        manager.saveOntology(ontology, format, outputStream);
    }

    /**
     * See.
     *
     * @param iri the iri
     * @param outFile the out file
     * @param defaultOnt -- e.g. "go". If the obo file contains no "ontology:" header tag, this is
     *        added
     * @param manager the manager to be used
     * @throws IOException Signals that an I/O exception has occurred.
     * @throws OWLOntologyCreationException ontology creation exception
     * @throws OWLOntologyStorageException ontology storage exception
     * @throws OBOFormatParserException OBO format parser exception
     *         {@link #convertURL(String, String, OWLOntologyManager)}
     */
    public static void convertURL(String iri, String outFile, String defaultOnt,
        OWLOntologyManager manager)
        throws IOException, OWLOntologyCreationException, OWLOntologyStorageException {
        OWLAPIObo2Owl bridge = new OWLAPIObo2Owl(manager);
        OBOFormatParser p = new OBOFormatParser();
        OBODoc obodoc = p.parse(new URL(iri));
        obodoc.addDefaultOntologyHeader(defaultOnt);
        OWLOntology ontology = bridge.convert(obodoc);
        IRI outputStream = IRI.create(outFile);
        OWLDocumentFormat format = new RDFXMLDocumentFormat();
        LOG.info("saving to {} fmt={}", outputStream, format);
        manager.saveOntology(ontology, format, outputStream);
    }

    /**
     * Table 5.8 Translation of Annotation Vocabulary.
     *
     * @return property map
     */
    protected static Map initAnnotationPropertyMap() {
        Map map = new HashMap<>();
        map.put(OboFormatTag.TAG_IS_OBSELETE.getTag(), OWLRDFVocabulary.OWL_DEPRECATED.getIRI());
        map.put(OboFormatTag.TAG_NAME.getTag(), OWLRDFVocabulary.RDFS_LABEL.getIRI());
        map.put(OboFormatTag.TAG_COMMENT.getTag(), OWLRDFVocabulary.RDFS_COMMENT.getIRI());
        for (Obo2OWLVocabulary vac : Obo2OWLVocabulary.values()) {
            map.put(vac.getMappedTag(), vac.getIRI());
        }
        return map;
    }

    /**
     * @param path the path
     * @return the URI string
     */
    protected static String getURI(String path) {
        if (path.startsWith("http://") || path.startsWith("https://") || path.startsWith("file:")) {
            return path;
        }
        File f = new File(path);
        return f.toURI().toString();
    }

    /**
     * Translate relation union of.
     *
     * @param id the id
     * @param p the p
     * @param clauses the clauses
     * @return the OWL axiom
     */
    @SuppressWarnings("unused")
    @Nullable
    protected static OWLAxiom trRelationUnionOf(String id, OWLProperty p,
        Collection clauses) {
        // TODO not expressible in OWL - use APs. SWRL?
        LOG.error(
            "The relation union_of for {} is currently non-translatable to OWL. Ignoring clauses: {}",
            id, clauses);
        return null;
    }

    /**
     * Translate relation intersection of.
     *
     * @param id the id
     * @param p the p
     * @param clauses the clauses
     * @return the OWL axiom
     */
    @SuppressWarnings("unused")
    @Nullable
    protected static OWLAxiom trRelationIntersectionOf(String id, OWLProperty p,
        Collection clauses) {
        // TODO not expressible in OWL - use APs. SWRL?
        LOG.error(
            "The relation intersection_of for {} is currently non-translatable to OWL. Ignoring clauses: {}",
            id, clauses);
        return null;
    }

    /**
     * Gets the qualifier value string.
     * 
     * @param q the qualifier value
     * @param quals the qualifier values
     * @return the qualifier value string
     */
    protected static String getQVString(String q, Collection quals) {
        for (QualifierValue qv : quals) {
            if (qv.getQualifier().equals(q)) {
                return qv.getValue();
            }
        }
        return "";
    }

    /**
     * Gets the qualifier value boolean.
     * 
     * @param q the qualifier value
     * @param quals the qualifier values
     * @return the qualifier value boolean
     */
    protected static boolean getQVBoolean(String q, Collection quals) {
        for (QualifierValue qv : quals) {
            if (qv.getQualifier().equals(q)) {
                Object v = qv.getValue();
                return Boolean.parseBoolean((String) v);
            }
        }
        return false;
    }

    /**
     * Gets the qualifier value int.
     * 
     * @param q the qualifier value
     * @param quals the qualifier values
     * @return the qualifier value int
     */
    @Nullable
    protected static Integer getQVInt(String q, Collection quals) {
        for (QualifierValue qv : quals) {
            if (qv.getQualifier().equals(q)) {
                Object v = qv.getValue();
                return Integer.valueOf((String) v);
            }
        }
        return null;
    }

    /**
     * Gets the id prefix.
     *
     * @param x the x
     * @return the id prefix
     */
    protected static String getIdPrefix(String x) {
        String[] parts = x.split(":", 2);
        return parts[0];
    }

    /**
     * Translate tag to iri.
     *
     * @param tag the tag
     * @return the iri
     */
    public static IRI trTagToIRI(String tag) {
        IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
        if (iri == null) {
            iri = IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, tag);
        }
        return iri;
    }

    protected void init(OWLOntologyManager m) {
        // use the given manager and its factory
        manager = m;
        fac = manager.getOWLDataFactory();
        int cacheSize = ConfigurationOptions.CACHE_SIZE
            .getValue(Integer.class, Collections.emptyMap()).intValue();
        idToIRICache = new IDCache(cacheSize);

        // clear all internal maps.
        idSpaceMap.clear();
        apToDeclare.clear();
        clsToDeclare.clear();
        typedefToAnnotationProperty.clear();
    }

    /**
     * Gets the manager.
     *
     * @return the manager
     */
    public OWLOntologyManager getManager() {
        return manager;
    }

    /**
     * Sets the manager.
     *
     * @param manager the new manager
     */
    public void setManager(OWLOntologyManager manager) {
        this.manager = manager;
    }

    /**
     * Gets the obodoc.
     *
     * @return the obodoc
     */
    public OBODoc getObodoc() {
        return obodoc;
    }

    /**
     * Sets the obodoc.
     *
     * @param obodoc the new obodoc
     */
    public void setObodoc(OBODoc obodoc) {
        this.obodoc = obodoc;
    }

    /**
     * Gets the owl ontology.
     *
     * @return the owlOntology
     */
    protected OWLOntology getOwlOntology() {
        return verifyNotNull(owlOntology);
    }

    /**
     * Sets the owl ontology.
     *
     * @param owlOntology the owlOntology to set
     */
    protected void setOwlOntology(OWLOntology owlOntology) {
        this.owlOntology = owlOntology;
    }

