Coverage for python/lsst/daf/butler/core/_butlerUri/file.py: 15%
Shortcuts on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
Shortcuts on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
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 Iterator,
38 List,
39 Optional,
40 Tuple,
41 Union,
42)
44from ..utils import safeMakeDir
45from .utils import NoTransaction, os2posix, posix2os
46from ._butlerUri import ButlerURI
49if TYPE_CHECKING: 49 ↛ 50line 49 didn't jump to line 50, because the condition on line 49 was never true
50 from ..datastore import DatastoreTransaction
53log = logging.getLogger(__name__)
56class ButlerFileURI(ButlerURI):
57 """URI for explicit ``file`` scheme."""
59 transferModes = ("copy", "link", "symlink", "hardlink", "relsymlink", "auto", "move")
60 transferDefault: str = "link"
62 # By definition refers to a local file
63 isLocal = True
65 @property
66 def ospath(self) -> str:
67 """Path component of the URI localized to current OS.
69 Will unquote URI path since a formal URI must include the quoting.
70 """
71 return urllib.parse.unquote(posix2os(self._uri.path))
73 def exists(self) -> bool:
74 """Indicate that the file exists."""
75 # Uses os.path.exists so if there is a soft link that points
76 # to a file that no longer exists this will return False
77 return os.path.exists(self.ospath)
79 def size(self) -> int:
80 """Return the size of the file in bytes."""
81 if not os.path.isdir(self.ospath):
82 stat = os.stat(self.ospath)
83 sz = stat.st_size
84 else:
85 sz = 0
86 return sz
88 def remove(self) -> None:
89 """Remove the resource."""
90 os.remove(self.ospath)
92 def _as_local(self) -> Tuple[str, bool]:
93 """Return the local path of the file.
95 This is an internal helper for ``as_local()``.
97 Returns
98 -------
99 path : `str`
100 The local path to this file.
101 temporary : `bool`
102 Always returns `False` (this is not a temporary file).
103 """
104 return self.ospath, False
106 def read(self, size: int = -1) -> bytes:
107 """Return the entire content of the file as bytes."""
108 with open(self.ospath, "rb") as fh:
109 return fh.read(size)
111 def write(self, data: bytes, overwrite: bool = True) -> None:
112 """Write the supplied data to the file."""
113 dir = os.path.dirname(self.ospath)
114 if not os.path.exists(dir):
115 safeMakeDir(dir)
116 if overwrite:
117 mode = "wb"
118 else:
119 mode = "xb"
120 with open(self.ospath, mode) as f:
121 f.write(data)
123 def mkdir(self) -> None:
124 """Make the directory associated with this URI."""
125 if not os.path.exists(self.ospath):
126 safeMakeDir(self.ospath)
127 elif not os.path.isdir(self.ospath):
128 raise FileExistsError(f"URI {self} exists but is not a directory!")
130 def isdir(self) -> bool:
131 """Return whether this URI is a directory.
133 Returns
134 -------
135 isdir : `bool`
136 `True` if this URI is a directory or looks like a directory,
137 else `False`.
138 """
139 return self.dirLike or os.path.isdir(self.ospath)
141 def transfer_from(self, src: ButlerURI, transfer: str,
142 overwrite: bool = False,
143 transaction: Optional[Union[DatastoreTransaction, NoTransaction]] = None) -> None:
144 """Transfer the current resource to a local file.
146 Parameters
147 ----------
148 src : `ButlerURI`
149 Source URI.
150 transfer : `str`
151 Mode to use for transferring the resource. Supports the following
152 options: copy, link, symlink, hardlink, relsymlink.
153 overwrite : `bool`, optional
154 Allow an existing file to be overwritten. Defaults to `False`.
155 transaction : `DatastoreTransaction`, optional
156 If a transaction is provided, undo actions will be registered.
157 """
158 # Fail early to prevent delays if remote resources are requested
159 if transfer not in self.transferModes:
160 raise ValueError(f"Transfer mode '{transfer}' not supported by URI scheme {self.scheme}")
162 # Existence checks can take time so only try if the log message
163 # will be issued.
164 if log.isEnabledFor(logging.DEBUG):
165 log.debug("Transferring %s [exists: %s] -> %s [exists: %s] (transfer=%s)",
166 src, src.exists(), self, self.exists(), transfer)
168 # We do not have to special case ButlerFileURI here because
169 # as_local handles that.
170 with src.as_local() as local_uri:
171 is_temporary = local_uri.isTemporary
172 local_src = local_uri.ospath
174 # Short circuit if the URIs are identical immediately.
175 if self == local_uri:
176 log.debug("Target and destination URIs are identical: %s, returning immediately."
177 " No further action required.", self)
178 return
180 # Default transfer mode depends on whether we have a temporary
181 # file or not.
