Coverage for python/lsst/resources/file.py: 91%
177 statements
« prev ^ index » next coverage.py v7.2.3, created at 2023-04-19 03:38 -0700
« prev ^ index » next coverage.py v7.2.3, created at 2023-04-19 03:38 -0700
1# This file is part of lsst-resources.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# Use of this source code is governed by a 3-clause BSD-style
10# license that can be found in the LICENSE file.
12from __future__ import annotations
14import contextlib
15import copy
16import logging
17import os
18import os.path
19import posixpath
20import re
21import shutil
22import urllib.parse
24__all__ = ("FileResourcePath",)
26from typing import IO, TYPE_CHECKING, Iterator, List, Optional, Tuple, Union
28from ._resourceHandles._fileResourceHandle import FileResourceHandle
29from ._resourcePath import ResourcePath
30from .utils import NoTransaction, os2posix, posix2os
32if TYPE_CHECKING:
33 from .utils import TransactionProtocol
36log = logging.getLogger(__name__)
39class FileResourcePath(ResourcePath):
40 """Path for explicit ``file`` URI scheme."""
42 transferModes = ("copy", "link", "symlink", "hardlink", "relsymlink", "auto", "move")
43 transferDefault: str = "link"
45 # By definition refers to a local file
46 isLocal = True
48 @property
49 def ospath(self) -> str:
50 """Path component of the URI localized to current OS.
52 Will unquote URI path since a formal URI must include the quoting.
53 """
54 return urllib.parse.unquote(posix2os(self._uri.path))
56 def exists(self) -> bool:
57 """Indicate that the file exists."""
58 # Uses os.path.exists so if there is a soft link that points
59 # to a file that no longer exists this will return False
60 return os.path.exists(self.ospath)
62 def size(self) -> int:
63 """Return the size of the file in bytes."""
64 if not os.path.isdir(self.ospath):
65 stat = os.stat(self.ospath)
66 sz = stat.st_size
67 else:
68 sz = 0
69 return sz
71 def remove(self) -> None:
72 """Remove the resource."""
73 os.remove(self.ospath)
75 def _as_local(self) -> Tuple[str, bool]:
76 """Return the local path of the file.
78 This is an internal helper for ``as_local()``.
80 Returns
81 -------
82 path : `str`
83 The local path to this file.
84 temporary : `bool`
85 Always returns the temporary nature of the input file resource.
86 """
87 return self.ospath, self.isTemporary
89 def read(self, size: int = -1) -> bytes:
90 """Return the entire content of the file as bytes."""
91 with open(self.ospath, "rb") as fh:
92 return fh.read(size)
94 def write(self, data: bytes, overwrite: bool = True) -> None:
95 """Write the supplied data to the file."""
96 dir = os.path.dirname(self.ospath)
97 if not os.path.exists(dir):
98 os.makedirs(dir, exist_ok=True)
99 if overwrite:
100 mode = "wb"
101 else:
102 mode = "xb"
103 with open(self.ospath, mode) as f:
104 f.write(data)
106 def mkdir(self) -> None:
107 """Make the directory associated with this URI.
109 An attempt will be made to create the directory even if the URI
110 looks like a file.
112 Raises
113 ------
114 NotADirectoryError:
115 Raised if a non-directory already exists.
116 """
117 try:
118 os.makedirs(self.ospath, exist_ok=True)
119 except FileExistsError:
120 raise NotADirectoryError(f"{self.ospath} exists but is not a directory.") from None
122 def isdir(self) -> bool:
123 """Return whether this URI is a directory.
125 Returns
126 -------
127 isdir : `bool`
128 `True` if this URI is a directory or looks like a directory,
129 else `False`.
130 """
131 return self.dirLike or os.path.isdir(self.ospath)
133 def transfer_from(
134 self,
135 src: ResourcePath,
136 transfer: str,
137 overwrite: bool = False,
138 transaction: Optional[TransactionProtocol] = None,
139 ) -> None:
140 """Transfer the current resource to a local file.
142 Parameters
143 ----------
144 src : `ResourcePath`
145 Source URI.
146 transfer : `str`
147 Mode to use for transferring the resource. Supports the following
148 options: copy, link, symlink, hardlink, relsymlink.
