llnl.util.filesystem.find: multiple entrypoints (#47436)
You can now provide multiple roots to a single `find()` call and all of them will be searched. The roots can overlap (e.g. can be parents of one another). This also adds a library function for taking a set of regular expression patterns and creating a single OR expression (and that library function is used in `find` to improve its performance).
This commit is contained in:
Harmen Stoppels
GitHub
parent
57a90c91a4
commit
73219e4b02
@ -20,11 +20,11 @@
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import tempfile
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from contextlib import contextmanager
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from itertools import accumulate
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from typing import Callable, Iterable, List, Match, Optional, Tuple, Union
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from typing import Callable, Deque, Dict, Iterable, List, Match, Optional, Set, Tuple, Union
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import llnl.util.symlink
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from llnl.util import tty
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from llnl.util.lang import dedupe, memoized
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from llnl.util.lang import dedupe, fnmatch_translate_multiple, memoized
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from llnl.util.symlink import islink, readlink, resolve_link_target_relative_to_the_link, symlink
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from ..path import path_to_os_path, system_path_filter
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@ -1673,32 +1673,40 @@ def find_first(root: str, files: Union[Iterable[str], str], bfs_depth: int = 2)
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return FindFirstFile(root, *files, bfs_depth=bfs_depth).find()
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def find(root, files, recursive=True, max_depth: Optional[int] = None):
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"""Search for ``files`` starting from the ``root`` directory.
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Like GNU/BSD find but written entirely in Python.
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Specifically this behaves like `find -type f`: it only returns
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results that are files. When searching recursively, this behaves
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as `find` with the `-L` option (follows symlinks).
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def find(
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root: Union[str, List[str]],
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files: Union[str, List[str]],
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recursive: bool = True,
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max_depth: Optional[int] = None,
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) -> List[str]:
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"""Finds all non-directory files matching the filename patterns from ``files`` starting from
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``root``. This function returns a deterministic result for the same input and directory
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structure when run multiple times. Symlinked directories are followed, and unique directories
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are searched only once. Each matching file is returned only once at lowest depth in case
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multiple paths exist due to symlinked directories. The function has similarities to the Unix
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``find`` utility.
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Examples:
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.. code-block:: console
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$ find -L /usr -name python
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$ find -L /usr -name python3 -type f
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is equivalent to:
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is roughly equivalent to
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>>> find('/usr', 'python')
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>>> find("/usr", "python3")
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with the notable difference that this function only lists a single path to each file in case of
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symlinked directories.
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.. code-block:: console
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$ find /usr/local/bin -maxdepth 1 -name python
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$ find -L /usr/local/bin /usr/local/sbin -maxdepth 1 '(' -name python3 -o -name getcap \\
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')' -type f
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is equivalent to:
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is roughly equivalent to:
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>>> find('/usr/local/bin', 'python', recursive=False)
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>>> find(["/usr/local/bin", "/usr/local/sbin"], ["python3", "getcap"], recursive=False)
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Accepts any glob characters accepted by fnmatch:
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@ -1712,17 +1720,17 @@ def find(root, files, recursive=True, max_depth: Optional[int] = None):
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========== ====================================
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Parameters:
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root (str): The root directory to start searching from
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files (str or collections.abc.Sequence): Library name(s) to search for
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recursive (bool): if False search only root folder,
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if True descends top-down from the root. Defaults to True.
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max_depth (int): if set, don't search below this depth. Cannot be set
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if recursive is False
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root: One or more root directories to start searching from
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files: One or more filename patterns to search for
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recursive: if False search only root, if True descends from roots. Defaults to True.
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max_depth: if set, don't search below this depth. Cannot be set if recursive is False
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Returns:
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list: The files that have been found
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Returns a list of absolute, matching file paths.
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"""
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if isinstance(files, str):
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if not isinstance(root, list):
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root = [root]
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if not isinstance(files, list):
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files = [files]
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# If recursive is false, max_depth can only be None or 0
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@ -1734,10 +1742,9 @@ def find(root, files, recursive=True, max_depth: Optional[int] = None):
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elif max_depth is None:
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max_depth = sys.maxsize
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tty.debug(f"Find (max depth = {max_depth}): {root} {str(files)}")
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result = find_max_depth(root, files, max_depth)
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tty.debug(f"Find complete: {root} {str(files)}")
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tty.debug(f"Find (max depth = {max_depth}): {root} {files}")
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result = _find_max_depth(root, files, max_depth)
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tty.debug(f"Find complete: {root} {files}")
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return result
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@ -1746,56 +1753,36 @@ def _log_file_access_issue(e: OSError, path: str) -> None:
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tty.debug(f"find must skip {path}: {errno_name} {e}")
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@system_path_filter(arg_slice=slice(1))
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def find_max_depth(root, globs, max_depth: Optional[int] = None):
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"""Given a set of non-recursive glob file patterns, finds all
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files matching those patterns up to a maximum specified depth.