182 if transfer == "auto":
183 transfer = self.transferDefault if not is_temporary else "copy"
185 if not os.path.exists(local_src):
186 if is_temporary:
187 msg = f"Local file {local_uri} downloaded from {src} has gone missing"
188 else:
189 msg = f"Source URI {src} does not exist"
190 raise FileNotFoundError(msg)
192 # Follow soft links
193 local_src = os.path.realpath(os.path.normpath(local_src))
195 # All the modes involving linking use "link" somewhere
196 if "link" in transfer and is_temporary:
197 raise RuntimeError("Can not use local file system transfer mode"
198 f" {transfer} for remote resource ({src})")
200 # For temporary files we can own them
201 requested_transfer = transfer
202 if is_temporary and transfer == "copy":
203 transfer = "move"
205 # The output location should not exist unless overwrite=True.
206 # Rather than use `exists()`, use os.stat since we might need
207 # the full answer later.
208 dest_stat: Optional[os.stat_result]
209 try:
210 # Do not read through links of the file itself.
211 dest_stat = os.lstat(self.ospath)
212 except FileNotFoundError:
213 dest_stat = None
215 # It is possible that the source URI and target URI refer
216 # to the same file. This can happen for a number of reasons
217 # (such as soft links in the path, or they really are the same).
218 # In that case log a message and return as if the transfer
219 # completed (it technically did). A temporary file download
220 # can't be the same so the test can be skipped.
221 if dest_stat and not is_temporary:
222 # Be consistent and use lstat here (even though realpath
223 # has been called). It does not harm.
224 local_src_stat = os.lstat(local_src)
225 if (dest_stat.st_ino == local_src_stat.st_ino
226 and dest_stat.st_dev == local_src_stat.st_dev):
227 log.debug("Destination URI %s is the same file as source URI %s, returning immediately."
228 " No further action required.", self, local_uri)
229 return
231 if not overwrite and dest_stat:
232 raise FileExistsError(f"Destination path '{self}' already exists. Transfer "
233 f"from {src} cannot be completed.")
235 # Make the path absolute (but don't follow links since that
236 # would possibly cause us to end up in the wrong place if the
237 # file existed already as a soft link)
238 newFullPath = os.path.abspath(self.ospath)
239 outputDir = os.path.dirname(newFullPath)
240 if not os.path.isdir(outputDir):
241 # Must create the directory -- this can not be rolled back
242 # since another transfer running concurrently may
243 # be relying on this existing.
244 safeMakeDir(outputDir)
246 if transaction is None:
247 # Use a no-op transaction to reduce code duplication
248 transaction = NoTransaction()
250 # For links the OS doesn't let us overwrite so if something does
251 # exist we have to remove it before we do the actual "transfer"
252 # below
253 if "link" in transfer and overwrite and dest_stat:
254 try:
255 self.remove()
256 except Exception:
257 # If this fails we ignore it since it's a problem
258 # that will manifest immediately below with a more relevant
259 # error message
260 pass
262 if transfer == "move":
263 with transaction.undoWith(f"move from {local_src}", shutil.move, newFullPath, local_src):
264 shutil.move(local_src, newFullPath)
265 elif transfer == "copy":
266 with transaction.undoWith(f"copy from {local_src}", os.remove, newFullPath):
267 shutil.copy(local_src, newFullPath)
268 elif transfer == "link":
269 # Try hard link and if that fails use a symlink
270 with transaction.undoWith(f"link to {local_src}", os.remove, newFullPath):
271 try:
272 os.link(local_src, newFullPath)
273 except OSError:
274 # Read through existing symlinks
275 os.symlink(local_src, newFullPath)
276 elif transfer == "hardlink":
277 with transaction.undoWith(f"hardlink to {local_src}", os.remove, newFullPath):
278 os.link(local_src, newFullPath)
279 elif transfer == "symlink":
280 # Read through existing symlinks
281 with transaction.undoWith(f"symlink to {local_src}", os.remove, newFullPath):
282 os.symlink(local_src, newFullPath)
283 elif transfer == "relsymlink":
284 # This is a standard symlink but using a relative path
285 # Need the directory name to give to relative root
286 # A full file path confuses it into an extra ../
287 newFullPathRoot = os.path.dirname(newFullPath)
288 relPath = os.path.relpath(local_src, newFullPathRoot)
289 with transaction.undoWith(f"relsymlink to {local_src}", os.remove, newFullPath):
290 os.symlink(relPath, newFullPath)
291 else:
292 raise NotImplementedError("Transfer type '{}' not supported.".format(transfer))
294 # This was an explicit move requested from a remote resource
295 # try to remove that remote resource. We check is_temporary because
296 # the local file would have been moved by shutil.move already.
