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QueryEBIOLS.py
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QueryEBIOLS.py
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__author__ = 'Stephen Ramsey'
__copyright__ = 'Oregon State University'
__credits__ = ['Stephen Ramsey']
__license__ = 'MIT'
__version__ = '0.1.0'
__maintainer__ = ''
__email__ = ''
__status__ = 'Prototype'
# import requests
# import requests_cache
from cache_control_helper import CacheControlHelper
import urllib.parse
import sys
import json
import time
class QueryEBIOLS:
TIMEOUT_SEC = 120
API_BASE_URL = "https://www.ebi.ac.uk/ols/api/ontologies"
HANDLER_MAP = {
'get_anatomy': '{ontology}/terms/{id}',
'get_phenotype': '{ontology}/terms/{id}',
'get_disease': '{ontology}/terms/{id}',
'get_bio_process': '{ontology}/terms/{id}',
'get_cellular_component': '{ontology}/terms/{id}',
'get_molecular_function': '{ontology}/terms/{id}'
}
@staticmethod
def send_query_get(handler, url_suffix):
requests = CacheControlHelper()
url_str = QueryEBIOLS.API_BASE_URL + '/' + handler + "/" + url_suffix
# print(url_str)
try:
res = requests.get(url_str, timeout=QueryEBIOLS.TIMEOUT_SEC)
except requests.exceptions.Timeout:
print('HTTP timeout in QueryNCBIeUtils.py; URL: ' + url_str, file=sys.stderr)
time.sleep(1) # take a timeout because NCBI rate-limits connections
return None
except requests.exceptions.ConnectionError:
print('HTTP connection error in QueryNCBIeUtils.py; URL: ' + url_str, file=sys.stderr)
time.sleep(1) # take a timeout because NCBI rate-limits connections
return None
except BaseException as e:
print(url_str, file=sys.stderr)
print('%s received in QueryEBIOLS for URL: %s' % (e, url_str), file=sys.stderr)
return None
status_code = res.status_code
if status_code != 200:
print('HTTP response status code: ' + str(status_code) + ' for URL:\n' + url_str, file=sys.stderr)
res = None
return res
@staticmethod
def get_bto_term_for_bto_id(bto_curie_id):
"""
Converts an anatomy BTO ID to the BTO term
:param bto_curie_id: eg. "BTO:0001259"
:return: a set of BTO terms (eg. {"blood"})
"""
bto_iri = "http://purl.obolibrary.org/obo/" + bto_curie_id.replace(":", "_")
bto_iri_double_encoded = urllib.parse.quote_plus(urllib.parse.quote_plus(bto_iri))
res = QueryEBIOLS.send_query_get("bto/terms/", bto_iri_double_encoded)
ret_label = None
if res is not None:
res_json = res.json()
ret_label = res_json.get("label", None)
return ret_label
@staticmethod
def get_bto_id_for_uberon_id(uberon_curie_id):
"""
Converts an anatomy uberon ID to BTO id
:param uberon_curie_id: eg. "UBERON:0001259"
:return: a set of BTO id's (eg. {"BTO:D008099"})
"""
uberon_iri = "http://purl.obolibrary.org/obo/" + uberon_curie_id.replace(":", "_")
uberon_iri_double_encoded = urllib.parse.quote_plus(urllib.parse.quote_plus(uberon_iri))
res = QueryEBIOLS.send_query_get("uberon/terms/", uberon_iri_double_encoded)
ret_list = list()
if res is not None:
res_json = res.json()
res_annotation = res_json.get("annotation", None)
if res_annotation is not None:
db_x_refs = res_annotation.get("database_cross_reference", None)
if db_x_refs is not None:
ret_list = [bto_id for bto_id in db_x_refs if "BTO:" in bto_id]
return set(ret_list)
@staticmethod
def get_mesh_id_for_uberon_id(uberon_curie_id):
"""
Converts an anatomy uberon ID to MeSH id
:param uberon_curie_id: eg. "UBERON:0001259"
:return: a set of MeSH id's (eg. {"MESH:D008099"})
"""
uberon_iri = "http://purl.obolibrary.org/obo/" + uberon_curie_id.replace(":", "_")
uberon_iri_double_encoded = urllib.parse.quote_plus(urllib.parse.quote_plus(uberon_iri))
