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import requests
from requests.auth import HTTPDigestAuth, HTTPBasicAuth
import ssl
import json
from joblib import Memory
cachedir = 'cached'
mem = Memory(cachedir, verbose=False)
@mem.cache
def execute_query(endpoint, query, auth):
headers = {
'Content-Type': 'application/x-www-form-urlencoded',
'Accept': 'application/sparql-results+json'
}
params = {
'query': query
}
response = requests.post(endpoint, headers=headers, params=params, auth=auth)
if response.status_code != 200:
raise Exception(f"Failed to execute query: {response.text}")
return response.text
def execute_query_no_cache(endpoint, query, auth):
headers = {
'Content-Type': 'application/x-www-form-urlencoded',
'Accept': 'application/sparql-results+json'
}
params = {
'query': query
}
response = requests.post(endpoint, headers=headers, params=params, auth=auth)
if response.status_code != 200:
raise Exception(f"Failed to execute query: {response.text}")
return response.text
def sparqlQuery(endpoint, query, usernameVirt, passwordVirt, USE_CACHE=True):
"""
Make a SPARQL query to a Virtuoso SPARQL endpoint.
Args:
- endpoint (str): The URL of the Virtuoso SPARQL endpoint.
- query (str): The SPARQL query to execute.
- username (str): The username for authentication.
- password (str): The password for authentication.
Returns:
- responseText (requests.Response): The responseText from the Virtuoso SPARQL endpoint.
"""
# Use SSL context to establish a secure connection
ssl_context = ssl.create_default_context()
# Try HTTP Digest authentication
try:
auth = HTTPDigestAuth(usernameVirt, passwordVirt)
if USE_CACHE:
responseText = execute_query(endpoint, query, auth)
else:
responseText = execute_query_no_cache(endpoint, query, auth)
except Exception as e:
print(f"HTTP Digest authentication failed: {str(e)}")
# Fallback to Basic Auth
try:
auth = HTTPBasicAuth(usernameVirt, passwordVirt)
if USE_CACHE:
responseText = execute_query(endpoint, query, auth)
else:
responseText = execute_query_no_cache(endpoint, query, auth)
except Exception as e:
print(f"Basic Auth failed: {str(e)}")
return None
return responseText
#
# def sparqlQuery(endpoint, query, usernameVirt, passwordVirt):
# """
# Make a SPARQL query to a Virtuoso SPARQL endpoint.
#
# Args:
# - endpoint (str): The URL of the Virtuoso SPARQL endpoint.
# - query (str): The SPARQL query to execute.
# - username (str): The username for authentication.
# - password (str): The password for authentication.
#
# Returns:
# - response (requests.Response): The response from the Virtuoso SPARQL endpoint.
# """
# headers = {
# 'Content-Type': 'application/x-www-form-urlencoded',
# 'Accept': 'application/sparql-results+json'
# }
#
# params = {
# 'query': query
# }
#
# # Use SSL context to establish a secure connection
# ssl_context = ssl.create_default_context()
#
# # Try HTTP Digest authentication
# try:
# auth = HTTPDigestAuth(usernameVirt, passwordVirt)
# response = requests.post(endpoint, headers=headers, params=params, auth=auth)
# except Exception as e:
# print(f"HTTP Digest authentication failed: {str(e)}")
#
# # Fallback to Basic Auth
# try:
# auth = HTTPBasicAuth(usernameVirt, passwordVirt)
# response = requests.post(endpoint, headers=headers, params=params, auth=auth)
# except Exception as e:
# print(f"Basic Auth failed: {str(e)}")
# return None
#
# if response.status_code != 200:
# raise Exception(f"Failed to execute query: {response.text}")
#
# return response
if __name__ == '__main__':
# Example usage
endpoint = 'https://api-vast.jrc.service.ec.europa.eu/sparql'
VirtuosoUsername = 'dba'
VirtuosoPassword = ''
Virtuosokey_filename = 'VIRTUOSO-dba.key'
USE_CACHE = False # True or False
#############
#choices = ['SNOMED', 'LOINC', 'ICD10', 'MESH', 'NCIT'] # restricts the input to these values only
choices = ["AI", "AIO", "AEO", "BFO", "BIM", "BCGO", "CL", "CHIRO", "CHEBI", "DCM", "FMA", "GO", "GENO",
"GeoSPARQL", "HL7", "DOID", "HP", "HP_O", "IDO", "IAO", "ICD10", "LOINC", "MESH",
"MONDO", "NCIT", "NCBITAXON", "NCBITaxon_", "NIFCELL", "NIFSTD", "GML", "OBCS", "OCHV", "OHPI",
"OPB", "TRANS", "PLOSTHES", "RADLEX", "RO", "STY", "SO", "SNOMED", "STATO",
"SYMP", "FoodOn", "UBERON", "ORDO", "HOOM", "VO", "OGMS", "EuroSciVoc"]
# Construct the FROM clauses
from_clauses = ' '.join([f"FROM <{choice}>" for choice in choices])
#word = "acute sinusitis"
word = "pure mathematics"
# Construct the full SPARQL query
query = f"""
prefix skosxl: <http://www.w3.org/2008/05/skos-xl#>
SELECT ?concept ?label (COUNT(?edge) AS ?score)
{from_clauses}
WHERE {{
?concept skos:prefLabel|rdfs:label|skos:altLabel|skosxl:literalForm|obo:hasRelatedSynonym ?label .
FILTER (LCASE(STR(?label)) = "{word.lower()}")
?concept ?edge ?o .
}}
GROUP BY ?concept ?label
ORDER BY DESC(?score)
"""
print(query)
###############
if Virtuosokey_filename:
fkeyname = Virtuosokey_filename
with open(fkeyname) as f:
VirtuosoPassword = f.read()
responseText = sparqlQuery(endpoint, query, VirtuosoUsername, VirtuosoPassword, USE_CACHE)
# Parse the response as JSON
results = json.loads(responseText)
# Print the results
if len(results) > 0 and results['results']['bindings']:
for result in results['results']['bindings']:
print(result)
else:
print("!!! VIRTUOSO NO RESULTS !!!") |