743 lines
22 KiB
Python
743 lines
22 KiB
Python
from __future__ import annotations
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import contextlib
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import logging
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import math
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import os
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import pathlib
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import re
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import sys
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import tempfile
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from functools import partial
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from hashlib import md5
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from importlib.metadata import version
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from typing import (
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IO,
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TYPE_CHECKING,
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Any,
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Callable,
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Iterable,
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Iterator,
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Sequence,
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TypeVar,
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)
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from urllib.parse import urlsplit
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if TYPE_CHECKING:
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from typing_extensions import TypeGuard
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from fsspec.spec import AbstractFileSystem
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DEFAULT_BLOCK_SIZE = 5 * 2**20
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T = TypeVar("T")
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def infer_storage_options(
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urlpath: str, inherit_storage_options: dict[str, Any] | None = None
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) -> dict[str, Any]:
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"""Infer storage options from URL path and merge it with existing storage
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options.
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Parameters
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----------
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urlpath: str or unicode
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Either local absolute file path or URL (hdfs://namenode:8020/file.csv)
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inherit_storage_options: dict (optional)
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Its contents will get merged with the inferred information from the
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given path
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Returns
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-------
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Storage options dict.
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Examples
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--------
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>>> infer_storage_options('/mnt/datasets/test.csv') # doctest: +SKIP
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{"protocol": "file", "path", "/mnt/datasets/test.csv"}
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>>> infer_storage_options(
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... 'hdfs://username:pwd@node:123/mnt/datasets/test.csv?q=1',
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... inherit_storage_options={'extra': 'value'},
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... ) # doctest: +SKIP
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{"protocol": "hdfs", "username": "username", "password": "pwd",
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"host": "node", "port": 123, "path": "/mnt/datasets/test.csv",
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"url_query": "q=1", "extra": "value"}
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"""
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# Handle Windows paths including disk name in this special case
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if (
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re.match(r"^[a-zA-Z]:[\\/]", urlpath)
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or re.match(r"^[a-zA-Z0-9]+://", urlpath) is None
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):
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return {"protocol": "file", "path": urlpath}
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parsed_path = urlsplit(urlpath)
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protocol = parsed_path.scheme or "file"
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if parsed_path.fragment:
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path = "#".join([parsed_path.path, parsed_path.fragment])
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else:
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path = parsed_path.path
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if protocol == "file":
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# Special case parsing file protocol URL on Windows according to:
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# https://msdn.microsoft.com/en-us/library/jj710207.aspx
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windows_path = re.match(r"^/([a-zA-Z])[:|]([\\/].*)$", path)
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if windows_path:
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path = "%s:%s" % windows_path.groups()
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if protocol in ["http", "https"]:
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# for HTTP, we don't want to parse, as requests will anyway
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return {"protocol": protocol, "path": urlpath}
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options: dict[str, Any] = {"protocol": protocol, "path": path}
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if parsed_path.netloc:
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# Parse `hostname` from netloc manually because `parsed_path.hostname`
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# lowercases the hostname which is not always desirable (e.g. in S3):
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# https://github.com/dask/dask/issues/1417
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options["host"] = parsed_path.netloc.rsplit("@", 1)[-1].rsplit(":", 1)[0]
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if protocol in ("s3", "s3a", "gcs", "gs"):
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options["path"] = options["host"] + options["path"]
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else:
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options["host"] = options["host"]
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if parsed_path.port:
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options["port"] = parsed_path.port
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if parsed_path.username:
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options["username"] = parsed_path.username
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if parsed_path.password:
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options["password"] = parsed_path.password
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if parsed_path.query:
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options["url_query"] = parsed_path.query
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if parsed_path.fragment:
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options["url_fragment"] = parsed_path.fragment
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if inherit_storage_options:
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update_storage_options(options, inherit_storage_options)
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return options
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def update_storage_options(
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options: dict[str, Any], inherited: dict[str, Any] | None = None
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) -> None:
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if not inherited:
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inherited = {}
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collisions = set(options) & set(inherited)
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if collisions:
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for collision in collisions:
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if options.get(collision) != inherited.get(collision):
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raise KeyError(
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f"Collision between inferred and specified storage "
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f"option:\n{collision}"
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)
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options.update(inherited)
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# Compression extensions registered via fsspec.compression.register_compression
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compressions: dict[str, str] = {}
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def infer_compression(filename: str) -> str | None:
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"""Infer compression, if available, from filename.
