edu.harvard.i2b2.eclipse.plugins.metadataLoader.util.FileUtil.java Source code

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Here is the source code for edu.harvard.i2b2.eclipse.plugins.metadataLoader.util.FileUtil.java

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/*
 * Copyright (c) 2006-2013 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v2.1 
 * which accompanies this distribution. 
 * 
 * Contributors:
 *       Lori Phillips
 */
package edu.harvard.i2b2.eclipse.plugins.metadataLoader.util;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Enumeration;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import java.util.zip.ZipInputStream;

import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.DefaultHttpClient;

import edu.harvard.i2b2.eclipse.plugins.metadataLoader.views.RunData;

/**
 * StringUtil class to perform string parsing tasks
 * This is singleton class.
 * @author lcp5
 */
public class FileUtil {

    //to make this class singleton
    private static FileUtil thisInstance;

    static {
        thisInstance = new FileUtil();
    }

    public static FileUtil getInstance() {
        return thisInstance;
    }

    public static void unzip(String zipname) throws IOException {

        FileInputStream fis = new FileInputStream(zipname);
        ZipInputStream zis = new ZipInputStream(new BufferedInputStream(fis));
        //??    GZIPInputStream gzis = new GZIPInputStream(new BufferedInputStream(fis));

        // get directory of the zip file
        if (zipname.contains("\\"))
            zipname = zipname.replace("\\", "/");
        //   String zipDirectory = zipname.substring(0, zipname.lastIndexOf("/")+1) ;
        String zipDirectory = zipname.substring(0, zipname.lastIndexOf("."));
        new File(zipDirectory).mkdir();

        RunData.getInstance().setMetadataDirectory(zipDirectory);

        ZipEntry entry;
        while ((entry = zis.getNextEntry()) != null) {
            System.out.println("Unzipping: " + entry.getName());
            if (entry.getName().contains("metadata")) {
                RunData.getInstance().setMetadataFile(zipDirectory + "/" + entry.getName());
            } else if (entry.getName().contains("schemes")) {
                RunData.getInstance().setSchemesFile(zipDirectory + "/" + entry.getName());
            } else if (entry.getName().contains("access")) {
                RunData.getInstance().setTableAccessFile(zipDirectory + "/" + entry.getName());
            }

            int size;
            byte[] buffer = new byte[2048];

            FileOutputStream fos = new FileOutputStream(zipDirectory + "/" + entry.getName());
            BufferedOutputStream bos = new BufferedOutputStream(fos, buffer.length);

            while ((size = zis.read(buffer, 0, buffer.length)) != -1) {
                bos.write(buffer, 0, size);
            }
            bos.flush();
            bos.close();
        }
        zis.close();
        fis.close();
    }

    //http://www.java2s.com/Code/Java/File-Input-Output/Zip-Tar-File.htm

    // this might work if the zip file contains a folder..
    public static void unZipAll(File source, File destination) throws IOException {
        System.out.println("Unzipping - " + source.getName());
        int BUFFER = 2048;

        ZipFile zip = new ZipFile(source);
        try {
            destination.getParentFile().mkdirs();
            Enumeration zipFileEntries = zip.entries();

            // Process each entry
            while (zipFileEntries.hasMoreElements()) {
                // grab a zip file entry
                ZipEntry entry = (ZipEntry) zipFileEntries.nextElement();
                String currentEntry = entry.getName();
                File destFile = new File(destination, currentEntry);
                //destFile = new File(newPath, destFile.getName());
                File destinationParent = destFile.getParentFile();

                // create the parent directory structure if needed
                destinationParent.mkdirs();

                if (!entry.isDirectory()) {
                    BufferedInputStream is = null;
                    FileOutputStream fos = null;
                    BufferedOutputStream dest = null;
                    try {
                        is = new BufferedInputStream(zip.getInputStream(entry));
                        int currentByte;
                        // establish buffer for writing file
                        byte data[] = new byte[BUFFER];

                        // write the current file to disk
                        fos = new FileOutputStream(destFile);
                        dest = new BufferedOutputStream(fos, BUFFER);

                        // read and write until last byte is encountered
                        while ((currentByte = is.read(data, 0, BUFFER)) != -1) {
                            dest.write(data, 0, currentByte);
                        }
                    } catch (Exception e) {
                        System.out.println("unable to extract entry:" + entry.getName());
                        throw e;
                    } finally {
                        if (dest != null) {
                            dest.close();
                        }
                        if (fos != null) {
                            fos.close();
                        }
                        if (is != null) {
                            is.close();
                        }
                    }
                } else {
                    //Create directory
                    destFile.mkdirs();
                }

                if (currentEntry.endsWith(".zip")) {
                    // found a zip file, try to extract
                    unZipAll(destFile, destinationParent);
                    if (!destFile.delete()) {
                        System.out.println("Could not delete zip");
                    }
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
            System.out.println("Failed to successfully unzip:" + source.getName());
        } finally {
            zip.close();
        }
        System.out.println("Done Unzipping:" + source.getName());
    }

    public static void download(String workingDir, String URL, String filename) throws IOException {
        workingDir = workingDir + filename;

        DefaultHttpClient httpclient = new DefaultHttpClient();
        HttpGet httpget = new HttpGet(URL);

        HttpResponse response = httpclient.execute(httpget);

        //      System.out.println(response.getStatusLine());
        HttpEntity entity = response.getEntity();
        if (entity != null) {

            InputStream instream = entity.getContent();

            try {
                BufferedInputStream bis = new BufferedInputStream(instream);
                BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(new File(workingDir)));
                int inByte;
                while ((inByte = bis.read()) != -1) {
                    bos.write(inByte);
                }
                bis.close();
                bos.close();
                //       unzip("ICD10.zip");
            } catch (IOException ex) {
                throw ex;
            } catch (RuntimeException ex) {
                httpget.abort();
                throw ex;
            } finally {
                instream.close();
            }
            httpclient.getConnectionManager().shutdown();

        }
    }

}