"""Common IO api utilities"""
import bz2
import codecs
from collections import abc
import dataclasses
import gzip
from io import BufferedIOBase, BytesIO, RawIOBase, StringIO, TextIOWrapper
import mmap
import os
from typing import IO, Any, AnyStr, Dict, List, Mapping, Optional, Tuple, Union, cast
from urllib.parse import (
urljoin,
urlparse as parse_url,
uses_netloc,
uses_params,
uses_relative,
)
import warnings
import zipfile
from pandas._typing import (
Buffer,
CompressionDict,
CompressionOptions,
FileOrBuffer,
FilePathOrBuffer,
StorageOptions,
)
from pandas.compat import get_lzma_file, import_lzma
from pandas.compat._optional import import_optional_dependency
from pandas.core.dtypes.common import is_file_like
lzma = import_lzma()
_VALID_URLS = set(uses_relative + uses_netloc + uses_params)
_VALID_URLS.discard("")
@dataclasses.dataclass
class IOArgs:
"""
Return value of io/common.py:_get_filepath_or_buffer.
Note (copy&past from io/parsers):
filepath_or_buffer can be Union[FilePathOrBuffer, s3fs.S3File, gcsfs.GCSFile]
though mypy handling of conditional imports is difficult.
See https://github.com/python/mypy/issues/1297
"""
filepath_or_buffer: FileOrBuffer
encoding: str
mode: str
compression: CompressionDict
should_close: bool = False
@dataclasses.dataclass
class IOHandles:
"""
Return value of io/common.py:get_handle
Can be used as a context manager.
This is used to easily close created buffers and to handle corner cases when
TextIOWrapper is inserted.
handle: The file handle to be used.
created_handles: All file handles that are created by get_handle
is_wrapped: Whether a TextIOWrapper needs to be detached.
"""
handle: Buffer
compression: CompressionDict
created_handles: List[Buffer] = dataclasses.field(default_factory=list)
is_wrapped: bool = False
is_mmap: bool = False
def close(self) -> None:
"""
Close all created buffers.
Note: If a TextIOWrapper was inserted, it is flushed and detached to
avoid closing the potentially user-created buffer.
"""
if self.is_wrapped:
assert isinstance(self.handle, TextIOWrapper)
self.handle.flush()
self.handle.detach()
self.created_handles.remove(self.handle)
try:
for handle in self.created_handles:
handle.close()
except (OSError, ValueError):
pass
self.created_handles = []
self.is_wrapped = False
def __enter__(self) -> "IOHandles":
return self
def __exit__(self, *args: Any) -> None:
self.close()
[docs]def is_url(url) -> bool:
"""
Check to see if a URL has a valid protocol.
Parameters
----------
url : str or unicode
Returns
-------
isurl : bool
If `url` has a valid protocol return True otherwise False.
"""
if not isinstance(url, str):
return False
return parse_url(url).scheme in _VALID_URLS
def _expand_user(filepath_or_buffer: FileOrBuffer[AnyStr]) -> FileOrBuffer[AnyStr]:
"""
Return the argument with an initial component of ~ or ~user
replaced by that user's home directory.
Parameters
----------
filepath_or_buffer : object to be converted if possible
Returns
-------
expanded_filepath_or_buffer : an expanded filepath or the
input if not expandable
"""
if isinstance(filepath_or_buffer, str):
return os.path.expanduser(filepath_or_buffer)
return filepath_or_buffer
def validate_header_arg(header) -> None:
if isinstance(header, bool):
raise TypeError(
"Passing a bool to header is invalid. Use header=None for no header or "
"header=int or list-like of ints to specify "
"the row(s) making up the column names"
)
def stringify_path(
filepath_or_buffer: FilePathOrBuffer[AnyStr],
convert_file_like: bool = False,
) -> FileOrBuffer[AnyStr]:
"""
Attempt to convert a path-like object to a string.
Parameters
----------
filepath_or_buffer : object to be converted
Returns
-------
str_filepath_or_buffer : maybe a string version of the object
Notes
-----
Objects supporting the fspath protocol (python 3.6+) are coerced
according to its __fspath__ method.