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Infer a named compression type, if registered and available, from filename
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extension. This includes builtin (gz, bz2, zip) compressions, as well as
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optional compressions. See fsspec.compression.register_compression.
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"""
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extension = os.path.splitext(filename)[-1].strip(".").lower()
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if extension in compressions:
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return compressions[extension]
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return None
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def build_name_function(max_int: float) -> Callable[[int], str]:
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"""Returns a function that receives a single integer
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and returns it as a string padded by enough zero characters
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to align with maximum possible integer
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>>> name_f = build_name_function(57)
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>>> name_f(7)
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'07'
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>>> name_f(31)
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'31'
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>>> build_name_function(1000)(42)
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'0042'
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>>> build_name_function(999)(42)
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'042'
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>>> build_name_function(0)(0)
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'0'
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"""
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# handle corner cases max_int is 0 or exact power of 10
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max_int += 1e-8
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pad_length = int(math.ceil(math.log10(max_int)))
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def name_function(i: int) -> str:
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return str(i).zfill(pad_length)
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return name_function
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def seek_delimiter(file: IO[bytes], delimiter: bytes, blocksize: int) -> bool:
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r"""Seek current file to file start, file end, or byte after delimiter seq.
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Seeks file to next chunk delimiter, where chunks are defined on file start,
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a delimiting sequence, and file end. Use file.tell() to see location afterwards.
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Note that file start is a valid split, so must be at offset > 0 to seek for
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delimiter.
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Parameters
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----------
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file: a file
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delimiter: bytes
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a delimiter like ``b'\n'`` or message sentinel, matching file .read() type
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blocksize: int
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Number of bytes to read from the file at once.
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Returns
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-------
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Returns True if a delimiter was found, False if at file start or end.
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"""
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if file.tell() == 0:
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# beginning-of-file, return without seek
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return False
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# Interface is for binary IO, with delimiter as bytes, but initialize last
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# with result of file.read to preserve compatibility with text IO.
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last: bytes | None = None
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while True:
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current = file.read(blocksize)
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if not current:
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# end-of-file without delimiter
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return False
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full = last + current if last else current
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try:
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if delimiter in full:
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i = full.index(delimiter)
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file.seek(file.tell() - (len(full) - i) + len(delimiter))
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return True
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elif len(current) < blocksize:
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# end-of-file without delimiter
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return False
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except (OSError, ValueError):
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pass
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last = full[-len(delimiter) :]
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def read_block(
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f: IO[bytes],
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offset: int,
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length: int | None,
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delimiter: bytes | None = None,
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split_before: bool = False,
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) -> bytes:
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"""Read a block of bytes from a file
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Parameters
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----------
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f: File
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Open file
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offset: int
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Byte offset to start read
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length: int
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Number of bytes to read, read through end of file if None
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delimiter: bytes (optional)
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Ensure reading starts and stops at delimiter bytestring
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split_before: bool (optional)
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Start/stop read *before* delimiter bytestring.
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If using the ``delimiter=`` keyword argument we ensure that the read
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starts and stops at delimiter boundaries that follow the locations
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``offset`` and ``offset + length``. If ``offset`` is zero then we
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start at zero, regardless of delimiter. The bytestring returned WILL
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include the terminating delimiter string.
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Examples
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--------
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>>> from io import BytesIO # doctest: +SKIP
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>>> f = BytesIO(b'Alice, 100\\nBob, 200\\nCharlie, 300') # doctest: +SKIP
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>>> read_block(f, 0, 13) # doctest: +SKIP
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b'Alice, 100\\nBo'
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>>> read_block(f, 0, 13, delimiter=b'\\n') # doctest: +SKIP
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b'Alice, 100\\nBob, 200\\n'
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>>> read_block(f, 10, 10, delimiter=b'\\n') # doctest: +SKIP
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b'Bob, 200\\nCharlie, 300'
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"""
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if delimiter:
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f.seek(offset)
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found_start_delim = seek_delimiter(f, delimiter, 2**16)
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if length is None:
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return f.read()
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start = f.tell()
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length -= start - offset
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f.seek(start + length)
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found_end_delim = seek_delimiter(f, delimiter, 2**16)
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end = f.tell()
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# Adjust split location to before delimiter if seek found the
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# delimiter sequence, not start or end of file.