    /**
     * Creates an OBOFormatParser object to parse a file and then converts it using the convert
     * method.
     *
     * @param oboFile the obo file
     * @return ontology
     * @throws OWLOntologyCreationException the OWL ontology creation exception
     */
    public OWLOntology convert(String oboFile) throws OWLOntologyCreationException {
        try {
            OBOFormatParser p = new OBOFormatParser();
            return convert(p.parse(oboFile));
        } catch (IOException ex) {
            throw new OWLOntologyCreationException(
                "Error Occured while parsing OBO '" + oboFile + '\'', ex);
        } catch (OBOFormatParserException ex) {
            throw new OWLOntologyCreationException(
                "Syntax error occured while parsing OBO '" + oboFile + '\'', ex);
        }
    }

    /**
     * Convert.
     *
     * @param doc the obodoc
     * @return ontology
     * @throws OWLOntologyCreationException the OWL ontology creation exception
     */
    public OWLOntology convert(OBODoc doc) throws OWLOntologyCreationException {
        obodoc = doc;
        init(manager);
        return tr(manager.createOntology());
    }

    /**
     * Convert.
     *
     * @param doc the obodoc
     * @param in the in
     * @return the OWL ontology
     */
    public OWLOntology convert(OBODoc doc, OWLOntology in) {
        obodoc = doc;
        init(in.getOWLOntologyManager());
        return tr(in);
    }

    /**
     * Translate ontology.
     *
     * @param in the in
     * @return the OWL ontology
     */
    protected OWLOntology tr(OWLOntology in) {
        setOwlOntology(in);
        Frame hf = verifyNotNull(obodoc.getHeaderFrame());
        Clause ontClause = hf.getClause(OboFormatTag.TAG_ONTOLOGY);
        if (ontClause != null) {
            String ontOboId = (String) ontClause.getValue();
            defaultIDSpace = ontOboId;
            IRI ontIRI;
            if (ontOboId.contains(":")) {
                ontIRI = IRI.create(ontOboId);
            } else {
                ontIRI = IRI.create(DEFAULT_IRI_PREFIX + ontOboId + ".owl");
            }
            Clause dvclause = hf.getClause(OboFormatTag.TAG_DATA_VERSION);
            if (dvclause != null) {
                String dv = dvclause.getValue().toString();
                IRI vIRI =
                    IRI.create(DEFAULT_IRI_PREFIX + ontOboId + '/' + dv + '/' + ontOboId + ".owl");
                OWLOntologyID oid = new OWLOntologyID(optional(ontIRI), optional(vIRI));
                // if the ontology being read has a differet id from the one
                // that was passed in, update it
                // when parsing, the original ontology is likely an anonymous,
                // empty one
                if (!oid.equals(in.getOntologyID())) {
                    manager.applyChange(new SetOntologyID(in, oid));
                }
            } else {
                // if the ontology being read has a differet id from the one
                // that was passed in, update it
                // when parsing, the original ontology is likely an anonymous,
                // empty one
                if (!ontIRI.equals(in.getOntologyID().getOntologyIRI().orElse(null))) {
                    manager.applyChange(new SetOntologyID(in,
                        new OWLOntologyID(optional(ontIRI), emptyOptional())));
                }
            }
        } else {
            defaultIDSpace = "TEMP";
            manager.applyChange(new SetOntologyID(in, new OWLOntologyID(
                optional(IRI.create(DEFAULT_IRI_PREFIX, defaultIDSpace)), emptyOptional())));
            // TODO - warn
        }
        trHeaderFrame(hf);
        obodoc.getTypedefFrames().forEach(this::trTypedefToAnnotationProperty);
        obodoc.getTypedefFrames().forEach(this::trTypedefFrame);
        obodoc.getTermFrames().forEach(this::trTermFrame);
        // TODO - individuals
        for (Clause cl : hf.getClauses(OboFormatTag.TAG_IMPORT)) {
            String path = getURI(cl.getValue().toString());
            IRI importIRI = IRI.create(path);
            OWLImportsDeclaration owlImportsDeclaration = fac.getOWLImportsDeclaration(importIRI);
            manager.makeLoadImportRequest(owlImportsDeclaration,
                new OWLOntologyLoaderConfiguration());
            AddImport ai = new AddImport(in, owlImportsDeclaration);
            manager.applyChange(ai);
        }
        postProcess(in);
        return in;
    }

    /**
     * perform any necessary post-processing. currently this only includes the experimental
     * logical-definitions-view-property
     *
     * @param ontology the ontology
     */
    protected void postProcess(OWLOntology ontology) {
        OWLAnnotationProperty p =
            fac.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_LogicalDefinitionViewRelation);
        Optional findAny = ontology.annotations().filter(a -> a.getProperty().equals(p))
            .map(a -> a.getValue().asLiteral()).filter(Optional::isPresent)
            .map(x -> x.get().getLiteral()).findAny();
        if (!findAny.isPresent()) {
            return;
        }
        IRI pIRI = oboIdToIRI(findAny.get());
        OWLObjectProperty vp = fac.getOWLObjectProperty(pIRI);
        Set rmAxioms = new HashSet<>();
        Set newAxioms = new HashSet<>();
        ontology.axioms(AxiomType.EQUIVALENT_CLASSES).forEach(eca -> {
            AtomicInteger numNamed = new AtomicInteger();
            Set xs = new HashSet<>();
            eca.classExpressions().forEach(x -> {
                if (x instanceof OWLClass) {
                    xs.add(x);
                    numNamed.incrementAndGet();
                } else {
                    // anonymous class expressions are 'prefixed' with view
                    // property
                    xs.add(fac.getOWLObjectSomeValuesFrom(vp, x));
                }
            });
            if (numNamed.get() == 1) {
                rmAxioms.add(eca);
                newAxioms.add(fac.getOWLEquivalentClassesAxiom(xs));
            }
        });
        ontology.remove(rmAxioms);
        ontology.add(newAxioms);
    }

