Python shutil.copy2() Examples

def copytree(src, dst, symlinks=False, ignore=None):
    """
    Correctly copy an entire directory

    :param src: source dir
    :param dst: destination dir
    :param symlinks: copy content of symlinks
    :param ignore: ignore
    """
    for item in os.listdir(src):
        s = os.path.join(src, item)
        d = os.path.join(dst, item)
        if os.path.isdir(s):
            shutil.copytree(s, d, symlinks, ignore)
        else:
            shutil.copy2(s, d) 

def copy_results(datanames, result_dir, output_dir, verbose):
    ''' This function copies all the [dataname.predict] results from result_dir to output_dir'''
    for basename in datanames:
        try:
            test_files = ls(result_dir + "/" + basename + "*_test*.predict")
            if len(test_files)==0: 
                vprint(verbose, "[-] Missing 'test' result files for " + basename) 
                return 0
            for f in test_files: copy2(f, output_dir)
            valid_files = ls(result_dir + "/" + basename + "*_valid*.predict")
            if len(valid_files)==0: 
                vprint(verbose, "[-] Missing 'valid' result files for " + basename) 
                return 0
            for f in valid_files: copy2(f, output_dir)
            vprint( verbose,  "[+] " + basename.capitalize() + " copied")
        except:
            vprint(verbose, "[-] Missing result files")
            return 0
    return 1

# ================ Display directory structure and code version (for debug purposes) ================= 

def install_user_service(service_file, socket_file):
    """
    Installs the service file and socket file into the xinetd
    service directory, sets the service to start on boot, and
    starts the service now.

    Args:
        service_file: The path to the systemd service file to install
        socket_file: The path to the systemd socket file to install
    """

    if service_file is None:
       return
    service_name = os.path.basename(service_file)

    logger.debug("...Installing user service '%s'.", service_name)

    # copy service file
    service_path = os.path.join(XINETD_SERVICE_PATH, service_name)
    shutil.copy2(service_file, service_path)

    execute(["service", "xinetd", "restart"], timeout=60) 

def copymessage(self, n, tofolder, ton):
        """Copy one message over a specific destination message,
        which may or may not already exist."""
        path = self.getmessagefilename(n)
        # Open it to check that it exists
        f = open(path)
        f.close()
        del f
        topath = tofolder.getmessagefilename(ton)
        backuptopath = tofolder.getmessagefilename(',%d' % ton)
        try:
            os.rename(topath, backuptopath)
        except os.error:
            pass
        ok = 0
        try:
            tofolder.setlast(None)
            shutil.copy2(path, topath)
            ok = 1
        finally:
            if not ok:
                try:
                    os.unlink(topath)
                except os.error:
                    pass 

def install():
    status_set('maintenance', 'Executing pre-install')
    execd_preinstall()
    configure_installation_source(config('openstack-origin'))
    status_set('maintenance', 'Installing apt packages')
    apt_update()
    apt_install(determine_packages(), fatal=True)

    _files = os.path.join(charm_dir(), 'files')
    if os.path.isdir(_files):
        for f in os.listdir(_files):
            f = os.path.join(_files, f)
            log('Installing {} to /usr/bin'.format(f))
            shutil.copy2(f, '/usr/bin')

    for port in API_PORTS.values():
        open_port(port) 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy(args, movelist, fromdir, todir):
    for p in sorted(movelist):
        logging.debug("mkdir %s" % os.path.join(todir, p))
        if not args.dryrun:
            try:
                os.makedirs(os.path.join(todir, p), exist_ok=True)
            except FileExistsError:
                pass
        logging.debug("copy from '%s' to '%s':" % (os.path.join(fromdir, p), os.path.join(todir, p)))
        for f in sorted(movelist[p]):
            if os.path.exists(os.path.join(fromdir, p, f)):
                logging.debug("%s" % (f))
                if not args.dryrun:
                    shutil.copy2(os.path.join(fromdir, p, f), os.path.join(todir, p, f))
            else:
                logging.error("%s can't be copied as it doesn't exist" % (f)) 

def copy(self, target, nameIsLeaf=False):
        """
        same as rename - except for copying.  returns the new target name
        """
        if self.isfile():
            target = Path(target)
            if nameIsLeaf:
                target = self.up() / target

            if self == target:
                return target

            targetDirpath = target.up()
            if not targetDirpath.exists():
                targetDirpath.create()

            shutil.copy2(str(self), str(target))

            return target
        elif self.isdir():
            shutil.copytree(str(self), str(target)) 

