org.biojava.nbio.structure.io.util.FileDownloadUtils Maven / Gradle / Ivy
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/**
* 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 Feb 23, 2012 Created by Andreas Prlic
*
* @since 3.0.2
*/
package org.biojava.nbio.structure.io.util;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.SocketTimeoutException;
import java.net.URL;
import java.net.URLConnection;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.nio.channels.ReadableByteChannel;
public class FileDownloadUtils {
private static final Logger logger = LoggerFactory.getLogger(FileDownloadUtils.class);
/**
* Copy the content of file src to dst TODO since java 1.7 this is provided
* in java.nio.file.Files
*
* @param src
* @param dst
* @throws IOException
*/
@SuppressWarnings("resource")
public static void copy(File src, File dst) throws IOException {
// Took following recipe from
// http://stackoverflow.com/questions/106770/standard-concise-way-to-copy-a-file-in-java
// The nio package seems to be the most efficient way to copy a file
FileChannel source = null;
FileChannel destination = null;
try {
// we need the supress warnings here (the warning that the stream is not closed is harmless)
// see http://stackoverflow.com/questions/12970407/does-filechannel-close-close-the-underlying-stream
source = new FileInputStream(src).getChannel();
destination = new FileOutputStream(dst).getChannel();
destination.transferFrom(source, 0, source.size());
} finally {
if (source != null) {
source.close();
}
if (destination != null) {
destination.close();
}
}
}
public static String getFileExtension(File f) {
String fileName = f.getName();
String ext = "";
int mid = fileName.lastIndexOf(".");
ext = fileName.substring(mid + 1, fileName.length());
return ext;
}
public static String getFilePrefix(File f) {
String fileName = f.getName();
String fname = "";
int mid = fileName.indexOf(".");
fname = fileName.substring(0, mid);
return fname;
}
/**
* Download the content provided at URL url and store the result to a local
* file, using a temp file to cache the content in case something goes wrong
* in download
*
* @param url
* @param destination
* @throws IOException
*/
public static void downloadFile(URL url, File destination) throws IOException {
int count = 0;
int maxTries = 10;
int timeout = 60000; //60 sec
File tempFile = File.createTempFile(getFilePrefix(destination), "." + getFileExtension(destination));
// Took following recipe from stackoverflow:
// http://stackoverflow.com/questions/921262/how-to-download-and-save-a-file-from-internet-using-java
// It seems to be the most efficient way to transfer a file
// See: http://docs.oracle.com/javase/7/docs/api/java/nio/channels/FileChannel.html
ReadableByteChannel rbc = null;
FileOutputStream fos = null;
while (true) {
try {
URLConnection connection = prepareURLConnection(url.toString(), timeout);
connection.connect();
InputStream inputStream = connection.getInputStream();
rbc = Channels.newChannel(inputStream);
fos = new FileOutputStream(tempFile);
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
break;
} catch (SocketTimeoutException e) {
if (++count == maxTries) throw e;
} finally {
if (rbc != null) {
rbc.close();
}
if (fos != null) {
fos.close();
}
}
}
logger.debug("Copying temp file {} to final location {}", tempFile, destination);
copy(tempFile, destination);
// delete the tmp file
tempFile.delete();
}
/**
* Converts path to Unix convention and adds a terminating slash if it was
* omitted
*
* @param path original platform dependent path
* @return path in Unix convention
* @author Peter Rose
* @since 3.2
*/
public static String toUnixPath(String path) {
String uPath = path;
if (uPath.contains("\\")) {
uPath = uPath.replaceAll("\\\\", "/");
}
// this should be removed, it's need since "\" is added AtomCache code
if (uPath.endsWith("//")) {
uPath = uPath.substring(0, uPath.length() - 1);
}
if (!uPath.endsWith("/")) {
uPath = uPath + "/";
}
return uPath;
}
/**
* Expands ~ in paths to the user's home directory.
*
*
* This does not work for some special cases for paths: Other users' homes
* (~user/...), and Tilde expansion within the path (/.../~/...)
*
* @param file
* @return
*/
public static String expandUserHome(String file) {
if (file.startsWith("~" + File.separator)) {
file = System.getProperty("user.home") + file.substring(1);
}
return file;
}
/**
* Pings a HTTP URL. This effectively sends a HEAD request and returns
* true if the response code is in the 200-399 range.
*
* @param url The HTTP URL to be pinged.
* @param timeout The timeout in millis for both the connection timeout and
* the response read timeout. Note that the total timeout is effectively two
* times the given timeout.
* @return true if the given HTTP URL has returned response
* code 200-399 on a HEAD request within the given timeout, otherwise
* false.
* @author BalusC,
* http://stackoverflow.com/questions/3584210/preferred-java-way-to-ping-a-http-url-for-availability
*/
public static boolean ping(String url, int timeout) {
//url = url.replaceFirst("https", "http"); // Otherwise an exception may be thrown on invalid SSL certificates.
try {
HttpURLConnection connection = (HttpURLConnection) prepareURLConnection(url, timeout);
connection.setRequestMethod("HEAD");
int responseCode = connection.getResponseCode();
return (200 <= responseCode && responseCode <= 399);
} catch (IOException exception) {
return false;
}
}
/**
* Prepare {@link URLConnection} with customised timeouts.
*
* @param url The URL
* @param timeout The timeout in millis for both the connection timeout and
* the response read timeout. Note that the total timeout is effectively two
* times the given timeout.
*
*
* Example of code.
* UrlConnection conn = prepareURLConnection("http://www.google.com/", 20000);
* conn.connect();
* conn.getInputStream();
*
*
*
* NB. User should execute connect() method before getting input
* stream.
* @return
* @throws IOException
* @author Jacek Grzebyta
*/
public static URLConnection prepareURLConnection(String url, int timeout) throws IOException {
URLConnection connection = new URL(url).openConnection();
connection.setReadTimeout(timeout);
connection.setConnectTimeout(timeout);
return connection;
}
public static void main(String[] args) {
String url;
url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/";
System.out.format("%s\t%s%n", ping(url, 200), url);
url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/foo";
System.out.format("%s\t%s%n", ping(url, 200), url);
url = "http://scopzzz.mrc-lmb.cam.ac.uk/scop/parse/";
System.out.format("%s\t%s%n", ping(url, 200), url);
url = "scop.mrc-lmb.cam.ac.uk";
System.out.format("%s\t%s%n", ping(url, 200), url);
url = "http://scop.mrc-lmb.cam.ac.uk";
System.out.format("%s\t%s%n", ping(url, 200), url);
}
}