    /**
     * Translate header frame.
     *
     * @param headerFrame the header frame
     */
    public void trHeaderFrame(Frame headerFrame) {
        for (String t : headerFrame.getTags()) {
            OboFormatTag tag = OBOFormatConstants.getTag(t);
            if (tag == OboFormatTag.TAG_ONTOLOGY) {
                // already processed
            } else if (tag == OboFormatTag.TAG_IMPORT) {
                // TODO
            } else if (tag == OboFormatTag.TAG_SUBSETDEF) {
                OWLAnnotationProperty parentAnnotProp = trTagToAnnotationProp(t);
                for (Clause clause : headerFrame.getClauses(t)) {
                    OWLAnnotationProperty childAnnotProp =
                        trAnnotationProp(clause.getValue(String.class));
                    Set annotations = trAnnotations(clause);
                    add(fac.getOWLSubAnnotationPropertyOfAxiom(childAnnotProp, parentAnnotProp,
                        annotations));
                    OWLAnnotationProperty ap =
                        trTagToAnnotationProp(OboFormatTag.TAG_COMMENT.getTag());
                    add(fac.getOWLAnnotationAssertionAxiom(ap, childAnnotProp.getIRI(),
                        trLiteral(clause.getValue2())));
                }
            } else if (tag == OboFormatTag.TAG_SYNONYMTYPEDEF) {
                OWLAnnotationProperty parentAnnotProp = trTagToAnnotationProp(t);
                for (Clause clause : headerFrame.getClauses(t)) {
                    Object[] values = clause.getValues().toArray();
                    OWLAnnotationProperty childAnnotProp = trAnnotationProp(values[0].toString());
                    IRI childIRI = childAnnotProp.getIRI();
                    Set annotations = trAnnotations(clause);
                    add(fac.getOWLSubAnnotationPropertyOfAxiom(childAnnotProp, parentAnnotProp,
                        annotations));
                    OWLAnnotationProperty ap =
                        trTagToAnnotationProp(OboFormatTag.TAG_NAME.getTag());
                    add(fac.getOWLAnnotationAssertionAxiom(ap, childIRI, trLiteral(values[1])));
                    if (values.length > 2 && !values[2].toString().isEmpty()) {
                        ap = trTagToAnnotationProp(OboFormatTag.TAG_SCOPE.getTag());
                        add(fac.getOWLAnnotationAssertionAxiom(ap, childIRI,
                            trTagToAnnotationProp(values[2].toString()).getIRI()));
                    }
                }
            } else if (tag == OboFormatTag.TAG_DATE) {
                handleDate(t, headerFrame.getClause(tag));
            } else if (tag == OboFormatTag.TAG_PROPERTY_VALUE) {
                addPropertyValueHeaders(headerFrame.getClauses(OboFormatTag.TAG_PROPERTY_VALUE));
            } else if (tag == OboFormatTag.TAG_DATA_VERSION) {
                // TODO Add versionIRI
            } else if (tag == OboFormatTag.TAG_REMARK) {
                // translate remark as rdfs:comment
                headerFrame.getClauses(t).forEach(c -> addOntologyAnnotation(fac.getRDFSComment(),
                    trLiteral(c.getValue()), trAnnotations(c)));
            } else if (tag == OboFormatTag.TAG_IDSPACE) {
                // do not translate, as they are just directives
            } else if (tag == OboFormatTag.TAG_OWL_AXIOMS) {
                // in theory, there should only be one tag
                // but we can silently collapse multiple tags
                headerFrame.getTagValues(tag, String.class)
                    .forEach(s -> OwlStringTools.translate(s, getOwlOntology()));
            } else {
                headerFrame.getClauses(t)
                    .forEach(c -> addOntologyAnnotation(trTagToAnnotationProp(t),
                        trLiteral(c.getValue()), trAnnotations(c)));
            }
        }
    }

    protected void handleDate(String t, @Nullable Clause clause) {
        if (clause != null) {
            Object value = clause.getValue();
            String dateString = null;
            if (value instanceof Date) {
                dateString = OBOFormatConstants.headerDateFormat().format((Date) value);
            } else if (value instanceof String) {
                dateString = (String) value;
            }
            if (dateString != null) {
                addOntologyAnnotation(trTagToAnnotationProp(t), trLiteral(dateString),
                    trAnnotations(clause));
            } else {
                // TODO: Throw Exceptions
                OBOFormatException e =
                    new OBOFormatException("Cannot translate clause «" + clause + '»');
                LOG.error("Cannot translate: {}", clause, e);
            }
        }
    }

    /**
     * Adds the property value headers.
     *
     * @param clauses the clauses
     */
    protected void addPropertyValueHeaders(Collection clauses) {
        for (Clause clause : clauses) {
            Set annotations = trAnnotations(clause);
            Collection values = clause.getValues();
            Object v = clause.getValue();
            Object v2 = clause.getValue2();
            if (values.size() == 2) {
                // property_value(Rel-ID Entity-ID Qualifiers)
                OWLAnnotationProperty prop = trAnnotationProp((String) v);
                OWLAnnotationValue value = trAnnotationProp(v2.toString()).getIRI();
                OWLAnnotation ontAnn = fac.getOWLAnnotation(prop, value, annotations);
                AddOntologyAnnotation addAnn = new AddOntologyAnnotation(getOwlOntology(), ontAnn);
                apply(addAnn);
            } else if (values.size() == 3) {
                // property_value(Rel-ID Value XSD-Type Qualifiers)
                Iterator it = clause.getValues().iterator();
                it.next();
                it.next();
                String v3String = (String) it.next();
                IRI valueIRI;
                if (v3String.startsWith("xsd:")) {
                    valueIRI = IRI.create(Namespaces.XSD.getPrefixIRI(), v3String.substring(4));
                } else {
                    valueIRI = IRI.create(v3String);
                }
                OWLAnnotationValue value =
                    fac.getOWLLiteral((String) v2, OWL2Datatype.getDatatype(valueIRI));
                OWLAnnotationProperty prop = trAnnotationProp((String) v);
                OWLAnnotation ontAnn = fac.getOWLAnnotation(prop, value, annotations);
                AddOntologyAnnotation addAnn = new AddOntologyAnnotation(getOwlOntology(), ontAnn);
                apply(addAnn);
            } else {
                LOG.error("Cannot translate: {}", clause);
                // TODO
            }
        }
    }

    /**
     * Adds the ontology annotation.
     *
     * @param ap the ap
     * @param v the v
     * @param annotations the annotations
     */
    protected void addOntologyAnnotation(OWLAnnotationProperty ap, OWLAnnotationValue v,
        Set annotations) {
        OWLAnnotation ontAnn = fac.getOWLAnnotation(ap, v, annotations);
        AddOntologyAnnotation addAnn = new AddOntologyAnnotation(getOwlOntology(), ontAnn);
        apply(addAnn);
    }

    /**
     * Translate term frame.
     *
     * @param termFrame the term frame
     * @return the OWL class expression
     */
    public OWLClassExpression trTermFrame(Frame termFrame) {
        OWLClass cls = trClass(checkNotNull(termFrame.getId()));
        add(fac.getOWLDeclarationAxiom(cls));
        termFrame.getTags().stream().filter(OboFormatTag.TAG_ALT_ID.getTag()::equals).forEach(t ->
        // Generate deprecated and replaced_by details for alternate
        // identifier
        add(translateAltIds(termFrame.getClauses(t), cls.getIRI(), true)));
        termFrame.getTags().forEach(t -> add(trTermFrameClauses(cls, termFrame.getClauses(t), t)));
        return cls;
    }

