/*
 * Copyright (c) 2007-2013 The Broad Institute, Inc.
 * SOFTWARE COPYRIGHT NOTICE
 * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 */

package org.broad.igv.util.stream;

import org.apache.log4j.Logger;
import org.broad.igv.util.HttpUtils;
import org.broad.tribble.util.URLHelper;

import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.HashMap;
import java.util.Map;

/**
 * @author jrobinso
 * @date Jul 6, 2011
 */
public class IGVUrlHelper implements URLHelper {

    static Logger log = Logger.getLogger(IGVUrlHelper.class);

    URL url;

    public IGVUrlHelper(URL url) {
        this.url = url;
    }

    public URL getUrl() {
        return url;
    }

    public long getContentLength() throws IOException {
        return HttpUtils.getInstance().getContentLength(url);
    }

    public InputStream openInputStream() throws IOException {
        return HttpUtils.getInstance().openConnectionStream(url);
    }

    public InputStream openInputStreamForRange(long start, long end) throws IOException {

        String byteRange = "bytes=" + start + "-" + end;
        Map<String, String> params = new HashMap();
        params.put("Range", byteRange);
        //Hack for web services which strip range header
        URL url = addStartEndQueryString(start, end);
        return HttpUtils.getInstance().openConnectionStream(url, params);
    }

    /**
     * Add query parameters which should more properly be in Range header field
     * to query string
     * @param start start byte
     * @param end end byte
     * @throws MalformedURLException
     */
    private URL addStartEndQueryString(long start, long end) throws MalformedURLException {

        log.debug("old url: " + this.url);
        String surl = url.toExternalForm();
        String nurl = surl;

        String toadd = String.format("start=%d&end=%d", start, end);
        String[] parts = surl.split("\\?", 2);
        //TODO For now only mess with the string if we already have query parameters
        //nurl = String.format("%s?%s", parts[0], toadd);
        if(parts.length == 2){
            nurl = String.format("%s?%s", parts[0], toadd);
            nurl += "&" + parts[1];
        }
        log.debug("new url: " + nurl);
        return new URL(nurl);
    }

    public boolean exists() {
        return HttpUtils.getInstance().resourceAvailable(url);
    }
}

@@ -2152,51 +2152,8 @@
  %7B%0A%0A
-        log.debug(%22old url: %22 + this.url);%0A
     
@@ -2617,16 +2617,97 @@
       %7D%0A
+        if(log.isDebugEnabled())%7B%0A            log.debug(%22old url: %22 + surl);%0A    
         
@@ -2733,24 +2733,34 @@
  %22 + nurl);%0A
+        %7D%0A
         retu

Improve logging in IGVUrlHelper