Examples with CountingInputStream org.apache.commons.compress.utils.CountingInputStream used on opensource projects

Example 1 with CountingInputStream

use of org.apache.commons.compress.utils.CountingInputStream in project android by cSploit.

the class UpdateService method extract.

/**
   * extract an archive into a directory
   *
   * @throws IOException if some I/O error occurs
   * @throws java.util.concurrent.CancellationException if task is cancelled by user
   * @throws java.lang.InterruptedException when the the running thread get cancelled.
   */
private void extract() throws RuntimeException, IOException, InterruptedException, ChildManager.ChildNotStartedException {
    ArchiveInputStream is = null;
    ArchiveEntry entry;
    CountingInputStream counter;
    OutputStream outputStream = null;
    File f, inFile;
    File[] list;
    String name;
    String envPath;
    final StringBuffer sb = new StringBuffer();
    int mode;
    int count;
    long total;
    boolean isTar, r, w, x, isElf, isScript;
    short percentage, old_percentage;
    Child which;
    if (mCurrentTask.path == null || mCurrentTask.outputDir == null)
        return;
    mBuilder.setContentTitle(getString(R.string.extracting)).setContentText("").setContentInfo("").setSmallIcon(android.R.drawable.ic_popup_sync).setProgress(100, 0, false);
    mNotificationManager.notify(NOTIFICATION_ID, mBuilder.build());
    Logger.info(String.format("extracting '%s' to '%s'", mCurrentTask.path, mCurrentTask.outputDir));
    envPath = null;
    which = null;
    try {
        if (mCurrentTask.fixShebang) {
            which = System.getTools().raw.async("which env", new Raw.RawReceiver() {

                @Override
                public void onNewLine(String line) {
                    sb.delete(0, sb.length());
                    sb.append(line);
                }
            });
        }
        inFile = new File(mCurrentTask.path);
        total = inFile.length();
        counter = new CountingInputStream(new FileInputStream(inFile));
        is = openArchiveStream(counter);
        isTar = mCurrentTask.archiver.equals(archiveAlgorithm.tar);
        old_percentage = -1;
        f = new File(mCurrentTask.outputDir);
        if (f.exists() && f.isDirectory() && (list = f.listFiles()) != null && list.length > 2)
            wipe();
        if (mCurrentTask.fixShebang) {
            if (execShell(which, "cancelled while retrieving env path") != 0) {
                throw new RuntimeException("cannot find 'env' executable");
            }
            envPath = sb.toString();
        }
        while (mRunning && (entry = is.getNextEntry()) != null) {
            name = entry.getName().replaceFirst("^\\./?", "");
            if (mCurrentTask.skipRoot) {
                if (name.contains("/"))
                    name = name.substring(name.indexOf('/') + 1);
                else if (entry.isDirectory())
                    continue;
            }
            f = new File(mCurrentTask.outputDir, name);
            isElf = isScript = false;
            if (entry.isDirectory()) {
                if (!f.exists()) {
                    if (!f.mkdirs()) {
                        throw new IOException(String.format("Couldn't create directory '%s'.", f.getAbsolutePath()));
                    }
                }
            } else {
                byte[] buffer = null;
                byte[] writeMe = null;
                outputStream = new FileOutputStream(f);
                // check il file is an ELF or a script
                if ((!isTar || mCurrentTask.fixShebang) && entry.getSize() > 4) {
                    writeMe = buffer = new byte[4];
                    IOUtils.readFully(is, buffer);
                    if (buffer[0] == 0x7F && buffer[1] == 0x45 && buffer[2] == 0x4C && buffer[3] == 0x46) {
                        isElf = true;
                    } else if (buffer[0] == '#' && buffer[1] == '!') {
                        isScript = true;
                        ByteArrayOutputStream firstLine = new ByteArrayOutputStream();
                        int newline = -1;
                        // assume that '\n' is more far then 4 chars.
                        firstLine.write(buffer);
                        buffer = new byte[1024];
                        count = 0;
                        while (mRunning && (count = is.read(buffer)) >= 0 && (newline = Arrays.binarySearch(buffer, 0, count, (byte) 0x0A)) < 0) {
                            firstLine.write(buffer, 0, count);
                        }
                        if (!mRunning) {
                            throw new CancellationException("cancelled while searching for newline.");
                        } else if (count < 0) {
                            newline = count = 0;
                        } else if (newline < 0) {
                            newline = count;
                        }
                        firstLine.write(buffer, 0, newline);
                        firstLine.close();
                        byte[] newFirstLine = new String(firstLine.toByteArray()).replace("/usr/bin/env", envPath).getBytes();
                        writeMe = new byte[newFirstLine.length + (count - newline)];
                        java.lang.System.arraycopy(newFirstLine, 0, writeMe, 0, newFirstLine.length);
                        java.lang.System.arraycopy(buffer, newline, writeMe, newFirstLine.length, count - newline);
                    }
                }
                if (writeMe != null) {
                    outputStream.write(writeMe);
                }
                IOUtils.copy(is, outputStream);
                outputStream.close();
                outputStream = null;
                percentage = (short) (((double) counter.getBytesRead() / total) * 100);
                if (percentage != old_percentage) {
                    mBuilder.setProgress(100, percentage, false).setContentInfo(percentage + "%");
                    mNotificationManager.notify(NOTIFICATION_ID, mBuilder.build());
                    old_percentage = percentage;
                }
            }
            // Zip does not store file permissions.
            if (isTar) {
                mode = ((TarArchiveEntry) entry).getMode();
                r = (mode & 0400) > 0;
                w = (mode & 0200) > 0;
                x = (mode & 0100) > 0;
            } else if (isElf || isScript) {
                r = w = x = true;
            } else {
                continue;
            }
            if (!f.setExecutable(x, true)) {
                Logger.warning(String.format("cannot set executable permission of '%s'", name));
            }
            if (!f.setWritable(w, true)) {
                Logger.warning(String.format("cannot set writable permission of '%s'", name));
            }
            if (!f.setReadable(r, true)) {
                Logger.warning(String.format("cannot set readable permission of '%s'", name));
            }
        }
        if (!mRunning)
            throw new CancellationException("extraction cancelled.");
        Logger.info("extraction completed");
        f = new File(mCurrentTask.outputDir, ".nomedia");
        if (f.createNewFile())
            Logger.info(".nomedia created");
        mBuilder.setContentInfo("").setProgress(100, 100, true);
        mNotificationManager.notify(NOTIFICATION_ID, mBuilder.build());
    } finally {
        if (is != null)
            is.close();
        if (outputStream != null)
            outputStream.close();
    }
}

