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 relative_to(self, other: ButlerURI) -> Optional[str]:
108 """Return the relative path from this URI to the other URI.
110 Parameters
111 ----------
112 other : `ButlerURI`
113 URI to use to calculate the relative path. Must be a parent
114 of this URI.
116 Returns
117 -------
118 subpath : `str`
119 The sub path of this URI relative to the supplied other URI.
120 Returns `None` if there is no parent child relationship.
121 Scheme and netloc must match but for file URIs schemeless
122 is also used. If this URI is a relative URI but the other is
123 absolute, it is assumed to be in the parent completely unless it
124 starts with ".." (in which case the path is combined and tested).
125 If both URIs are relative, the relative paths are compared
126 for commonality.
128 Notes
129 -----
130 By definition a relative path will be relative to the enclosing
131 absolute parent URI. It will be returned unchanged if it does not
132 use a parent directory specification.
133 """
134 # We know self is a file so check the other. Anything other than
135 # file or schemeless means by definition these have no paths in common
136 if other.scheme and other.scheme != "file":
137 return None
139 # for case where both URIs are relative use the normal logic
140 # where a/b/c.txt and a/b/ returns c.txt.
141 if not self.isabs() and not other.isabs():
142 return super().relative_to(other)
144 # if we have a relative path convert it to absolute
145 # relative to the supplied parent. This is solely to handle
146 # the case where the relative path includes ".." but somehow
147 # then goes back inside the directory of the parent
148 if not self.isabs():
149 childUri = other.join(self.path)
150 return childUri.relative_to(other)
152 # By this point if the schemes are identical we can use the
153 # base class implementation.
154 if self.scheme == other.scheme:
155 return super().relative_to(other)
157 # if one is schemeless and the other is not the base implementation
158 # will fail so we need to fix that -- they are both absolute so
159 # forcing to file is fine.
160 # Use a cast to convince mypy that other has to be a ButlerFileURI
161 # in order to get to this part of the code.
162 return self.abspath().relative_to(cast(ButlerFileURI, other).abspath())
164 def read(self, size: int = -1) -> bytes:
165 """Return the entire content of the file as bytes."""
166 with open(self.ospath, "rb") as fh:
167 return fh.read(size)
169 def write(self, data: bytes, overwrite: bool = True) -> None:
170 """Write the supplied data to the file."""
171 dir = os.path.dirname(self.ospath)
172 if not os.path.exists(dir):
173 safeMakeDir(dir)
174 if overwrite:
175 mode = "wb"
176 else:
177 mode = "xb"
178 with open(self.ospath, mode) as f:
179 f.write(data)
181 def mkdir(self) -> None:
182 """Make the directory associated with this URI."""
183 if not os.path.exists(self.ospath):
184 safeMakeDir(self.ospath)
185 elif not os.path.isdir(self.ospath):
186 raise FileExistsError(f"URI {self} exists but is not a directory!")
188 def isdir(self) -> bool:
189 """Return whether this URI is a directory.
191 Returns
192 -------
193 isdir : `bool`
194 `True` if this URI is a directory or looks like a directory,
195 else `False`.
196 """
197 return self.dirLike or os.path.isdir(self.ospath)
199 def transfer_from(self, src: ButlerURI, transfer: str,
200 overwrite: bool = False,
201 transaction: Optional[Union[DatastoreTransaction, NoTransaction]] = None) -> None:
202 """Transfer the current resource to a local file.
204 Parameters
205 ----------
206 src : `ButlerURI`
207 Source URI.
208 transfer : `str`
209 Mode to use for transferring the resource. Supports the following
210 options: copy, link, symlink, hardlink, relsymlink.
211 overwrite : `bool`, optional
212 Allow an existing file to be overwritten. Defaults to `False`.
213 transaction : `DatastoreTransaction`, optional
214 If a transaction is provided, undo actions will be registered.
215 """
216 # Fail early to prevent delays if remote resources are requested
217 if transfer not in self.transferModes:
218 raise ValueError(f"Transfer mode '{transfer}' not supported by URI scheme {self.scheme}")
220 # Existence checks can take time so only try if the log message
221 # will be issued.
222 if log.isEnabledFor(logging.DEBUG):
223 log.debug("Transferring %s [exists: %s] -> %s [exists: %s] (transfer=%s)",
224 src, src.exists(), self, self.exists(), transfer)
226 # We do not have to special case ButlerFileURI here because
227 # as_local handles that.