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def _dir_id(s: os.stat_result) -> Tuple[int, int]:
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# Note: on windows, st_ino is the file index and st_dev is the volume serial number. See
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# https://github.com/python/cpython/blob/3.9/Python/fileutils.c
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return (s.st_ino, s.st_dev)
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If a directory has a name which matches an input pattern, it will
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not be included in the results.
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If ``max_depth`` is specified, does not search below that depth.
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def _find_max_depth(roots: List[str], globs: List[str], max_depth: int = sys.maxsize) -> List[str]:
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"""See ``find`` for the public API."""
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# Apply normcase to file patterns and filenames to respect case insensitive filesystems
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regex, groups = fnmatch_translate_multiple([os.path.normcase(x) for x in globs])
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# Ordered dictionary that keeps track of the files found for each pattern
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capture_group_to_paths: Dict[str, List[str]] = {group: [] for group in groups}
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# Ensure returned paths are always absolute
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roots = [os.path.abspath(r) for r in roots]
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# Breadth-first search queue. Each element is a tuple of (depth, directory)
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dir_queue: Deque[Tuple[int, str]] = collections.deque()
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# Set of visited directories. Each element is a tuple of (inode, device)
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visited_dirs: Set[Tuple[int, int]] = set()
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If ``globs`` is a list, files matching earlier entries are placed
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in the return value before files matching later entries.
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"""
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try:
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stat_root = os.stat(root)
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except OSError:
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return []
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for root in roots:
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try:
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stat_root = os.stat(root)
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except OSError as e:
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_log_file_access_issue(e, root)
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continue
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dir_id = _dir_id(stat_root)
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if dir_id not in visited_dirs:
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dir_queue.appendleft((0, root))
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visited_dirs.add(dir_id)
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if max_depth is None:
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max_depth = sys.maxsize
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if isinstance(globs, str):
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globs = [globs]
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# Apply normcase to regular expressions and to the filenames:
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# this respects case-sensitivity semantics of different OSes
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# (e.g. file search is typically case-insensitive on Windows)
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regexes = [re.compile(fnmatch.translate(os.path.normcase(x))) for x in globs]
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# Note later calls to os.scandir etc. return abspaths if the
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# input is absolute, see https://docs.python.org/3/library/os.html#os.DirEntry.path
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root = os.path.abspath(root)
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found_files = collections.defaultdict(list)
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def _dir_id(stat_info):
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# Note: on windows, st_ino is the file index and st_dev
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# is the volume serial number. See
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# https://github.com/python/cpython/blob/3.9/Python/fileutils.c
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return (stat_info.st_ino, stat_info.st_dev)
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visited_dirs = set([_dir_id(stat_root)])
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# Each queue item stores the depth and path
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# This achieves a consistent traversal order by iterating through
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# each directory in alphabetical order.
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# This also traverses in BFS order to ensure finding the shortest
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# path to any file (or one of the shortest paths, if there are
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# several - the one returned will be consistent given the prior
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# point).
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dir_queue = collections.deque([(0, root)])
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while dir_queue:
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depth, next_dir = dir_queue.pop()
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try:
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@ -1810,20 +1797,18 @@ def _dir_id(stat_info):
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try:
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it_is_a_dir = dir_entry.is_dir(follow_symlinks=True)
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except OSError as e:
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# Possible permission issue, or a symlink that cannot
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# be resolved (ELOOP).
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# Possible permission issue, or a symlink that cannot be resolved (ELOOP).
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_log_file_access_issue(e, dir_entry.path)
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continue
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if it_is_a_dir and (depth < max_depth):
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if it_is_a_dir and depth < max_depth:
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try:
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# The stat should be performed in a try/except block.
