Source code for

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"""File system abstraction for file-based sources and sinks.

Note to implementors:
  "path" arguments will be URLs in the form scheme://foo/bar. The exception is
  LocalFileSystem, which gets unix-style paths in the form /foo/bar.

# pytype: skip-file

import abc
import bz2
import io
import logging
import lzma
import os
import posixpath
import re
import time
import zlib
from typing import BinaryIO  # pylint: disable=unused-import
from typing import Iterator
from typing import List
from typing import Optional
from typing import Tuple

import zstandard

from apache_beam.utils.plugin import BeamPlugin

logger = logging.getLogger(__name__)

DEFAULT_READ_BUFFER_SIZE = 16 * 1024 * 1024

__all__ = [

[docs]class CompressionTypes(object): """Enum-like class representing known compression types.""" # Detect compression based on filename extension. # # The following extensions are currently recognized by auto-detection: # .bz2 (implies BZIP2 as described below). # .gz (implies GZIP as described below) # .deflate (implies DEFLATE as described below) # .zst (implies ZSTD as described below) # .zst (implies ZSTD as described below) # .xz (implies LZMA as described below) # .lzma (implies LZMA as described below) # Any non-recognized extension implies UNCOMPRESSED as described below. AUTO = 'auto' # BZIP2 compression. BZIP2 = 'bzip2' # DEFLATE compression DEFLATE = 'deflate' # ZSTD compression ZSTD = 'zstd' # GZIP compression (deflate with GZIP headers). GZIP = 'gzip' # LZMA compression LZMA = 'lzma' # Uncompressed (i.e., may be split). UNCOMPRESSED = 'uncompressed'
[docs] @classmethod def is_valid_compression_type(cls, compression_type): """Returns True for valid compression types, False otherwise.""" types = set([ CompressionTypes.AUTO, CompressionTypes.BZIP2, CompressionTypes.DEFLATE, CompressionTypes.GZIP, CompressionTypes.ZSTD, CompressionTypes.LZMA, CompressionTypes.UNCOMPRESSED ]) return compression_type in types
[docs] @classmethod def mime_type(cls, compression_type, default='application/octet-stream'): mime_types_by_compression_type = { cls.BZIP2: 'application/x-bz2', cls.DEFLATE: 'application/x-deflate', cls.GZIP: 'application/x-gzip', cls.ZSTD: 'application/zstd', cls.LZMA: 'application/lzma' } return mime_types_by_compression_type.get(compression_type, default)
[docs] @classmethod def detect_compression_type(cls, file_path): """Returns the compression type of a file (based on its suffix).""" compression_types_by_suffix = { '.bz2': cls.BZIP2, '.deflate': cls.DEFLATE, '.gz': cls.GZIP, '.zst': cls.ZSTD, '.zstd': cls.ZSTD, '.xz': cls.LZMA, '.lzma': cls.LZMA } lowercased_path = file_path.lower() for suffix, compression_type in compression_types_by_suffix.items(): if lowercased_path.endswith(suffix): return compression_type return cls.UNCOMPRESSED
[docs]class CompressedFile(object): """File wrapper for easier handling of compressed files.""" # XXX: This class is not thread safe in the read path. # The bit mask to use for the wbits parameters of the zlib compressor and # decompressor objects. _gzip_mask = zlib.MAX_WBITS | 16 # Mask when using GZIP headers. def __init__( self, fileobj, # type: BinaryIO compression_type=CompressionTypes.GZIP, read_size=DEFAULT_READ_BUFFER_SIZE): if not fileobj: raise ValueError('File object must not be None') if not CompressionTypes.is_valid_compression_type(compression_type): raise TypeError( 'compression_type must be CompressionType object but ' 'was %s' % type(compression_type)) if compression_type in (CompressionTypes.AUTO, CompressionTypes.UNCOMPRESSED): raise ValueError( 'Cannot create object with unspecified or no compression') self._file = fileobj self._compression_type = compression_type if self._file.tell() != 0: raise ValueError( 'File object must be at position 0 but was %d' % self._file.tell()) self._uncompressed_position = 0 self._uncompressed_size = None # type: Optional[int] if self.readable(): self._read_size = read_size self._read_buffer = io.BytesIO() self._read_position = 0 self._read_eof = False self._initialize_decompressor() else: self._decompressor = None if self.writeable(): self._initialize_compressor() else: self._compressor = None def _initialize_decompressor(self): if self._compression_type == CompressionTypes.BZIP2: self._decompressor = bz2.BZ2Decompressor() elif self._compression_type == CompressionTypes.DEFLATE: self._decompressor = zlib.decompressobj() elif self._compression_type == CompressionTypes.ZSTD: # hardcoded max_window_size to avoid too much memory # errors when reading big files, please refer # to the following issue for further explanation: # self._decompressor = zstandard.ZstdDecompressor( max_window_size=2147483648).decompressobj() elif self._compression_type == CompressionTypes.LZMA: self._decompressor = lzma.LZMADecompressor() else: assert self._compression_type == CompressionTypes.GZIP self._decompressor = zlib.decompressobj(self._gzip_mask) def _initialize_compressor(self): if self._compression_type == CompressionTypes.BZIP2: self._compressor = bz2.BZ2Compressor() elif self._compression_type == CompressionTypes.DEFLATE: self._compressor = zlib.compressobj( zlib.Z_DEFAULT_COMPRESSION, zlib.DEFLATED) elif self._compression_type == CompressionTypes.ZSTD: self._compressor = zstandard.ZstdCompressor().compressobj() elif self._compression_type == CompressionTypes.LZMA: self._compressor = lzma.LZMACompressor() else: assert self._compression_type == CompressionTypes.GZIP self._compressor = zlib.compressobj( zlib.Z_DEFAULT_COMPRESSION, zlib.DEFLATED, self._gzip_mask)
[docs] def readable(self): # type: () -> bool mode = self._file.mode return 'r' in mode or 'a' in mode
[docs] def writeable(self): # type: () -> bool mode = self._file.mode return 'w' in mode or 'a' in mode
[docs] def write(self, data): # type: (bytes) -> None """Write data to file.""" if not self._compressor: raise ValueError('compressor not initialized') self._uncompressed_position += len(data) compressed = self._compressor.compress(data) if compressed: self._file.write(compressed)
def _fetch_to_internal_buffer(self, num_bytes: int) -> None: """Fetch up to num_bytes into the internal buffer.""" if (not self._read_eof and self._read_position > 0 and (self._read_buffer.tell() - self._read_position) < num_bytes): # There aren't enough number of bytes to accommodate a read, so we # prepare for a possibly large read by clearing up all internal buffers # but without dropping any previous held data. data = self._clear_read_buffer() self._read_buffer.write(data) assert self._decompressor while not self._read_eof and (self._read_buffer.tell() - self._read_position) < num_bytes: # Continue reading from the underlying file object until enough bytes are # available, or EOF is reached. if not self._decompressor.unused_data: buf = else: # Any uncompressed data at the end of the stream of a gzip or bzip2 # file that is not corrupted points to a concatenated compressed # file. We read concatenated files by recursively creating decompressor # objects for the unused compressed data. buf = self._decompressor.unused_data self._initialize_decompressor() if buf: decompressed = self._decompressor.decompress(buf) del buf # Free up some possibly large and no-longer-needed memory. self._read_buffer.write(decompressed) else: # EOF of current stream reached. if (self._compression_type == CompressionTypes.BZIP2 or self._compression_type == CompressionTypes.DEFLATE or self._compression_type == CompressionTypes.ZSTD or self._compression_type == CompressionTypes.GZIP or self._compression_type == CompressionTypes.LZMA): pass else: # Deflate, Gzip and bzip2 formats do not require flushing # remaining data in the decompressor into the read buffer when # fully decompressing files. self._read_buffer.write(self._decompressor.flush()) # Record that we have hit the end of file, so we won't unnecessarily # repeat the completeness verification step above. self._read_eof = True def _read_from_internal_buffer(self, read_fn): """Read from the internal buffer by using the supplied read_fn.""" result = read_fn() self._read_position += len(result) self._uncompressed_position += len(result), os.SEEK_END) # Allow future writes. return result
[docs] def read(self, num_bytes: Optional[int] = None) -> bytes: if not self._decompressor: raise ValueError('decompressor not initialized') self._fetch_to_internal_buffer(num_bytes) return self._read_from_internal_buffer( lambda:
[docs] def readline(self): # type: () -> bytes """Equivalent to standard file.readline(). Same return conventions apply.""" if not self._decompressor: raise ValueError('decompressor not initialized') bytes_io = io.BytesIO() while True: # Ensure that the internal buffer has at least half the read_size. Going # with half the _read_size (as opposed to a full _read_size) to ensure # that actual fetches are more evenly spread out, as opposed to having 2 # consecutive reads at the beginning of a read. self._fetch_to_internal_buffer(self._read_size // 2) line = self._read_from_internal_buffer( lambda: self._read_buffer.readline()) bytes_io.write(line) if line.endswith(b'\n') or not line: break # Newline or EOF reached. return bytes_io.getvalue()
[docs] def closed(self) -> bool: return not self._file or self._file.closed
[docs] def close(self) -> None: if self.readable(): self._read_buffer.close() if self.writeable(): assert self._compressor self._file.write(self._compressor.flush()) self._file.close()
[docs] def flush(self) -> None: if self.writeable(): assert self._compressor self._file.write(self._compressor.flush()) self._file.flush()
@property def seekable(self): # type: () -> bool return 'r' in self._file.mode def _clear_read_buffer(self): # type: () -> None """Clears the read buffer by removing all the contents and resetting _read_position to 0""" self._read_position = 0 self._read_buffer.truncate(0) def _rewind_file(self): # type: () -> None """Seeks to the beginning of the input file. Input file's EOF marker is cleared and _uncompressed_position is reset to zero""", os.SEEK_SET) self._read_eof = False self._uncompressed_position = 0 def _rewind(self): # type: () -> None """Seeks to the beginning of the input file and resets the internal read buffer. The decompressor object is re-initialized to ensure that no data left in it's buffer.""" self._clear_read_buffer() self._rewind_file() # Re-initialize decompressor to clear any data buffered prior to rewind self._initialize_decompressor()
[docs] def seek(self, offset, whence=os.SEEK_SET): # type: (int, int) -> None """Set the file's current offset. Seeking behavior: * seeking from the end :data:`os.SEEK_END` the whole file is decompressed once to determine its size. Therefore it is preferred to use :data:`os.SEEK_SET` or :data:`os.SEEK_CUR` to avoid the processing overhead * seeking backwards from the current position rewinds the file to ``0`` and decompresses the chunks to the requested offset * seeking is only supported in files opened for reading * if the new offset is out of bound, it is adjusted to either ``0`` or ``EOF``. Args: offset (int): seek offset in the uncompressed content represented as number whence (int): seek mode. Supported modes are :data:`os.SEEK_SET` (absolute seek), :data:`os.SEEK_CUR` (seek relative to the current position), and :data:`os.SEEK_END` (seek relative to the end, offset should be negative). Raises: IOError: When this buffer is closed. ValueError: When whence is invalid or the file is not seekable """ if whence == os.SEEK_SET: absolute_offset = offset elif whence == os.SEEK_CUR: absolute_offset = self._uncompressed_position + offset elif whence == os.SEEK_END: # Determine and cache the uncompressed size of the file if not self._uncompressed_size: logger.warning( "Seeking relative from end of file is requested. " "Need to decompress the whole file once to determine " "its size. This might take a while...") uncompress_start_time = time.time() while pass uncompress_end_time = time.time() logger.warning( "Full file decompression for seek " "from end took %.2f secs", (uncompress_end_time - uncompress_start_time)) self._uncompressed_size = self._uncompressed_position absolute_offset = self._uncompressed_size + offset else: raise ValueError("Whence mode %r is invalid." % whence) # Determine how many bytes needs to be read before we reach # the requested offset. Rewind if we already passed the position. if absolute_offset < self._uncompressed_position: self._rewind() bytes_to_skip = absolute_offset - self._uncompressed_position # Read until the desired position is reached or EOF occurs. while bytes_to_skip: data =, bytes_to_skip)) if not data: break bytes_to_skip -= len(data)
[docs] def tell(self): # type: () -> int """Returns current position in uncompressed file.""" return self._uncompressed_position
def __enter__(self): return self def __exit__(self, exception_type, exception_value, traceback): self.close()
