galaxy.util.path package¶

Path manipulation functions.

galaxy.util.path.safe_contains(prefix, path, allowlist=None, real=None)[source]¶

Ensure a path is contained within another path.

Given any two filesystem paths, ensure that path is contained in prefix. If path exists (either as an absolute path or relative to prefix), it is canonicalized with os.path.realpath() to ensure it is not a symbolic link that points outside of prefix. If it is a symbolic link and allowlist is set, the symbolic link may also point inside a allowlist path.

The path is checked against allowlist using either its absolute pathname (if passed in as absolute) or relative to prefix and canonicalized (if applicable). It is not os.path.join()``ed with each ``allowlist directory.

Parameters:	prefix (string) – a directory under which `path` is to be checked path (string) – a filename to check allowlist (list of strings) – list of additional paths under which `path` may be located
Return type:	bool
Returns:	`True` if `path` is contained within `prefix` or `allowlist`, `False` otherwise.

galaxy.util.path.safe_makedirs(path)[source]¶

Safely make a directory, do not fail if it already exists or is created during execution.

Parameters:	path (string) – a directory to create

galaxy.util.path.safe_relpath(path)[source]¶

Determine whether a relative path references a path outside its root.

This is a path computation: the filesystem is not accessed to confirm the existence or nature of path.

Parameters:	path (string) – a path to check
Return type:	bool
Returns:	`True` if path is relative and does not reference a path in a parent directory, `False` otherwise.

galaxy.util.path.safe_walk(path, allowlist=None)[source]¶

Walk a path and return only the contents that are not symlinks outside the path.

Symbolic links are followed if a allowlist is provided. The path itself cannot be a symbolic link unless the pointed to location is in the allowlist.

Parameters:	path (string) – a directory to check for unsafe contents allowlist (list of strings) – list of additional paths under which contents may be located
Return type:	iterator
Returns:	Iterator of “safe” `os.walk()` tuples found under `path`

galaxy.util.path.unsafe_walk(path, allowlist=None, username=None)[source]¶

Walk a path and ensure that none of its contents are symlinks outside the path.

It is assumed that path itself has already been validated e.g. with safe_relpath() or safe_contains(). This function is most useful for the case where you want to test whether a directory contains safe paths, but do not want to actually walk the safe contents.

Parameters:	path (string) – a directory to check for unsafe contents allowlist (list of strings) – list of additional paths under which contents may be located
Return type:	list of strings
Returns:	A list of “bad” files found under `path`

galaxy.util.path.joinext(root, ext)[source]¶

Roughly the reverse of os.path.splitext.

Parameters:	root (string) – part of the filename before the extension ext – the extension
Return type:	string
Returns:	`root` joined with `ext` separated by a single `os.extsep`

galaxy.util.path.has_ext(path, ext, aliases=False, ignore=None)[source]¶

Determine whether path has extension ext

Parameters:	path (string) – Path to check ext (string) – Extension to check aliases (bool) – Check any known aliases for the given extension ignore (string) – Ignore this extension at the end of the path (e.g. `sample`)
Return type:	bool
Returns:	`True` if path is a YAML file, `False` otherwise.

galaxy.util.path.get_ext(path, ignore=None, canonicalize=True)[source]¶

Return the extension of path

Parameters:	path (string) – Path to check ignore (string) – Ignore this extension at the end of the path (e.g. `sample`) canonicalize (bool) – If the extension is known to this module, return the canonicalized extension instead of the file’s actual extension
Return type:	string

Submodules¶

galaxy.util.path.ntpath module¶

Galaxy “safe” path functions forced to work with Windows-style paths regardless of current platform

galaxy.util.path.posixpath module¶

Galaxy “safe” path functions forced to work with POSIX-style paths regardless of current platform