149 overwrite : `bool`, optional
150 Allow an existing file to be overwritten. Defaults to `False`.
151 transaction : `~lsst.resources.utils.TransactionProtocol`, optional
152 If a transaction is provided, undo actions will be registered.
153 """
154 # Fail early to prevent delays if remote resources are requested
155 if transfer not in self.transferModes:
156 raise ValueError(f"Transfer mode '{transfer}' not supported by URI scheme {self.scheme}")
158 # Existence checks can take time so only try if the log message
159 # will be issued.
160 if log.isEnabledFor(logging.DEBUG): 160 ↛ 172line 160 didn't jump to line 172, because the condition on line 160 was never false
161 log.debug(
162 "Transferring %s [exists: %s] -> %s [exists: %s] (transfer=%s)",
163 src,
164 src.exists(),
165 self,
166 self.exists(),
167 transfer,
168 )
170 # We do not have to special case FileResourcePath here because
171 # as_local handles that.
172 with src.as_local() as local_uri:
173 is_temporary = local_uri.isTemporary
174 local_src = local_uri.ospath
176 # Short circuit if the URIs are identical immediately.
177 if self == local_uri:
178 log.debug(
179 "Target and destination URIs are identical: %s, returning immediately."
180 " No further action required.",
181 self,
182 )
183 return
185 # Default transfer mode depends on whether we have a temporary
186 # file or not.
187 if transfer == "auto":
188 transfer = self.transferDefault if not is_temporary else "copy"
190 if not os.path.exists(local_src):
191 if is_temporary:
192 if src == local_uri: 192 ↛ 196line 192 didn't jump to line 196, because the condition on line 192 was never false
193 msg = f"Local temporary file {src} has gone missing."
194 else:
195 # This will not happen in normal scenarios.
196 msg = f"Local file {local_uri} downloaded from {src} has gone missing"
197 else:
198 msg = f"Source URI {src} does not exist"
199 raise FileNotFoundError(msg)
201 # Follow soft links
202 local_src = os.path.realpath(os.path.normpath(local_src))
204 # Creating a symlink to a local copy of a remote resource
205 # should never work. Creating a hardlink will work but should
206 # not be allowed since it is highly unlikely that this is ever
207 # an intended option and depends on the local target being
208 # on the same file system as was used for the temporary file
209 # download.
210 # If a symlink is being requested for a local temporary file
211 # that is likely undesirable but should not be refused.
212 if is_temporary and src != local_uri and "link" in transfer:
213 raise RuntimeError(
214 f"Can not use local file system transfer mode {transfer} for remote resource ({src})"
215 )
216 elif is_temporary and src == local_uri and "symlink" in transfer:
217 log.debug(
218 "Using a symlink for a temporary resource may lead to unexpected downstream failures."
219 )
221 # For temporary files we can own them if we created it.
222 requested_transfer = transfer
223 if src != local_uri and is_temporary and transfer == "copy":
224 transfer = "move"
226 # The output location should not exist unless overwrite=True.
227 # Rather than use `exists()`, use os.stat since we might need
228 # the full answer later.
229 dest_stat: Optional[os.stat_result]
230 try:
231 # Do not read through links of the file itself.
232 dest_stat = os.lstat(self.ospath)
233 except FileNotFoundError:
234 dest_stat = None
236 # It is possible that the source URI and target URI refer
237 # to the same file. This can happen for a number of reasons
238 # (such as soft links in the path, or they really are the same).
239 # In that case log a message and return as if the transfer
240 # completed (it technically did). A temporary file download
241 # can't be the same so the test can be skipped.
242 if dest_stat and not is_temporary:
243 # Be consistent and use lstat here (even though realpath
244 # has been called). It does not harm.
245 local_src_stat = os.lstat(local_src)
246 if dest_stat.st_ino == local_src_stat.st_ino and dest_stat.st_dev == local_src_stat.st_dev:
247 log.debug(
248 "Destination URI %s is the same file as source URI %s, returning immediately."
249 " No further action required.",
250 self,
251 local_uri,
252 )
253 return
255 if not overwrite and dest_stat:
256 raise FileExistsError(
257 f"Destination path '{self}' already exists. Transfer from {src} cannot be completed."
258 )
260 # Make the path absolute (but don't follow links since that
261 # would possibly cause us to end up in the wrong place if the
262 # file existed already as a soft link)
263 newFullPath = os.path.abspath(self.ospath)
264 outputDir = os.path.dirname(newFullPath)
265 if not os.path.isdir(outputDir):
266 # Must create the directory -- this can not be rolled back
267 # since another transfer running concurrently may
268 # be relying on this existing.