def csvwrite(_imagefile, _feature_data, write_dir):
    print("Writing FEATURE.CSV file...")
    feature_file = os.path.splitext(_imagefile)[0]
    feature_file = feature_file.replace("IR", "Features")

    name = feature_file + '.csv';
    with open(name, 'w') as csvfile:
        fieldnames = ['mean_value', 'euler_number', 'major_axis', 'area', 'solidity', 'std', 'eccentricity',
                      'eq_diameter', 'minor_axis']
        fieldnames.extend(getHistFeatureKeys())

        writer = csv.DictWriter(csvfile, fieldnames=fieldnames);
        writer.writeheader()

        for cluster in _feature_data:
            data = {key:value for key, value in cluster.items() if key in fieldnames}
            writer.writerow(data)
    print write_dir
    
    os.rename(name, write_dir + "\\" + "output.csv")
    #copy2(outpu, _junk)
    #os.rename(_junk, "output.csv")
    print("FEATURE.CSV file is Written") 

def write(self, dbfile=None):
        if dbfile is None:
            dbfile = self.dbfile
        # Make a backup
        if os.path.exists(dbfile):
            shutil.copy2(dbfile, dbfile+"_bak")

        # write main database file
        with open(dbfile, "wb") as db:
            self.header_main.tofile(db)
            for entry in self.entries.values():
                db.write(entry)
            # Update database header
            num_entries = len(self.entries)
            db.seek(0)
            db.write(b"\0%c%c" % (num_entries>>8, num_entries&0xFF)) 

def copymessage(self, n, tofolder, ton):
        """Copy one message over a specific destination message,
        which may or may not already exist."""
        path = self.getmessagefilename(n)
        # Open it to check that it exists
        f = open(path)
        f.close()
        del f
        topath = tofolder.getmessagefilename(ton)
        backuptopath = tofolder.getmessagefilename(',%d' % ton)
        try:
            os.rename(topath, backuptopath)
        except os.error:
            pass
        ok = 0
        try:
            tofolder.setlast(None)
            shutil.copy2(path, topath)
            ok = 1
        finally:
            if not ok:
                try:
                    os.unlink(topath)
                except os.error:
                    pass 

def copytree(src, dst, symlinks=False, ignore=None):
	names = os.listdir(src)
	if ignore is not None:
		ignored_names = ignore(src, names)
	else:
		ignored_names = set()

	if not os.path.isdir(dst):
		os.makedirs(dst)

	errors = []
	for name in names:
		if name in ignored_names:
			continue

		srcname = os.path.join(src, name)
		dstname = os.path.join(dst, name)
		if os.path.isdir(srcname):
			copytree(srcname, dstname, symlinks, ignore)
		else:
			shutil.copy2(srcname, dstname)

	return

# ???????????????????? 

def _do_tree(root_src, root_dest, tmpl_dict, tmpl_ext, tag_delim, level=0):
    if level == 0:
        _mkdir(root_dest)

    for entry in os.scandir(root_src):
        src_path = os.path.join(root_src, entry.name)
        dest_path = os.path.join(root_dest,
                                 do_text(entry.name, tmpl_dict, tag_delim))

        if entry.is_dir():
            _mkdir(dest_path, copy_stats_from=src_path)
            _do_tree(src_path, dest_path, tmpl_dict, tmpl_ext, tag_delim,
                     level + 1)
        elif entry.is_file():
            was_tmpl = False
            for ext in tmpl_ext:
                ext = ext.lower()
                if entry.name.lower().endswith(ext):
                    was_tmpl = True
                    dest_path = dest_path[0:-len(ext)]
                    do_file(src_path, dest_path, tmpl_dict, tag_delim)
                    break

            if not was_tmpl:
                shutil.copy2(src_path, dest_path, follow_symlinks=False) 

def handle(self, *args, **kwargs):
        export_dir = os.path.join('.', 'export-{}'.format(now().strftime('%Y-%m-%d-%H%M%S')))
        os.mkdir(export_dir)
        successful_exports = 0
        failed_exports = []

        for session in CashdeskSession.objects.filter(end__isnull=False):
            report_path = session.get_report_path()
            if report_path:
                shutil.copy2(report_path, export_dir)
                successful_exports += 1
            else:
                failed_exports.append(session.pk)

        success_msg = 'Exported {} reports to directory {}.'.format(successful_exports, export_dir)
        self.stdout.write(self.style.SUCCESS(success_msg))

        if failed_exports:
            warn_msg = 'Could not find reports for {} finished sessions (IDs: {}).'.format(
                len(failed_exports),
                failed_exports,
            )
            self.stdout.write(self.style.WARNING(warn_msg)) 

