ClassAnnotationVisitor.java

/*
 * Copyright 2012 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package uk.ac.ebi.fg.annotare2.magetabcheck.efo;

import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.util.OWLObjectVisitorAdapter;

/**
 * @author Olga Melnichuk
 */
class ClassAnnotationVisitor extends OWLObjectVisitorAdapter {

    private enum Literal {
        LABEL {
            @Override
            public boolean matches(OWLAnnotationProperty property) {
                return property.isLabel();
            }

            @Override
            public void updateNode(String literal, EfoNodeImpl node) {
                node.setLabel(literal);
            }
        },
        DEFINITION {
            @Override
            public boolean matches(OWLAnnotationProperty property) {
                return "definition".equals(property.getIRI().getFragment());
            }

            @Override
            public void updateNode(String literal, EfoNodeImpl node) {
                node.setDefinition(literal);
            }
        },
        ORGANIZATIONAL_CLASS {
            @Override
            public boolean matches(OWLAnnotationProperty property) {
                return "organizational_class".equals(property.getIRI().getFragment());
            }

            @Override
            public void updateNode(String literal, EfoNodeImpl node) {
                node.setOrganizational(Boolean.valueOf(literal));
            }
        },
        ALTERNATIVE_TERM {
            @Override
            public boolean matches(OWLAnnotationProperty property) {
                return "alternative_term".equals(property.getIRI().getFragment())
                        || "definition_citation".equals(property.getIRI().getFragment());
            }

            @Override
            public void updateNode(String literal, EfoNodeImpl node) {
                node.addAlternativeTerm(preprocessAlternativeTermString(literal));
            }

            private String preprocessAlternativeTermString(String str) {
                return str == null ? null :
                        str.replaceAll("(\\[accessedResource:[^\\]]+\\])|(\\[accessDate:[^\\]]+\\])", "").trim();
            }
        };

        public abstract boolean matches(OWLAnnotationProperty property);

        public abstract void updateNode(String literal, EfoNodeImpl node);

        public static Literal find(OWLAnnotation annotation) {
            if (!(annotation.getValue() instanceof OWLLiteral)) {
                return null;
            }
            for (Literal lit : values()) {
                if (lit.matches(annotation.getProperty())) {
                    return lit;
                }
            }
            return null;
        }
    }

    private final EfoNodeImpl node;

    ClassAnnotationVisitor(String nodeId) {
        node = new EfoNodeImpl(nodeId);
    }

    @Override
    public void visit(OWLAnnotation annot) {
        Literal lit = Literal.find(annot);
        if (lit == null) {
            return;
        }

        lit.updateNode(((OWLLiteral) annot.getValue()).getLiteral(), node);
    }

    EfoNodeImpl getNode() {
        return node;
    }
}