def test_is_in_efo(self):
with requests_mock.mock() as m:
url = "http://www.ebi.ac.uk/ols/api/ontologies/efo/terms/http%253A%252F%252Fwww.orpha.net%252FORDO%252FOrphanet_425"
m.get(url,
json=test_ols_data.TestIsInEfoData.orphanet_425_ols_efo_json)
self.assertEqual(
ols.is_in_efo("http://www.orpha.net/ORDO/Orphanet_425"), True)
def test_is_in_efo(self):
with requests_mock.mock() as m:
url = "https://www.ebi.ac.uk/ols/api/ontologies/efo/terms/http%253A%252F%252Fwww.orpha.net%252FORDO%252FOrphanet_425"
m.get(url,
json=test_ols_data.TestIsInEfoData.orphanet_425_ols_efo_json)
self.assertEqual(ols.is_in_efo("http://www.orpha.net/ORDO/Orphanet_425"),
True)
def find_previous_mapping(trait_name, previous_mappings):
if trait_name not in previous_mappings:
return ''
uri = previous_mappings[trait_name]
label = get_ontology_label_from_ols(uri)
uri_is_current_and_in_efo = is_current_and_in_efo(uri)
uri_in_efo = is_in_efo(uri)
if uri_in_efo:
trait_status = 'EFO_CURRENT' if uri_is_current_and_in_efo else 'EFO_OBSOLETE'
else:
trait_status = 'NOT_CONTAINED'
trait_string = '|'.join([uri, label, 'NOT_SPECIFIED', 'previously-used', trait_status])
return trait_string
def find_previous_mapping(trait_name, previous_mappings):
if trait_name not in previous_mappings:
return ''
uri = previous_mappings[trait_name]
label = get_ontology_label_from_ols(uri)
uri_is_current_and_in_efo = is_current_and_in_efo(uri)
uri_in_efo = is_in_efo(uri)
if uri_in_efo:
trait_status = 'EFO_CURRENT' if uri_is_current_and_in_efo else 'EFO_OBSOLETE'
else:
trait_status = 'NOT_CONTAINED'
trait_string = '|'.join(
[uri, label, 'NOT_SPECIFIED', 'previously-used', trait_status])
return trait_string
def get_zooma_results(trait_name: str, filters: dict, zooma_host: str) -> list:
"""
Given a trait name, Zooma filters in a dict and a hostname to use, query Zooma and return a list
of Zooma mappings for this trait.
First get the URI, label from a selected source, confidence and source:
http://snarf.ebi.ac.uk:8580/spot/zooma/v2/api/services/annotate?propertyValue=intellectual+disability
Then the ontology label to replace the label from a source:
http://www.ebi.ac.uk/ols/api/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0003847
:param trait_name: A string containing a trait name from a ClinVar record.
:param filters: A dictionary containing filters used when querying OxO
:param zooma_host: Hostname of a Zooma instance to query.
:return: List of ZoomaResults
"""
url = build_zooma_query(trait_name, filters, zooma_host)
zooma_response_list = request_retry_helper(zooma_query_helper, 4, url)
if zooma_response_list is None:
return None
zooma_result_list = get_zooma_results_for_trait(zooma_response_list)
for zooma_result in zooma_result_list:
for zooma_mapping in zooma_result.mapping_list:
label = get_ontology_label_from_ols(zooma_mapping.uri)
# If no label is returned (shouldn't really happen) keep the existing one
if label is not None:
zooma_mapping.ontology_label = label
else:
logging.warning(
"Couldn't retrieve ontology label from OLS for trait '{}'".