[docs]class FileMetadata(object): """Metadata about a file path that is the output of FileSystem.match. Fields: path: [Required] file path. size_in_bytes: [Required] file size in bytes. last_updated_in_seconds: [Optional] last modified timestamp of the file, or valued 0.0 if not specified. """ def __init__( self, path: str, size_in_bytes: int, last_updated_in_seconds: float = 0.0): assert isinstance(path, str) and path, "Path should be a string" assert isinstance(size_in_bytes, int) and size_in_bytes >= 0, \ "Invalid value for size_in_bytes should %s (of type %s)" % ( size_in_bytes, type(size_in_bytes)) self.path = path self.size_in_bytes = size_in_bytes self.last_updated_in_seconds = last_updated_in_seconds def __eq__(self, other): """Note: This is only used in tests where we verify that mock objects match. """ return ( isinstance(other, FileMetadata) and self.path == other.path and self.size_in_bytes == other.size_in_bytes and self.last_updated_in_seconds == other.last_updated_in_seconds) def __hash__(self): return hash((self.path, self.size_in_bytes, self.last_updated_in_seconds)) def __repr__(self): if self.last_updated_in_seconds == 0.0: return 'FileMetadata(%s, %s)' % (self.path, self.size_in_bytes) else: return 'FileMetadata(%s, %s, %s)' % ( self.path, self.size_in_bytes, self.last_updated_in_seconds)
[docs]class MatchResult(object): """Result from the ``FileSystem`` match operation which contains the list of matched ``FileMetadata``. """ def __init__(self, pattern, metadata_list): # type: (str, List[FileMetadata]) -> None self.metadata_list = metadata_list self.pattern = pattern
class BeamIOError(IOError): def __init__(self, msg, exception_details=None): """Class representing the errors thrown in the batch file operations. Args: msg: Message string for the exception thrown exception_details: Optional map of individual input to exception for failed operations in batch. This parameter is optional so if specified the user can assume that the all errors in the filesystem operation have been reported. When the details are missing then the operation may have failed anywhere so the user should use match to determine the current state of the system. """ message = "%s with exceptions %s" % (msg, exception_details) super().__init__(message) self.exception_details = exception_details
[docs]class FileSystem(BeamPlugin, metaclass=abc.ABCMeta): """A class that defines the functions that can be performed on a filesystem. All methods are abstract and they are for file system providers to implement. Clients should use the FileSystems class to interact with the correct file system based on the provided file pattern scheme. """ CHUNK_SIZE = 1 # Chuck size in the batch operations def __init__(self, pipeline_options): """ Args: pipeline_options: Instance of ``PipelineOptions`` or dict of options and values (like ``RuntimeValueProvider.runtime_options``). """ @staticmethod def _get_compression_type(path, compression_type): if compression_type == CompressionTypes.AUTO: compression_type = CompressionTypes.detect_compression_type(path) elif not CompressionTypes.is_valid_compression_type(compression_type): raise TypeError( 'compression_type must be CompressionType object but ' 'was %s' % type(compression_type)) return compression_type
[docs] @classmethod def scheme(cls): """URI scheme for the FileSystem """ raise NotImplementedError
[docs] @abc.abstractmethod def join(self, basepath, *paths): # type: (str, *str) -> str """Join two or more pathname components for the filesystem Args: basepath: string path of the first component of the path paths: path components to be added Returns: full path after combining all the passed components """ raise NotImplementedError
[docs] @abc.abstractmethod def split(self, path): # type: (str) -> Tuple[str, str] """Splits the given path into two parts. Splits the path into a pair (head, tail) such that tail contains the last component of the path and head contains everything up to that. For file-systems other than the local file-system, head should include the prefix. Args: path: path as a string Returns: a pair of path components as strings. """ raise NotImplementedError
[docs] @abc.abstractmethod def mkdirs(self, path): """Recursively create directories for the provided path. Args: path: string path of the directory structure that should be created Raises: IOError: if leaf directory already exists. """ raise NotImplementedError
[docs] @abc.abstractmethod def has_dirs(self): """Whether this FileSystem supports directories.""" raise NotImplementedError