def copy_files(source_folder, target_folder):

    for root, dirs, files in os.walk(source_folder):
        for file in files:
            next = False
            #Obtenemos archivo origen a copiar
            tf = os.path.join(root, file)
            #Comprobamos la lista negra para no copiar
            for nc in NO_COPY:
                if nc.strip() in tf:
                    next = True
                    break
            if next: continue
            tf = tf.replace(source_folder, target_folder)
            #Si el archivo existe en el destino
            if os.path.exists(tf): continue
            else:
                try:
                    os.makedirs(root.replace(source_folder, target_folder))
                except:
                    None
                shutil.copy2(os.path.join(root, file), tf) 

def copy_results(datanames, result_dir, output_dir, verbose):
    ''' This function copies all the [dataname.predict] results from result_dir to output_dir'''
    for basename in datanames:
        try:
            test_files = ls(result_dir + "/" + basename + "*_test*.predict")
            if len(test_files)==0: 
                vprint(verbose, "[-] Missing 'test' result files for " + basename) 
                return 0
            for f in test_files: copy2(f, output_dir)
            valid_files = ls(result_dir + "/" + basename + "*_valid*.predict")
            if len(valid_files)==0: 
                vprint(verbose, "[-] Missing 'valid' result files for " + basename) 
                return 0
            for f in valid_files: copy2(f, output_dir)
            vprint( verbose,  "[+] " + basename.capitalize() + " copied")
        except:
            vprint(verbose, "[-] Missing result files")
            return 0
    return 1

# ================ Display directory structure and code version (for debug purposes) ================= 

def _configure(self, context):
            if not os.path.exists(self.build_path):
                shutil.copytree(self.source_path, self.build_path, symlinks=True)
            try:
                shutil.rmtree(pj(self.build_path, 'kiwixlib', 'src', 'main'))
            except FileNotFoundError:
                pass
            shutil.copytree(pj(self.buildEnv.install_dir, 'kiwix-lib'),
                            pj(self.build_path, 'kiwixlib', 'src', 'main'))
            os.makedirs(
                pj(self.build_path, 'app', 'src', 'main', 'assets', 'icu'),
                exist_ok=True)
            shutil.copy2(pj(self.buildEnv.install_dir, 'share', 'icu', '58.2',
                            'icudt58l.dat'),
                         pj(self.build_path, 'app', 'src', 'main', 'assets',
                            'icu', 'icudt58l.dat')) 

def ExecRecursiveMirror(self, source, dest):
    """Emulation of rm -rf out && cp -af in out."""
    if os.path.exists(dest):
      if os.path.isdir(dest):
        def _on_error(fn, path, dummy_excinfo):
          # The operation failed, possibly because the file is set to
          # read-only. If that's why, make it writable and try the op again.
          if not os.access(path, os.W_OK):
            os.chmod(path, stat.S_IWRITE)
          fn(path)
        shutil.rmtree(dest, onerror=_on_error)
      else:
        if not os.access(dest, os.W_OK):
          # Attempt to make the file writable before deleting it.
          os.chmod(dest, stat.S_IWRITE)
        os.unlink(dest)

    if os.path.isdir(source):
      shutil.copytree(source, dest)
    else:
      shutil.copy2(source, dest)
      # Try to diagnose crbug.com/741603
      if not os.path.exists(dest):
        raise Exception("Copying of %s to %s failed" % (source, dest)) 

def _CopyRuntimeImpl(target, source, verbose=True):
  """Copy |source| to |target| if it doesn't already exist or if it needs to be
  updated (comparing last modified time as an approximate float match as for
  some reason the values tend to differ by ~1e-07 despite being copies of the
  same file... https://crbug.com/603603).
  """
  if (os.path.isdir(os.path.dirname(target)) and
      (not os.path.isfile(target) or
       abs(os.stat(target).st_mtime - os.stat(source).st_mtime) >= 0.01)):
    if verbose:
      print 'Copying %s to %s...' % (source, target)
    if os.path.exists(target):
      # Make the file writable so that we can delete it now, and keep it
      # readable.
      os.chmod(target, stat.S_IWRITE | stat.S_IREAD)
      os.unlink(target)
    shutil.copy2(source, target)
    # Make the file writable so that we can overwrite or delete it later,
    # keep it readable.
    os.chmod(target, stat.S_IWRITE | stat.S_IREAD) 

def GetHeadersFromGN(out_dir, q):
  """Return all the header files from GN"""

