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"""Test fixtures to set up a test named graph for loading RDF data."""
from requests.auth import HTTPDigestAuth
from flask import config
import os
import requests
import pytest
def get_sparql_auth_conf() -> dict:
"""Fetch SPARQL auth configuration for the GN3_SECRETS file."""
sparql_conf = config.Config("")
# When loading from the environment, GN3_CONF precedes
# GN3_SECRETS. Don't change this order.
sparql_conf.from_envvar("GN3_CONF")
sparql_conf.from_envvar("GN3_SECRETS")
return {
"sparql_user": sparql_conf["SPARQL_USER"],
"sparql_auth_uri": sparql_conf["SPARQL_AUTH_URI"],
"sparql_crud_auth_uri": sparql_conf["SPARQL_CRUD_AUTH_URI"],
"sparql_endpoint": sparql_conf["SPARQL_ENDPOINT"],
"sparql_password": sparql_conf["SPARQL_PASSWORD"],
}
@pytest.fixture(scope="module")
def rdf_setup():
"""Upload RDF to a Virtuoso named graph"""
# Define the URL and file
sparql_conf = get_sparql_auth_conf()
url = sparql_conf["sparql_crud_auth_uri"]
file_path = os.path.join(
os.path.dirname(__file__).split("fixtures")[0],
"test_data/ttl-files/test-data.ttl",
)
# Define the query parameters and authentication
params = {"graph": "http://cd-test.genenetwork.org"}
auth = HTTPDigestAuth(
sparql_conf["sparql_user"], sparql_conf["sparql_password"])
# Make sure this graph does not exist before running anything
requests.delete(url, params=params, auth=auth)
# Open the file in binary mode and send the request
with open(file_path, "rb") as file:
response = requests.put(url, params=params, auth=auth, data=file)
yield response
requests.delete(url, params=params, auth=auth)
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