org.mcisb.util.io.StreamReader.java Source code

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Here is the source code for org.mcisb.util.io.StreamReader.java

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/*******************************************************************************
 * Manchester Centre for Integrative Systems Biology
 * University of Manchester
 * Manchester M1 7ND
 * United Kingdom
 * 
 * Copyright (C) 2007 University of Manchester
 * 
 * This program is released under the Academic Free License ("AFL") v3.0.
 * (http://www.opensource.org/licenses/academic.php)
 *******************************************************************************/
package org.mcisb.util.io;

import java.io.*;
import java.net.*;
import java.util.zip.*;
import org.apache.commons.io.*;

/**
 * 
 * @author Neil Swainston
 */
public class StreamReader implements Runnable {
    /**
     * Output stream.
     */
    protected final OutputStream os;

    /**
     * Error stream.
     */
    protected final OutputStream es;

    /**
     * Input stream.
     */
    protected InputStream is;

    /**
     * 
     * @param os
     */
    public StreamReader(final OutputStream os) {
        this(null, os, System.err);
    }

    /**
     * 
     * @param is
     * @param os
     */
    public StreamReader(final InputStream is, final OutputStream os) {
        this(is, os, System.err);
    }

    /**
     * 
     * @param is
     * @param os
     * @param es
     */
    public StreamReader(final InputStream is, final OutputStream os, final OutputStream es) {
        setInputStream(is);
        this.os = new BufferedOutputStream(os);
        this.es = new BufferedOutputStream(es);
    }

    /**
     * 
     * @param is
     */
    public void setInputStream(final InputStream is) {
        this.is = new BufferedInputStream(is);
    }

    /**
     * 
     * @throws IOException
     */
    public void read() throws IOException {
        IOUtils.copy(is, os);
        is.close();
        os.close();
    }

    /*
     * (non-Javadoc)
     * 
     * @see java.lang.Runnable#run()
     */
    @Override
    public void run() {
        try {
            read();
        } catch (IOException e) {
            e.printStackTrace(new PrintStream(es));
        }
    }

    /**
     * 
     * @param is
     * @return String
     * @throws IOException
     */
    public static byte[] read(final InputStream is) throws IOException {
        ByteArrayOutputStream os = null;

        try {
            os = new ByteArrayOutputStream();
            new StreamReader(is, os).read();
            final byte[] b = os.toByteArray();
            os.close();
            return b;
        } finally {
            if (os != null) {
                os.close();
            }
        }
    }

    /**
     * 
     * @param zipUrl
     * @param root
     * @throws IOException
     */
    public static void unzip(final URL zipUrl, final File root) throws IOException {
        try (final InputStream is = new BufferedInputStream(zipUrl.openStream());
                final ZipInputStream zis = new ZipInputStream(is)) {
            ZipEntry entry;

            while ((entry = zis.getNextEntry()) != null) {
                final File entryFile = new File(root, entry.getName());

                if (entry.getName().endsWith("/")) //$NON-NLS-1$
                {
                    if (!entryFile.mkdir()) {
                        throw new IOException();
                    }
                } else {
                    try (final OutputStream os = new FileOutputStream(entryFile)) {
                        new StreamReader(zis, os).read();
                    }
                }
            }
        }
    }
}