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# We repeat that here vs. moving to the above block
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# because we only want to call `stat` if we haven't
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# exceeded our max_depth
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# The stat should be performed in a try/except block. We repeat that here
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# vs. moving to the above block because we only want to call `stat` if we
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# haven't exceeded our max_depth
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if sys.platform == "win32":
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# Note: st_ino/st_dev on DirEntry.stat are not set on
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# Windows, so we have to call os.stat
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# Note: st_ino/st_dev on DirEntry.stat are not set on Windows, so we
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# have to call os.stat
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stat_info = os.stat(dir_entry.path, follow_symlinks=True)
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else:
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stat_info = dir_entry.stat(follow_symlinks=True)
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@ -1836,15 +1821,15 @@ def _dir_id(stat_info):
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dir_queue.appendleft((depth + 1, dir_entry.path))
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visited_dirs.add(dir_id)
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else:
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fname = os.path.basename(dir_entry.path)
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for pattern in regexes:
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if pattern.match(os.path.normcase(fname)):
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found_files[pattern].append(os.path.join(next_dir, fname))
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m = regex.match(os.path.normcase(os.path.basename(dir_entry.path)))
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if not m:
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continue
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for group in capture_group_to_paths:
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if m.group(group):
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capture_group_to_paths[group].append(dir_entry.path)
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break
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# TODO: for fully-recursive searches, we can print a warning after
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# after having searched everything up to some fixed depth
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return list(itertools.chain(*[found_files[x] for x in regexes]))
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return [path for paths in capture_group_to_paths.values() for path in paths]
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# Utilities for libraries and headers
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@ -5,12 +5,14 @@
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import collections.abc
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import contextlib
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import fnmatch
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import functools
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import itertools
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import os
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import re
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import sys
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import traceback
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import typing
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import warnings
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from datetime import datetime, timedelta
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from typing import Callable, Iterable, List, Tuple, TypeVar
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@ -859,6 +861,32 @@ def elide_list(line_list: List[str], max_num: int = 10) -> List[str]:
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return line_list
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if sys.version_info >= (3, 9):
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PatternStr = re.Pattern[str]
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else:
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PatternStr = typing.Pattern[str]
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def fnmatch_translate_multiple(patterns: List[str]) -> Tuple[PatternStr, List[str]]:
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"""Same as fnmatch.translate, but creates a single regex of the form
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``(?P<pattern0>...)|(?P<pattern1>...)|...`` for each pattern in the iterable, where
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``patternN`` is a named capture group that matches the corresponding pattern translated by
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``fnmatch.translate``. This can be used to match multiple patterns in a single pass. No case
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normalization is performed on the patterns.
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Args:
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patterns: list of fnmatch patterns
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Returns:
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Tuple of the combined regex and the list of named capture groups corresponding to each
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pattern in the input list.
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"""
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groups = [f"pattern{i}" for i in range(len(patterns))]
