def get_oxo_results(id_list: list, target_list: list, distance: int) -> list:
"""
Use list of ontology IDs, datasource targets and distance call function to query OxO and return
a list of OxOResults.
:param id_list: List of ontology IDs with which to find xrefs using OxO
:param target_list: List of ontology datasources to include
:param distance: Number of steps to take through xrefs to find mappings
:return: List of OxOResults based upon results from request made to OxO
"""
url = "https://www.ebi.ac.uk/spot/oxo/api/search?size=5000"
payload = build_oxo_payload(id_list, target_list, distance)
try:
oxo_response = json_request(url, payload, requests.post)
except requests.HTTPError:
# Sometimes, OxO fails to process a completely valid request even after several attempts.
# See https://github.com/EBISPOT/OXO/issues/26 for details
logger.error(
'OxO failed to process request for id_list {} (probably a known bug in OxO)'
.format(id_list))
return []
if oxo_response is None:
return []
if "_embedded" not in oxo_response:
logger.warning(
"Cannot parse the response from OxO for the following identifiers: {}"
.format(','.join(id_list)))
return []
return get_oxo_results_from_response(oxo_response)
def get_ontology_label_from_ols(ontology_uri: str) -> str:
"""
Using provided ontology URI, build an OLS URL with which to make a request to find the term label for this URI.
:param ontology_uri: A URI for a term in an ontology.
:return: Term label for the ontology URI provided in the parameters.
"""
url = build_ols_query(ontology_uri)
json_response = json_request(url)
if not json_response:
return None
# If the '_embedded' section is missing from the response, it means that the term is not found in OLS
if '_embedded' not in json_response:
if '/medgen/' not in url and '/omim/' not in url:
logger.warning(
'OLS queried OK but did not return any results for URL {}'.
format(url))
return None
# Go through all terms found by the requested identifier and try to find the one where the _identifier_ and the
# _term_ come from the same ontology (marked by a special flag). Example of such a situation would be a MONDO term
# in the MONDO ontology. Example of a reverse situation is a MONDO term in EFO ontology (being *imported* into it
# at some point).
for term in json_response["_embedded"]["terms"]:
if term["is_defining_ontology"]:
return term["label"]
if '/medgen/' not in url and '/omim/' not in url:
logger.warning(
'OLS queried OK, but there is no defining ontology in its results for URL {}'
.format(url))
return None
def get_zooma_uris(trait_name, zooma_host, filters):
url = build_zooma_query(trait_name, filters, zooma_host)
json_response = json_request(url)
if json_response is None:
return None
uri_set = set()
for result in json_response:
if result["confidence"].lower() == "high":
uri_set.update(result["semanticTags"])
return uri_set