228 with src.as_local() as local_uri:
229 is_temporary = local_uri.isTemporary
230 local_src = local_uri.ospath
232 # Default transfer mode depends on whether we have a temporary
233 # file or not.
234 if transfer == "auto":
235 transfer = self.transferDefault if not is_temporary else "copy"
237 if not os.path.exists(local_src):
238 if is_temporary:
239 msg = f"Local file {local_uri} downloaded from {src} has gone missing"
240 else:
241 msg = f"Source URI {src} does not exist"
242 raise FileNotFoundError(msg)
244 # Follow soft links
245 local_src = os.path.realpath(os.path.normpath(local_src))
247 # All the modes involving linking use "link" somewhere
248 if "link" in transfer and is_temporary:
249 raise RuntimeError("Can not use local file system transfer mode"
250 f" {transfer} for remote resource ({src})")
252 # For temporary files we can own them
253 requested_transfer = transfer
254 if is_temporary and transfer == "copy":
255 transfer = "move"
257 # The output location should not exist
258 dest_exists = self.exists()
259 if not overwrite and dest_exists:
260 raise FileExistsError(f"Destination path '{self}' already exists. Transfer "
261 f"from {src} cannot be completed.")
263 # Make the path absolute (but don't follow links since that
264 # would possibly cause us to end up in the wrong place if the
265 # file existed already as a soft link)
266 newFullPath = os.path.abspath(self.ospath)
267 outputDir = os.path.dirname(newFullPath)
268 if not os.path.isdir(outputDir):
269 # Must create the directory -- this can not be rolled back
270 # since another transfer running concurrently may
271 # be relying on this existing.
272 safeMakeDir(outputDir)
274 if transaction is None:
275 # Use a no-op transaction to reduce code duplication
276 transaction = NoTransaction()
278 # For links the OS doesn't let us overwrite so if something does
279 # exist we have to remove it before we do the actual "transfer"
280 # below
281 if "link" in transfer and overwrite and dest_exists:
282 try:
283 self.remove()
284 except Exception:
285 # If this fails we ignore it since it's a problem
286 # that will manifest immediately below with a more relevant
287 # error message
288 pass
290 if transfer == "move":
291 with transaction.undoWith(f"move from {local_src}", shutil.move, newFullPath, local_src):
292 shutil.move(local_src, newFullPath)
293 elif transfer == "copy":
294 with transaction.undoWith(f"copy from {local_src}", os.remove, newFullPath):
295 shutil.copy(local_src, newFullPath)
296 elif transfer == "link":
297 # Try hard link and if that fails use a symlink
298 with transaction.undoWith(f"link to {local_src}", os.remove, newFullPath):
299 try:
300 os.link(local_src, newFullPath)
301 except OSError:
302 # Read through existing symlinks
303 os.symlink(local_src, newFullPath)
304 elif transfer == "hardlink":
305 with transaction.undoWith(f"hardlink to {local_src}", os.remove, newFullPath):
306 os.link(local_src, newFullPath)
307 elif transfer == "symlink":
308 # Read through existing symlinks
309 with transaction.undoWith(f"symlink to {local_src}", os.remove, newFullPath):
310 os.symlink(local_src, newFullPath)
311 elif transfer == "relsymlink":
312 # This is a standard symlink but using a relative path
313 # Need the directory name to give to relative root
314 # A full file path confuses it into an extra ../
315 newFullPathRoot = os.path.dirname(newFullPath)
316 relPath = os.path.relpath(local_src, newFullPathRoot)
317 with transaction.undoWith(f"relsymlink to {local_src}", os.remove, newFullPath):
318 os.symlink(relPath, newFullPath)
319 else:
320 raise NotImplementedError("Transfer type '{}' not supported.".format(transfer))
322 # This was an explicit move requested from a remote resource
323 # try to remove that remote resource. We check is_temporary because
324 # the local file would have been moved by shutil.move already.
325 if requested_transfer == "move" and is_temporary:
326 # Transactions do not work here
327 src.remove()
329 def walk(self, file_filter: Optional[Union[str, re.Pattern]] = None) -> Iterator[Union[List,
330 Tuple[ButlerURI,
331 List[str],
332 List[str]]]]:
333 """Walk the directory tree returning matching files and directories.