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if found_start_delim and split_before:
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start -= len(delimiter)
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if found_end_delim and split_before:
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end -= len(delimiter)
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offset = start
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length = end - start
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f.seek(offset)
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# TODO: allow length to be None and read to the end of the file?
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assert length is not None
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b = f.read(length)
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return b
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def tokenize(*args: Any, **kwargs: Any) -> str:
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"""Deterministic token
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(modified from dask.base)
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>>> tokenize([1, 2, '3'])
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'9d71491b50023b06fc76928e6eddb952'
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>>> tokenize('Hello') == tokenize('Hello')
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True
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"""
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if kwargs:
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args += (kwargs,)
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try:
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h = md5(str(args).encode())
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except ValueError:
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# FIPS systems: https://github.com/fsspec/filesystem_spec/issues/380
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h = md5(str(args).encode(), usedforsecurity=False)
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return h.hexdigest()
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|
|
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def stringify_path(filepath: str | os.PathLike[str] | pathlib.Path) -> str:
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"""Attempt to convert a path-like object to a string.
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|
Parameters
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----------
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filepath: object to be converted
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|
Returns
|
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-------
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filepath_str: maybe a string version of the object
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|
Notes
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-----
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Objects supporting the fspath protocol are coerced according to its
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__fspath__ method.
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For backwards compatibility with older Python version, pathlib.Path
|
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objects are specially coerced.
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Any other object is passed through unchanged, which includes bytes,
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strings, buffers, or anything else that's not even path-like.
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"""
|
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if isinstance(filepath, str):
|
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return filepath
|
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elif hasattr(filepath, "__fspath__"):
|
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return filepath.__fspath__()
|
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elif isinstance(filepath, pathlib.Path):
|
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return str(filepath)
|
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elif hasattr(filepath, "path"):
|
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return filepath.path
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else:
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return filepath # type: ignore[return-value]
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|
|
|
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def make_instance(
|
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cls: Callable[..., T], args: Sequence[Any], kwargs: dict[str, Any]
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) -> T:
|
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inst = cls(*args, **kwargs)
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inst._determine_worker() # type: ignore[attr-defined]
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return inst
|
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|
|
|
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def common_prefix(paths: Iterable[str]) -> str:
|
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"""For a list of paths, find the shortest prefix common to all"""
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parts = [p.split("/") for p in paths]
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lmax = min(len(p) for p in parts)
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end = 0
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for i in range(lmax):
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end = all(p[i] == parts[0][i] for p in parts)
|
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if not end:
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break
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i += end
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return "/".join(parts[0][:i])
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|
|
|
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def other_paths(
|
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paths: list[str],
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path2: str | list[str],
|
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exists: bool = False,
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|
flatten: bool = False,
|
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) -> list[str]:
|
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"""In bulk file operations, construct a new file tree from a list of files
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|
Parameters
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|
----------
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paths: list of str
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The input file tree
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path2: str or list of str
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|
Root to construct the new list in. If this is already a list of str, we just
|
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assert it has the right number of elements.
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exists: bool (optional)
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|
For a str destination, it is already exists (and is a dir), files should
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end up inside.