@abc.abstractmethod def _list(self, dir_or_prefix): """List files in a location. Listing is non-recursive (for filesystems that support directories). Args: dir_or_prefix: (string) A directory or location prefix (for filesystems that don't have directories). Returns: Generator of ``FileMetadata`` objects. Raises: ``BeamIOError``: if listing fails, but not if no files were found. """ raise NotImplementedError @staticmethod def _split_scheme(url_or_path): match = re.match(r'(^[a-z]+)://(.*)', url_or_path) if match is not None: return match.groups() return None, url_or_path @staticmethod def _combine_scheme(scheme, path): if scheme is None: return path return '{}://{}'.format(scheme, path) def _url_dirname(self, url_or_path): """Like posixpath.dirname, but preserves scheme:// prefix. Args: url_or_path: A string in the form of scheme://some/path OR /some/path. """ scheme, path = self._split_scheme(url_or_path) return self._combine_scheme(scheme, posixpath.dirname(path))
[docs] def match_files(self, file_metas, pattern): # type: (List[FileMetadata], str) -> Iterator[FileMetadata] """Filter :class:`FileMetadata` objects by *pattern* Args: file_metas (list of :class:`FileMetadata`): Files to consider when matching pattern (str): File pattern See Also: :meth:`translate_pattern` Returns: Generator of matching :class:`FileMetadata` """ re_pattern = re.compile(self.translate_pattern(pattern)) match = re_pattern.match for file_metadata in file_metas: if match(file_metadata.path): yield file_metadata
[docs] @staticmethod def translate_pattern(pattern): # type: (str) -> str """ Translate a *pattern* to a regular expression. There is no way to quote meta-characters. Pattern syntax: The pattern syntax is based on the fnmatch_ syntax, with the following differences: - ``*`` Is equivalent to ``[^/\\]*`` rather than ``.*``. - ``**`` Is equivalent to ``.*``. See also: :meth:`match` uses this method This method is based on `Python 2.7's fnmatch.translate`_. The code in this method is licensed under PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2. .. _`fnmatch`: .. _`Python 2.7's fnmatch.translate`:\ /blob/170ea8ccd4235d28538ab713041502d07ad1cacd/Lib/ """ i, n = 0, len(pattern) res = '' while i < n: c = pattern[i] i = i + 1 if c == '*': # One char lookahead for "**" if i < n and pattern[i] == "*": res = res + '.*' i = i + 1 else: res = res + r'[^/\\]*' elif c == '?': res = res + '.' elif c == '[': j = i if j < n and pattern[j] == '!': j = j + 1 if j < n and pattern[j] == ']': j = j + 1 while j < n and pattern[j] != ']': j = j + 1 if j >= n: res = res + r'\[' else: stuff = pattern[i:j].replace('\\', '\\\\') i = j + 1 if stuff[0] == '!': stuff = '^' + stuff[1:] elif stuff[0] == '^': stuff = '\\' + stuff res = '%s[%s]' % (res, stuff) else: res = res + re.escape(c) logger.debug('translate_pattern: %r -> %r', pattern, res) return r'(?ms)' + res + r'\Z'
[docs] def match(self, patterns, limits=None): """Find all matching paths to the patterns provided. See Also: :meth:`translate_pattern` Patterns ending with '/' or '\\' will be appended with '*'. Args: patterns: list of string for the file path pattern to match against limits: list of maximum number of responses that need to be fetched Returns: list of ``MatchResult`` objects. Raises: ``BeamIOError``: if any of the pattern match operations fail """ if limits is None: limits = [None] * len(patterns) else: err_msg = "Patterns and limits should be equal in length" assert len(patterns) == len(limits), err_msg def _match(pattern, limit): """Find all matching paths to the pattern provided.""" if pattern.endswith('/') or pattern.endswith('\\'): pattern += '*' # Get the part of the pattern before the first globbing character. # For example scheme://path/foo* will become scheme://path/foo for # filesystems like GCS, or converted to scheme://path for filesystems with # directories. prefix_or_dir = re.match('^[^[*?]*', pattern).group(0) file_metadatas = [] if prefix_or_dir == pattern: # Short-circuit calling self.list() if there's no glob pattern to match. if self.exists(pattern): file_metadatas = [self.metadata(pattern)] else: if self.has_dirs(): prefix_dirname = self._url_dirname(prefix_or_dir) if not prefix_dirname == prefix_or_dir: logger.debug( "Changed prefix_or_dir %r -> %r", prefix_or_dir, prefix_dirname) prefix_or_dir = prefix_dirname logger.debug("Listing files in %r", prefix_or_dir) file_metadatas = self._list(prefix_or_dir) metadata_list = [] for file_metadata in self.match_files(file_metadatas, pattern): if limit is not None and len(metadata_list) >= limit: break metadata_list.append(file_metadata) return MatchResult(pattern, metadata_list) exceptions = {} result = [] for pattern, limit in zip(patterns, limits): try: result.append(_match(pattern, limit)) except Exception as e: # pylint: disable=broad-except exceptions[pattern] = e if exceptions: raise BeamIOError("Match operation failed", exceptions) return result