335 Parameters
336 ----------
337 file_filter : `str` or `re.Pattern`, optional
338 Regex to filter out files from the list before it is returned.
340 Yields
341 ------
342 dirpath : `ButlerURI`
343 Current directory being examined.
344 dirnames : `list` of `str`
345 Names of subdirectories within dirpath.
346 filenames : `list` of `str`
347 Names of all the files within dirpath.
348 """
349 if not self.isdir():
350 raise ValueError("Can not walk a non-directory URI")
352 if isinstance(file_filter, str):
353 file_filter = re.compile(file_filter)
355 for root, dirs, files in os.walk(self.ospath):
356 # Filter by the regex
357 if file_filter is not None:
358 files = [f for f in files if file_filter.search(f)]
359 yield type(self)(root, forceAbsolute=False, forceDirectory=True), dirs, files
361 @classmethod
362 def _fixupPathUri(cls, parsed: urllib.parse.ParseResult, root: Optional[Union[str, ButlerURI]] = None,
363 forceAbsolute: bool = False,
364 forceDirectory: bool = False) -> Tuple[urllib.parse.ParseResult, bool]:
365 """Fix up relative paths in URI instances.
367 Parameters
368 ----------
369 parsed : `~urllib.parse.ParseResult`
370 The result from parsing a URI using `urllib.parse`.
371 root : `str` or `ButlerURI`, optional
372 Path to use as root when converting relative to absolute.
373 If `None`, it will be the current working directory. This
374 is a local file system path, or a file URI. It is only used if
375 a file-scheme is used incorrectly with a relative path.
376 forceAbsolute : `bool`, ignored
377 Has no effect for this subclass. ``file`` URIs are always
378 absolute.
379 forceDirectory : `bool`, optional
380 If `True` forces the URI to end with a separator, otherwise given
381 URI is interpreted as is.
383 Returns
384 -------
385 modified : `~urllib.parse.ParseResult`
386 Update result if a URI is being handled.
387 dirLike : `bool`
388 `True` if given parsed URI has a trailing separator or
389 forceDirectory is True. Otherwise `False`.
391 Notes
392 -----
393 Relative paths are explicitly not supported by RFC8089 but `urllib`
394 does accept URIs of the form ``file:relative/path.ext``. They need
395 to be turned into absolute paths before they can be used. This is
396 always done regardless of the ``forceAbsolute`` parameter.
397 """
398 # assume we are not dealing with a directory like URI
399 dirLike = False
401 # file URI implies POSIX path separators so split as POSIX,
402 # then join as os, and convert to abspath. Do not handle
403 # home directories since "file" scheme is explicitly documented
404 # to not do tilde expansion.
405 sep = posixpath.sep
407 # For local file system we can explicitly check to see if this
408 # really is a directory. The URI might point to a location that
409 # does not exists yet but all that matters is if it is a directory
410 # then we make sure use that fact. No need to do the check if
411 # we are already being told.
412 if not forceDirectory and posixpath.isdir(parsed.path):
413 forceDirectory = True
415 # For an absolute path all we need to do is check if we need
416 # to force the directory separator
417 if posixpath.isabs(parsed.path):
418 if forceDirectory:
419 if not parsed.path.endswith(sep):
420 parsed = parsed._replace(path=parsed.path+sep)
421 dirLike = True
422 return copy.copy(parsed), dirLike
424 # Relative path so must fix it to be compliant with the standard
426 # Replacement values for the URI
427 replacements = {}
429 if root is None:
430 root = os.path.abspath(os.path.curdir)
431 elif isinstance(root, ButlerURI):
432 if root.scheme and root.scheme != "file":
433 raise RuntimeError(f"The override root must be a file URI not {root.scheme}")
434 root = os.path.abspath(root.ospath)
436 replacements["path"] = posixpath.normpath(posixpath.join(os2posix(root), parsed.path))
438 # normpath strips trailing "/" so put it back if necessary
439 # Acknowledge that trailing separator exists.
440 if forceDirectory or (parsed.path.endswith(sep) and not replacements["path"].endswith(sep)):
441 replacements["path"] += sep
442 dirLike = True
444 # ParseResult is a NamedTuple so _replace is standard API
445 parsed = parsed._replace(**replacements)
447 if parsed.params or parsed.query:
448 log.warning("Additional items unexpectedly encountered in file URI: %s", parsed.geturl())
450 return parsed, dirLike