  tmp = None
  ans, err = set(), None
  try:
    # Argument |dir| is needed to make sure it's on the same drive on Windows.
    # dir='' means dir='.', but doesn't introduce an unneeded prefix.
    tmp = tempfile.mkdtemp(dir='')
    shutil.copy2(os.path.join(out_dir, 'args.gn'),
                 os.path.join(tmp, 'args.gn'))
    # Do "gn gen" in a temp dir to prevent dirtying |out_dir|.
    gn_exe = 'gn.bat' if sys.platform == 'win32' else 'gn'
    subprocess.check_call([
        os.path.join(DEPOT_TOOLS_DIR, gn_exe), 'gen', tmp, '--ide=json', '-q'])
    gn_json = json.load(open(os.path.join(tmp, 'project.json')))
    ans = ParseGNProjectJSON(gn_json, out_dir, tmp)
  except Exception as e:
    err = str(e)
  finally:
    if tmp:
      shutil.rmtree(tmp)
  q.put((ans, err)) 

def GenerateV14LayoutResource(input_filename, output_v14_filename,
                              output_v17_filename):
  """Convert API 17 layout resource to API 14 compatible layout resource.

  It's mostly a simple replacement, s/Start/Left s/End/Right,
  on the attribute names.
  If the generated resource is identical to the original resource,
  don't do anything. If not, write the generated resource to
  output_v14_filename, and copy the original resource to output_v17_filename.
  """
  dom = ParseAndReportErrors(input_filename)
  is_modified = GenerateV14LayoutResourceDom(dom, input_filename)

  if is_modified:
    # Write the generated resource.
    WriteDomToFile(dom, output_v14_filename)

    # Copy the original resource.
    build_utils.MakeDirectory(os.path.dirname(output_v17_filename))
    shutil.copy2(input_filename, output_v17_filename) 

def copy2(src, dst):
    """
    Similar to shutil.copy(), but metadata (permissions etc., as mentioned in
    copy_stat above) is copied as well  in fact, this is just shutil.copy()
    followed by copystat(). This is similar to the Unix command cp -p.
    :Arguments:
        src - file and metadata to be copied
        dst - file/dir on which to be copied
    :Return:
        True/False - based on the success/failure of the operation
    """
    status = False
    try:
        shutil.copy2(src, dst)
        print_info("src {} copied to dst {} successfully along with metadata".
                   format(src, dst))
        status = True
    except Exception as e:
        print_error("copying file {} with metadata to file {} raised exception"
                    " {}".format(src, dst, str(e)))
    return status 

def move(src, dst):
    """
    Recursively move a file or directory (src) to another location (dst).
    If the destination is an existing directory, then src is moved inside that
    directory. If the destination already exists but is not a directory, it may
    be overwritten depending on os.rename() semantics.If the destination is on
    the current filesystem, then os.rename() is used. Otherwise, src is copied
    (using shutil.copy2()) to dst and then removed.
    :Arguments:
        src - source file to be moved
        dst - target file/directory on which to be moved
    :Return:
        True/False - based on the success/failure of the operation
    """
    status = False
    try:
        shutil.move(src, dst)
        print_info("move of src {} to dst {} successful".format(src, dst))
        status = True
    except Exception as e:
        print_error("moving file {} to file {} raised exception {}".
                    format(src, dst, str(e)))
    return status 

def copy_results(datanames, result_dir, output_dir, verbose):
    ''' This function copies all the [dataname.predict] results from result_dir to output_dir'''
    for basename in datanames:
        try:
            test_files = ls(result_dir + "/" + basename + "*_test*.predict")
            if len(test_files)==0: 
                vprint(verbose, "[-] Missing 'test' result files for " + basename) 
                return 0
            for f in test_files: copy2(f, output_dir)
            valid_files = ls(result_dir + "/" + basename + "*_valid*.predict")
            if len(valid_files)==0: 
                vprint(verbose, "[-] Missing 'valid' result files for " + basename) 
                return 0
            for f in valid_files: copy2(f, output_dir)
            vprint( verbose,  "[+] " + basename.capitalize() + " copied")
        except:
            vprint(verbose, "[-] Missing result files")
            return 0
    return 1

# ================ Display directory structure and code version (for debug purposes) ================= 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def uploadfile(srcfile, dstfolder):
    '''
    Copy a file to the upload folder
    srcfile: Full source filename including path
    '''

    uploadfile = os.path.join(dstfolder, os.path.basename(srcfile))

    folderinit(dstfolder, 'Upload file destination folder')

    try:
        shutil.copy2(srcfile, uploadfile)
    except Exception as e:
        logger.error('File "{}" could not be copied to upload folder "{}".\n\tException Message: {}'.format(srcfile, dstfolder))

    return 

def copy_cwl_files(from_dir=CWL_PATH):
    """Copy cwl files to a directory where the cwl-runner can find them.

    cwl files are copied to $XDG_DATA_HOME/commonwl/ This is one of the default
    locations where the cwl-runner looks for cwl files.