Any other object is passed through unchanged, which includes bytes,
strings, buffers, or anything else that's not even path-like.
"""
if not convert_file_like and is_file_like(filepath_or_buffer):
# GH 38125: some fsspec objects implement os.PathLike but have already opened a
# file. This prevents opening the file a second time. infer_compression calls
# this function with convert_file_like=True to infer the compression.
return cast(FileOrBuffer[AnyStr], filepath_or_buffer)
if isinstance(filepath_or_buffer, os.PathLike):
filepath_or_buffer = filepath_or_buffer.__fspath__()
return _expand_user(filepath_or_buffer)
def urlopen(*args, **kwargs):
"""
Lazy-import wrapper for stdlib urlopen, as that imports a big chunk of
the stdlib.
"""
import urllib.request
return urllib.request.urlopen(*args, **kwargs)
def is_fsspec_url(url: FilePathOrBuffer) -> bool:
"""
Returns true if the given URL looks like
something fsspec can handle
"""
return (
isinstance(url, str)
and "://" in url
and not url.startswith(("http://", "https://"))
)
def _get_filepath_or_buffer(
filepath_or_buffer: FilePathOrBuffer,
encoding: str = "utf-8",
compression: CompressionOptions = None,
mode: str = "r",
storage_options: StorageOptions = None,
) -> IOArgs:
"""
If the filepath_or_buffer is a url, translate and return the buffer.
Otherwise passthrough.
Parameters
----------
filepath_or_buffer : a url, filepath (str, py.path.local or pathlib.Path),
or buffer
compression : {{'gzip', 'bz2', 'zip', 'xz', None}}, optional
encoding : the encoding to use to decode bytes, default is 'utf-8'
mode : str, optional
storage_options : dict, optional
Extra options that make sense for a particular storage connection, e.g.
host, port, username, password, etc., if using a URL that will
be parsed by ``fsspec``, e.g., starting "s3://", "gcs://". An error
will be raised if providing this argument with a local path or
a file-like buffer. See the fsspec and backend storage implementation
docs for the set of allowed keys and values
.. versionadded:: 1.2.0
..versionchange:: 1.2.0
Returns the dataclass IOArgs.
"""
filepath_or_buffer = stringify_path(filepath_or_buffer)
# handle compression dict
compression_method, compression = get_compression_method(compression)
compression_method = infer_compression(filepath_or_buffer, compression_method)
# GH21227 internal compression is not used for non-binary handles.
if compression_method and hasattr(filepath_or_buffer, "write") and "b" not in mode:
warnings.warn(
"compression has no effect when passing a non-binary object as input.",
RuntimeWarning,
stacklevel=2,
)
compression_method = None
compression = dict(compression, method=compression_method)
# uniform encoding names
if encoding is not None:
encoding = encoding.replace("_", "-").lower()
# bz2 and xz do not write the byte order mark for utf-16 and utf-32
# print a warning when writing such files
if (
"w" in mode
and compression_method in ["bz2", "xz"]
and encoding in ["utf-16", "utf-32"]
):
warnings.warn(
f"{compression} will not write the byte order mark for {encoding}",
UnicodeWarning,
)
