org.intermine.bio.web.logic.LiftOverService.java Source code

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Here is the source code for org.intermine.bio.web.logic.LiftOverService.java

Source

package org.intermine.bio.web.logic;

/*
 * Copyright (C) 2002-2013 FlyMine
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  See the LICENSE file for more
 * information or http://www.gnu.org/copyleft/lesser.html.
 *
 */

import java.io.OutputStreamWriter;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.intermine.bio.web.model.GenomicRegion;
import org.intermine.bio.web.model.GenomicRegionSearchConstraint;
import org.json.JSONArray;
import org.json.JSONObject;

/**
 * Communication between intermine and liftover server in a way as
 * posting http request from the webapp, avoiding cross-domian issue.
 *
 * @author Fengyuan Hu
 *
 */
public class LiftOverService {
    private static final Logger LOG = Logger.getLogger(LiftOverService.class);

    private static final Map<String, String> ORGANISM_COMMON_NAME_MAP;
    static {
        Map<String, String> tempMap = new HashMap<String, String>();
        tempMap.put("H. sapiens", "human");
        tempMap.put("M. musculus", "mouse");
        tempMap.put("D. melanogaster", "fly");
        tempMap.put("C. elegans", "worm");
        ORGANISM_COMMON_NAME_MAP = Collections.unmodifiableMap(tempMap);
    }

    private static final Map<String, String> HUMAN_GENOME_BUILD_MAP;
    static {
        Map<String, String> tempMap = new HashMap<String, String>();
        tempMap.put("GRCh37", "hg19");
        tempMap.put("NCBI36", "hg18");
        tempMap.put("NCBI35", "hg17");
        tempMap.put("NCBI34", "hg16");
        HUMAN_GENOME_BUILD_MAP = Collections.unmodifiableMap(tempMap);
    }

    private static final Map<String, String> MOUSE_GENOME_BUILD_MAP;
    static {
        Map<String, String> tempMap = new HashMap<String, String>();
        tempMap.put("GRCm38", "mm10");
        tempMap.put("NCBIM37", "mm9");
        tempMap.put("NCBIM36", "mm8");
        MOUSE_GENOME_BUILD_MAP = Collections.unmodifiableMap(tempMap);
    }

    /**
     * Send a HTTP POST request to liftOver service.
     *
     * @param grsc the Genomic Region Search constraint
     * @param org human or mouse
     * @param genomeVersionSource older genome version
     * @param genomeVersionTarget intermine genome version
     * @param liftOverServerURL url
     * @return a list of GenomicRegion
     */
    public String doLiftOver(GenomicRegionSearchConstraint grsc, String org, String genomeVersionSource,
            String genomeVersionTarget, String liftOverServerURL) {

        List<GenomicRegion> genomicRegionList = grsc.getGenomicRegionList();
        String liftOverResponse;

        String coords = converToBED(genomicRegionList);
        String organism = ORGANISM_COMMON_NAME_MAP.get(org);

        try {
            // Construct data
            String data = URLEncoder.encode("coords", "UTF-8") + "=" + URLEncoder.encode(coords, "UTF-8");
            data += "&" + URLEncoder.encode("source", "UTF-8") + "="
                    + URLEncoder.encode(genomeVersionSource, "UTF-8");
            data += "&" + URLEncoder.encode("target", "UTF-8") + "="
                    + URLEncoder.encode(genomeVersionTarget, "UTF-8");

            // Send data
            URL url;
            // liftOverServerURL ends with "/"
            if (!liftOverServerURL.endsWith("/")) {
                url = new URL(liftOverServerURL + "/" + organism);
            } else {
                url = new URL(liftOverServerURL + organism);
            }
            URLConnection conn = url.openConnection();
            conn.setDoOutput(true);
            OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream());
            wr.write(data);
            wr.flush();
            wr.close();

            liftOverResponse = new String(IOUtils.toCharArray(conn.getInputStream()));

            LOG.info("LiftOver response message: \n" + liftOverResponse);

        } catch (Exception e) {
            e.printStackTrace();
            return null;
        }

        return liftOverResponse;
    }

    private String converToBED(List<GenomicRegion> genomicRegionList) {

        StringBuffer coords = new StringBuffer();

        for (GenomicRegion gr : genomicRegionList) {
            coords.append(gr.getChr()).append("\t").append(gr.getStart()).append("\t").append(gr.getEnd())
                    .append("\n");
        }
        return coords.toString();
    }
}