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"""Test fixtures to set up a test named graph for loading RDF data."""
import os
from requests.auth import HTTPDigestAuth
from flask import config
import requests
import pytest
def get_sparql_auth_conf() -> dict:
"""Fetch SPARQL auth configuration for the GN3_SECRETS file."""
sparql_conf = config.Config("")
if os.environ.get("GN3_CONF"):
# Check whether GN3_CONF has been set, and ignore GN3_CONF
# otherwise. In CD, we use a mixed-text file, so we don't
# have an explicit PATH to point this to.
# https://git.genenetwork.org/gn-machines/tree/genenetwork-development.scm#n517
sparql_conf.from_envvar("GN3_CONF")
# Set sane defaults for GN3_SECRETS to CD's secret file. In CD,
# this file is set in the genenetwork3 cd gexp:
# https://git.genenetwork.org/gn-machines/tree/genenetwork-development.scm#n516
# However, during testing GN3_SECRETS isn't set; and by default,
# we run guix's default tests for python projects: `pytest`
# https://git.genenetwork.org/guix-bioinformatics/tree/gn/packages/genenetwork.scm#n182
if not os.environ.get("GN3_SECRETS"):
os.environ["GN3_SECRETS"] = "/etc/genenetwork/conf/gn3/secrets.py"
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"],
}
# XXXX: Currently we run the tests against CD's virtuoso instance.
# This is not idempotent. Consider having a special virtuoso instance
# just for running tests.
@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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