io.scigraph.annotation.EntityRecognizer.java Source code

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Here is the source code for io.scigraph.annotation.EntityRecognizer.java

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/**
 * Copyright (C) 2014 The SciGraph authors
 *
 * 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 io.scigraph.annotation;

import static com.google.common.collect.Iterables.getFirst;
import static com.google.common.collect.Sets.newHashSet;
import static java.util.Collections.disjoint;
import io.scigraph.frames.Concept;
import io.scigraph.owlapi.curies.CurieUtil;
import io.scigraph.vocabulary.Vocabulary;
import io.scigraph.vocabulary.Vocabulary.Query;

import java.io.IOException;
import java.util.Collection;
import java.util.List;
import java.util.Set;

import javax.inject.Inject;

import com.google.common.base.Optional;

public class EntityRecognizer {

    private final Vocabulary vocabulary;
    private final CurieUtil curieUtil;

    @Inject
    EntityRecognizer(Vocabulary vocabulary, CurieUtil curieUtil) throws IOException {
        this.vocabulary = vocabulary;
        this.curieUtil = curieUtil;
    }

    public String getCssClass() {
        return "sciCrunchAnnotation";
    }

    boolean shouldAnnotate(Concept concept, EntityFormatConfiguration config) {
        Collection<String> conceptCategories = newHashSet(concept.getCategories());

        if (!disjoint(config.getExcludeCategories(), conceptCategories)) {
            return false;
        }
        if (!config.isIncludeNumbers() && getFirst(concept.getLabels(), "").matches("(\\d|\\-|_)+")) {
            return false;
        }

        if (!config.getIncludeCategories().isEmpty()
                && disjoint(config.getIncludeCategories(), conceptCategories)) {
            return false;
        }

        return true;
    }

    public Collection<Entity> getEntities(String token, EntityFormatConfiguration config) {
        Query query = new Vocabulary.Query.Builder(token).build();
        List<Concept> terms = vocabulary.getConceptsFromTerm(query);

        Set<Entity> entities = newHashSet();
        for (Concept term : terms) {
            if (shouldAnnotate(term, config)) {
                Optional<String> id = curieUtil.getCurie(term.getIri());
                entities.add(new Entity(term.getLabels(), id.or(term.getIri()), term.getCategories()));
            }
        }

        return entities;
    }

}