io.leishvl.core.xml.PubMedXmlBinder.java Source code

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Here is the source code for io.leishvl.core.xml.PubMedXmlBinder.java

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/*
 * Copyright 2014-2015 EUBrazilCC (EU?Brazil Cloud Connect)
 * 
 * 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.
 *
 * This product combines work with different licenses. See the "NOTICE" text
 * file for details on the various modules and licenses.
 *
 * The "NOTICE" text file is part of the distribution. Any derivative works
 * that you distribute must include a readable copy of the "NOTICE" text file.
 */

package io.leishvl.core.xml;

import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkState;
import static com.google.common.collect.Lists.newArrayList;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

import java.util.List;

import javax.annotation.Nullable;
import javax.xml.bind.JAXBElement;

import io.leishvl.core.ncbi.pubmed.ObjectFactory;
import io.leishvl.core.ncbi.pubmed.PubmedArticle;
import io.leishvl.core.ncbi.pubmed.PubmedArticleSet;
import io.leishvl.core.ncbi.pubmed.Year;

/**
 * NCBI PubMed article XML binding helper.
 * @author Erik Torres <ertorser@upv.es>
 */
public class PubMedXmlBinder extends XmlBinder {

    private static final Class<?>[] SUPPORTED_CLASSES = { PubmedArticleSet.class, PubmedArticle.class };

    public static final ObjectFactory PUBMED_XML_FACTORY = new ObjectFactory();

    public static final PubMedXmlBinder PUBMED_XMLB = new PubMedXmlBinder();

    private PubMedXmlBinder() {
        super(SUPPORTED_CLASSES);
    }

    @Override
    @SuppressWarnings("unchecked")
    protected <T> JAXBElement<T> createType(final T obj) {
        Object element;
        Class<?> clazz = obj.getClass();
        if (clazz.equals(PubmedArticleSet.class)) {
            element = PUBMED_XML_FACTORY.createPubmedArticleSet();
        } else if (clazz.equals(PubmedArticle.class)) {
            element = PUBMED_XML_FACTORY.createPubmedArticle();
        } else {
            throw new IllegalArgumentException("Unsupported type: " + clazz.getCanonicalName());
        }
        return (JAXBElement<T>) element;
    }

    /**
     * Gets the PubMed identifier (PMID) from a PubMed article.
     * @param article - PubMed article
     * @return if found, the PubMed identifier (PMID), otherwise {@code null}.
     */
    public static @Nullable String getPubMedId(final PubmedArticle article) {
        checkArgument(article != null && article.getMedlineCitation() != null
                && article.getMedlineCitation().getPMID() != null, "Uninitialized or invalid article.");
        return isNotBlank(article.getMedlineCitation().getPMID().getvalue())
                ? article.getMedlineCitation().getPMID().getvalue().trim()
                : null;
    }

    public static int getYear(final PubmedArticle article) {
        checkArgument(
                article != null && article.getMedlineCitation() != null
                        && article.getMedlineCitation().getArticle() != null
                        && article.getMedlineCitation().getArticle().getJournal() != null
                        && article.getMedlineCitation().getArticle().getJournal().getJournalIssue() != null
                        && article.getMedlineCitation().getArticle().getJournal().getJournalIssue()
                                .getPubDate() != null
                        && article.getMedlineCitation().getArticle().getJournal().getJournalIssue().getPubDate()
                                .getYearOrMonthOrDayOrSeasonOrMedlineDate() != null
                        && !article.getMedlineCitation().getArticle().getJournal().getJournalIssue().getPubDate()
                                .getYearOrMonthOrDayOrSeasonOrMedlineDate().isEmpty(),
                "Uninitialized or invalid article");
        int year = -1;
        final List<Object> pubDate = article.getMedlineCitation().getArticle().getJournal().getJournalIssue()
                .getPubDate().getYearOrMonthOrDayOrSeasonOrMedlineDate();
        for (final Object obj : pubDate) {
            if (obj instanceof Year) {
                year = Integer.valueOf(((Year) obj).getvalue());
            }
        }
        checkState(year > 1900, "No valid year found");
        return year;
    }

    public static List<String> getSequences(final PubmedArticle article) {
        final List<String> sequences = newArrayList();
        checkArgument(article != null && article.getMedlineCitation() != null
                && article.getMedlineCitation().getArticle() != null, "Uninitialized or invalid article");
        if (article.getMedlineCitation().getArticle().getDataBankList() != null
                && article.getMedlineCitation().getArticle().getDataBankList().getDataBank() != null) {
            article.getMedlineCitation().getArticle().getDataBankList().getDataBank().forEach(db -> {
                if (db != null && "GENBANK".equalsIgnoreCase(db.getDataBankName())
                        && db.getAccessionNumberList() != null
                        && db.getAccessionNumberList().getAccessionNumber() != null) {
                    db.getAccessionNumberList().getAccessionNumber().forEach(an -> {
                        if (isNotBlank(an.getvalue())) {
                            sequences.add(an.getvalue().trim());
                        }
                    });
                }
            });
        }
        return sequences;
    }

}