    Args:
        from_dir (str): Path to directory where to copy files from (default:
            the cwl directory of nlppln).
    """
    cwl_data_dir = os.environ.get('XDG_DATA_HOME')
    if not cwl_data_dir:
        cwl_data_dir = DEFAULT_DATA_DIR

    cwl_data_dir = os.path.join(cwl_data_dir, CWL_DATA_DIR_PREFIX)

    create_dirs(cwl_data_dir)

    cwl_files = glob.glob('{}{}*.cwl'.format(from_dir, os.sep))
    for fi in cwl_files:
        fo = os.path.join(cwl_data_dir, os.path.basename(fi))
        shutil.copy2(fi, fo) 

def rename_file(entry, pdf, bib, dry_run):
    if entry['author']:
        authors = entry['author'].split(',')
        if len(authors) <= 3:
            author = ', '.join(authors[:-1])
        else:
            author = authors[0] + ' et al.'

    if author and 'year' in entry and 'title' in entry:
        newname = author + ' - ' + '{}'.format(entry['year']) + ' - ' + algo.tex_to_unicode(algo.title_case(entry['title'])).replace("/", " ") + '.pdf'

        if os.path.exists(pdf):
            shutil.copy2(pdf, os.path.expanduser("~") + papers_path +  newname)
            entry.set_tag('file', ':' + pdf + ':PDF' )

            if not dry_run:
                shutil.move(pdf, os.path.expanduser("~") + '/.local/share/Trash/files/')
                return True
    return False 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy_files(src, dst, symlinks=False, ignore=None):
    """Copy files from src to dst."""
    for item in os.listdir(src):
        s = os.path.join(src, item)
        d = os.path.join(dst, item)
        if os.path.isdir(s):
            shutil.copytree(s, d, symlinks, ignore)
        else:
            shutil.copy2(s, d) 

def gen_setup(self, filename, fragment, tmpdir):
        match = EGG_FRAGMENT.match(fragment)
        dists = match and [
            d for d in
            interpret_distro_name(filename, match.group(1), None) if d.version
        ] or []

        if len(dists) == 1:  # unambiguous ``#egg`` fragment
            basename = os.path.basename(filename)

            # Make sure the file has been downloaded to the temp dir.
            if os.path.dirname(filename) != tmpdir:
                dst = os.path.join(tmpdir, basename)
                from setuptools.command.easy_install import samefile
                if not samefile(filename, dst):
                    shutil.copy2(filename, dst)
                    filename = dst

            with open(os.path.join(tmpdir, 'setup.py'), 'w') as file:
                file.write(
                    "from setuptools import setup\n"
                    "setup(name=%r, version=%r, py_modules=[%r])\n"
                    % (
                        dists[0].project_name, dists[0].version,
                        os.path.splitext(basename)[0]
                    )
                )
            return filename

        elif match:
            raise DistutilsError(
                "Can't unambiguously interpret project/version identifier %r; "
                "any dashes in the name or version should be escaped using "
                "underscores. %r" % (fragment, dists)
            )
        else:
            raise DistutilsError(
                "Can't process plain .py files without an '#egg=name-version'"
                " suffix to enable automatic setup script generation."
            ) 

def gen_setup(self, filename, fragment, tmpdir):
        match = EGG_FRAGMENT.match(fragment)
        dists = match and [
            d for d in
            interpret_distro_name(filename, match.group(1), None) if d.version
        ] or []

        if len(dists) == 1:  # unambiguous ``#egg`` fragment
            basename = os.path.basename(filename)

            # Make sure the file has been downloaded to the temp dir.
            if os.path.dirname(filename) != tmpdir:
                dst = os.path.join(tmpdir, basename)
                from setuptools.command.easy_install import samefile
                if not samefile(filename, dst):
                    shutil.copy2(filename, dst)
                    filename = dst

            with open(os.path.join(tmpdir, 'setup.py'), 'w') as file:
                file.write(
                    "from setuptools import setup\n"
                    "setup(name=%r, version=%r, py_modules=[%r])\n"
                    % (
                        dists[0].project_name, dists[0].version,
                        os.path.splitext(basename)[0]
                    )
                )
            return filename

        elif match:
            raise DistutilsError(
                "Can't unambiguously interpret project/version identifier %r; "
                "any dashes in the name or version should be escaped using "
                "underscores. %r" % (fragment, dists)
            )
        else:
            raise DistutilsError(
                "Can't process plain .py files without an '#egg=name-version'"
                " suffix to enable automatic setup script generation."
            ) 

def local_update(repo_path, deb_paths=[]):
    """
    Updates a local deb repository by copying debs and running scanpackages.