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flatten: bool (optional)
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|
Whether to flatten the input directory tree structure so that the output files
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|
are in the same directory.
|
|
|
|
Returns
|
|
-------
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|
list of str
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|
"""
|
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|
|
if isinstance(path2, str):
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path2 = path2.rstrip("/")
|
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|
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if flatten:
|
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path2 = ["/".join((path2, p.split("/")[-1])) for p in paths]
|
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else:
|
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cp = common_prefix(paths)
|
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if exists:
|
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cp = cp.rsplit("/", 1)[0]
|
|
if not cp and all(not s.startswith("/") for s in paths):
|
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path2 = ["/".join([path2, p]) for p in paths]
|
|
else:
|
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path2 = [p.replace(cp, path2, 1) for p in paths]
|
|
else:
|
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assert len(paths) == len(path2)
|
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return path2
|
|
|
|
|
|
def is_exception(obj: Any) -> bool:
|
|
return isinstance(obj, BaseException)
|
|
|
|
|
|
def isfilelike(f: Any) -> TypeGuard[IO[bytes]]:
|
|
for attr in ["read", "close", "tell"]:
|
|
if not hasattr(f, attr):
|
|
return False
|
|
return True
|
|
|
|
|
|
def get_protocol(url: str) -> str:
|
|
url = stringify_path(url)
|
|
parts = re.split(r"(\:\:|\://)", url, 1)
|
|
if len(parts) > 1:
|
|
return parts[0]
|
|
return "file"
|
|
|
|
|
|
def can_be_local(path: str) -> bool:
|
|
"""Can the given URL be used with open_local?"""
|
|
from fsspec import get_filesystem_class
|
|
|
|
try:
|
|
return getattr(get_filesystem_class(get_protocol(path)), "local_file", False)
|
|
except (ValueError, ImportError):
|
|
# not in registry or import failed
|
|
return False
|
|
|
|
|
|
def get_package_version_without_import(name: str) -> str | None:
|
|
"""For given package name, try to find the version without importing it
|
|
|
|
Import and package.__version__ is still the backup here, so an import
|
|
*might* happen.
|
|
|
|
Returns either the version string, or None if the package
|
|
or the version was not readily found.
|
|
"""
|
|
if name in sys.modules:
|
|
mod = sys.modules[name]
|
|
if hasattr(mod, "__version__"):
|
|
return mod.__version__
|
|
try:
|
|
return version(name)
|
|
except: # noqa: E722
|
|
pass
|
|
try:
|
|
import importlib
|
|
|
|
mod = importlib.import_module(name)
|
|
return mod.__version__
|
|
except (ImportError, AttributeError):
|
|
return None
|
|
|
|
|
|
def setup_logging(
|
|
logger: logging.Logger | None = None,
|
|
logger_name: str | None = None,
|
|
level: str = "DEBUG",
|
|
clear: bool = True,
|
|
) -> logging.Logger:
|
|
if logger is None and logger_name is None:
|
|
raise ValueError("Provide either logger object or logger name")
|
|
logger = logger or logging.getLogger(logger_name)
|
|
handle = logging.StreamHandler()
|
|
formatter = logging.Formatter(
|
|
"%(asctime)s - %(name)s - %(levelname)s - %(funcName)s -- %(message)s"
|
|
)
|
|
handle.setFormatter(formatter)
|
|
if clear:
|
|
logger.handlers.clear()
|
|
logger.addHandler(handle)
|
|
logger.setLevel(level)
|
|
return logger
|
|
|
|
|
|
def _unstrip_protocol(name: str, fs: AbstractFileSystem) -> str:
|
|
return fs.unstrip_protocol(name)
|
|
|
|
|
|
def mirror_from(
|
|
origin_name: str, methods: Iterable[str]
|
|
) -> Callable[[type[T]], type[T]]:
|
|
"""Mirror attributes and methods from the given
|
|
origin_name attribute of the instance to the
|
|
decorated class"""
|
|
|
|
def origin_getter(method: str, self: Any) -> Any:
|
|
origin = getattr(self, origin_name)
|
|
return getattr(origin, method)
|
|
|
|
def wrapper(cls: type[T]) -> type[T]:
|
|
for method in methods:
|
|
wrapped_method = partial(origin_getter, method)
|
|
setattr(cls, method, property(wrapped_method))
|
|
return cls
|
|
|
|
return wrapper
|
|
|
|
|
|
@contextlib.contextmanager
|
|
def nullcontext(obj: T) -> Iterator[T]:
|
|
yield obj
|
|
|
|
|
|
def merge_offset_ranges(
|
|
paths: list[str],
|
|
starts: list[int] | int,
|
|
ends: list[int] | int,
|
|
max_gap: int = 0,
|
|
max_block: int | None = None,
|
|
sort: bool = True,
|
|
) -> tuple[list[str], list[int], list[int]]:
|
|
"""Merge adjacent byte-offset ranges when the inter-range
|
|
gap is <= `max_gap`, and when the merged byte range does not
|
|
exceed `max_block` (if specified). By default, this function
|
|
will re-order the input paths and byte ranges to ensure sorted
|
|
order. If the user can guarantee that the inputs are already
|
|
sorted, passing `sort=False` will skip the re-ordering.