    /**
     * Generate axioms for the alternate identifiers of an {@link OWLClass} or
     * {@link OWLObjectProperty}.
     *
     * @param clauses collection of alt_id clauses
     * @param replacedBy IRI of the entity
     * @param isClass set to true if the alt_id is represents a class, false in case of an property
     * @return set of axioms generated for the alt_id clauses
     */
    protected Set translateAltIds(Collection clauses, IRI replacedBy,
        boolean isClass) {
        Set axioms = new HashSet<>();
        for (Clause clause : clauses) {
            String altId = clause.getValue(String.class);
            OWLEntity altIdEntity;
            if (isClass) {
                altIdEntity = trClass(altId);
            } else {
                IRI altIdIRI = oboIdToIRI(altId);
                altIdEntity = fac.getOWLObjectProperty(altIdIRI);
            }
            // entity declaration axiom
            axioms.add(fac.getOWLDeclarationAxiom(altIdEntity));
            // annotate as deprecated
            axioms.add(fac.getOWLAnnotationAssertionAxiom(altIdEntity.getIRI(),
                fac.getOWLAnnotation(fac.getOWLDeprecated(), fac.getOWLLiteral(true))));
            // annotate with replaced_by (IAO_0100001)
            axioms.add(fac.getOWLAnnotationAssertionAxiom(altIdEntity.getIRI(),
                fac.getOWLAnnotation(
                    fac.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0100001.iri),
                    replacedBy)));
            // annotate with obo:IAO_0000231=obo:IAO_0000227
            // 'has obsolescence reason' 'terms merged'
            axioms.add(fac.getOWLAnnotationAssertionAxiom(altIdEntity.getIRI(),
                fac.getOWLAnnotation(fac.getOWLAnnotationProperty(Obo2OWLConstants.IRI_IAO_0000231),
                    Obo2OWLConstants.IRI_IAO_0000227)));
        }
        return axioms;
    }

    /**
     * Translate term frame clauses.
     *
     * @param cls the cls
     * @param clauses the clauses
     * @param t the t
     * @return the sets the
     */
    public Set trTermFrameClauses(OWLClass cls, Collection clauses, String t) {
        OboFormatTag tag = OBOFormatConstants.getTag(t);
        Set axioms = new HashSet<>();
        if (tag == OboFormatTag.TAG_INTERSECTION_OF) {
            axioms.add(trIntersectionOf(cls, clauses));
        } else if (tag == OboFormatTag.TAG_UNION_OF) {
            axioms.add(trUnionOf(cls, clauses));
        } else {
            clauses.forEach(c -> axioms.add(trTermClause(cls, t, c)));
        }
        return axioms;
    }

    /**
     * Translate typedef to annotation property.
     *
     * @param typedefFrame the typedef frame
     * @return the OWL named object
     */
    @Nullable
    protected OWLNamedObject trTypedefToAnnotationProperty(Frame typedefFrame) {
        Object tagValue = typedefFrame.getTagValue(OboFormatTag.TAG_IS_METADATA_TAG);
        if (Boolean.TRUE.equals(tagValue)) {
            String id = checkNotNull(typedefFrame.getId());
            OWLAnnotationProperty p = trAnnotationProp(id);
            add(fac.getOWLDeclarationAxiom(p));
            // handle xrefs also for meta data tags
            String xid = translateShorthandIdToExpandedId(id);
            if (!id.equals(xid)) {
                OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp("shorthand"),
                    p.getIRI(), trLiteral(id), new HashSet());
                add(ax);
            }
            typedefToAnnotationProperty.put(p.getIRI().toString(), p);
            for (String tag : typedefFrame.getTags()) {
                OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
                if (tagConstant == OboFormatTag.TAG_IS_A) {
                    // todo - subAnnotationProperty
                } else {
                    typedefFrame.getClauses(tag).forEach(c -> add(trGenericClause(p, tag, c)));
                }
            }
            return p;
        }
        return null;
    }

    /**
     * Translate typedef frame.
     *
     * @param typedefFrame the typedef frame
     * @return the OWL named object
     */
    @Nullable
    public OWLNamedObject trTypedefFrame(Frame typedefFrame) {
        // TODO - annotation props
        Object tagValue = typedefFrame.getTagValue(OboFormatTag.TAG_IS_METADATA_TAG);
        if (Boolean.TRUE.equals(tagValue)) {
            // already handled
            // see: trTypedefToAnnotationProperty(Frame typedefFrame)
            return null;
        } else {
            String id = checkNotNull(typedefFrame.getId());
            OWLObjectProperty p = trObjectProp(id);
            add(fac.getOWLDeclarationAxiom(p));
            String xid = translateShorthandIdToExpandedId(id);
            if (!xid.equals(id)) {
                OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp("shorthand"),
                    p.getIRI(), trLiteral(id), new HashSet());
                add(ax);
            }
            // TODO See 5.9.3 Special Rules for Relations
            for (String tag : typedefFrame.getTags()) {
                Collection clauses = typedefFrame.getClauses(tag);
                OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
                if (tagConstant == OboFormatTag.TAG_INTERSECTION_OF) {
                    OWLAxiom axiom = trRelationIntersectionOf(id, p, clauses);
                    if (axiom != null) {
                        add(axiom);
                    }
                } else if (tagConstant == OboFormatTag.TAG_UNION_OF) {
                    OWLAxiom axiom = trRelationUnionOf(id, p, clauses);
                    if (axiom != null) {
                        add(axiom);
                    }
                } else if (tagConstant == OboFormatTag.TAG_ALT_ID) {
                    add(translateAltIds(clauses, p.getIRI(), false));
                } else {
                    clauses.forEach(c -> add(trTypedefClause(p, tag, c)));
                }
            }
            return p;
        }
    }

    /**
     * Translate union of.
     *
     * @param cls the cls
     * @param clauses the clauses
     * @return the OWL axiom
     */
    protected OWLAxiom trUnionOf(OWLClass cls, Collection clauses) {
        Set annotations = trAnnotations(clauses);
        Set eSet = new HashSet<>();
        eSet.add(cls);
        Set iSet = new HashSet<>();
        for (Clause clause : clauses) {
            Collection qvs = clause.getQualifierValues();
            // TODO - quals
            if (clause.getValues().size() == 1) {
                iSet.add(trClass(clause.getValue()));
            } else {
                LOG.error("union_of n-ary slots not is standard - converting anyway");
                iSet.add(trRel((String) clause.getValue(), (String) clause.getValue2(), qvs));
            }
        }
        eSet.add(fac.getOWLObjectUnionOf(iSet));
        // TODO - fix this
        if (annotations.isEmpty()) {
            return fac.getOWLEquivalentClassesAxiom(eSet);
        } else {
            return fac.getOWLEquivalentClassesAxiom(eSet, annotations);
        }
    }