297 if requested_transfer == "move" and is_temporary:
298 # Transactions do not work here
299 src.remove()
301 def walk(self, file_filter: Optional[Union[str, re.Pattern]] = None) -> Iterator[Union[List,
302 Tuple[ButlerURI,
303 List[str],
304 List[str]]]]:
305 """Walk the directory tree returning matching files and directories.
307 Parameters
308 ----------
309 file_filter : `str` or `re.Pattern`, optional
310 Regex to filter out files from the list before it is returned.
312 Yields
313 ------
314 dirpath : `ButlerURI`
315 Current directory being examined.
316 dirnames : `list` of `str`
317 Names of subdirectories within dirpath.
318 filenames : `list` of `str`
319 Names of all the files within dirpath.
320 """
321 if not self.isdir():
322 raise ValueError("Can not walk a non-directory URI")
324 if isinstance(file_filter, str):
325 file_filter = re.compile(file_filter)
327 for root, dirs, files in os.walk(self.ospath):
328 # Filter by the regex
329 if file_filter is not None:
330 files = [f for f in files if file_filter.search(f)]
331 yield type(self)(root, forceAbsolute=False, forceDirectory=True), dirs, files
333 @classmethod
334 def _fixupPathUri(cls, parsed: urllib.parse.ParseResult, root: Optional[Union[str, ButlerURI]] = None,
335 forceAbsolute: bool = False,
336 forceDirectory: bool = False) -> Tuple[urllib.parse.ParseResult, bool]:
337 """Fix up relative paths in URI instances.
339 Parameters
340 ----------
341 parsed : `~urllib.parse.ParseResult`
342 The result from parsing a URI using `urllib.parse`.
343 root : `str` or `ButlerURI`, optional
344 Path to use as root when converting relative to absolute.
345 If `None`, it will be the current working directory. This
346 is a local file system path, or a file URI. It is only used if
347 a file-scheme is used incorrectly with a relative path.
348 forceAbsolute : `bool`, ignored
349 Has no effect for this subclass. ``file`` URIs are always
350 absolute.
351 forceDirectory : `bool`, optional
352 If `True` forces the URI to end with a separator, otherwise given
353 URI is interpreted as is.
355 Returns
356 -------
357 modified : `~urllib.parse.ParseResult`
358 Update result if a URI is being handled.
359 dirLike : `bool`
360 `True` if given parsed URI has a trailing separator or
361 forceDirectory is True. Otherwise `False`.
363 Notes
364 -----
365 Relative paths are explicitly not supported by RFC8089 but `urllib`
366 does accept URIs of the form ``file:relative/path.ext``. They need
367 to be turned into absolute paths before they can be used. This is
368 always done regardless of the ``forceAbsolute`` parameter.
369 """
370 # assume we are not dealing with a directory like URI
371 dirLike = False
373 # file URI implies POSIX path separators so split as POSIX,
374 # then join as os, and convert to abspath. Do not handle
375 # home directories since "file" scheme is explicitly documented
376 # to not do tilde expansion.
377 sep = posixpath.sep
379 # For local file system we can explicitly check to see if this
380 # really is a directory. The URI might point to a location that
381 # does not exists yet but all that matters is if it is a directory
382 # then we make sure use that fact. No need to do the check if
383 # we are already being told.
384 if not forceDirectory and posixpath.isdir(parsed.path):
385 forceDirectory = True
387 # For an absolute path all we need to do is check if we need
388 # to force the directory separator
389 if posixpath.isabs(parsed.path):
390 if forceDirectory:
391 if not parsed.path.endswith(sep):
392 parsed = parsed._replace(path=parsed.path+sep)
393 dirLike = True
394 return copy.copy(parsed), dirLike
396 # Relative path so must fix it to be compliant with the standard
398 # Replacement values for the URI
399 replacements = {}
401 if root is None:
402 root = os.path.abspath(os.path.curdir)
403 elif isinstance(root, ButlerURI):
404 if root.scheme and root.scheme != "file":
405 raise RuntimeError(f"The override root must be a file URI not {root.scheme}")
406 root = os.path.abspath(root.ospath)
408 replacements["path"] = posixpath.normpath(posixpath.join(os2posix(root), parsed.path))
410 # normpath strips trailing "/" so put it back if necessary
411 # Acknowledge that trailing separator exists.
412 if forceDirectory or (parsed.path.endswith(sep) and not replacements["path"].endswith(sep)):
413 replacements["path"] += sep
414 dirLike = True
416 # ParseResult is a NamedTuple so _replace is standard API
417 parsed = parsed._replace(**replacements)
419 if parsed.params or parsed.query:
420 log.warning("Additional items unexpectedly encountered in file URI: %s", parsed.geturl())
422 return parsed, dirLike