pt.ua.tm.neji.web.annotate.pubmed.Pubmed.java Source code

Introduction

Here is the source code for pt.ua.tm.neji.web.annotate.pubmed.Pubmed.java

Source

/*
 * Copyright (c) 2016 BMD Software and University of Aveiro.
 *
 * Neji is a flexible and powerful platform for biomedical information extraction from text.
 *
 * This project is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
 * To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
 *
 * This project is a free software, you are free to copy, distribute, change and transmit it.
 * However, you may not use it for commercial purposes.
 *
 * It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
 * without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 */

package pt.ua.tm.neji.web.annotate.pubmed;

import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.WebResource;
import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.StringUtils;

import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.UriBuilder;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.util.Arrays;
import java.util.Map;

/**
 * @author David Campos (<a href="mailto:david.campos@ua.pt">david.campos@ua.pt</a>)
 * @version 1.0
 * @since 1.0
 */
public class Pubmed {

    public static void main(String... args) {
        File outputFolder = new File(FilenameUtils.separatorsToSystem("/Users/david/Downloads/neji_ppi/in/"));

        //Map<String, Document> map = getCleanTextFromPM(new String[]{"11748933", "11700088", "15282350", "15282345"});
        Map<String, Document> map = getCleanTextFromPM(new String[] { "23142263", "23299379", "23430246",
                "23477989", "23536070", "23365075", "23400560", "23202730", "23576130", "23374228", "23118350",
                "23575824", "23172224", "23155407", "23152192", "23446677", "23481704", "23233058", "23138650",
                "23109154", "23161037", "23082203", "23372648", "23209315", "23211594", "23183882", "23286786",
                "23173713", "23467355", "23122958", "23092137", "23486975", "23236499", "23486882", "23289174",
                "23296102", "23173743", "23224319", "23314196", "23474306", "23650720", "23280791", "23100439",
                "23584199", "23595759", "23085935", "23114667", "23486963", "23109151", "23144955", "23364356",
                "23076628", "23552688", "23227576", "23109153", "23197725", "23155049", "23178565", "23365250",
                "23178660", "23276553", "23262393", "23184605", "23789343", "23420027", "23468550", "23642578",
                "23143229", "23149447", "23226438", "23386614", "23064434", "23368879", "23083210", "23071606",
                "23295908", "23276639", "23223301", "23152628", "23159938", "23403102", "23249765", "23383156",
                "23327526", "23656991", "23100049", "23284610", "23123349", "23097297", "23390179", "23142262",
                "23109807", "23238159", "23284867", "23479184", "23237352", "23370287", "23546882", "23115165",
                "23278858" });

        for (String pmid : map.keySet()) {
            File file = new File(outputFolder, pmid + ".txt");

            try {
                FileWriter fileWriter = new FileWriter(file);
                fileWriter.write(map.get(pmid).toString());
                fileWriter.close();
            } catch (IOException e) {
                System.err.println("ERROR: ");
                e.printStackTrace();
            }
        }

    }

    /**
     * @param pmids
     * @return
     */
    public static Map<String, Document> getCleanTextFromPM(final String[] pmids) {
        // Join PMCIDs
        String pmidsQuery = StringUtils.join(Arrays.asList(pmids), ',');

        // Build URL
        StringBuilder url = new StringBuilder(
                "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=");
        url.append(pmidsQuery);
        url.append("&retmode=xml");

        // Build URI
        URI uri = UriBuilder.fromUri(url.toString()).build();

        ClientConfig config = new DefaultClientConfig();
        Client client = Client.create(config);
        WebResource service = client.resource(uri);

        // Get input stream
        InputStream inputStream = service.accept(MediaType.APPLICATION_XML).get(InputStream.class);

        // Parse and return result
        return new PubmedXMLParser().parse(inputStream);
    }

    /**
     * @param pmid
     * @return
     */
    public static Document getCleanTextFromPM(final String pmid) {

        // Build URL
        StringBuilder url = new StringBuilder(
                "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=");
        url.append(pmid);
        url.append("&retmode=xml");

        // Build URI
        URI uri = UriBuilder.fromUri(url.toString()).build();

        ClientConfig config = new DefaultClientConfig();
        Client client = Client.create(config);
        WebResource service = client.resource(uri);

        // Get input stream
        InputStream inputStream = service.accept(MediaType.APPLICATION_XML).get(InputStream.class);

        // Parse and return result
        return new PubmedXMLParser().parse(inputStream).get(pmid);
    }
}