nexusLIMS.utils.paths#

Path manipulation utilities for NexusLIMS.

Module Contents#

Functions#

is_subpath

Return if this path is a subpath of other paths.

join_instrument_filestore_path

Safely join NX_INSTRUMENT_DATA_PATH with an instrument’s filestore_path.

replace_instrument_data_path

Given an “NX_INSTRUMENT_DATA_PATH” path, generate equivalent”NX_DATA_PATH” path.

API#

nexusLIMS.utils.paths.is_subpath(path: Path, of_paths: Union[Path, List[Path]])[source]#

Return if this path is a subpath of other paths.

Helper function to determine if a given path is a “subpath” of a set of paths. Useful to help determine which instrument a given file comes from, given the instruments filestore_path and the path of the file to test.

Parameters:

  • path – The path of the file (or directory) to test. This will usually be the absolute path to a file on the local filesystem (to be compared using the host-specific nx_instrument_data_path.

  • of_paths – The “higher-level” path to test against (or list thereof). In typical use, this will be a path joined of an instruments filestore_path with the root-level nx_instrument_data_path

Returns:

result – Whether or not path is a subpath of one of the directories in of_paths

Return type:

bool

Examples:

>>> is_subpath(Path('/path/to/file.dm3'),
...            settings.NX_INSTRUMENT_DATA_PATH /
...                titan.filestore_path))
True
nexusLIMS.utils.paths.join_instrument_filestore_path(filestore_path: str) → Path[source]#

Safely join NX_INSTRUMENT_DATA_PATH with an instrument’s filestore_path.

This helper handles filestore_path values with leading slashes gracefully. If filestore_path starts with ‘/’, the leading slash is stripped before joining to ensure the path remains relative to NX_INSTRUMENT_DATA_PATH.

Parameters:

filestore_path – The instrument’s filestore_path (may contain leading ‘/’)

Returns:

A resolved Path object: NX_INSTRUMENT_DATA_PATH / filestore_path

Return type:

Path

Examples:

>>> join_instrument_filestore_path("./Titan_STEM")
PosixPath('/mnt/data/Titan_STEM')

>>> join_instrument_filestore_path("/Titan_STEM")  # Leading slash stripped
PosixPath('/mnt/data/Titan_STEM')

>>> join_instrument_filestore_path("Titan_STEM")
PosixPath('/mnt/data/Titan_STEM')
nexusLIMS.utils.paths.replace_instrument_data_path(path: Path, suffix: str) → Path[source]#

Given an “NX_INSTRUMENT_DATA_PATH” path, generate equivalent”NX_DATA_PATH” path.

If the given path is not a subpath of “NX_INSTRUMENT_DATA_PATH”, a warning will be logged and the suffix will just be added at the end.

Parameters:

  • path – The input path, which is expected to be a subpath of the NX_INSTRUMENT_DATA_PATH directory

  • suffix – Any added suffix to add to the path (useful for appending with a new extension, such as .json)

Returns:

A resolved pathlib.Path object pointing to the new path

Return type:

Path