    /**
     * Translate intersection of.
     *
     * @param cls the cls
     * @param clauses the clauses
     * @return the OWL axiom
     */
    protected OWLAxiom trIntersectionOf(OWLClass cls, Collection clauses) {
        Set annotations = trAnnotations(clauses);
        Set eSet = new HashSet<>();
        eSet.add(cls);
        Set iSet = new HashSet<>();
        for (Clause clause : clauses) {
            Collection qvs = clause.getQualifierValues();
            if (clause.getValues().size() == 1) {
                iSet.add(trClass(clause.getValue()));
            } else {
                iSet.add(trRel((String) clause.getValue(), (String) clause.getValue2(), qvs));
            }
        }
        eSet.add(fac.getOWLObjectIntersectionOf(iSet));
        // TODO - fix this
        if (annotations.isEmpty()) {
            return fac.getOWLEquivalentClassesAxiom(eSet);
        } else {
            return fac.getOWLEquivalentClassesAxiom(eSet, annotations);
        }
    }

    // no data properties in obo

    /**
     * @param axiom the axiom to add
     */
    protected void add(@Nullable OWLAxiom axiom) {
        if (axiom == null) {
            LOG.error("no axiom");
            return;
        }
        add(Collections.singleton(axiom));
    }

    /**
     * @param axioms the axioms to add
     */
    protected void add(@Nullable Set axioms) {
        if (axioms == null || axioms.isEmpty()) {
            LOG.error("no axiom");
            return;
        }
        getOwlOntology().add(axioms);
    }

    /**
     * Apply the change.
     *
     * @param change the change
     */
    protected void apply(OWLOntologyChange change) {
        apply(CollectionFactory.list(change));
    }

    /**
     * Apply the changes.
     *
     * @param changes the changes
     */
    protected void apply(List changes) {
        try {
            manager.applyChanges(changes);
        } catch (Exception e) {
            LOG.error("COULD NOT TRANSLATE AXIOM", e);
        }
    }

    /**
     * #5.2
     *
     * @param cls the cls
     * @param tag the tag
     * @param clause the clause
     * @return axiom
     */
    @Nullable
    protected OWLAxiom trTermClause(OWLClass cls, String tag, Clause clause) {
        Collection qvs = clause.getQualifierValues();
        Set annotations = trAnnotations(clause);
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        // 5.2.2
        // The gci_relation qualifier translate cls to a class expression
        OWLClassExpression clsx = cls;
        String gciRel = getQVString("gci_relation", qvs);
        String gciFiller = getQVString("gci_filler", qvs);
        if (!gciRel.isEmpty() && !gciFiller.isEmpty()) {
            OWLClassExpression r = trRel(gciRel, gciFiller, Collections.emptySet());
            clsx = fac.getOWLObjectIntersectionOf(cls, r);
        }
        OWLAxiom ax;
        if (tagConstant == OboFormatTag.TAG_IS_A) {
            ax = fac.getOWLSubClassOfAxiom(clsx, trClass((String) clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_RELATIONSHIP) {
            // TODO
            IRI relId = oboIdToIRI((String) clause.getValue());
            OWLAnnotationProperty prop = typedefToAnnotationProperty.get(relId.toString());
            if (prop != null) {
                ax = fac.getOWLAnnotationAssertionAxiom(prop, cls.getIRI(),
                    oboIdToIRI((String) clause.getValue2()), annotations);
            } else {
                ax = fac.getOWLSubClassOfAxiom(clsx,
                    trRel((String) clause.getValue(), (String) clause.getValue2(), qvs),
                    annotations);
            }
        } else if (tagConstant == OboFormatTag.TAG_DISJOINT_FROM) {
            Set cSet = new HashSet<>();
            cSet.add(clsx);
            cSet.add(trClass((String) clause.getValue()));
            ax = fac.getOWLDisjointClassesAxiom(cSet, annotations);
        } else if (tagConstant == OboFormatTag.TAG_EQUIVALENT_TO) {
            Set cSet = new HashSet<>();
            cSet.add(clsx);
            cSet.add(trClass((String) clause.getValue()));
            ax = fac.getOWLEquivalentClassesAxiom(cSet, annotations);
        } else {
            return trGenericClause(cls, tag, clause);
        }
        return ax;
    }