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regexes = (fnmatch.translate(p) for p in patterns)
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combined = re.compile("|".join(f"(?P<{g}>{r})" for g, r in zip(groups, regexes)))
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return combined, groups
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@contextlib.contextmanager
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def nullcontext(*args, **kwargs):
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"""Empty context manager.
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@ -1072,16 +1072,16 @@ def test_find_max_depth(dir_structure_with_things_to_find):
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# Make sure the paths we use to verify are absolute
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assert os.path.isabs(locations["file_one"])
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assert set(fs.find_max_depth(root, "file_*", 0)) == {locations["file_four"]}
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assert set(fs.find_max_depth(root, "file_*", 1)) == {
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assert set(fs.find(root, "file_*", max_depth=0)) == {locations["file_four"]}
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assert set(fs.find(root, "file_*", max_depth=1)) == {
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locations["file_one"],
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locations["file_three"],
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locations["file_four"],
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}
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assert set(fs.find_max_depth(root, "file_two", 2)) == {locations["file_two"]}
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assert not set(fs.find_max_depth(root, "file_two", 1))
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assert set(fs.find_max_depth(root, "file_two")) == {locations["file_two"]}
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assert set(fs.find_max_depth(root, "file_*")) == set(locations.values())
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assert set(fs.find(root, "file_two", max_depth=2)) == {locations["file_two"]}
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assert not set(fs.find(root, "file_two", max_depth=1))
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assert set(fs.find(root, "file_two")) == {locations["file_two"]}
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assert set(fs.find(root, "file_*")) == set(locations.values())
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def test_find_max_depth_relative(dir_structure_with_things_to_find):
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@ -1090,8 +1090,8 @@ def test_find_max_depth_relative(dir_structure_with_things_to_find):
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"""
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root, locations = dir_structure_with_things_to_find
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with fs.working_dir(root):
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assert set(fs.find_max_depth(".", "file_*", 0)) == {locations["file_four"]}
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assert set(fs.find_max_depth(".", "file_two", 2)) == {locations["file_two"]}
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assert set(fs.find(".", "file_*", max_depth=0)) == {locations["file_four"]}
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assert set(fs.find(".", "file_two", max_depth=2)) == {locations["file_two"]}
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@pytest.mark.parametrize("recursive,max_depth", [(False, -1), (False, 1)])
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@ -1105,7 +1105,8 @@ def test_max_depth_and_recursive_errors(tmpdir, recursive, max_depth):
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fs.find_libraries(["some_lib"], root, recursive=recursive, max_depth=max_depth)
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def dir_structure_with_things_to_find_links(tmpdir, use_junctions=False):
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@pytest.fixture(params=[True, False])
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def complex_dir_structure(request, tmpdir):
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"""
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"lx-dy" means "level x, directory y"
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"lx-fy" means "level x, file y"
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@ -1128,8 +1129,11 @@ def dir_structure_with_things_to_find_links(tmpdir, use_junctions=False):
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l1-s3 -> l3-d4 # a link that "skips" a directory level
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l1-s4 -> l2-s3 # a link to a link to a dir
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"""
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if sys.platform == "win32" and (not use_junctions) and (not _windows_can_symlink()):
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use_junctions = request.param
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if sys.platform == "win32" and not use_junctions and not _windows_can_symlink():
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pytest.skip("This Windows instance is not configured with symlink support")
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elif sys.platform != "win32" and use_junctions:
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pytest.skip("Junctions are a Windows-only feature")
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l1_d1 = tmpdir.join("l1-d1").ensure(dir=True)
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l2_d1 = l1_d1.join("l2-d1").ensure(dir=True)
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@ -1150,44 +1154,60 @@ def dir_structure_with_things_to_find_links(tmpdir, use_junctions=False):
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link_fn(l2_d2, l2_s3)
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link_fn(l2_s3, pathlib.Path(tmpdir) / "l1-s4")
