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/*
* The MIT License
*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import htsjdk.samtools.SAMException;
import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.math.BigInteger;
import java.nio.file.Files;
import java.nio.file.Path;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
/**
* Class to generate an MD5 string for a file as it is being read
*
* @author [email protected]
*/
public class Md5CalculatingOutputStream extends OutputStream {
private final OutputStream os;
private final MessageDigest md5;
private final Path digestFile;
private String hash;
/**
* Constructor that takes in the OutputStream that we are wrapping
* and creates the MD5 MessageDigest
*/
public Md5CalculatingOutputStream(OutputStream os, Path digestFile) {
super();
this.hash = null;
this.os = os;
this.digestFile = digestFile;
try {
md5 = MessageDigest.getInstance("MD5");
md5.reset();
}
catch (NoSuchAlgorithmException e) {
throw new RuntimeException("MD5 algorithm not found", e);
}
}
public Md5CalculatingOutputStream(OutputStream os, File digestFile) {
this(os, IOUtil.toPath(digestFile));
}
@Override
public void write(int b) throws IOException {
md5.update((byte)b);
os.write(b);
}
@Override
public void write(byte[] b) throws IOException {
md5.update(b);
os.write(b);
}
@Override
public void write(byte[] b, int off, int len) throws IOException {
md5.update(b, off, len);
os.write(b, off, len);
}
public String md5() {
if(hash == null) {
throw new SAMException("Attempting to access md5 digest before the entire file is written! Call close first.");
}
return hash;
}
private String makeHash() {
if(hash == null) {
hash = new BigInteger(1, md5.digest()).toString(16);
if (hash.length() != 32) {
final String zeros = "00000000000000000000000000000000";
hash = zeros.substring(0, 32 - hash.length()) + hash;
}
return hash;
} else {
throw new SAMException("Calling close on Md5CalculatingOutputStream twice!");
}
}
@Override
public void close() throws IOException {
os.close();
makeHash();
if(digestFile != null) {
BufferedWriter writer = Files.newBufferedWriter(digestFile);
writer.write(hash);
writer.close();
}
}
// Pass-through method
@Override
public void flush() throws IOException { os.flush(); }
}