    /**
     * Translate typedef clause.
     *
     * @param p the p
     * @param tag the tag
     * @param clause the clause
     * @return the OWL axiom
     */
    @Nullable
    protected OWLAxiom trTypedefClause(OWLObjectProperty p, String tag, Clause clause) {
        OWLAxiom ax = null;
        Object v = clause.getValue();
        assert v != null;
        Set annotations = trAnnotations(clause);
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        if (tagConstant == OboFormatTag.TAG_IS_A) {
            ax = fac.getOWLSubObjectPropertyOfAxiom(p, trObjectProp((String) v), annotations);
        } else if (tagConstant == OboFormatTag.TAG_RELATIONSHIP) {
            IRI relId = oboIdToIRI((String) v);
            OWLAnnotationProperty metaProp = typedefToAnnotationProperty.get(relId.toString());
            if (metaProp != null) {
                ax = fac.getOWLAnnotationAssertionAxiom(metaProp, p.getIRI(),
                    oboIdToIRI((String) clause.getValue2()), annotations);
            }
        } else if (tagConstant == OboFormatTag.TAG_DISJOINT_FROM) {
            Set cSet = new HashSet<>();
            cSet.add(p);
            cSet.add(trObjectProp((String) v));
            ax = fac.getOWLDisjointObjectPropertiesAxiom(cSet, annotations);
        } else if (tagConstant == OboFormatTag.TAG_INVERSE_OF) {
            ax = fac.getOWLInverseObjectPropertiesAxiom(p, trObjectProp((String) v), annotations);
        } else if (tagConstant == OboFormatTag.TAG_EQUIVALENT_TO) {
            Set cSet = new HashSet<>();
            cSet.add(p);
            cSet.add(trObjectProp((String) v));
            ax = fac.getOWLEquivalentObjectPropertiesAxiom(cSet, annotations);
        } else if (tagConstant == OboFormatTag.TAG_DOMAIN) {
            ax = fac.getOWLObjectPropertyDomainAxiom(p, trClass(v), annotations);
        } else if (tagConstant == OboFormatTag.TAG_RANGE) {
            ax = fac.getOWLObjectPropertyRangeAxiom(p, trClass(v), annotations);
        } else if (tagConstant == OboFormatTag.TAG_TRANSITIVE_OVER) {
            List chain = new ArrayList<>(2);
            chain.add(p);
            chain.add(trObjectProp(v));
            ax = fac.getOWLSubPropertyChainOfAxiom(chain, p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_HOLDS_OVER_CHAIN
            || tagConstant == OboFormatTag.TAG_EQUIVALENT_TO_CHAIN) {
            if (tagConstant == OboFormatTag.TAG_EQUIVALENT_TO_CHAIN) {
                OWLAnnotation ann = fac.getOWLAnnotation(
                    trAnnotationProp(IRI_PROP_ISREVERSIBLEPROPERTYCHAIN), trLiteral(TRUE));
                annotations.add(ann);
            }
            List chain = new ArrayList<>();
            chain.add(trObjectProp(v));
            chain.add(trObjectProp(clause.getValue2()));
            ax = fac.getOWLSubPropertyChainOfAxiom(chain, p, annotations);
            // TODO - annotations for equivalent to
        } else if (tagConstant == OboFormatTag.TAG_IS_TRANSITIVE
            && TRUE.equals(clause.getValue().toString())) {
            ax = fac.getOWLTransitiveObjectPropertyAxiom(p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_IS_REFLEXIVE
            && TRUE.equals(clause.getValue().toString())) {
            ax = fac.getOWLReflexiveObjectPropertyAxiom(p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_IS_SYMMETRIC
            && TRUE.equals(clause.getValue().toString())) {
            ax = fac.getOWLSymmetricObjectPropertyAxiom(p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_IS_ASYMMETRIC
            && TRUE.equals(clause.getValue().toString())) {
            ax = fac.getOWLAsymmetricObjectPropertyAxiom(p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_IS_FUNCTIONAL
            && TRUE.equals(clause.getValue().toString())) {
            ax = fac.getOWLFunctionalObjectPropertyAxiom(p, annotations);
        } else if (tagConstant == OboFormatTag.TAG_IS_INVERSE_FUNCTIONAL
            && TRUE.equals(clause.getValue().toString())) {
            ax = fac.getOWLInverseFunctionalObjectPropertyAxiom(p, annotations);
        } else {
            return trGenericClause(p, tag, clause);
        }
        // TODO - disjointOver
        return ax;
    }

    /**
     * Translate generic clause.
     *
     * @param e the e
     * @param tag the tag
     * @param clause the clause
     * @return the OWL axiom
     */
    @Nullable
    protected OWLAxiom trGenericClause(OWLNamedObject e, String tag, Clause clause) {
        return trGenericClause(e.getIRI(), tag, clause);
    }

    /**
     * Translate generic clause.
     *
     * @param sub the sub
     * @param tag the tag
     * @param clause the clause
     * @return the OWL axiom
     */
    @Nullable
    protected OWLAxiom trGenericClause(OWLAnnotationSubject sub, String tag, Clause clause) {
        Set annotations = trAnnotations(clause);
        OWLAxiom ax = null;
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        if (tagConstant == OboFormatTag.TAG_NAME) {
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
                trLiteral(clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_DEF) {
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
                trLiteral(clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_SUBSET) {
            String v = clause.getValue(String.class);
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
                trAnnotationProp(v).getIRI(), annotations);
        } else if (tagConstant == OboFormatTag.TAG_PROPERTY_VALUE) {
            Collection values = clause.getValues();
            Object v = clause.getValue();
            Object v2 = clause.getValue2();
            if (values.size() == 2) {
                // property_value(Rel-ID Entity-ID Qualifiers)
                ax = fac.getOWLAnnotationAssertionAxiom(trAnnotationProp((String) v), sub,
                    trAnnotationProp(v2.toString()).getIRI(), annotations);
            } else if (values.size() == 3) {
                // property_value(Rel-ID Value XSD-Type Qualifiers)
                Iterator it = clause.getValues().iterator();
                it.next();
                it.next();
                String v3String = (String) it.next();
                IRI valueIRI;
                if (v3String.startsWith("xsd:")) {
                    valueIRI = IRI.create(Namespaces.XSD.getPrefixIRI(), v3String.substring(4));
                } else {
                    valueIRI = IRI.create(v3String);
                }
                OWLAnnotationValue value =
                    fac.getOWLLiteral((String) v2, OWL2Datatype.getDatatype(valueIRI));
                ax = fac.getOWLAnnotationAssertionAxiom(trAnnotationProp((String) v), sub, value,
                    annotations);
            } else {
                LOG.error("Cannot translate: {}", clause);
                // TODO
            }
        } else if (tagConstant == OboFormatTag.TAG_SYNONYM) {
            Object[] values = clause.getValues().toArray();
            String synType;
            if (values.length > 1) {
                synType = values[1].toString();
                if (values.length > 2) {
                    OWLAnnotation ann = fac.getOWLAnnotation(
                        trTagToAnnotationProp(OboFormatTag.TAG_HAS_SYNONYM_TYPE.getTag()),
                        trAnnotationProp(values[2].toString()).getIRI());
                    annotations.add(ann);
                }
            } else {
                LOG.warn("Assume 'RELATED'for missing scope in synonym clause: {}", clause);
                // we make allowances for obof1.0, where the synonym scope is
                // optional
                synType = OboFormatTag.TAG_RELATED.getTag();
            }
            ax = fac.getOWLAnnotationAssertionAxiom(trSynonymType(synType), sub,
                trLiteral(clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_XREF) {
            Xref xref = (Xref) clause.getValue();
            String xrefAnnotation = xref.getAnnotation();
            if (xrefAnnotation != null) {
                annotations.add(fac.getRDFSLabel(xrefAnnotation));
            }
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
                trLiteral(clause.getValue()), annotations);
        } else {
            // generic
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
                trLiteral(clause.getValue()), annotations);
        }
        return ax;
    }

    /**
     * Translate synonym type.
     *
     * @param type the type
     * @return the OWL annotation property
     */
    protected OWLAnnotationProperty trSynonymType(String type) {
        if (type.equals(OboFormatTag.TAG_RELATED.getTag())
            || type.equals(OboFormatTag.TAG_EXACT.getTag())
            || type.equals(OboFormatTag.TAG_NARROW.getTag())
            || type.equals(OboFormatTag.TAG_BROAD.getTag())) {
            return trTagToAnnotationProp(type);
        }
        return trAnnotationProp(type);
    }

    /**
     * Translate annotations.
     *
     * @param clause the clause
     * @return the sets the
     */
    protected Set trAnnotations(Clause clause) {
        if (clause.hasNoAnnotations()) {
            return CollectionFactory.createSet();
        }
        Set anns = new HashSet<>();
        trAnnotations(clause, anns);
        return anns;
    }

