uk.ac.ebi.embl.api.validation.helper.FileUtils.java Source code

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Here is the source code for uk.ac.ebi.embl.api.validation.helper.FileUtils.java

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/*******************************************************************************
 * Copyright 2012 EMBL-EBI, Hinxton outstation
 * 
 * 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 uk.ac.ebi.embl.api.validation.helper;

import java.io.*;
import java.util.zip.GZIPInputStream;

import org.apache.commons.lang.StringUtils;

import uk.ac.ebi.embl.api.validation.FileType;

/**
 * Created by IntelliJ IDEA.
 * User: lbower
 * Date: 08-Feb-2012
 * Time: 16:08:06
 */
public class FileUtils {

    public static final String embl_filetoken = "ID";
    public static final String genbank_filetoken = "LOCUS";
    public static final String gff_filetoken = "##gff-version 3";
    public static final String fasta_filetoken = ">";
    private static final String[] AssemblyFileToken = { "assembly", "chromosome", "unlocalised", "unplaced",
            "placed" };

    public static void copyFile(File src, File dst) throws IOException, FileNotFoundException, SecurityException {

        InputStream in = new FileInputStream(src);
        OutputStream out = new FileOutputStream(dst);

        // Transfer bytes from in to out
        byte[] buf = new byte[1024];
        int len;
        while ((len = in.read(buf)) > 0) {
            out.write(buf, 0, len);
        }
        in.close();
        out.close();
    }

    public static String readFile(InputStream inputStream) throws IOException {

        if (inputStream != null) {
            BufferedInputStream stream = new BufferedInputStream(inputStream);
            BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
            StringBuffer fileData = new StringBuffer(1000);

            char[] buf = new char[1024];
            int numRead = 0;
            while ((numRead = reader.read(buf)) != -1) {
                String readData = String.valueOf(buf, 0, numRead);
                fileData.append(readData);
                buf = new char[1024];
            }
            reader.close();

            return fileData.toString();
        }
        return null;
    }

    public static void moveFile(String oldFileString, String newFileDirString) throws Exception {
        File oldFile = new File(oldFileString);
        File newFileDir = new File(newFileDirString);

        if (!oldFile.exists()) {
            throw new Exception("file does not exist " + oldFileString);
        }

        if (!newFileDir.isDirectory()) {
            throw new Exception("copy file is not a directory " + newFileDirString);
        }

        boolean success = oldFile.renameTo(new File(newFileDir, oldFile.getName()));

        if (!success) {
            throw new Exception("problem moving file\n " + oldFileString + " to \n " + newFileDirString);
        }
    }

    public static String getdeCompressedFile(String file) throws IOException {
        if (file == null) {
            return null;
        }
        File zipFile = new File(file);
        if (!zipFile.exists()) {
            return null;
        }

        if (!zipFile.getName().matches("^.+\\.gz$")) {
            return file;
        }
        byte[] buffer = new byte[1024];
        GZIPInputStream zis = new GZIPInputStream(new FileInputStream(zipFile));
        File tempFile = new File(zipFile.getParent() + File.separator
                + zipFile.getName().substring(0, zipFile.getName().lastIndexOf(".gz")));
        if (!tempFile.exists()) {
            tempFile.createNewFile();
        }

        FileOutputStream fos = new FileOutputStream(tempFile);
        int len;
        while ((len = zis.read(buffer)) > 0) {
            fos.write(buffer, 0, len);
        }

        fos.close();

        zis.close();

        return tempFile.getAbsolutePath();
    }

    public static FileType getFileType(File formatFile) throws IOException {
        BufferedReader fileFormatReader = new BufferedReader(new FileReader(formatFile));
        // FINDING THE TYPE OF FILE BY READING THE FIRST LINE OF THE FILE
        String firstLineofFile = fileFormatReader.readLine();
        fileFormatReader.close();
        if (firstLineofFile.startsWith(embl_filetoken)) {
            return FileType.EMBL;
        } else if (firstLineofFile.startsWith(genbank_filetoken)) {
            return FileType.GENBANK;
        } else if (firstLineofFile.startsWith(gff_filetoken)) {
            return FileType.GFF3;
        } else if (StringUtils.indexOfAny(formatFile.getName(), AssemblyFileToken) != -1) {
            return FileType.GENOMEASSEMBLY;
        } else if (firstLineofFile.startsWith(fasta_filetoken)) {
            return FileType.FASTA;
        }
        return null;
    }

}