def process_trait(trait: Trait, filters: dict, zooma_host: str,
oxo_target_list: list, oxo_distance: int) -> Trait:
"""
Process a single trait. Find any mappings in Zooma. If there are no high confidence Zooma
mappings that are in EFO then query OxO with any high confidence mappings not in EFO.
:param trait: The trait to be processed.
:param filters: A dictionary of filters to use for querying Zooma.
:param zooma_host: A string with the hostname to use for querying Zooma
:param oxo_target_list: A list of strings, each being an OxO ID for an ontology. Used to specify
which ontologies should be queried using OxO.
:param oxo_distance: int specifying the maximum number of steps to use to query OxO. i.e. OxO's
"distance" parameter.
:return: The original trait after querying Zooma and possibly OxO, with any results found.
"""
trait.zooma_result_list = get_zooma_results(trait.name, filters,
zooma_host)
trait.process_zooma_results()
if (trait.is_finished or len(trait.zooma_result_list) == 0 or any([
entry.is_current for mapping in trait.zooma_result_list
for entry in mapping.mapping_list
])):
return trait
uris_for_oxo_set = get_uris_for_oxo(trait.zooma_result_list)
if len(uris_for_oxo_set) == 0:
return trait
oxo_input_id_list = uris_to_oxo_format(uris_for_oxo_set)
trait.oxo_result_list = get_oxo_results(oxo_input_id_list, oxo_target_list,
oxo_distance)
trait.process_oxo_mappings()
return trait
def process_trait(trait: Trait, filters: dict, zooma_host: str, oxo_target_list: list,
oxo_distance: int) -> Trait:
"""
Process a single trait. Find any mappings in Zooma. If there are no high confidence Zooma
mappings that are in EFO then query OxO with any high confidence mappings not in EFO.
:param trait: The trait to be processed.
:param filters: A dictionary of filters to use for querying Zooma.
:param zooma_host: A string with the hostname to use for querying Zooma
:param oxo_target_list: A list of strings, each being an OxO ID for an ontology. Used to specify
which ontologies should be queried using OxO.
:param oxo_distance: int specifying the maximum number of steps to use to query OxO. i.e. OxO's
"distance" parameter.
:return: The original trait after querying Zooma and possibly OxO, with any results found.
"""
trait.zooma_result_list = get_zooma_results(trait.name, filters, zooma_host)
trait.process_zooma_results()
if (trait.is_finished
or len(trait.zooma_result_list) == 0
or any([entry.is_current
for mapping in trait.zooma_result_list
for entry in mapping.mapping_list])):
return trait
uris_for_oxo_set = get_uris_for_oxo(trait.zooma_result_list)
if len(uris_for_oxo_set) == 0:
return trait
oxo_input_id_list = uris_to_oxo_format(uris_for_oxo_set)
trait.oxo_result_list = get_oxo_results(oxo_input_id_list, oxo_target_list, oxo_distance)
trait.process_oxo_mappings()
return trait
def test_get_result_without_ols_label(self):
"""If OLS does not provide a label for a trait, ZOOMA original label must be used instead."""
requested_trait_name = 'Mucopolysaccharidosis type VI'
expected_trait_label = 'Mucopolysaccharidosis type 6'
zooma_result = zooma.get_zooma_results(requested_trait_name, self.filters, self.zooma_host)
self.assertEqual(len(zooma_result), 1)
mappings = zooma_result[0].mapping_list
self.assertEqual(len(mappings), 3)
self.assertIn(expected_trait_label, [m.ontology_label for m in mappings])