    /**
     * Translate annotations.
     *
     * @param clause the clause
     * @param anns the anns
     */
    protected void trAnnotations(Clause clause, Set anns) {
        Collection xrefs = clause.getXrefs();
        for (Xref x : xrefs) {
            if (!x.getIdref().isEmpty()) {
                OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_XREF.getTag());
                OWLAnnotation ann = fac.getOWLAnnotation(ap, trLiteral(x));
                anns.add(ann);
            }
        }
        Collection qvs = clause.getQualifierValues();
        for (QualifierValue qv : qvs) {
            String qTag = qv.getQualifier();
            if (SKIPPED_QUALIFIERS.contains(qTag)) {
                continue;
            }
            OWLAnnotationProperty ap = trTagToAnnotationProp(qTag);
            OWLAnnotation ann = fac.getOWLAnnotation(ap, trLiteral(qv.getValue()));
            anns.add(ann);
        }
    }

    /**
     * Translate annotations.
     *
     * @param clauses the clauses
     * @return the set of annotations
     */
    protected Set trAnnotations(Collection clauses) {
        Set anns = new HashSet<>();
        clauses.forEach(c -> trAnnotations(c, anns));
        return anns;
    }

    /**
     * Translate rel.
     *
     * @param relId the rel id
     * @param classId the class id
     * @param quals the quals
     * @return the OWL class expression
     */
    public OWLClassExpression trRel(String relId, String classId,
        Collection quals) {
        Frame relFrame = obodoc.getTypedefFrame(relId);
        OWLObjectPropertyExpression pe = trObjectProp(relId);
        OWLClassExpression ce = trClass(classId);
        Integer exact = getQVInt("cardinality", quals);
        Integer min = getQVInt("minCardinality", quals);
        Integer max = getQVInt("maxCardinality", quals);
        boolean allSome = getQVBoolean("all_some", quals);
        boolean allOnly = getQVBoolean("all_only", quals);
        // obo-format allows dangling references to classes in class
        // expressions.
        // Create an explicit class declaration to be sure
        if (ce instanceof OWLClass) {
            add(fac.getOWLDeclarationAxiom((OWLClass) ce));
        }
        OWLClassExpression ex;
        if (exact != null && exact.intValue() > 0) {
            ex = fac.getOWLObjectExactCardinality(exact.intValue(), pe, ce);
        } else if (exact != null && exact.intValue() == 0 || max != null && max.intValue() == 0) {
            OWLObjectComplementOf ceCompl = fac.getOWLObjectComplementOf(ce);
            ex = fac.getOWLObjectAllValuesFrom(pe, ceCompl);
        } else if (max != null && min != null) {
            ex = fac.getOWLObjectIntersectionOf(
                fac.getOWLObjectMinCardinality(min.intValue(), pe, ce),
                fac.getOWLObjectMaxCardinality(max.intValue(), pe, ce));
        } else if (min != null) {
            ex = fac.getOWLObjectMinCardinality(min.intValue(), pe, ce);
        } else if (max != null) {
            ex = fac.getOWLObjectMaxCardinality(max.intValue(), pe, ce);
        } else if (allSome && allOnly) {
            ex = fac.getOWLObjectIntersectionOf(fac.getOWLObjectSomeValuesFrom(pe, ce),
                fac.getOWLObjectAllValuesFrom(pe, ce));
        } else if (allOnly) {
            ex = fac.getOWLObjectAllValuesFrom(pe, ce);
        } else if (relFrame != null
            && Boolean.TRUE.equals(relFrame.getTagValue(OboFormatTag.TAG_IS_CLASS_LEVEL_TAG))) {
            // pun
            ex = fac.getOWLObjectHasValue(pe, trIndividual(classId));
        } else {
            // default
            ex = fac.getOWLObjectSomeValuesFrom(pe, ce);
        }
        return ex;
    }

    /**
     * Translate class.
     *
     * @param classId the class id
     * @return the OWL class
     */
    protected OWLClass trClass(String classId) {
        return fac.getOWLClass(oboIdToIRI(classId));
    }

    /**
     * Translate class.
     *
     * @param v the v
     * @return the OWL class expression
     */
    protected OWLClassExpression trClass(Object v) {
        return trClass((String) v);
    }

    /**
     * See section "header macros" and treat-xrefs-as-equivalent.
     *
     * @param id the id
     * @return mapped id
     */
    protected String mapPropId(String id) {
        Frame f = obodoc.getTypedefFrame(id);
        if (f != null) {
            Collection xrefs = f.getTagValues(OboFormatTag.TAG_XREF, Xref.class);
            for (Xref x : xrefs) {
                String xid = x.getIdref();
                if (OBODoc.isTreatXrefsAsEquivalent(getIdPrefix(xid))) {
                    return xid;
                }
            }
        }
        return id;
    }

    /**
     * Translate individual.
     *
     * @param instId the individual id
     * @return the OWL individual
     */
    protected OWLIndividual trIndividual(String instId) {
        IRI iri = oboIdToIRI(instId);
        return fac.getOWLNamedIndividual(iri);
    }

    private IRI trTagToIRIIncludingTypedefs(String tag) {
        IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
        if (iri == null) {
            iri = oboIdToIRI(tag, true);
        }
        return iri;
    }

    /**
     * Translate tag to annotation prop.
     * 
     * @param tag the tag
     * @return the OWL annotation property
     */
    protected OWLAnnotationProperty trTagToAnnotationProp(String tag) {
        IRI iri = trTagToIRIIncludingTypedefs(tag);
        OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri);
        if (!apToDeclare.contains(ap)) {
            apToDeclare.add(ap);
            add(fac.getOWLDeclarationAxiom(ap));
            Obo2OWLVocabulary vocab = Obo2OWLConstants.getVocabularyObj(tag);
            if (vocab != null) {
                add(fac.getOWLAnnotationAssertionAxiom(iri, fac.getRDFSLabel(trLiteral(vocab.getLabel()))));
            }
        }
        return ap;
    }

    /**
     * Adds the declared annotation properties.
     *
     * @param declaredProperties the declared properties
     */
    protected void addDeclaredAnnotationProperties(
        @Nullable Collection declaredProperties) {
        if (declaredProperties != null) {
            apToDeclare.addAll(declaredProperties);
        }
    }

    /**
     * Translate annotation prop.
     *
     * @param relId the rel id
     * @return the OWL annotation property
     */
    protected OWLAnnotationProperty trAnnotationProp(String relId) {
        return fac.getOWLAnnotationProperty(oboIdToIRI(mapPropId(relId)));
    }

