org.apache.parquet.tools.submit.FileFormat.java Source code

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Here is the source code for org.apache.parquet.tools.submit.FileFormat.java

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/*
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 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package org.apache.parquet.tools.submit;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;

//import org.apache.commons.io.FileUtils;
/*
import org.apache.parquet.tools.Main;
import static org.apache.parquet.tools.Main.OPTIONS;
import static org.apache.parquet.tools.Main.mergeOptions;
    
import org.apache.parquet.tools.command.Command;
import org.apache.parquet.tools.command.Registry;
import org.apache.parquet.tools.command.ShowSchemaCommand;
*/
/**
 *
 * @author someya
 */

public class FileFormat {

    public boolean checkfilenamn;

    // public   Main main = new Main();
    //public ShowSchemaCommand show = new   ShowSchemaCommand (); 

    public TerminalCommands terminalCall = new TerminalCommands();

    public boolean checkFileName(String filename, String endsWith) {

        checkfilenamn = filename.endsWith(endsWith);

        return checkfilenamn;

    }

    public String checkAdam(String fileNamn) throws IOException, Exception {
        String filtyp = terminalCall.myArrr(fileNamn);
        return filtyp;

    }

    public void setFile(String fileNamn, ArrayList<String> contentsOfFile) {
        BufferedWriter writer = null;
        try {

            if (getFolder(fileNamn) == true) {

                File logFile = new File(fileNamn);

                writer = new BufferedWriter(new FileWriter(logFile));

                String listString = "";

                for (String s : contentsOfFile) {
                    listString += s + "\t";

                }

                //  System.out.println(i);
                writer.write(listString);

            }

        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            try {
                // Close the writer regardless of what happens...
                writer.close();
            } catch (Exception e) {
            }
        }
    }

    public String getFile(String fileNamn) {
        return fileNamn;
    }

    public boolean getFolder(String fileNamn) {

        File folder = new File("/home/someya/NetBeansProjects/AdamBackend/Files/");
        File[] listOfFiles = folder.listFiles();

        for (int i = 0; i < listOfFiles.length; i++) {
            if (fileNamn.equals(listOfFiles[i].getName())) {
                //   System.out.println("File ");
                return false;
            }

        }
        return true;
    }

    public void writeFile(String adamSubmitCommand, String fileName, String outputFileName, String kmers)
            throws IOException, InterruptedException {

        setFile(outputFileName, terminalCall.setCommand(adamSubmitCommand, fileName, "", ""));
    }

    public static void main(String[] a) throws Exception {
        FileFormat fileTyp = new FileFormat();
        //fileTyp.zipFolder("/home/someya/NetBeansProjects/AdamBackend/Files/igen9", "/home/someya/NetBeansProjects/AdamBackend/Files/igen9.zip");

        //fileTyp.zipSam("bqsr1.sam","frt");

    }

    public void zipFolder(String srcFolder, String destZipFile) throws Exception {
        ZipOutputStream zip = null;
        FileOutputStream fileWriter = null;
        fileWriter = new FileOutputStream(destZipFile);
        zip = new ZipOutputStream(fileWriter);
        addFolderToZip("", srcFolder, zip);
        zip.flush();
        zip.close();
    }

    private void addFileToZip(String path, String srcFile, ZipOutputStream zip) throws Exception {
        File folder = new File(srcFile);
        if (folder.isDirectory()) {
            addFolderToZip(path, srcFile, zip);
        } else {
            byte[] buf = new byte[1024];
            int len;
            FileInputStream in = new FileInputStream(srcFile);
            zip.putNextEntry(new ZipEntry(path + "/" + folder.getName()));
            while ((len = in.read(buf)) > 0) {
                zip.write(buf, 0, len);
            }
        }
    }

    private void addFolderToZip(String path, String srcFolder, ZipOutputStream zip) throws Exception {
        File folder = new File(srcFolder);

        for (String fileName : folder.list()) {
            if (path.equals("")) {
                addFileToZip(folder.getName(), srcFolder + "/" + fileName, zip);
            } else {
                addFileToZip(path + "/" + folder.getName(), srcFolder + "/" + fileName, zip);
            }
        }
    }

    public String CreateDirectory(String namn) {

        String folder = namn;

        Path path = Paths.get(folder);
        //if directory exists?
        if (!Files.exists(path)) {
            try {
                Files.createDirectories(path);
            } catch (IOException e) {
                //fail to create directory
                e.printStackTrace();
            }
        }

        return folder;

    }

    public void CopyFiles(String srcDir, String dstDir) throws IOException {
        File source = new File(srcDir);
        File dest = new File(dstDir);

        if (source.isFile()) {
            FileUtils.copyFileToDirectory(source, dest);
        } else if (source.isDirectory()) {
            FileUtils.copyDirectoryToDirectory(source, dest);

        }
    }

    public String zipSam(String FilePath) throws IOException, Exception {

        String folder = FilePath + ".folder";
        String rgdict = FilePath + ".rgdict";
        String seqdict = FilePath + ".seqdict";

        CreateDirectory(folder);
        CopyFiles(FilePath, folder);
        CopyFiles(rgdict, folder);
        CopyFiles(seqdict, folder);

        String zipFile = folder + ".zip";
        zipFolder(folder, zipFile);

        return folder;

    }

}