# Use binary mode when converting path-like objects to file-like objects (fsspec)
# except when text mode is explicitly requested. The original mode is returned if
# fsspec is not used.
fsspec_mode = mode
if "t" not in fsspec_mode and "b" not in fsspec_mode:
fsspec_mode += "b"
if isinstance(filepath_or_buffer, str) and is_url(filepath_or_buffer):
# TODO: fsspec can also handle HTTP via requests, but leaving this unchanged
if storage_options:
raise ValueError(
"storage_options passed with file object or non-fsspec file path"
)
req = urlopen(filepath_or_buffer)
content_encoding = req.headers.get("Content-Encoding", None)
if content_encoding == "gzip":
# Override compression based on Content-Encoding header
compression = {"method": "gzip"}
reader = BytesIO(req.read())
req.close()
return IOArgs(
filepath_or_buffer=reader,
encoding=encoding,
compression=compression,
should_close=True,
mode=fsspec_mode,
)
if is_fsspec_url(filepath_or_buffer):
assert isinstance(
filepath_or_buffer, str
) # just to appease mypy for this branch
# two special-case s3-like protocols; these have special meaning in Hadoop,
# but are equivalent to just "s3" from fsspec's point of view
# cc #11071
if filepath_or_buffer.startswith("s3a://"):
filepath_or_buffer = filepath_or_buffer.replace("s3a://", "s3://")
if filepath_or_buffer.startswith("s3n://"):
filepath_or_buffer = filepath_or_buffer.replace("s3n://", "s3://")
fsspec = import_optional_dependency("fsspec")
# If botocore is installed we fallback to reading with anon=True
# to allow reads from public buckets
err_types_to_retry_with_anon: List[Any] = []
try:
import_optional_dependency("botocore")
from botocore.exceptions import ClientError, NoCredentialsError
err_types_to_retry_with_anon = [
ClientError,
NoCredentialsError,
PermissionError,
]
except ImportError:
pass
try:
file_obj = fsspec.open(
filepath_or_buffer, mode=fsspec_mode, **(storage_options or {})
).open()
# GH 34626 Reads from Public Buckets without Credentials needs anon=True
except tuple(err_types_to_retry_with_anon):
if storage_options is None:
storage_options = {"anon": True}
else:
# don't mutate user input.
storage_options = dict(storage_options)
storage_options["anon"] = True
file_obj = fsspec.open(
filepath_or_buffer, mode=fsspec_mode, **(storage_options or {})
).open()
return IOArgs(
filepath_or_buffer=file_obj,
encoding=encoding,
compression=compression,
should_close=True,
mode=fsspec_mode,
)
elif storage_options:
raise ValueError(
"storage_options passed with file object or non-fsspec file path"
)
if isinstance(filepath_or_buffer, (str, bytes, mmap.mmap)):
return IOArgs(
filepath_or_buffer=_expand_user(filepath_or_buffer),
encoding=encoding,
compression=compression,
should_close=False,
mode=mode,
)
if not is_file_like(filepath_or_buffer):
msg = f"Invalid file path or buffer object type: {type(filepath_or_buffer)}"
raise ValueError(msg)
return IOArgs(
filepath_or_buffer=filepath_or_buffer,
encoding=encoding,
compression=compression,
should_close=False,
mode=mode,
)
def file_path_to_url(path: str) -> str:
"""
converts an absolute native path to a FILE URL.
Parameters
----------
path : a path in native format
Returns
-------
a valid FILE URL
"""
# lazify expensive import (~30ms)
from urllib.request import pathname2url
return urljoin("file:", pathname2url(path))
_compression_to_extension = {"gzip": ".gz", "bz2": ".bz2", "zip": ".zip", "xz": ".xz"}
def get_compression_method(
compression: CompressionOptions,
) -> Tuple[Optional[str], CompressionDict]:
"""
Simplifies a compression argument to a compression method string and
a mapping containing additional arguments.
Parameters
----------
compression : str or mapping
If string, specifies the compression method. If mapping, value at key
'method' specifies compression method.
Returns
-------
tuple of ({compression method}, Optional[str]
{compression arguments}, Dict[str, Any])
Raises
------
ValueError on mapping missing 'method' key
"""
compression_method: Optional[str]
if isinstance(compression, Mapping):
compression_args = dict(compression)
try:
compression_method = compression_args.pop("method")
except KeyError as err:
raise ValueError("If mapping, compression must have key 'method'") from err
else:
compression_args = {}
compression_method = compression
return compression_method, compression_args
def infer_compression(
filepath_or_buffer: FilePathOrBuffer, compression: Optional[str]
) -> Optional[str]:
"""
Get the compression method for filepath_or_buffer. If compression='infer',
the inferred compression method is returned. Otherwise, the input
compression method is returned unchanged, unless it's invalid, in which
case an error is raised.
