com.roche.sequencing.bioinformatics.common.utils.Md5CheckSumUtil.java Source code

Introduction

Here is the source code for com.roche.sequencing.bioinformatics.common.utils.Md5CheckSumUtil.java

Source

/*
 *    Copyright 2016 Roche NimbleGen Inc.
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *    http://www.apache.org/licenses/LICENSE-2.0
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 */
package com.roche.sequencing.bioinformatics.common.utils;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.zip.GZIPInputStream;

import org.apache.commons.codec.binary.Hex;
import org.apache.commons.codec.digest.DigestUtils;

import com.roche.sequencing.bioinformatics.common.utils.gzip.GZipUtil;

public class Md5CheckSumUtil {

    private Md5CheckSumUtil() {
        throw new AssertionError();
    }

    /**
     * return the md5 checksum for the string (note: this would be equivalent to writing this string to a file and asking for the md5sum of the file)
     * 
     * @param string
     * @return the md5sum of the string or null if there was an error calculating the md5sum
     */
    public static String md5sum(String string) {
        return DigestUtils.md5Hex(string);
    }

    public static String md5Sum(File file) throws FileNotFoundException, IOException {
        String md5Sum = null;
        try (FileInputStream fis = new FileInputStream(file)) {
            md5Sum = DigestUtils.md5Hex(fis);
        }
        return md5Sum;
    }

    public static String md5Sum(Class<?> resourceReferenceClass, String resourceName)
            throws FileNotFoundException, IOException {
        String md5Sum = null;
        try (InputStream is = resourceReferenceClass.getResourceAsStream(resourceName)) {
            md5Sum = DigestUtils.md5Hex(is);
        }
        return md5Sum;
    }

    public static String md5SumWithSkippingCommentLines(File file) throws FileNotFoundException, IOException {
        return md5SumWithSkippingCommentLines(new InputStreamFactory(file));
    }

    public static String md5SumWithSkippingCommentLines(IInputStreamFactory inputStreamFactory)
            throws FileNotFoundException, IOException {
        InputStream inputStream;
        if (GZipUtil.isCompressed(inputStreamFactory)) {
            inputStream = new GZIPInputStream(inputStreamFactory.createInputStream());
        } else {
            inputStream = new BufferedInputStream(inputStreamFactory.createInputStream());
        }

        MessageDigest md5SumDigest = null;
        try {
            md5SumDigest = MessageDigest.getInstance("MD5");
        } catch (NoSuchAlgorithmException e) {
            throw new AssertionError();
        }

        try {
            byte[] character = new byte[1024];
            StringBuilder currentLine = new StringBuilder();
            int readChars = 0;
            while ((readChars = inputStream.read(character)) != -1) {
                for (int i = 0; i < readChars; ++i) {
                    char currentCharacter = (char) character[i];
                    if (currentCharacter == StringUtil.NEWLINE_SYMBOL) {
                        currentLine.append(currentCharacter);
                        String line = currentLine.toString();
                        if (!line.startsWith("#")) {
                            md5SumDigest.update(line.getBytes());
                        }

                        currentLine = new StringBuilder();

                    } else {
                        currentLine.append(currentCharacter);
                    }
                }
            }
        } finally {
            inputStream.close();
        }
        String md5Sum = Hex.encodeHexString(md5SumDigest.digest());
        return md5Sum;
    }
}