269 os.makedirs(outputDir, exist_ok=True)
271 if transaction is None: 271 ↛ 278line 271 didn't jump to line 278, because the condition on line 271 was never false
272 # Use a no-op transaction to reduce code duplication
273 transaction = NoTransaction()
275 # For links the OS doesn't let us overwrite so if something does
276 # exist we have to remove it before we do the actual "transfer"
277 # below
278 if "link" in transfer and overwrite and dest_stat:
279 try:
280 self.remove()
281 except Exception:
282 # If this fails we ignore it since it's a problem
283 # that will manifest immediately below with a more relevant
284 # error message
285 pass
287 if transfer == "move":
288 # If a rename works we try that since that is guaranteed to
289 # be atomic. If that fails we copy and rename. We do this
290 # in case other processes are trying to move to the same
291 # file and we want the "winner" to not be corrupted.
292 try:
293 with transaction.undoWith(f"move from {local_src}", os.rename, newFullPath, local_src):
294 os.rename(local_src, newFullPath)
295 except OSError:
296 with self.temporary_uri(prefix=self.parent(), suffix=self.getExtension()) as temp_copy:
297 shutil.copy(local_src, temp_copy.ospath)
298 with transaction.undoWith(
299 f"move from {local_src}",
300 shutil.move,
301 newFullPath,
302 local_src,
303 copy_function=shutil.copy,
304 ):
305 os.rename(temp_copy.ospath, newFullPath)
306 os.remove(local_src)
307 elif transfer == "copy":
308 # We want atomic copies so first copy to a temp location in
309 # the same output directory. This at least guarantees that
310 # if multiple processes are writing to the same file
311 # simultaneously the file we end up with will not be corrupt.
312 with self.temporary_uri(prefix=self.parent(), suffix=self.getExtension()) as temp_copy:
313 shutil.copy(local_src, temp_copy.ospath)
314 with transaction.undoWith(f"copy from {local_src}", os.remove, newFullPath):
315 # os.rename works even if the file exists.
316 # It's possible that another process has copied a file
317 # in whilst this one was copying. If overwrite
318 # protection is needed then another stat() call should
319 # happen here.
320 os.rename(temp_copy.ospath, newFullPath)
321 elif transfer == "link":
322 # Try hard link and if that fails use a symlink
323 with transaction.undoWith(f"link to {local_src}", os.remove, newFullPath):
324 try:
325 os.link(local_src, newFullPath)
326 except OSError:
327 # Read through existing symlinks
328 os.symlink(local_src, newFullPath)
329 elif transfer == "hardlink":
330 with transaction.undoWith(f"hardlink to {local_src}", os.remove, newFullPath):
331 os.link(local_src, newFullPath)
332 elif transfer == "symlink":
333 # Read through existing symlinks
334 with transaction.undoWith(f"symlink to {local_src}", os.remove, newFullPath):
335 os.symlink(local_src, newFullPath)
336 elif transfer == "relsymlink":
337 # This is a standard symlink but using a relative path
338 # Need the directory name to give to relative root
339 # A full file path confuses it into an extra ../
340 newFullPathRoot = os.path.dirname(newFullPath)
341 relPath = os.path.relpath(local_src, newFullPathRoot)
342 with transaction.undoWith(f"relsymlink to {local_src}", os.remove, newFullPath):
343 os.symlink(relPath, newFullPath)
344 else:
345 raise NotImplementedError("Transfer type '{}' not supported.".format(transfer))
347 # This was an explicit move requested from a remote resource
348 # try to remove that remote resource. We check is_temporary because
349 # the local file would have been moved by shutil.move already.
350 if requested_transfer == "move" and is_temporary and src != local_uri:
351 # Transactions do not work here
352 src.remove()
354 def walk(
355 self, file_filter: Optional[Union[str, re.Pattern]] = None
356 ) -> Iterator[Union[List, Tuple[ResourcePath, List[str], List[str]]]]:
357 """Walk the directory tree returning matching files and directories.
