Wags-TAILS

Technology-Assisted Information Loading and Structure (TAILS) for Wagnerds.

This tool provides data acquisition and access utilities for several projects developed by the Wagner Lab. It designates a storage location in user-space where external data files can be saved, and provides methods to download and update them when available.

It is currently used in:

• Thera-Py
• Gene Normalizer
• Disease Normalizer
• and more!

Documentation · Installation · Usage · API reference

Installation

Install from PyPI:

python3 -m pip install wags_tails

Usage

Data source classes provide a get_latest() method that acquires the most recent available data file and returns a pathlib.Path object with its location:

>>> from wags_tails.mondo import MondoData
>>> m = MondoData()
>>> m.get_latest(force_refresh=True)
Downloading mondo.obo: 100%|█████████████████| 171M/171M [00:28<00:00, 6.23MB/s]
PosixPath('/Users/genomicmedlab/.local/share/wags_tails/mondo/mondo_v2023-09-12.obo'), 'v2023-09-12'

Initialize the source class with the silent parameter set to True to suppress console output:

>>> from wags_tails.mondo import MondoData
>>> m = MondoData(silent=True)
>>> latest_file, version = m.get_latest(force_refresh=True)

Configuration

All data is stored within source-specific subdirectories of a designated WagsTails data directory. By default, this location is ~/.local/share/wags_tails/, but it can be configured by passing a Path directly to a data class on initialization, via the $WAGS_TAILS_DIR environment variable, or via XDG data environment variables.

Feedback and contributing

We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The documentation contains guidance for submitting feedback and contributing new code.