|
|
"""
|
|
# Check input
|
|
if not isinstance(paths, list):
|
|
raise TypeError
|
|
if not isinstance(starts, list):
|
|
starts = [starts] * len(paths)
|
|
if not isinstance(ends, list):
|
|
ends = [ends] * len(paths)
|
|
if len(starts) != len(paths) or len(ends) != len(paths):
|
|
raise ValueError
|
|
|
|
# Early Return
|
|
if len(starts) <= 1:
|
|
return paths, starts, ends
|
|
|
|
starts = [s or 0 for s in starts]
|
|
# Sort by paths and then ranges if `sort=True`
|
|
if sort:
|
|
paths, starts, ends = (
|
|
list(v)
|
|
for v in zip(
|
|
*sorted(
|
|
zip(paths, starts, ends),
|
|
)
|
|
)
|
|
)
|
|
|
|
if paths:
|
|
# Loop through the coupled `paths`, `starts`, and
|
|
# `ends`, and merge adjacent blocks when appropriate
|
|
new_paths = paths[:1]
|
|
new_starts = starts[:1]
|
|
new_ends = ends[:1]
|
|
for i in range(1, len(paths)):
|
|
if paths[i] == paths[i - 1] and new_ends[-1] is None:
|
|
continue
|
|
elif (
|
|
paths[i] != paths[i - 1]
|
|
or ((starts[i] - new_ends[-1]) > max_gap)
|
|
or (max_block is not None and (ends[i] - new_starts[-1]) > max_block)
|
|
):
|
|
# Cannot merge with previous block.
|
|
# Add new `paths`, `starts`, and `ends` elements
|
|
new_paths.append(paths[i])
|
|
new_starts.append(starts[i])
|
|
new_ends.append(ends[i])
|
|
else:
|
|
# Merge with previous block by updating the
|
|
# last element of `ends`
|
|
new_ends[-1] = ends[i]
|
|
return new_paths, new_starts, new_ends
|
|
|
|
# `paths` is empty. Just return input lists
|
|
return paths, starts, ends
|
|
|
|
|
|
def file_size(filelike: IO[bytes]) -> int:
|
|
"""Find length of any open read-mode file-like"""
|
|
pos = filelike.tell()
|
|
try:
|
|
return filelike.seek(0, 2)
|
|
finally:
|
|
filelike.seek(pos)
|
|
|
|
|
|
@contextlib.contextmanager
|
|
def atomic_write(path: str, mode: str = "wb"):
|
|
"""
|
|
A context manager that opens a temporary file next to `path` and, on exit,
|
|
replaces `path` with the temporary file, thereby updating `path`
|
|
atomically.
|
|
"""
|
|
fd, fn = tempfile.mkstemp(
|
|
dir=os.path.dirname(path), prefix=os.path.basename(path) + "-"
|
|
)
|
|
try:
|
|
with open(fd, mode) as fp:
|
|
yield fp
|
|
except BaseException:
|
|
with contextlib.suppress(FileNotFoundError):
|
|
os.unlink(fn)
|
|
raise
|
|
else:
|
|
os.replace(fn, path)
|
|
|
|
|
|
def _translate(pat, STAR, QUESTION_MARK):