359 Parameters
360 ----------
361 file_filter : `str` or `re.Pattern`, optional
362 Regex to filter out files from the list before it is returned.
364 Yields
365 ------
366 dirpath : `ResourcePath`
367 Current directory being examined.
368 dirnames : `list` of `str`
369 Names of subdirectories within dirpath.
370 filenames : `list` of `str`
371 Names of all the files within dirpath.
372 """
373 if not self.isdir():
374 raise ValueError("Can not walk a non-directory URI")
376 if isinstance(file_filter, str): 376 ↛ 377line 376 didn't jump to line 377, because the condition on line 376 was never true
377 file_filter = re.compile(file_filter)
379 for root, dirs, files in os.walk(self.ospath, followlinks=True):
380 # Filter by the regex
381 if file_filter is not None:
382 files = [f for f in files if file_filter.search(f)]
383 yield type(self)(root, forceAbsolute=False, forceDirectory=True), dirs, files
385 @classmethod
386 def _fixupPathUri(
387 cls,
388 parsed: urllib.parse.ParseResult,
389 root: Optional[ResourcePath] = None,
390 forceAbsolute: bool = False,
391 forceDirectory: bool = False,
392 ) -> Tuple[urllib.parse.ParseResult, bool]:
393 """Fix up relative paths in URI instances.
395 Parameters
396 ----------
397 parsed : `~urllib.parse.ParseResult`
398 The result from parsing a URI using `urllib.parse`.
399 root : `ResourcePath`, optional
400 Path to use as root when converting relative to absolute.
401 If `None`, it will be the current working directory. It is only
402 used if a file-scheme is used incorrectly with a relative path.
403 forceAbsolute : `bool`, ignored
404 Has no effect for this subclass. ``file`` URIs are always
405 absolute.
406 forceDirectory : `bool`, optional
407 If `True` forces the URI to end with a separator, otherwise given
408 URI is interpreted as is.
410 Returns
411 -------
412 modified : `~urllib.parse.ParseResult`
413 Update result if a URI is being handled.
414 dirLike : `bool`
415 `True` if given parsed URI has a trailing separator or
416 forceDirectory is True. Otherwise `False`.
418 Notes
419 -----
420 Relative paths are explicitly not supported by RFC8089 but `urllib`
421 does accept URIs of the form ``file:relative/path.ext``. They need
422 to be turned into absolute paths before they can be used. This is
423 always done regardless of the ``forceAbsolute`` parameter.
424 """
425 # assume we are not dealing with a directory like URI
426 dirLike = False
428 # file URI implies POSIX path separators so split as POSIX,
429 # then join as os, and convert to abspath. Do not handle
430 # home directories since "file" scheme is explicitly documented
431 # to not do tilde expansion.
432 sep = posixpath.sep
434 # For local file system we can explicitly check to see if this
435 # really is a directory. The URI might point to a location that
436 # does not exists yet but all that matters is if it is a directory
437 # then we make sure use that fact. No need to do the check if
438 # we are already being told.
439 if not forceDirectory and posixpath.isdir(parsed.path): 439 ↛ 440line 439 didn't jump to line 440, because the condition on line 439 was never true
440 forceDirectory = True
442 # For an absolute path all we need to do is check if we need
443 # to force the directory separator
444 if posixpath.isabs(parsed.path):
445 if forceDirectory:
446 if not parsed.path.endswith(sep):
447 parsed = parsed._replace(path=parsed.path + sep)
448 dirLike = True
449 return copy.copy(parsed), dirLike
451 # Relative path so must fix it to be compliant with the standard
453 # Replacement values for the URI
454 replacements = {}
456 if root is None:
457 root_str = os.path.abspath(os.path.curdir)
458 else:
459 if root.scheme and root.scheme != "file": 459 ↛ 460line 459 didn't jump to line 460, because the condition on line 459 was never true
460 raise RuntimeError(f"The override root must be a file URI not {root.scheme}")
461 root_str = os.path.abspath(root.ospath)
463 replacements["path"] = posixpath.normpath(posixpath.join(os2posix(root_str), parsed.path))
465 # normpath strips trailing "/" so put it back if necessary
466 # Acknowledge that trailing separator exists.
467 if forceDirectory or (parsed.path.endswith(sep) and not replacements["path"].endswith(sep)):
468 replacements["path"] += sep
469 dirLike = True
471 # ParseResult is a NamedTuple so _replace is standard API
472 parsed = parsed._replace(**replacements)
474 if parsed.params or parsed.query: 474 ↛ 475line 474 didn't jump to line 475, because the condition on line 474 was never true
475 log.warning("Additional items unexpectedly encountered in file URI: %s", parsed.geturl())
477 return parsed, dirLike
479 @contextlib.contextmanager
480 def _openImpl(
481 self,
482 mode: str = "r",
483 *,
484 encoding: Optional[str] = None,
485 ) -> Iterator[IO]:
486 with FileResourceHandle(mode=mode, log=log, filename=self.ospath, encoding=encoding) as buffer:
487 yield buffer # type: ignore