ubic.gemma.loader.entrez.pubmed.PubMedXMLFetcher.java Source code

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Here is the source code for ubic.gemma.loader.entrez.pubmed.PubMedXMLFetcher.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2006 University of British Columbia
 * 
 * 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 ubic.gemma.loader.entrez.pubmed;

import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Collection;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import ubic.gemma.model.common.description.BibliographicReference;
import ubic.gemma.util.ConfigUtils;

/**
 * Class that can retrieve pubmed records (in XML format) via HTTP. The url used is configured via a resource.
 * 
 * @author pavlidis
 * @version $Id: PubMedXMLFetcher.java,v 1.10 2011/10/20 15:51:42 paul Exp $
 */
public class PubMedXMLFetcher {

    protected static final Log log = LogFactory.getLog(PubMedXMLFetcher.class);
    private String uri;

    private final static int MAX_TRIES = 2;

    public PubMedXMLFetcher() {
        String baseURL = ConfigUtils.getString("entrez.efetch.baseurl");
        String db = ConfigUtils.getString("entrez.efetch.pubmed.db");
        String idtag = ConfigUtils.getString("entrez.efetch.pubmed.idtag");
        String retmode = ConfigUtils.getString("entrez.efetch.pubmed.retmode");
        String rettype = ConfigUtils.getString("entrez.efetch.pubmed.rettype");
        uri = baseURL + "&" + db + "&" + retmode + "&" + rettype + "&" + idtag;
    }

    /**
     * For collection of integer pubmed ids.
     * 
     * @param pubMedIds
     * @return Collection<BibliographicReference>
     * @throws IOException
     */
    public Collection<BibliographicReference> retrieveByHTTP(Collection<Integer> pubMedIds) throws IOException {
        StringBuilder buf = new StringBuilder();
        for (Integer integer : pubMedIds) {
            buf.append(integer + ",");
        }
        URL toBeGotten = new URL(uri + StringUtils.chomp(buf.toString()));
        log.debug("Fetching " + toBeGotten);
        PubMedXMLParser pmxp = new PubMedXMLParser();
        return pmxp.parse(toBeGotten.openStream());
    }

    /**
     * For an integer pubmed id
     * 
     * @param pubMedId
     * @return BibliographicReference for the id given.
     */
    public BibliographicReference retrieveByHTTP(int pubMedId) {
        Collection<BibliographicReference> results = null;
        try {
            for (int i = 0; i < MAX_TRIES; i++) {
                URL toBeGotten = new URL(uri + pubMedId);
                log.debug("Fetching " + toBeGotten);
                PubMedXMLParser pmxp = new PubMedXMLParser();
                results = pmxp.parse(toBeGotten.openStream());
                if (results != null && results.size() > 0)
                    break;
                try {
                    Thread.sleep(500);
                } catch (InterruptedException e) {
                    // noop
                }
            }
            if (results == null || results.size() == 0) {
                return null;
            }
            assert results.size() == 1;
            return results.iterator().next();
        } catch (MalformedURLException e) {
            throw new RuntimeException(e);
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
    }
}