Coverage for python/lsst/daf/butler/core/_butlerUri/file.py : 15%

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1# This file is part of daf_butler.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22from __future__ import annotations
24import os
25import os.path
26import shutil
27import urllib.parse
28import posixpath
29import copy
30import logging
31import re
33__all__ = ('ButlerFileURI',)
35from typing import (
36 TYPE_CHECKING,
37 cast,
38 Iterator,
39 List,
40 Optional,
41 Tuple,
42 Union,
43)
45from ..utils import safeMakeDir
46from .utils import NoTransaction, os2posix, posix2os
47from ._butlerUri import ButlerURI
50if TYPE_CHECKING: 50 ↛ 51line 50 didn't jump to line 51, because the condition on line 50 was never true
51 from ..datastore import DatastoreTransaction
54log = logging.getLogger(__name__)
57class ButlerFileURI(ButlerURI):
58 """URI for explicit ``file`` scheme."""
60 transferModes = ("copy", "link", "symlink", "hardlink", "relsymlink", "auto", "move")
61 transferDefault: str = "link"
63 # By definition refers to a local file
64 isLocal = True
66 @property
67 def ospath(self) -> str:
68 """Path component of the URI localized to current OS.
70 Will unquote URI path since a formal URI must include the quoting.
71 """
72 return urllib.parse.unquote(posix2os(self._uri.path))
74 def exists(self) -> bool:
75 """Indicate that the file exists."""
76 # Uses os.path.exists so if there is a soft link that points
77 # to a file that no longer exists this will return False
78 return os.path.exists(self.ospath)
80 def size(self) -> int:
81 """Return the size of the file in bytes."""
82 if not os.path.isdir(self.ospath):
83 stat = os.stat(self.ospath)
84 sz = stat.st_size
85 else:
86 sz = 0
87 return sz
89 def remove(self) -> None:
90 """Remove the resource."""
91 os.remove(self.ospath)
93 def _as_local(self) -> Tuple[str, bool]:
94 """Return the local path of the file.
96 This is an internal helper for ``as_local()``.
98 Returns
99 -------
100 path : `str`
101 The local path to this file.
102 temporary : `bool`
103 Always returns `False` (this is not a temporary file).
104 """
105 return self.ospath, False
107 def _force_to_file(self) -> ButlerFileURI:
108 """Force a schemeless URI to a file URI and returns a new URI.
110 Returns
111 -------
112 file : `ButlerFileURI`
113 A copy of the URI using file scheme. If already a file scheme
114 the copy will be identical.
116 Raises
117 ------
118 ValueError
119 Raised if this URI is schemeless and relative path and so can
120 not be forced to file absolute path without context.
121 """
122 # This is always a file scheme so always return copy
123 return copy.copy(self)
125 def relative_to(self, other: ButlerURI) -> Optional[str]:
126 """Return the relative path from this URI to the other URI.
128 Parameters
129 ----------
130 other : `ButlerURI`
131 URI to use to calculate the relative path. Must be a parent
132 of this URI.
134 Returns
135 -------
136 subpath : `str`
137 The sub path of this URI relative to the supplied other URI.
138 Returns `None` if there is no parent child relationship.
139 Scheme and netloc must match but for file URIs schemeless
140 is also used. If this URI is a relative URI but the other is
141 absolute, it is assumed to be in the parent completely unless it
142 starts with ".." (in which case the path is combined and tested).
143 If both URIs are relative, the relative paths are compared
144 for commonality.
146 Notes
147 -----
148 By definition a relative path will be relative to the enclosing
149 absolute parent URI. It will be returned unchanged if it does not
150 use a parent directory specification.
151 """
152 # We know self is a file so check the other. Anything other than
153 # file or schemeless means by definition these have no paths in common
154 if other.scheme and other.scheme != "file":
155 return None
157 # for case where both URIs are relative use the normal logic
158 # where a/b/c.txt and a/b/ returns c.txt.