Parameters
----------
filepath_or_buffer : str or file handle
File path or object.
compression : {'infer', 'gzip', 'bz2', 'zip', 'xz', None}
If 'infer' and `filepath_or_buffer` is path-like, then detect
compression from the following extensions: '.gz', '.bz2', '.zip',
or '.xz' (otherwise no compression).
Returns
-------
string or None
Raises
------
ValueError on invalid compression specified.
"""
if compression is None:
return None
# Infer compression
if compression == "infer":
# Convert all path types (e.g. pathlib.Path) to strings
filepath_or_buffer = stringify_path(filepath_or_buffer, convert_file_like=True)
if not isinstance(filepath_or_buffer, str):
# Cannot infer compression of a buffer, assume no compression
return None
# Infer compression from the filename/URL extension
for compression, extension in _compression_to_extension.items():
if filepath_or_buffer.lower().endswith(extension):
return compression
return None
# Compression has been specified. Check that it's valid
if compression in _compression_to_extension:
return compression
msg = f"Unrecognized compression type: {compression}"
valid = ["infer", None] + sorted(_compression_to_extension)
msg += f"\nValid compression types are {valid}"
raise ValueError(msg)
[docs]def get_handle(
path_or_buf: FilePathOrBuffer,
mode: str,
encoding: Optional[str] = None,
compression: CompressionOptions = None,
memory_map: bool = False,
is_text: bool = True,
errors: Optional[str] = None,
storage_options: StorageOptions = None,
) -> IOHandles:
"""
Get file handle for given path/buffer and mode.
Parameters
----------
path_or_buf : str or file handle
File path or object.
mode : str
Mode to open path_or_buf with.
encoding : str or None
Encoding to use.
compression : str or dict, default None
If string, specifies compression mode. If dict, value at key 'method'
specifies compression mode. Compression mode must be one of {'infer',
'gzip', 'bz2', 'zip', 'xz', None}. If compression mode is 'infer'
and `filepath_or_buffer` is path-like, then detect compression from
the following extensions: '.gz', '.bz2', '.zip', or '.xz' (otherwise
no compression). If dict and compression mode is one of
{'zip', 'gzip', 'bz2'}, or inferred as one of the above,
other entries passed as additional compression options.
.. versionchanged:: 1.0.0
May now be a dict with key 'method' as compression mode
and other keys as compression options if compression
mode is 'zip'.
.. versionchanged:: 1.1.0
Passing compression options as keys in dict is now
supported for compression modes 'gzip' and 'bz2' as well as 'zip'.
memory_map : boolean, default False
See parsers._parser_params for more information.
is_text : boolean, default True
Whether the type of the content passed to the file/buffer is string or
bytes. This is not the same as `"b" not in mode`. If a string content is
passed to a binary file/buffer, a wrapper is inserted.
errors : str, default 'strict'
Specifies how encoding and decoding errors are to be handled.
See the errors argument for :func:`open` for a full list
of options.
