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The protein structure modules of BioJava.
There is a newer version: 7.2.2

/*
 * This file is originally coming from the Dasobert library.
 * Author: Andreas Prlic
 *
 *                  BioJava development code
 *
 * 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.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on Jul 25, 2006
 *
 */

package org.biojava.nbio.structure.align.util;

import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.lang.reflect.Method;
import java.net.ConnectException;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.zip.GZIPInputStream;



/** a class that takes care about opening HttpURLConnections and sets the proper timeouts
 *
 * @author Andreas Prlic
 * @since 9:58:25 AM
 * @version %I% %G%
 */
public class HTTPConnectionTools {

	public static final String USERAGENT = "JFatCat Java client";

	public static final int    DEFAULT_CONNECTION_TIMEOUT = 15000; // timeout for http connection = 15. sec


	public HTTPConnectionTools() {
		super();

	}

	/**open HttpURLConnection. Recommended way to open
	 * HttpURLConnections, since this take care of setting timeouts
	 * properly for java 1.4 and 1.5
	 *
	 * @param url URL to oopen
	 * @param timeout timeout in milli seconds
	 * @return a HttpURLConnection
	 * @throws IOException
	 * @throws ConnectException
	 *
	 *
	 */
	@SuppressWarnings({ "rawtypes", "unchecked" })
public static HttpURLConnection openHttpURLConnection(URL url, int timeout)
	throws IOException, ConnectException{

		HttpURLConnection huc = null;

		huc = (HttpURLConnection) url.openConnection();
		huc.addRequestProperty("User-Agent", USERAGENT);

		// this sets the timeouts for Java 1.4
		System.setProperty("sun.net.client.defaultConnectTimeout", ""+timeout);
		System.setProperty("sun.net.client.defaultReadTimeout", ""+timeout);

		// for Java 1.5 we need to do this:
		// use reflection to determine if get and set timeout methods for urlconnection are available
		// seems java 1.5 does not watch the System properties any longer...
		// and java 1.4 did not provide the new classes...

		try {
			// try to use reflection to set timeout property
			Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");

			Method setconnecttimeout = urlconnectionClass.getMethod (
					"setConnectTimeout", new Class [] {int.class}
			);
			setconnecttimeout.invoke(huc,new Object[] {new Integer(timeout)});

			Method setreadtimeout = urlconnectionClass.getMethod (
					"setReadTimeout", new Class[] {int.class}
			);
			setreadtimeout.invoke(huc,new Object[] {new Integer(timeout)});
			//System.out.println("successfully set java 1.5 timeout");
		} catch (Exception e) {
			e.printStackTrace(); // TODO dmyersturnbull: should we rethrow this?
			// most likely it was a NoSuchMEthodException and we are running java 1.4.
		}
		return huc;
	}


	/** open HttpURLConnection. Recommended way to open
	 * HttpURLConnections, since this take care of setting timeouts
	 * properly for java 1.4 and 1.5
	 * uses the DEFAULT_CONNECTION_TIMEOUT (= 15 seconds)
	 *
	 * @param url a URL to open a http connection to
	 * @return HttpURLConnect the opened connection
	 * @throws IOException
	 * @throws ConnectException
	 *
	 * */
	public static HttpURLConnection openHttpURLConnection(URL url)
	throws IOException, ConnectException {

		return openHttpURLConnection(url,DEFAULT_CONNECTION_TIMEOUT);

	}

	/** connect to DAS server and return result as an InputStream.
	 * always asks for response to be in GZIP encoded
	 *
	 * @param url the URL to connect to
	 * @param timeout the timeout for the connection
	 * @return an InputStream
	 * @throws IOException
	 * @throws DASException if DAS server returns error response code
	 *
	 */
	public static InputStream getInputStream(URL url, int timeout)
	throws IOException
	{
		return getInputStream(url,true, timeout);
	}


	/** connect to DAS server and return result as an InputStream.
	 * always asks for response to be in GZIP encoded
	 *
	 * @param url the URL to connect to
	 * @return an InputStream
	 * @throws IOException
	 * @throws DASException if DAS server returns error response code
	 *
	 */
	public static InputStream getInputStream(URL url)
	throws IOException
	{
		return getInputStream(url,true, DEFAULT_CONNECTION_TIMEOUT);
	}

	/** open a URL and return an InputStream to it
	 *  if acceptGzipEncoding == true, use GZIPEncoding to
	 *  compress communication
	 *
	 * @param url
	 * @param acceptGzipEncoding
	 * @return an InputStream to the URL
	 * @throws IOException
	 * @throws DASException if DAS server returns error response code
	 */
	@SuppressWarnings("unused")
public static InputStream getInputStream(URL url, boolean acceptGzipEncoding, int timeout)
	throws IOException {
		InputStream inStream = null ;

		//System.out.println("opening connection to "+url);
		HttpURLConnection huc = HTTPConnectionTools.openHttpURLConnection(url,timeout);

		if ( acceptGzipEncoding) {
			// should make communication faster
			huc.setRequestProperty("Accept-Encoding", "gzip");
		}


		// check the HTTP response code
		int httpCode = huc.getResponseCode();

		String contentEncoding = huc.getContentEncoding();

		inStream = huc.getInputStream();

		if (contentEncoding != null) {
			if (contentEncoding.contains("gzip")) {
				// we have gzip encoding
				inStream = new GZIPInputStream(inStream);
			}
		}

		return inStream;

	}

	/** do a POST to a URL and return the response stream for further processing elsewhere.
	 *
	 *
	 * @param url
	 * @return InputStream of response
	 * @throws IOException
	 */
	public static InputStream doPOST(URL url, String data)
	throws IOException
	{
		return doPOST(url,data,DEFAULT_CONNECTION_TIMEOUT);
	}

	/** do a POST to a URL and return the response stream for further processing elsewhere.
	 *
	 *
	 * @param url
	 * @return InputStream of response
	 * @throws IOException
	 */
	public static InputStream doPOST(URL url, String data, int timeout)
	throws IOException
	{

	// Send data

	  HttpURLConnection conn = openHttpURLConnection(url, timeout);

		//URLConnection conn = url.openConnection();
		conn.setDoOutput(true);

		OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream());
		wr.write(data);
		wr.flush();

		// Get the response
		return conn.getInputStream();


	}


}