[docs] @abc.abstractmethod def create( self, path, mime_type='application/octet-stream', compression_type=CompressionTypes.AUTO): # type: (...) -> BinaryIO """Returns a write channel for the given file path. Args: path: string path of the file object to be written to the system mime_type: MIME type to specify the type of content in the file object compression_type: Type of compression to be used for this object Returns: file handle with a close function for the user to use """ raise NotImplementedError
[docs] @abc.abstractmethod def open( self, path, mime_type='application/octet-stream', compression_type=CompressionTypes.AUTO): # type: (...) -> BinaryIO """Returns a read channel for the given file path. Args: path: string path of the file object to be read mime_type: MIME type to specify the type of content in the file object compression_type: Type of compression to be used for this object Returns: file handle with a close function for the user to use """ raise NotImplementedError
[docs] @abc.abstractmethod def copy(self, source_file_names, destination_file_names): """Recursively copy the file tree from the source to the destination Args: source_file_names: list of source file objects that needs to be copied destination_file_names: list of destination of the new object Raises: ``BeamIOError``: if any of the copy operations fail """ raise NotImplementedError
[docs] @abc.abstractmethod def rename(self, source_file_names, destination_file_names): """Rename the files at the source list to the destination list. Source and destination lists should be of the same size. Args: source_file_names: List of file paths that need to be moved destination_file_names: List of destination_file_names for the files Raises: ``BeamIOError``: if any of the rename operations fail """ raise NotImplementedError
[docs] @abc.abstractmethod def exists(self, path): # type: (str) -> bool """Check if the provided path exists on the FileSystem. Args: path: string path that needs to be checked. Returns: boolean flag indicating if path exists """ raise NotImplementedError
[docs] @abc.abstractmethod def size(self, path): # type: (str) -> int """Get size in bytes of a file on the FileSystem. Args: path: string filepath of file. Returns: int size of file according to the FileSystem. Raises: ``BeamIOError``: if path doesn't exist. """ raise NotImplementedError
[docs] @abc.abstractmethod def last_updated(self, path): """Get UNIX Epoch time in seconds on the FileSystem. Args: path: string path of file. Returns: float UNIX Epoch time Raises: ``BeamIOError``: if path doesn't exist. """ raise NotImplementedError
[docs] def checksum(self, path): """Fetch checksum metadata of a file on the :class:``. This operation returns checksum metadata as stored in the underlying FileSystem. It should not need to read file data to obtain this value. Checksum type and format are FileSystem dependent and are not compatible between FileSystems. FileSystem implementations may return file size if a checksum isn't available. Args: path: string path of a file. Returns: string containing checksum Raises: ``BeamIOError``: if path isn't a file or doesn't exist. """ raise NotImplementedError
[docs] @abc.abstractmethod def metadata(self, path): """Fetch metadata of a file on the :class:``. This operation returns metadata as stored in the underlying FileSystem. It should not need to read file data to obtain this value. For web based file systems, this method should also incur as few as possible requests. Args: path: string path of a file. Returns: :class:``. Raises: ``BeamIOError``: if path isn't a file or doesn't exist. """ raise NotImplementedError
[docs] @abc.abstractmethod def delete(self, paths): """Deletes files or directories at the provided paths. Directories will be deleted recursively. Args: paths: list of paths that give the file objects to be deleted Raises: ``BeamIOError``: if any of the delete operations fail """ raise NotImplementedError