159 if not self.isabs() and not other.isabs():
160 return super().relative_to(other)
162 # if we have a relative path convert it to absolute
163 # relative to the supplied parent. This is solely to handle
164 # the case where the relative path includes ".." but somehow
165 # then goes back inside the directory of the parent
166 if not self.isabs():
167 childUri = other.join(self.path)
168 return childUri.relative_to(other)
170 # By this point if the schemes are identical we can use the
171 # base class implementation.
172 if self.scheme == other.scheme:
173 return super().relative_to(other)
175 # if one is schemeless and the other is not the base implementation
176 # will fail so we need to fix that -- they are both absolute so
177 # forcing to file is fine.
178 # Use a cast to convince mypy that other has to be a ButlerFileURI
179 # in order to get to this part of the code.
180 return self._force_to_file().relative_to(cast(ButlerFileURI, other)._force_to_file())
182 def read(self, size: int = -1) -> bytes:
183 """Return the entire content of the file as bytes."""
184 with open(self.ospath, "rb") as fh:
185 return fh.read(size)
187 def write(self, data: bytes, overwrite: bool = True) -> None:
188 """Write the supplied data to the file."""
189 dir = os.path.dirname(self.ospath)
190 if not os.path.exists(dir):
191 safeMakeDir(dir)
192 if overwrite:
193 mode = "wb"
194 else:
195 mode = "xb"
196 with open(self.ospath, mode) as f:
197 f.write(data)
199 def mkdir(self) -> None:
200 """Make the directory associated with this URI."""
201 if not os.path.exists(self.ospath):
202 safeMakeDir(self.ospath)
203 elif not os.path.isdir(self.ospath):
204 raise FileExistsError(f"URI {self} exists but is not a directory!")
206 def isdir(self) -> bool:
207 """Return whether this URI is a directory.
209 Returns
210 -------
211 isdir : `bool`
212 `True` if this URI is a directory or looks like a directory,
213 else `False`.
214 """
215 return self.dirLike or os.path.isdir(self.ospath)
217 def transfer_from(self, src: ButlerURI, transfer: str,
218 overwrite: bool = False,
219 transaction: Optional[Union[DatastoreTransaction, NoTransaction]] = None) -> None:
220 """Transfer the current resource to a local file.
222 Parameters
223 ----------
224 src : `ButlerURI`
225 Source URI.
226 transfer : `str`
227 Mode to use for transferring the resource. Supports the following
228 options: copy, link, symlink, hardlink, relsymlink.
229 overwrite : `bool`, optional
230 Allow an existing file to be overwritten. Defaults to `False`.
231 transaction : `DatastoreTransaction`, optional
232 If a transaction is provided, undo actions will be registered.
233 """
234 # Fail early to prevent delays if remote resources are requested
235 if transfer not in self.transferModes:
236 raise ValueError(f"Transfer mode '{transfer}' not supported by URI scheme {self.scheme}")
238 log.debug(f"Transferring {src} [exists: {src.exists()}] -> "
239 f"{self} [exists: {self.exists()}] (transfer={transfer})")
241 # We do not have to special case ButlerFileURI here because
242 # as_local handles that.
243 with src.as_local() as local_uri:
244 is_temporary = local_uri.isTemporary
245 local_src = local_uri.ospath
247 # Default transfer mode depends on whether we have a temporary
248 # file or not.
249 if transfer == "auto":
250 transfer = self.transferDefault if not is_temporary else "copy"
252 if not os.path.exists(local_src):
253 if is_temporary:
254 msg = f"Local file {local_uri} downloaded from {src} has gone missing"
255 else:
256 msg = f"Source URI {src} does not exist"
257 raise FileNotFoundError(msg)
259 # Follow soft links
260 local_src = os.path.realpath(os.path.normpath(local_src))
262 # All the modes involving linking use "link" somewhere
263 if "link" in transfer and is_temporary:
264 raise RuntimeError("Can not use local file system transfer mode"
265 f" {transfer} for remote resource ({src})")
267 # For temporary files we can own them
268 requested_transfer = transfer
269 if is_temporary and transfer == "copy":
270 transfer = "move"
272 # The output location should not exist
273 dest_exists = self.exists()
274 if not overwrite and dest_exists:
275 raise FileExistsError(f"Destination path '{self}' already exists. Transfer "
276 f"from {src} cannot be completed.")