    Args:
        repo_path: the path to the local repository.
        dep_paths: list of problem deb paths to copy.
    """

    if not exists(repo_path):
        logger.info("Creating repository at '%s'.", repo_path)
        makedirs(repo_path)
    elif not isdir(repo_path):
        logger.error("Repository '%s' is not a directory!", repo_path)
        raise FatalException

    [copy2(deb_path, repo_path) for deb_path in deb_paths]

    shell = spur.LocalShell()
    result = shell.run(["dpkg-scanpackages", ".", "/dev/null"], cwd=repo_path)

    packages_path = join(repo_path, "Packages.gz")
    with gzip.open(packages_path, "wb") as packages:
        packages.write(result.output)

    logger.info("Repository '%s' updated successfully. Copied %d packages.", repo_path, len(deb_paths)) 

def deploy_files(staging_directory, instance_directory, file_list, username, problem_class):
    """
    Copies the list of files from the staging directory to the instance directory.
    Will properly set permissions and setgid files based on their type.
    """

    # get uid and gid for default and problem user
    user = getpwnam(username)
    default = getpwnam(deploy_config.default_user)

    for f in file_list:
        # copy the file over, making the directories as needed
        output_path = join(instance_directory, f.path)
        if not os.path.isdir(os.path.dirname(output_path)):
            os.makedirs(os.path.dirname(output_path))

        if not isinstance(f, Directory):
          if isinstance(f, PreTemplatedFile):
              file_source = join(staging_directory, "__pre_templated", f.path)
          else:
              file_source = join(staging_directory, f.path)

          shutil.copy2(file_source, output_path)

        # set the ownership based on the type of file
        if isinstance(f, ProtectedFile) or isinstance(f, ExecutableFile):
            os.chown(output_path, default.pw_uid, user.pw_gid)
        else:
            uid = default.pw_uid if f.user is None else getpwnam(f.user).pw_uid
            gid = default.pw_gid if f.group is None else getgrnam(f.group).gr_gid
            os.chown(output_path, uid, gid)

        # set the permissions appropriately
        os.chmod(output_path, f.permissions)

    if issubclass(problem_class, Service):
        os.chown(instance_directory, default.pw_uid, user.pw_gid)
        os.chmod(instance_directory, 0o750) 

def copy_files(src, dst, symlinks=False, ignore=None):
    """Copy files from src to dst."""
    for item in os.listdir(src):
        s = os.path.join(src, item)
        d = os.path.join(dst, item)
        if os.path.isdir(s):
            shutil.copytree(s, d, symlinks, ignore)
        else:
            shutil.copy2(s, d) 

def copy_nrpe_checks():
    """
    Copy the nrpe checks into place

    """
    NAGIOS_PLUGINS = '/usr/local/lib/nagios/plugins'
    nrpe_files_dir = os.path.join(os.getenv('CHARM_DIR'), 'hooks',
                                  'charmhelpers', 'contrib', 'openstack',
                                  'files')

    if not os.path.exists(NAGIOS_PLUGINS):
        os.makedirs(NAGIOS_PLUGINS)
    for fname in glob.glob(os.path.join(nrpe_files_dir, "check_*")):
        if os.path.isfile(fname):
            shutil.copy2(fname,
                         os.path.join(NAGIOS_PLUGINS, os.path.basename(fname))) 

def copy_files(src, dst, symlinks=False, ignore=None):
    """Copy files from src to dst."""
    for item in os.listdir(src):
        s = os.path.join(src, item)
        d = os.path.join(dst, item)
        if os.path.isdir(s):
            shutil.copytree(s, d, symlinks, ignore)
        else:
            shutil.copy2(s, d) 

def main():
  beam_data = np.load(ARGS.data)

  # Optionally load vocabulary data
  vocab = None
  if ARGS.vocab:
    with open(ARGS.vocab) as file:
      vocab = file.readlines()
    vocab = [_.strip() for _ in vocab]
    vocab += ["UNK", "SEQUENCE_START", "SEQUENCE_END"]

  if not os.path.exists(ARGS.output_dir):
    os.makedirs(ARGS.output_dir)

