Use existing fixture to retrieve settings.

2 files changed, 15 insertions, 30 deletions

diff --git a/tests/fixtures/rdf.py b/tests/fixtures/rdf.py
index 0bafeaa..b942282 100644
--- a/tests/fixtures/rdf.py
+++ b/tests/fixtures/rdf.py
@@ -6,30 +6,14 @@ 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")
+def get_sparql_auth_conf(config_obj) -> dict:
+    """Fetch SPARQL auth configuration from the configuration object."""
     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"],
+        "sparql_user": config_obj["SPARQL_USER"],
+        "sparql_auth_uri": config_obj["SPARQL_AUTH_URI"],
+        "sparql_crud_auth_uri": config_obj["SPARQL_CRUD_AUTH_URI"],
+        "sparql_endpoint": config_obj["SPARQL_ENDPOINT"],
+        "sparql_password": config_obj["SPARQL_PASSWORD"],
     }
 
 
@@ -37,10 +21,10 @@ def get_sparql_auth_conf() -> dict:
 # This is not idempotent.  Consider having a special virtuoso instance
 # just for running tests.
 @pytest.fixture(scope="module")
-def rdf_setup():
+def rdf_setup(fxtr_app_config):
     """Upload RDF to a Virtuoso named graph"""
     # Define the URL and file
-    sparql_conf = get_sparql_auth_conf()
+    sparql_conf = get_sparql_auth_conf(fxtr_app_config)
     url = sparql_conf["sparql_crud_auth_uri"]
     file_path = os.path.join(
         os.path.dirname(__file__).split("fixtures")[0],
diff --git a/tests/unit/db/rdf/test_wiki.py b/tests/unit/db/rdf/test_wiki.py
index 5f36034..c737f29 100644
--- a/tests/unit/db/rdf/test_wiki.py
+++ b/tests/unit/db/rdf/test_wiki.py
@@ -29,8 +29,6 @@ from gn3.db.rdf.wiki import (
     update_wiki_comment,
 )
 
-
-SPARQL_CONF = get_sparql_auth_conf()
 GRAPH = "<http://cd-test.genenetwork.org>"
 
 
@@ -187,8 +185,9 @@ def test_sanitize_result(result, expected):
 
 
 @pytest.mark.rdf
-def test_get_wiki_entries_by_symbol(rdf_setup):  # pylint: disable=W0613,W0621
+def test_get_wiki_entries_by_symbol(fxtr_app_config, rdf_setup):  # pylint: disable=W0613,W0621
     """Test that wiki entries are fetched correctly by symbol"""
+    SPARQL_CONF = get_sparql_auth_conf(fxtr_app_config)
     result = get_wiki_entries_by_symbol(
         symbol="ckb",
         sparql_uri=SPARQL_CONF["sparql_endpoint"],
@@ -261,8 +260,9 @@ and C1QL3 (CTRP13).",
 
 
 @pytest.mark.rdf
-def test_get_comment_history(rdf_setup):  # pylint: disable=W0613,W0621
+def test_get_comment_history(fxtr_app_config, rdf_setup):  # pylint: disable=W0613,W0621
     """Test fetching a comment's history from RDF"""
+    SPARQL_CONF = get_sparql_auth_conf(fxtr_app_config)
     result = get_comment_history(
         comment_id=1158,
         sparql_uri=SPARQL_CONF["sparql_endpoint"],
@@ -353,8 +353,9 @@ Possible 3' UTR variants.",
 
 
 @pytest.mark.rdf
-def test_update_wiki_comment(rdf_setup):  # pylint: disable=W0613,W0621
+def test_update_wiki_comment(fxtr_app_config, rdf_setup):  # pylint: disable=W0613,W0621
     """Test that a comment is updated correctly"""
+    SPARQL_CONF = get_sparql_auth_conf(fxtr_app_config)
     update_wiki_comment(
         insert_dict={
             "Id": 230,