278 # Make the path absolute (but don't follow links since that
279 # would possibly cause us to end up in the wrong place if the
280 # file existed already as a soft link)
281 newFullPath = os.path.abspath(self.ospath)
282 outputDir = os.path.dirname(newFullPath)
283 if not os.path.isdir(outputDir):
284 # Must create the directory -- this can not be rolled back
285 # since another transfer running concurrently may
286 # be relying on this existing.
287 safeMakeDir(outputDir)
289 if transaction is None:
290 # Use a no-op transaction to reduce code duplication
291 transaction = NoTransaction()
293 # For links the OS doesn't let us overwrite so if something does
294 # exist we have to remove it before we do the actual "transfer"
295 # below
296 if "link" in transfer and overwrite and dest_exists:
297 try:
298 self.remove()
299 except Exception:
300 # If this fails we ignore it since it's a problem
301 # that will manifest immediately below with a more relevant
302 # error message
303 pass
305 if transfer == "move":
306 with transaction.undoWith(f"move from {local_src}", shutil.move, newFullPath, local_src):
307 shutil.move(local_src, newFullPath)
308 elif transfer == "copy":
309 with transaction.undoWith(f"copy from {local_src}", os.remove, newFullPath):
310 shutil.copy(local_src, newFullPath)
311 elif transfer == "link":
312 # Try hard link and if that fails use a symlink
313 with transaction.undoWith(f"link to {local_src}", os.remove, newFullPath):
314 try:
315 os.link(local_src, newFullPath)
316 except OSError:
317 # Read through existing symlinks
318 os.symlink(local_src, newFullPath)
319 elif transfer == "hardlink":
320 with transaction.undoWith(f"hardlink to {local_src}", os.remove, newFullPath):
321 os.link(local_src, newFullPath)
322 elif transfer == "symlink":
323 # Read through existing symlinks
324 with transaction.undoWith(f"symlink to {local_src}", os.remove, newFullPath):
325 os.symlink(local_src, newFullPath)
326 elif transfer == "relsymlink":
327 # This is a standard symlink but using a relative path
328 # Need the directory name to give to relative root
329 # A full file path confuses it into an extra ../
330 newFullPathRoot = os.path.dirname(newFullPath)
331 relPath = os.path.relpath(local_src, newFullPathRoot)
332 with transaction.undoWith(f"relsymlink to {local_src}", os.remove, newFullPath):
333 os.symlink(relPath, newFullPath)
334 else:
335 raise NotImplementedError("Transfer type '{}' not supported.".format(transfer))
337 # This was an explicit move requested from a remote resource
338 # try to remove that remote resource. We check is_temporary because
339 # the local file would have been moved by shutil.move already.
340 if requested_transfer == "move" and is_temporary:
341 # Transactions do not work here
342 src.remove()
344 def walk(self, file_filter: Optional[Union[str, re.Pattern]] = None) -> Iterator[Union[List,
345 Tuple[ButlerURI,
346 List[str],
347 List[str]]]]:
348 """Walk the directory tree returning matching files and directories.