storage_options: StorageOptions = None
Passed to _get_filepath_or_buffer
.. versionchanged:: 1.2.0
Returns the dataclass IOHandles
"""
# Windows does not default to utf-8. Set to utf-8 for a consistent behavior
encoding_passed, encoding = encoding, encoding or "utf-8"
# read_csv does not know whether the buffer is opened in binary/text mode
if _is_binary_mode(path_or_buf, mode) and "b" not in mode:
mode += "b"
# open URLs
ioargs = _get_filepath_or_buffer(
path_or_buf,
encoding=encoding,
compression=compression,
mode=mode,
storage_options=storage_options,
)
handle = ioargs.filepath_or_buffer
handles: List[Buffer]
# memory mapping needs to be the first step
handle, memory_map, handles = _maybe_memory_map(
handle, memory_map, ioargs.encoding, ioargs.mode, errors
)
is_path = isinstance(handle, str)
compression_args = dict(ioargs.compression)
compression = compression_args.pop("method")
if compression:
# compression libraries do not like an explicit text-mode
ioargs.mode = ioargs.mode.replace("t", "")
# GZ Compression
if compression == "gzip":
if is_path:
assert isinstance(handle, str)
handle = gzip.GzipFile(
filename=handle,
mode=ioargs.mode,
**compression_args,
)
else:
handle = gzip.GzipFile(
fileobj=handle, # type: ignore[arg-type]
mode=ioargs.mode,
**compression_args,
)
# BZ Compression
elif compression == "bz2":
handle = bz2.BZ2File(
handle, # type: ignore[arg-type]
mode=ioargs.mode,
**compression_args,
)
# ZIP Compression
elif compression == "zip":
handle = _BytesZipFile(handle, ioargs.mode, **compression_args)
if handle.mode == "r":
handles.append(handle)
zip_names = handle.namelist()
if len(zip_names) == 1:
handle = handle.open(zip_names.pop())
elif len(zip_names) == 0:
raise ValueError(f"Zero files found in ZIP file {path_or_buf}")
else:
raise ValueError(
"Multiple files found in ZIP file. "
f"Only one file per ZIP: {zip_names}"
)
# XZ Compression
elif compression == "xz":
handle = get_lzma_file(lzma)(handle, ioargs.mode)
# Unrecognized Compression
else:
msg = f"Unrecognized compression type: {compression}"
raise ValueError(msg)
assert not isinstance(handle, str)
handles.append(handle)
elif isinstance(handle, str):
# Check whether the filename is to be opened in binary mode.
# Binary mode does not support 'encoding' and 'newline'.
if ioargs.encoding and "b" not in ioargs.mode:
if errors is None and encoding_passed is None:
# ignore errors when no encoding is specified
errors = "replace"
# Encoding
handle = open(
handle,
ioargs.mode,
encoding=ioargs.encoding,
errors=errors,
newline="",
)
else:
# Binary mode
handle = open(handle, ioargs.mode)
handles.append(handle)
# Convert BytesIO or file objects passed with an encoding
is_wrapped = False
if is_text and (compression or _is_binary_mode(handle, ioargs.mode)):
handle = TextIOWrapper(
handle, # type: ignore[arg-type]
encoding=ioargs.encoding,
errors=errors,
newline="",
)
handles.append(handle)
# only marked as wrapped when the caller provided a handle
is_wrapped = not (
isinstance(ioargs.filepath_or_buffer, str) or ioargs.should_close
)
handles.reverse() # close the most recently added buffer first
if ioargs.should_close:
assert not isinstance(ioargs.filepath_or_buffer, str)
handles.append(ioargs.filepath_or_buffer)
assert not isinstance(handle, str)
return IOHandles(
handle=handle,
created_handles=handles,
is_wrapped=is_wrapped,
is_mmap=memory_map,
compression=ioargs.compression,
)
# error: Definition of "__exit__" in base class "ZipFile" is incompatible with
# definition in base class "BytesIO" [misc]
# error: Definition of "__enter__" in base class "ZipFile" is incompatible with
# definition in base class "BytesIO" [misc]
# error: Definition of "__enter__" in base class "ZipFile" is incompatible with
# definition in base class "BinaryIO" [misc]
# error: Definition of "__enter__" in base class "ZipFile" is incompatible with
# definition in base class "IO" [misc]
# error: Definition of "read" in base class "ZipFile" is incompatible with
# definition in base class "BytesIO" [misc]
# error: Definition of "read" in base class "ZipFile" is incompatible with
# definition in base class "IO" [misc]
class _BytesZipFile(zipfile.ZipFile, BytesIO): # type: ignore[misc]
"""
Wrapper for standard library class ZipFile and allow the returned file-like
handle to accept byte strings via `write` method.
BytesIO provides attributes of file-like object and ZipFile.writestr writes
bytes strings into a member of the archive.