  # Copy required files
  shutil.copy2("./bin/tools/beam_search_viz/tree.css", ARGS.output_dir)
  shutil.copy2("./bin/tools/beam_search_viz/tree.js", ARGS.output_dir)

  for idx in range(len(beam_data["predicted_ids"])):
    predicted_ids = beam_data["predicted_ids"][idx]
    parent_ids = beam_data["beam_parent_ids"][idx]
    scores = beam_data["scores"][idx]

    graph = create_graph(
        predicted_ids=predicted_ids,
        parent_ids=parent_ids,
        scores=scores,
        vocab=vocab)

    json_str = json.dumps(
        json_graph.tree_data(graph, (0, 0)),
        ensure_ascii=False)

    html_str = HTML_TEMPLATE.substitute(DATA=json_str)
    output_path = os.path.join(ARGS.output_dir, "{:06d}.html".format(idx))
    with open(output_path, "w") as file:
      file.write(html_str)
    print(output_path) 

def refilemessages(self, list, tofolder, keepsequences=0):
        """Refile one or more messages -- may raise os.error.
        'tofolder' is an open folder object."""
        errors = []
        refiled = {}
        for n in list:
            ton = tofolder.getlast() + 1
            path = self.getmessagefilename(n)
            topath = tofolder.getmessagefilename(ton)
            try:
                os.rename(path, topath)
            except os.error:
                # Try copying
                try:
                    shutil.copy2(path, topath)
                    os.unlink(path)
                except (IOError, os.error), msg:
                    errors.append(msg)
                    try:
                        os.unlink(topath)
                    except os.error:
                        pass
                    continue
            tofolder.setlast(ton)
            refiled[n] = ton
        if refiled:
            if keepsequences:
                tofolder._copysequences(self, refiled.items())
            self.removefromallsequences(refiled.keys())
        if errors:
            if len(errors) == 1:
                raise os.error, errors[0]
            else:
                raise os.error, ('multiple errors:', errors) 

def movemessage(self, n, tofolder, ton):
        """Move one message over a specific destination message,
        which may or may not already exist."""
        path = self.getmessagefilename(n)
        # Open it to check that it exists
        f = open(path)
        f.close()
        del f
        topath = tofolder.getmessagefilename(ton)
        backuptopath = tofolder.getmessagefilename(',%d' % ton)
        try:
            os.rename(topath, backuptopath)
        except os.error:
            pass
        try:
            os.rename(path, topath)
        except os.error:
            # Try copying
            ok = 0
            try:
                tofolder.setlast(None)
                shutil.copy2(path, topath)
                ok = 1
            finally:
                if not ok:
                    try:
                        os.unlink(topath)
                    except os.error:
                        pass
            os.unlink(path)
        self.removefromallsequences([n]) 

def extract_targz(tarname, filename=None, target_dir='.'):
    """filename must be a valid path in the tar"""
    import tarfile
    tmp_dir = '._tmp_'
    if filename is None:
        tarfile.TarFile.gzopen(tarname).extractall(target_dir)
    else:
        import shutil
        tarfile.TarFile.gzopen(tarname).extractall(tmp_dir)
        shutil.copy2(os.path.join(tmp_dir, filename),
                     os.path.join(target_dir, filename.split(os.path.sep)[-1]))
        shutil.rmtree(tmp_dir) 

def prepare_model_dir(self):
        if self.config.load_path:
            self.model_dir=self.config.load_path
        else:
            pth=datetime.now().strftime("%m%d_%H%M%S")+'_'+self.data_type
            self.model_dir=os.path.join(self.config.model_dir,pth)


        if not os.path.exists(self.model_dir):
            os.mkdir(self.model_dir)
        print('Model directory is ',self.model_dir)

        self.save_model_dir=os.path.join(self.model_dir,'checkpoints')
        if not os.path.exists(self.save_model_dir):
            os.mkdir(self.save_model_dir)
        self.save_model_name=os.path.join(self.save_model_dir,'Model')


        param_path = os.path.join(self.model_dir, "params.json")
        print("[*] MODEL dir: %s" % self.model_dir)
        print("[*] PARAM path: %s" % param_path)
        with open(param_path, 'w') as fp:
            json.dump(self.config.__dict__, fp, indent=4, sort_keys=True)

        config=self.config
        if config.is_train and not config.load_path:
            config.log_code_dir=os.path.join(self.model_dir,'code')
            for path in [self.model_dir, config.log_code_dir]:
                if not os.path.exists(path):
                    os.makedirs(path)