format(trait_name))
uri_is_current_and_in_efo = is_current_and_in_efo(
zooma_mapping.uri)
if not uri_is_current_and_in_efo:
uri_is_in_efo = is_in_efo(zooma_mapping.uri)
zooma_mapping.in_efo = uri_is_in_efo
else:
zooma_mapping.in_efo = uri_is_current_and_in_efo
zooma_mapping.is_current = uri_is_current_and_in_efo
return zooma_result_list
def get_oxo_results_from_response(oxo_response: dict) -> list:
"""
For a json(/dict) response from an OxO request, parse the data into a list of OxOResults
:param oxo_response: Response from OxO request
:return: List of OxOResults based upon the response from OxO
"""
oxo_result_list = []
results = oxo_response["_embedded"]["searchResults"]
for result in results:
if len(result["mappingResponseList"]) == 0:
continue
query_id = result["queryId"]
label = result["label"]
curie = result["curie"]
oxo_result = OxOResult(query_id, label, curie)
for mapping_response in result["mappingResponseList"]:
mapping_label = mapping_response["label"]
mapping_curie = mapping_response["curie"]
mapping_distance = mapping_response["distance"]
oxo_mapping = OxOMapping(mapping_label, mapping_curie,
mapping_distance, query_id)
uri = str(oxo_mapping.uri)
ontology_label = get_ontology_label_from_ols(uri)
if ontology_label is not None:
oxo_mapping.ontology_label = ontology_label
uri_is_current_and_in_efo = is_current_and_in_efo(uri)
if not uri_is_current_and_in_efo:
uri_is_in_efo = is_in_efo(uri)
oxo_mapping.in_efo = uri_is_in_efo
else:
oxo_mapping.in_efo = uri_is_current_and_in_efo
oxo_mapping.is_current = uri_is_current_and_in_efo
oxo_result.mapping_list.append(oxo_mapping)
oxo_result_list.append(oxo_result)
return oxo_result_list
def get_oxo_results_from_response(oxo_response: dict) -> list:
"""
For a json(/dict) response from an OxO request, parse the data into a list of OxOResults
:param oxo_response: Response from OxO request
:return: List of OxOResults based upon the response from OxO
"""
oxo_result_list = []
results = oxo_response["_embedded"]["searchResults"]
for result in results:
if len(result["mappingResponseList"]) == 0:
continue
query_id = result["queryId"]
label = result["label"]
curie = result["curie"]
oxo_result = OxOResult(query_id, label, curie)
for mapping_response in result["mappingResponseList"]:
mapping_label = mapping_response["label"]
mapping_curie = mapping_response["curie"]
mapping_distance = mapping_response["distance"]
oxo_mapping = OxOMapping(mapping_label, mapping_curie, mapping_distance, query_id)
uri = str(oxo_mapping.uri)
ontology_label = get_ontology_label_from_ols(uri)
if ontology_label is not None:
oxo_mapping.ontology_label = ontology_label
uri_is_current_and_in_efo = is_current_and_in_efo(uri)
if not uri_is_current_and_in_efo:
uri_is_in_efo = is_in_efo(uri)
oxo_mapping.in_efo = uri_is_in_efo
else:
oxo_mapping.in_efo = uri_is_current_and_in_efo
oxo_mapping.is_current = uri_is_current_and_in_efo
oxo_result.mapping_list.append(oxo_mapping)
oxo_result_list.append(oxo_result)
return oxo_result_list
def get_zooma_results(trait_name: str, filters: dict, zooma_host: str) -> list:
"""
Given a trait name, Zooma filters in a dict and a hostname to use, query Zooma and return a list
of Zooma mappings for this trait.
First get the URI, label from a selected source, confidence and source:
http://snarf.ebi.ac.uk:8580/spot/zooma/v2/api/services/annotate?propertyValue=intellectual+disability
Then the ontology label to replace the label from a source:
https://www.ebi.ac.uk/ols/api/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0003847
:param trait_name: A string containing a trait name from a ClinVar record.
:param filters: A dictionary containing filters used when querying OxO
:param zooma_host: Hostname of a Zooma instance to query.
:return: List of ZoomaResults
"""
url = build_zooma_query(trait_name, filters, zooma_host)
zooma_response_list = request_retry_helper(zooma_query_helper, 4, url)
if zooma_response_list is None:
return None
zooma_result_list = get_zooma_results_for_trait(zooma_response_list)
for zooma_result in zooma_result_list:
for zooma_mapping in zooma_result.mapping_list:
label = get_ontology_label_from_ols(zooma_mapping.uri)
# If no label is returned (shouldn't really happen) keep the existing one
if label is not None:
zooma_mapping.ontology_label = label
else:
logging.warning("Couldn't retrieve ontology label from OLS for trait '{}'".format(trait_name))
uri_is_current_and_in_efo = is_current_and_in_efo(zooma_mapping.uri)
if not uri_is_current_and_in_efo:
uri_is_in_efo = is_in_efo(zooma_mapping.uri)
zooma_mapping.in_efo = uri_is_in_efo
else:
zooma_mapping.in_efo = uri_is_current_and_in_efo
zooma_mapping.is_current = uri_is_current_and_in_efo
return zooma_result_list