|
|
# Copied from: https://github.com/python/cpython/pull/106703.
|
|
res: list[str] = []
|
|
add = res.append
|
|
i, n = 0, len(pat)
|
|
while i < n:
|
|
c = pat[i]
|
|
i = i + 1
|
|
if c == "*":
|
|
# compress consecutive `*` into one
|
|
if (not res) or res[-1] is not STAR:
|
|
add(STAR)
|
|
elif c == "?":
|
|
add(QUESTION_MARK)
|
|
elif c == "[":
|
|
j = i
|
|
if j < n and pat[j] == "!":
|
|
j = j + 1
|
|
if j < n and pat[j] == "]":
|
|
j = j + 1
|
|
while j < n and pat[j] != "]":
|
|
j = j + 1
|
|
if j >= n:
|
|
add("\\[")
|
|
else:
|
|
stuff = pat[i:j]
|
|
if "-" not in stuff:
|
|
stuff = stuff.replace("\\", r"\\")
|
|
else:
|
|
chunks = []
|
|
k = i + 2 if pat[i] == "!" else i + 1
|
|
while True:
|
|
k = pat.find("-", k, j)
|
|
if k < 0:
|
|
break
|
|
chunks.append(pat[i:k])
|
|
i = k + 1
|
|
k = k + 3
|
|
chunk = pat[i:j]
|
|
if chunk:
|
|
chunks.append(chunk)
|
|
else:
|
|
chunks[-1] += "-"
|
|
# Remove empty ranges -- invalid in RE.
|
|
for k in range(len(chunks) - 1, 0, -1):
|
|
if chunks[k - 1][-1] > chunks[k][0]:
|
|
chunks[k - 1] = chunks[k - 1][:-1] + chunks[k][1:]
|
|
del chunks[k]
|
|
# Escape backslashes and hyphens for set difference (--).
|
|
# Hyphens that create ranges shouldn't be escaped.
|
|
stuff = "-".join(
|
|
s.replace("\\", r"\\").replace("-", r"\-") for s in chunks
|
|
)
|
|
# Escape set operations (&&, ~~ and ||).
|
|
stuff = re.sub(r"([&~|])", r"\\\1", stuff)
|
|
i = j + 1
|
|
if not stuff:
|
|
# Empty range: never match.
|
|
add("(?!)")
|
|
elif stuff == "!":
|
|
# Negated empty range: match any character.
|
|
add(".")
|
|
else:
|
|
if stuff[0] == "!":
|
|
stuff = "^" + stuff[1:]
|
|
elif stuff[0] in ("^", "["):
|
|
stuff = "\\" + stuff
|
|
add(f"[{stuff}]")
|
|
else:
|
|
add(re.escape(c))
|
|
assert i == n
|
|
return res
|
|
|
|
|
|
def glob_translate(pat):
|
|
# Copied from: https://github.com/python/cpython/pull/106703.
|
|
# The keyword parameters' values are fixed to:
|
|
# recursive=True, include_hidden=True, seps=None
|
|
"""Translate a pathname with shell wildcards to a regular expression."""
|
|
if os.path.altsep:
|
|
seps = os.path.sep + os.path.altsep
|
|
else:
|
|
seps = os.path.sep
|
|
escaped_seps = "".join(map(re.escape, seps))
|
|
any_sep = f"[{escaped_seps}]" if len(seps) > 1 else escaped_seps
|
|
not_sep = f"[^{escaped_seps}]"
|
|
one_last_segment = f"{not_sep}+"
|
|
one_segment = f"{one_last_segment}{any_sep}"
|
|
any_segments = f"(?:.+{any_sep})?"
|
|
any_last_segments = ".*"
|
|
results = []
|
|
parts = re.split(any_sep, pat)
|
|
last_part_idx = len(parts) - 1
|
|
for idx, part in enumerate(parts):
|
|
if part == "*":
|
|
results.append(one_segment if idx < last_part_idx else one_last_segment)
|
|
continue
|
|
if part == "**":
|
|
results.append(any_segments if idx < last_part_idx else any_last_segments)
|
|
continue
|
|
elif "**" in part:
|
|
raise ValueError(
|
|
"Invalid pattern: '**' can only be an entire path component"
|
|
)
|
|
if part:
|
|
results.extend(_translate(part, f"{not_sep}*", not_sep))
|
|
if idx < last_part_idx:
|
|
results.append(any_sep)
|
|
res = "".join(results)
|
|
return rf"(?s:{res})\Z"
|