            #Copy python code in directory into model_dir/code for future reference:
            code_dir=os.path.dirname(os.path.realpath(sys.argv[0]))
            model_files = [f for f in listdir(code_dir) if isfile(join(code_dir, f))]
            for f in model_files:
                if f.endswith('.py'):
                    shutil.copy2(f,config.log_code_dir) 

def prepare_dirs_and_logger(config):
    formatter = logging.Formatter("%(asctime)s:%(levelname)s::%(message)s")
    logger = logging.getLogger()

    for hdlr in logger.handlers:
        logger.removeHandler(hdlr)

    handler = logging.StreamHandler()
    handler.setFormatter(formatter)

    logger.addHandler(handler)

    if config.load_path:
        if config.load_path.startswith(config.log_dir):
            config.model_dir = config.load_path
        else:
            if config.load_path.startswith(config.dataset):
                config.model_name = config.load_path
            else:
                config.model_name = "{}_{}".format(config.dataset, config.load_path)
    else:
        config.model_name = "{}_{}".format(config.dataset, get_time())

    if not hasattr(config, 'model_dir'):
        config.model_dir = os.path.join(config.log_dir, config.model_name)
    config.data_path = os.path.join(config.data_dir, config.dataset)

    if config.is_train:
        config.log_code_dir=os.path.join(config.model_dir,'code')
        for path in [config.log_dir, config.data_dir,
                     config.model_dir, config.log_code_dir]:
            if not os.path.exists(path):
                os.makedirs(path)

        #Copy python code in directory into model_dir/code for future reference:
        code_dir=os.path.dirname(os.path.realpath(sys.argv[0]))
        model_files = [f for f in listdir(code_dir) if isfile(join(code_dir, f))]
        for f in model_files:
            if f.endswith('.py'):
                shutil.copy2(f,config.log_code_dir) 

def prepare_dirs_and_logger(config):
    formatter = logging.Formatter("%(asctime)s:%(levelname)s::%(message)s")
    logger = logging.getLogger()

    for hdlr in logger.handlers:
        logger.removeHandler(hdlr)

    handler = logging.StreamHandler()
    handler.setFormatter(formatter)

    logger.addHandler(handler)

    if config.load_path:
        if config.load_path.startswith(config.log_dir):
            config.model_dir = config.load_path
        else:
            if config.load_path.startswith(config.dataset):
                config.model_name = config.load_path
            else:
                config.model_name = "{}_{}".format(config.dataset, config.load_path)
    else:
        config.model_name = "{}_{}".format(config.dataset, get_time())

    if not hasattr(config, 'model_dir'):
        config.model_dir = os.path.join(config.log_dir, config.model_name)
    config.data_path = os.path.join(config.data_dir, config.dataset)

    if not config.load_path:
        config.log_code_dir=os.path.join(config.model_dir,'code')
        for path in [config.log_dir, config.data_dir,
                     config.model_dir, config.log_code_dir]:
            if not os.path.exists(path):
                os.makedirs(path)

        #Copy python code in directory into model_dir/code for future reference:
        code_dir=os.path.dirname(os.path.realpath(sys.argv[0]))
        model_files = [f for f in listdir(code_dir) if isfile(join(code_dir, f))]
        for f in model_files:
            if f.endswith('.py'):
                shutil.copy2(f,config.log_code_dir) 

def copytree(src, dst, symlinks = False, ignore = None):
	if not os.path.exists(dst):
		os.makedirs(dst)
		shutil.copystat(src, dst)
	lst = os.listdir(src)
	if ignore:
		excl = ignore(src, lst)
		lst = [x for x in lst if x not in excl]
	for item in lst:
		s = os.path.join(src, item)
		d = os.path.join(dst, item)
		if symlinks and os.path.islink(s):
			if os.path.lexists(d):
				os.remove(d)
			os.symlink(os.readlink(s), d)
			try:
				st = os.lstat(s)
				mode = stat.S_IMODE(st.st_mode)
				os.lchmod(d, mode)
			except:
				pass # lchmod not available
		elif os.path.isdir(s):
			copytree(s, d, symlinks, ignore)
		else:
			shutil.copy2(s, d) 

def set_image(self, file_):
		"""Select currently active image"""
		shutil.copy2(file_, self.temporary.name)  # create temporary copy
		self.current = self.load_image_data(file_, self.temporary.name)  # parse SVG data