350 Parameters
351 ----------
352 file_filter : `str` or `re.Pattern`, optional
353 Regex to filter out files from the list before it is returned.
355 Yields
356 ------
357 dirpath : `ButlerURI`
358 Current directory being examined.
359 dirnames : `list` of `str`
360 Names of subdirectories within dirpath.
361 filenames : `list` of `str`
362 Names of all the files within dirpath.
363 """
364 if not self.isdir():
365 raise ValueError("Can not walk a non-directory URI")
367 if isinstance(file_filter, str):
368 file_filter = re.compile(file_filter)
370 for root, dirs, files in os.walk(self.ospath):
371 # Filter by the regex
372 if file_filter is not None:
373 files = [f for f in files if file_filter.search(f)]
374 yield type(self)(root, forceAbsolute=False, forceDirectory=True), dirs, files
376 @classmethod
377 def _fixupPathUri(cls, parsed: urllib.parse.ParseResult, root: Optional[Union[str, ButlerURI]] = None,
378 forceAbsolute: bool = False,
379 forceDirectory: bool = False) -> Tuple[urllib.parse.ParseResult, bool]:
380 """Fix up relative paths in URI instances.
382 Parameters
383 ----------
384 parsed : `~urllib.parse.ParseResult`
385 The result from parsing a URI using `urllib.parse`.
386 root : `str` or `ButlerURI`, optional
387 Path to use as root when converting relative to absolute.
388 If `None`, it will be the current working directory. This
389 is a local file system path, or a file URI. It is only used if
390 a file-scheme is used incorrectly with a relative path.
391 forceAbsolute : `bool`, ignored
392 Has no effect for this subclass. ``file`` URIs are always
393 absolute.
394 forceDirectory : `bool`, optional
395 If `True` forces the URI to end with a separator, otherwise given
396 URI is interpreted as is.
398 Returns
399 -------
400 modified : `~urllib.parse.ParseResult`
401 Update result if a URI is being handled.
402 dirLike : `bool`
403 `True` if given parsed URI has a trailing separator or
404 forceDirectory is True. Otherwise `False`.
406 Notes
407 -----
408 Relative paths are explicitly not supported by RFC8089 but `urllib`
409 does accept URIs of the form ``file:relative/path.ext``. They need
410 to be turned into absolute paths before they can be used. This is
411 always done regardless of the ``forceAbsolute`` parameter.
412 """
413 # assume we are not dealing with a directory like URI
414 dirLike = False
416 # file URI implies POSIX path separators so split as POSIX,
417 # then join as os, and convert to abspath. Do not handle
418 # home directories since "file" scheme is explicitly documented
419 # to not do tilde expansion.
420 sep = posixpath.sep
422 # For local file system we can explicitly check to see if this
423 # really is a directory. The URI might point to a location that
424 # does not exists yet but all that matters is if it is a directory
425 # then we make sure use that fact. No need to do the check if
426 # we are already being told.
427 if not forceDirectory and posixpath.isdir(parsed.path):
428 forceDirectory = True
430 # For an absolute path all we need to do is check if we need
431 # to force the directory separator
432 if posixpath.isabs(parsed.path):
433 if forceDirectory:
434 if not parsed.path.endswith(sep):
435 parsed = parsed._replace(path=parsed.path+sep)
436 dirLike = True
437 return copy.copy(parsed), dirLike
439 # Relative path so must fix it to be compliant with the standard
441 # Replacement values for the URI
442 replacements = {}
444 if root is None:
445 root = os.path.abspath(os.path.curdir)
446 elif isinstance(root, ButlerURI):
447 if root.scheme and root.scheme != "file":
448 raise RuntimeError(f"The override root must be a file URI not {root.scheme}")
449 root = os.path.abspath(root.ospath)
451 replacements["path"] = posixpath.normpath(posixpath.join(os2posix(root), parsed.path))
453 # normpath strips trailing "/" so put it back if necessary
454 # Acknowledge that trailing separator exists.
455 if forceDirectory or (parsed.path.endswith(sep) and not replacements["path"].endswith(sep)):
456 replacements["path"] += sep
457 dirLike = True
459 # ParseResult is a NamedTuple so _replace is standard API
460 parsed = parsed._replace(**replacements)
462 if parsed.params or parsed.query:
463 log.warning("Additional items unexpectedly encountered in file URI: %s", parsed.geturl())
465 return parsed, dirLike