    /**
     * Translate object prop.
     *
     * @param relId the rel id
     * @return the OWL object property
     */
    protected OWLObjectProperty trObjectProp(String relId) {
        return fac.getOWLObjectProperty(oboIdToIRI(mapPropId(relId)));
    }

    /**
     * Translate object prop.
     *
     * @param v the v
     * @return the OWL object property expression
     */
    protected OWLObjectPropertyExpression trObjectProp(Object v) {
        return trObjectProp((String) v);
    }

    /**
     * Translate literal.
     *
     * @param inputValue the value
     * @return the OWL annotation value
     */
    protected OWLAnnotationValue trLiteral(Object inputValue) {
        Object value = inputValue;
        if (value instanceof Xref) {
            value = ((Xref) value).getIdref();
        } else if (value instanceof Date) {
            // use proper OWL2 data type, write lexical value as ISO 8601 date
            // string
            String lexicalValue = OBOFormatConstants.headerDateFormat().format((Date) value);
            return fac.getOWLLiteral(lexicalValue, OWL2Datatype.XSD_DATE_TIME);
        } else if (value instanceof Boolean) {
            return fac.getOWLLiteral(((Boolean) value).booleanValue());
        } else if (!(value instanceof String)) {
            // TODO
            // e.g. boolean
            value = value.toString();
        }
        String value2 = (String) value;
        // TODO
        return fac.getOWLLiteral(value2);
    }

    /**
     * Obo id to iri.
     *
     * @param id the id
     * @return the iri
     */
    public IRI oboIdToIRI(String id) {
    	return oboIdToIRI(id, false);
    }

    /**
     * Obo id to iri.
     *
     * @param id the id
     * @return the iri
     */
    public IRI oboIdToIRI(String id, boolean oboInOwlDefault) {
        IRI iri = idToIRICache.get(id);
        if (iri == null) {
            iri = loadOboToIRI(id, oboInOwlDefault);
            idToIRICache.put(id, iri);
        }
        return iri;
    }

    /**
     * Obo id to iri.
     *
     * @param id the id
     * @return the iri
     */
    public IRI loadOboToIRI(String id) {
    	return loadOboToIRI(id, false);
    }

    /**
     * Obo id to iri.
     *
     * @param id the id
     * @return the iri
     */
    public IRI loadOboToIRI(String id, boolean oboInOwlDefault) {
        if (id.contains(" ")) {
            LOG.error("id contains space: \"{}\"", id);
            throw new OWLParserException("spaces not allowed: '" + id + '\'');
        }
        // No conversion is required if this is already an IRI (ID-as-URI rule)
        if (id.startsWith("http:")) {
            // TODO - roundtrip from other schemes
            return IRI.create(id);
        } else if (id.startsWith("https:")) {
            // TODO - roundtrip from other schemes
            return IRI.create(id);
        } else if (id.startsWith("ftp:")) {
            // TODO - roundtrip from other schemes
            return IRI.create(id);
        } else if (id.startsWith("urn:")) {
            // TODO - roundtrip from other schemes
            return IRI.create(id);
        } else if (id.startsWith("owl:") || id.startsWith("xsd:") || id.startsWith("rdf:")
            || id.startsWith("rdfs:")) {
            for (OWL2Datatype d : OWL2Datatype.values()) {
                if (d.getPrefixedName().equals(id)) {
                    return d.getIRI();
                }
            }
            for (OWLRDFVocabulary d : OWLRDFVocabulary.values()) {
                if (d.getPrefixedName().equals(id)) {
                    return d.getIRI();
                }
            }
            for (OWLXMLVocabulary d : OWLXMLVocabulary.values()) {
                if (d.getPrefixedName().equals(id)) {
                    return d.getIRI();
                }
            }
        }

        String[] idParts = id.split(":", 2);
        String uriPrefix;
        String localId;
        if (idParts.length > 1) { // Prefixed-ID (canonical or not)
            localId = idParts[1];
            uriPrefix = idSpaceMap.getOrDefault(idParts[0], DEFAULT_IRI_PREFIX + idParts[0] + '_');

            // Non-canonical prefixed IDs use a '#' separator
            // TODO - recognize all non-canonical prefixed IDs
            if (localId.contains("_")) {
                uriPrefix += "#";
            }
        } else { // Unprefixed-ID
            // Special case for relation xrefs (5.9.3. Special Rules for Relations)
            String xid = translateShorthandIdToExpandedId(id);
            if (!xid.equals(id)) {
                return oboIdToIRI(xid);
            }

            localId = id;
            if (oboInOwlDefault) {
                uriPrefix = OIOVOCAB_IRI_PREFIX;
            } else {
                // TODO - use ontology ID as specified in OBO-Format 5.9.2?
                uriPrefix = DEFAULT_IRI_PREFIX + getDefaultIDSpace() + '#';
            }
        }

        String safeId;
        try {
            safeId = java.net.URLEncoder.encode(localId, "US-ASCII");
        } catch (UnsupportedEncodingException e1) {
            throw new OWLRuntimeException(e1);
        }
        if (safeId.contains(" ")) {
            safeId = safeId.replace(" ", "_");
        }
        IRI iri = null;
        try {
            iri = IRI.create(uriPrefix + safeId);
        } catch (IllegalArgumentException e) {
            throw new OWLRuntimeException(e);
        }
        return iri;
    }

    // 5.9.3. Special Rules for Relations
    /**
     * Translate shorthand id to expanded id.
     * 
     * @param id the id
     * @return the string
     */
    protected String translateShorthandIdToExpandedId(String id) {
        if (id.contains(":")) {
            return id;
        }
        Frame tdf = obodoc.getTypedefFrame(id);
        if (tdf == null) {
            return id;
        }
        Collection xrefs = tdf.getTagValues(OboFormatTag.TAG_XREF, Xref.class);
        String matchingExpandedId = null;
        for (Xref xref : xrefs) {
            matchingExpandedId = handleXref(id, matchingExpandedId, xref);
        }
        if (matchingExpandedId == null) {
            return id;
        }
        return matchingExpandedId;
    }

    @Nullable
    protected String handleXref(String id, @Nullable String matchingExpandedId,
        @Nullable Xref xref) {
        if (xref != null) {
            String xid = xref.getIdref();
            if (xid.equals(id)) {
                return matchingExpandedId;
            }
            if (matchingExpandedId == null) {
                return xid;
            }
            // RO and BFO take precedence over others
            if (xid.startsWith("RO") || xid.startsWith("BFO")) {
                return xid;
            }
        }
        return matchingExpandedId;
    }

    /**
     * Gets the default id space.
     *
     * @return the default id space
     */
    protected String getDefaultIDSpace() {
        return defaultIDSpace;
    }
}
    

    

    

            

    

            



    
    






    
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