GenomicMedLab / wags-tails

Data acquisition tools for Wagnerds

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!

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Documentation · Installation · Usage · API reference

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Installation

Install from PyPI:

python3 -m pip install wags_tails

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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)

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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.

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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.