"""
# GH 17778
def __init__(
self,
file: FilePathOrBuffer,
mode: str,
archive_name: Optional[str] = None,
**kwargs,
):
mode = mode.replace("b", "")
self.archive_name = archive_name
self.multiple_write_buffer: Optional[Union[StringIO, BytesIO]] = None
kwargs_zip: Dict[str, Any] = {"compression": zipfile.ZIP_DEFLATED}
kwargs_zip.update(kwargs)
super().__init__(file, mode, **kwargs_zip) # type: ignore[arg-type]
def write(self, data):
# buffer multiple write calls, write on flush
if self.multiple_write_buffer is None:
self.multiple_write_buffer = (
BytesIO() if isinstance(data, bytes) else StringIO()
)
self.multiple_write_buffer.write(data)
def flush(self) -> None:
# write to actual handle and close write buffer
if self.multiple_write_buffer is None or self.multiple_write_buffer.closed:
return
# ZipFile needs a non-empty string
archive_name = self.archive_name or self.filename or "zip"
with self.multiple_write_buffer:
super().writestr(archive_name, self.multiple_write_buffer.getvalue())
def close(self):
self.flush()
super().close()
@property
def closed(self):
return self.fp is None
class _MMapWrapper(abc.Iterator):
"""
Wrapper for the Python's mmap class so that it can be properly read in
by Python's csv.reader class.
Parameters
----------
f : file object
File object to be mapped onto memory. Must support the 'fileno'
method or have an equivalent attribute
"""
def __init__(self, f: IO):
self.attributes = {}
for attribute in ("seekable", "readable", "writeable"):
if not hasattr(f, attribute):
continue
self.attributes[attribute] = getattr(f, attribute)()
self.mmap = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
def __getattr__(self, name: str):
if name in self.attributes:
return lambda: self.attributes[name]
return getattr(self.mmap, name)
def __iter__(self) -> "_MMapWrapper":
return self
def __next__(self) -> str:
newbytes = self.mmap.readline()
# readline returns bytes, not str, but Python's CSV reader
# expects str, so convert the output to str before continuing
newline = newbytes.decode("utf-8")
# mmap doesn't raise if reading past the allocated
# data but instead returns an empty string, so raise
# if that is returned
if newline == "":
raise StopIteration
return newline
def _maybe_memory_map(
handle: FileOrBuffer,
memory_map: bool,
encoding: str,
mode: str,
errors: Optional[str],
) -> Tuple[FileOrBuffer, bool, List[Buffer]]:
"""Try to memory map file/buffer."""
handles: List[Buffer] = []
memory_map &= hasattr(handle, "fileno") or isinstance(handle, str)
if not memory_map:
return handle, memory_map, handles
# need to open the file first
if isinstance(handle, str):
if encoding and "b" not in mode:
# Encoding
handle = open(handle, mode, encoding=encoding, errors=errors, newline="")
else:
# Binary mode
handle = open(handle, mode)
handles.append(handle)
try:
wrapped = cast(mmap.mmap, _MMapWrapper(handle)) # type: ignore[arg-type]
handle.close()
handles.remove(handle)
handles.append(wrapped)
handle = wrapped
except Exception:
# we catch any errors that may have occurred
# because that is consistent with the lower-level
# functionality of the C engine (pd.read_csv), so
# leave the file handler as is then
memory_map = False
return handle, memory_map, handles
def file_exists(filepath_or_buffer: FilePathOrBuffer) -> bool:
"""Test whether file exists."""
exists = False
filepath_or_buffer = stringify_path(filepath_or_buffer)
if not isinstance(filepath_or_buffer, str):
return exists
try:
exists = os.path.exists(filepath_or_buffer)
# gh-5874: if the filepath is too long will raise here
except (TypeError, ValueError):
pass
return exists
def _is_binary_mode(handle: FilePathOrBuffer, mode: str) -> bool:
"""Whether the handle is opened in binary mode"""
# specified by user
if "t" in mode or "b" in mode:
return "b" in mode
# classes that expect string but have 'b' in mode
text_classes = (codecs.StreamWriter, codecs.StreamReader, codecs.StreamReaderWriter)
if issubclass(type(handle), text_classes):
return False
# classes that expect bytes
binary_classes = (BufferedIOBase, RawIOBase)
return isinstance(handle, binary_classes) or "b" in getattr(handle, "mode", mode)