res = QueryEBIOLS.send_query_get("uberon/terms/", uberon_iri_double_encoded)
ret_list = list()
if res is not None:
res_json = res.json()
res_annotation = res_json.get("annotation", None)
if res_annotation is not None:
db_x_refs = res_annotation.get("database_cross_reference", None)
if db_x_refs is not None:
ret_list = [mesh_id for mesh_id in db_x_refs if "MESH:" in mesh_id]
return set(ret_list)
@staticmethod
def __access_api(handler):
requests = CacheControlHelper()
url = QueryEBIOLS.API_BASE_URL + '/' + handler
# print(url)
try:
res = requests.get(url, timeout=QueryEBIOLS.TIMEOUT_SEC)
except requests.exceptions.Timeout:
print(url, file=sys.stderr)
print('Timeout in QueryEBIOLSExtended for URL: ' + url, file=sys.stderr)
return None
except KeyboardInterrupt:
sys.exit(0)
except BaseException as e:
print(url, file=sys.stderr)
print('%s received in QueryEBIOLSExtended for URL: %s' % (e, url), file=sys.stderr)
return None
status_code = res.status_code
if status_code != 200:
print(url, file=sys.stderr)
print('Status code ' + str(status_code) + ' for url: ' + url, file=sys.stderr)
return None
return res.text
@staticmethod
def __get_entity(entity_type, entity_id):
ontology_id = entity_id[:entity_id.find(":")]
iri = "http://purl.obolibrary.org/obo/" + entity_id.replace(":", "_")
iri_double_encoded = urllib.parse.quote_plus(urllib.parse.quote_plus(iri))
handler = QueryEBIOLS.HANDLER_MAP[entity_type].format(ontology=ontology_id.lower(), id=iri_double_encoded)
results = QueryEBIOLS.__access_api(handler)
result_str = "None"
if results is not None:
res_json = json.loads(results)
# print(res_json)
res_description = res_json.get("description", None)
if res_description is not None:
if len(res_description) > 0:
result_str = res_description[0]
return result_str
@staticmethod
def get_anatomy_description(anatomy_id):
return QueryEBIOLS.__get_entity("get_anatomy", anatomy_id)
@staticmethod
def get_bio_process_description(bio_process_id):
return QueryEBIOLS.__get_entity("get_bio_process", bio_process_id)
@staticmethod
def get_phenotype_description(phenotype_id):
return QueryEBIOLS.__get_entity("get_phenotype", phenotype_id)
@staticmethod
def get_disease_description(disease_id):
return QueryEBIOLS.__get_entity("get_disease", disease_id)
@staticmethod
def get_cellular_component_description(cc_id):
return QueryEBIOLS.__get_entity("get_cellular_component", cc_id)
@staticmethod
def get_molecular_function_description(mf_id):
return QueryEBIOLS.__get_entity("get_molecular_function", mf_id)
if __name__ == "__main__":
print(QueryEBIOLS.get_bto_id_for_uberon_id("UBERON:0000178"))
print(QueryEBIOLS.get_bto_term_for_bto_id("BTO:0000089"))
print(QueryEBIOLS.get_mesh_id_for_uberon_id("UBERON:0002107"))
print(QueryEBIOLS.get_mesh_id_for_uberon_id("UBERON:0001162"))
def save_to_test_file(key, value):
f = open('tests/query_desc_test_data.json', 'r+')
try:
json_data = json.load(f)
except ValueError:
json_data = {}
f.seek(0)
f.truncate()
json_data[key] = value
json.dump(json_data, f)
f.close()
save_to_test_file('UBERON:0004476', QueryEBIOLS.get_anatomy_description('UBERON:0004476'))
save_to_test_file('CL:0000038', QueryEBIOLS.get_anatomy_description('CL:0000038'))
save_to_test_file('GO:0042535', QueryEBIOLS.get_bio_process_description('GO:0042535'))
save_to_test_file('HP:0011105', QueryEBIOLS.get_phenotype_description('HP:0011105'))
save_to_test_file('GO:0005573', QueryEBIOLS.get_cellular_component_description('GO:0005573'))
save_to_test_file('GO:0004689', QueryEBIOLS.get_molecular_function_description('GO:0004689'))
save_to_test_file('OMIM:604348', QueryEBIOLS.get_disease_description('OMIM:604348'))