Datasets

shedding_hub.load_dataset(dataset, *, repo='shedding-hub/shedding-hub', ref=None, pr=None, local=None)

Load a dataset from GitHub or a local directory.

Parameters:

Name	Type	Description	Default
dataset	str	Dataset identifier, e.g., :code:woelfel2020virological.	required
repo	str	GitHub repository to load data from.	'shedding-hub/shedding-hub'
ref	Optional[str]	Git reference to load. Defaults to the most recent data on the :code:main branch of https://github.com/shedding-hub/shedding-hub and is automatically fetched if a :code:pr number is specified.	None
pr	Optional[int]	Pull request to fetch data from.	None
local	Optional[str]	Local directory to load data from.	None

Returns:

Type	Description
dict	Loaded dataset.

Examples:

>>> import shedding_hub as sh
>>> data = sh.load_dataset('woelfel2020virological', local='./data')
>>> sorted(data.keys())
['analytes', 'dataset_id', 'description', 'doi', 'participants', 'title']
>>> data['dataset_id']
'woelfel2020virological'

shedding_hub.check_dataset(*, doi=None, title=None, local=None, similarity_threshold=0.6)

Check whether a paper is in the curated datasets.

Parameters:

Name	Type	Description	Default
doi	Optional[str]	DOI of the paper to check.	None
title	Optional[str]	Title of the paper to check.	None
local	Optional[str]	Local directory containing datasets. Defaults to the data directory in the repository root.	None
similarity_threshold	float	Minimum similarity ratio (0 to 1) for reporting near-matches when no exact title match is found.	0.6

Returns:

Type	Description
bool	True if the paper is found (exact DOI or exact title match), False
bool	otherwise. When a title is provided and no exact match is found, a
bool	warning is issued for the most similar dataset above the threshold.

Examples:

>>> import shedding_hub as sh
>>> sh.check_dataset(doi='10.1038/s41586-020-2196-x', local='./data')
True
>>> sh.check_dataset(doi='10.1000/nonexistent-doi', local='./data')
False

shedding_hub.normalize_str(value, *, dedent=True, strip=True, unwrap=True)

Normalize a string.

Parameters:

Name	Type	Description	Default
value	str	String to normalize.	required
dedent	bool	Remove any common leading whitespace.	True
strip	bool	Remove leading and trailing whitespace.	True
unwrap	bool	Unwrap lines separated by a single line break.	True

Examples:

>>> import shedding_hub as sh
>>> sh.normalize_str("\n    line one\n    line two\n")
'line one line two'

shedding_hub.folded_str

Bases: str

Folded string in yaml representation.

Examples:

>>> import yaml
>>> import shedding_hub as sh
>>> print(yaml.dump({"description": sh.folded_str("This is a long description that will be wrapped nicely.")}))
description: >-
  This is a long description that will be wrapped nicely.

shedding_hub.literal_str

Bases: str

Literal string in yaml representation.

Examples:

>>> import yaml
>>> import shedding_hub as sh
>>> print(yaml.dump({"description": sh.literal_str("Line one.\nLine two.\n")}))
description: |
  Line one.
  Line two.