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locations = {}
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locations["l4-f1"] = str(l3_d2.join("l4-f1").ensure())
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locations["l4-f2-full"] = str(l3_d4.join("l4-f2").ensure())
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locations["l4-f2-link"] = str(pathlib.Path(tmpdir) / "l1-s3" / "l4-f2")
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locations["l2-f1"] = str(l1_d2.join("l2-f1").ensure())
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locations["l2-f1-link"] = str(pathlib.Path(tmpdir) / "l1-d1" / "l2-d1" / "l3-s1" / "l2-f1")
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locations["l3-f3-full"] = str(l2_d2.join("l3-f3").ensure())
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locations["l3-f3-link-l1"] = str(pathlib.Path(tmpdir) / "l1-s4" / "l3-f3")
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locations = {
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"l4-f1": str(l3_d2.join("l4-f1").ensure()),
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"l4-f2-full": str(l3_d4.join("l4-f2").ensure()),
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"l4-f2-link": str(pathlib.Path(tmpdir) / "l1-s3" / "l4-f2"),
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"l2-f1": str(l1_d2.join("l2-f1").ensure()),
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"l2-f1-link": str(pathlib.Path(tmpdir) / "l1-d1" / "l2-d1" / "l3-s1" / "l2-f1"),
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"l3-f3-full": str(l2_d2.join("l3-f3").ensure()),
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"l3-f3-link-l1": str(pathlib.Path(tmpdir) / "l1-s4" / "l3-f3"),
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}
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return str(tmpdir), locations
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def _check_find_links(root, locations):
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def test_find_max_depth_symlinks(complex_dir_structure):
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root, locations = complex_dir_structure
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root = pathlib.Path(root)
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assert set(fs.find_max_depth(root, "l4-f1")) == {locations["l4-f1"]}
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assert set(fs.find_max_depth(root / "l1-s3", "l4-f2", 0)) == {locations["l4-f2-link"]}
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||||
assert set(fs.find_max_depth(root / "l1-d1", "l2-f1")) == {locations["l2-f1-link"]}
|
||||
assert set(fs.find(root, "l4-f1")) == {locations["l4-f1"]}
|
||||
assert set(fs.find(root / "l1-s3", "l4-f2", max_depth=0)) == {locations["l4-f2-link"]}
|
||||
assert set(fs.find(root / "l1-d1", "l2-f1")) == {locations["l2-f1-link"]}
|
||||
# File is accessible via symlink and subdir, the link path will be
|
||||
# searched first, and the directory will not be searched again when
|
||||
# it is encountered the second time (via not-link) in the traversal
|
||||
assert set(fs.find_max_depth(root, "l4-f2")) == {locations["l4-f2-link"]}
|
||||
assert set(fs.find(root, "l4-f2")) == {locations["l4-f2-link"]}
|
||||
# File is accessible only via the dir, so the full file path should
|
||||
# be reported
|
||||
assert set(fs.find_max_depth(root / "l1-d1", "l4-f2")) == {locations["l4-f2-full"]}
|
||||
assert set(fs.find(root / "l1-d1", "l4-f2")) == {locations["l4-f2-full"]}
|
||||
# Check following links to links
|
||||
assert set(fs.find_max_depth(root, "l3-f3")) == {locations["l3-f3-link-l1"]}
|
||||
assert set(fs.find(root, "l3-f3")) == {locations["l3-f3-link-l1"]}
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"use_junctions",
|
||||
[
|
||||
False,
|
||||
pytest.param(
|
||||
True,
|
||||
marks=pytest.mark.skipif(sys.platform != "win32", reason="Only Windows has junctions"),
|
||||
),
|
||||
],
|
||||
)
|
||||
def test_find_max_depth_symlinks(tmpdir, use_junctions):
|
||||
root, locations = dir_structure_with_things_to_find_links(tmpdir, use_junctions=use_junctions)
|
||||
_check_find_links(root, locations)
|
||||
def test_find_max_depth_multiple_and_repeated_entry_points(complex_dir_structure):
|
||||
root, locations = complex_dir_structure
|
||||
|
||||
fst = str(pathlib.Path(root) / "l1-d1" / "l2-d1")
|
||||
snd = str(pathlib.Path(root) / "l1-d2")
|
||||
nonexistent = str(pathlib.Path(root) / "nonexistent")
|
||||
|
||||
assert set(fs.find([fst, snd, fst, snd, nonexistent], ["l*-f*"], max_depth=1)) == {
|
||||
locations["l2-f1"],
|
||||
locations["l4-f1"],
|
||||
locations["l4-f2-full"],
|
||||
locations["l3-f3-full"],
|
||||
}
|
||||
|
||||
|
||||
def test_multiple_patterns(complex_dir_structure):
|
||||
root, _ = complex_dir_structure
|
||||
paths = fs.find(root, ["l2-f1", "l3-f3", "*"])
|
||||
# There shouldn't be duplicate results with multiple, overlapping patterns
|
||||
assert len(set(paths)) == len(paths)
|
||||
# All files should be found
|
||||
filenames = [os.path.basename(p) for p in paths]
|
||||
assert set(filenames) == {"l2-f1", "l3-f3", "l4-f1", "l4-f2"}
|
||||
# They are ordered by first matching pattern (this is a bit of an implementation detail,
|
||||
# and we could decide to change the exact order in the future)
|
||||
assert filenames[0] == "l2-f1"
|
||||
assert filenames[1] == "l3-f3"
|
||||
|
||||
@ -373,3 +373,18 @@ class _SomeClass:
|
||||
_SomeClass.deprecated.error_lvl = 2
|
||||
with pytest.raises(AttributeError):
|
||||
_ = s.deprecated
|
||||
|
||||
|
||||
def test_fnmatch_multiple():
|
||||
regex, groups = llnl.util.lang.fnmatch_translate_multiple(["libf*o.so", "libb*r.so"])
|
||||
|
||||
a = regex.match("libfoo.so")
|
||||
assert a and a.group(groups[0]) == "libfoo.so"
|
||||
|
||||
b = regex.match("libbar.so")
|
||||
assert b and b.group(groups[1]) == "libbar.so"
|
||||
|
||||
assert not regex.match("libfoo.so.1")
|
||||
assert not regex.match("libbar.so.1")
|
||||
assert not regex.match("libfoo.solibbar.so")
|
||||
assert not regex.match("libbaz.so")
|
||||
|
||||
Loading…
Reference in New Issue
Block a user