Example 2 with CountingInputStream

use of org.apache.commons.compress.utils.CountingInputStream in project android by cSploit.

the class UpdateService method verifyArchiveIntegrity.

/**
   * check if an archive is valid by reading it.
   * @throws RuntimeException if trying to run this with no archive
   */
private void verifyArchiveIntegrity() throws RuntimeException, KeyException {
    File f;
    long total;
    short old_percentage, percentage;
    CountingInputStream counter;
    ArchiveInputStream is;
    byte[] buffer;
    String rootDirectory;
    Logger.info("verifying archive integrity");
    if (mCurrentTask == null || mCurrentTask.path == null)
        throw new RuntimeException("no archive to test");
    mBuilder.setContentTitle(getString(R.string.checking)).setSmallIcon(android.R.drawable.ic_popup_sync).setContentText("").setContentInfo("").setProgress(100, 0, true);
    mNotificationManager.notify(NOTIFICATION_ID, mBuilder.build());
    f = new File(mCurrentTask.path);
    try {
        counter = new CountingInputStream(new FileInputStream(f));
    } catch (FileNotFoundException e) {
        throw new RuntimeException(String.format("archive '%s' does not exists", mCurrentTask.path));
    }
    try {
        is = openArchiveStream(counter);
        ArchiveEntry entry;
        buffer = new byte[2048];
        total = f.length();
        old_percentage = -1;
        rootDirectory = null;
        // consume the archive
        while (mRunning && (entry = is.getNextEntry()) != null) {
            if (!mCurrentTask.skipRoot)
                continue;
            String name = entry.getName();
            if (rootDirectory == null) {
                if (name.contains("/")) {
                    rootDirectory = name.substring(0, name.indexOf('/'));
                } else if (entry.isDirectory()) {
                    rootDirectory = name;
                } else {
                    throw new IOException(String.format("archive '%s' contains files under it's root", mCurrentTask.path));
                }
            } else {
                if (!name.startsWith(rootDirectory)) {
                    throw new IOException("multiple directories found in the archive root");
                }
            }
        }
        while (mRunning && is.read(buffer) > 0) {
            percentage = (short) (((double) counter.getBytesRead() / total) * 100);
            if (percentage != old_percentage) {
                mBuilder.setProgress(100, percentage, false).setContentInfo(percentage + "%");
                mNotificationManager.notify(NOTIFICATION_ID, mBuilder.build());
                old_percentage = percentage;
            }
        }
    } catch (IOException e) {
        throw new KeyException("corrupted archive: " + e.getMessage());
    } finally {
        try {
            counter.close();
        } catch (IOException ignore) {
        }
    }
    if (!mRunning)
        throw new CancellationException("archive integrity check cancelled");
    if (mCurrentTask.skipRoot && rootDirectory == null)
        throw new KeyException(String.format("archive '%s' is empty", mCurrentTask.path));
}

Example 3 with CountingInputStream

use of org.apache.commons.compress.utils.CountingInputStream in project bboxdb by jnidzwetzki.

the class FileLineIndex method indexFile.

/**
 * Index the given file
 * @throws IOException
 */
public void indexFile() throws IOException {
    final File file = new File(filename);
    if (!file.canRead()) {
        throw new IOException("Unable to open file: " + filename);
    }
    openDatabase();
    logger.info("Indexing file: {}", filename);
    indexedLines = 1;
    registerLine(indexedLines, 0);
    indexedLines++;
    try (final CountingInputStream inputStream = new CountingInputStream(new BufferedInputStream(new FileInputStream(file)))) {
        while (inputStream.available() > 0) {
            final char readChar = (char) inputStream.read();
            if (readChar == '\n') {
                registerLine(indexedLines, inputStream.getBytesRead());
                indexedLines++;
            }
        }
    }
    logger.info("Indexing file done: {}", filename);
}