#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the `pypath` python module
#
# Copyright 2014-2023
# EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
# Authors: see the file `README.rst`
# Contact: Dénes Türei (turei.denes@gmail.com)
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# https://www.gnu.org/licenses/gpl-3.0.html
#
# Website: https://pypath.omnipathdb.org/
#
from typing import Dict, List, Optional, Union
import glom
import pypath.share.session as session
import pypath.share.common as common
import pypath.resources.urls as urls
import pypath.inputs.ebi as ebi
_logger = session.Logger(name = 'ontology_input')
[docs]
def ontology(
ontology: str,
fields: Optional[Union[List, str, dict]] = None,
) -> Union[List[tuple], Dict[str, str]]:
"""
Downloads an ontology using the EBI Ontology Lookup Service.
Args
ontology: The ID of an ontology available in EBI OLS. For a
full list, call ``listof_ontologies``.
fields: Additional fields to include, apart from the default
ones. Can be a dict of glom specs or simply keys in the
terms section of the OLS Terms query response.
"""
_logger._log('Retrieving ontology `%s` from EBI OLS.' % ontology)
url = urls.urls['ols']['url'] + '/%s/terms' % ontology.lower()
_fields = {
'label': ('_embedded.terms', ['label']),
'obo_id': ('_embedded.terms', ['obo_id']),
}
if not isinstance(fields, dict):
fields = dict(
(
f.rsplit('.', maxsplit = 1)[-1],
('_embedded.terms', [glom.Coalesce(f, default = None)])
)
for f in common.to_list(fields)
)
_fields.update(fields)
result = ebi.ebi_rest(
url = url,
fields = _fields,
page_param = 'page',
page_field = 'page.number',
paginate = True,
)
if not fields:
result = dict(
(i.obo_id, i.label)
for i in result
)
result.pop(None, None)
return result
[docs]
def listof_ontologies(
fields: Optional[Union[List, str]] = None,
full_config: bool = False,
) -> Union[List[tuple], Dict[str, str]]:
"""
Returns a list of available ontologies in the EBI Ontology Lookup Service.
Args
fields: Additional field(s) to include, apart from the default
ones.
full_config: Keep the full config dict.
Return
If no extra fields and no full config are requested: a dict with
ontology abbreviations as keys and ontology names as values.
Otherwise a list of named tuples, each representing an ontology
described by the requested fields.
"""
_fields = {
'config': ('_embedded.ontologies', ['config']),
'ontologyId': ('_embedded.ontologies', ['ontologyId']),
}
_fields.update(
dict(
(f, ('_embedded.ontologies', [f]))
for f in common.to_list(fields)
)
)
result = ebi.ebi_rest(
url = urls.urls['ols']['url'],
fields = _fields,
page_param = 'page',
page_field = 'page.number',
paginate = True,
)
if not fields and not full_config:
result = dict(
(i.ontologyId, i.config['title'])
for i in result
)
result.pop(None, None)
return result
