Set a default password for sparql.

* tests/fixtures/rdf.py: Import config.
(get_sparql_auth_conf):  Load GN3 config from GN3_SECRETS and GN3_CONF
if the respective envs are set.  Set sane defaults for sparql_conf.
(rdf_setup): Remove "fxtr_app_config".
* tests/unit/db/rdf/test_wiki.py (test_get_wiki_entries_by_symbol): Ditto.
(test_get_comment_history): Ditto.
(test_update_wiki_comment): Ditto.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

2 files changed, 40 insertions, 15 deletions

diff --git a/tests/fixtures/rdf.py b/tests/fixtures/rdf.py
index 9bf297b..028ef8d 100644
--- a/tests/fixtures/rdf.py
+++ b/tests/fixtures/rdf.py
@@ -1,19 +1,44 @@
 """Test fixtures to set up a test named graph for loading RDF data."""
 import os
+from flask import config
 
 import pytest
 import requests
 from requests.auth import HTTPDigestAuth
 
 
-def get_sparql_auth_conf(config_obj) -> dict:
-    """Fetch SPARQL auth configuration from the configuration object."""
+def get_sparql_auth_conf() -> dict:
+    """Fetch SPARQL auth configuration from the configurafrom flask
+    import configuration object."""
+    # When loading from the environment, GN3_CONF precedes
+    # GN3_SECRETS.  Don't change this order.
+    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 os.environ.get("GN3_SECRETS"):
+        sparql_conf.from_envvar("GN3_SECRETS")
+    # If the sparql configurations aren't loaded, set sane defaults.
+    # This way, the genenetwork3 package builds.
     return {
-        "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"],
+        "sparql_user": sparql_conf.get("SPARQL_USER", "dba"),
+        "sparql_auth_uri": sparql_conf.get(
+            "SPARQL_AUTH_URI", "http://localhost:8890/sparql-auth/"
+        ),
+        "sparql_crud_auth_uri": sparql_conf.get(
+            "SPARQL_CRUD_AUTH_URI", "http://localhost:8890/sparql-graph-crud-auth"
+        ),
+        "sparql_endpoint": sparql_conf.get("SPARQL_ENDPOINT", "http://localhost:8890"),
+        "sparql_password": sparql_conf.get("SPARQL_PASSWORD", "dba"),
     }
 
 
@@ -21,10 +46,10 @@ def get_sparql_auth_conf(config_obj) -> dict:
 # This is not idempotent.  Consider having a special virtuoso instance
 # just for running tests.
 @pytest.fixture(scope="module")
-def rdf_setup(fxtr_app_config):
+def rdf_setup():
     """Upload RDF to a Virtuoso named graph"""
     # Define the URL and file
-    sparql_conf = get_sparql_auth_conf(fxtr_app_config)
+    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],
diff --git a/tests/unit/db/rdf/test_wiki.py b/tests/unit/db/rdf/test_wiki.py
index 7627dbf..8dd4f3a 100644
--- a/tests/unit/db/rdf/test_wiki.py
+++ b/tests/unit/db/rdf/test_wiki.py
@@ -185,9 +185,9 @@ def test_sanitize_result(result, expected):
 
 
 @pytest.mark.rdf
-def test_get_wiki_entries_by_symbol(fxtr_app_config, rdf_setup):  # pylint: disable=W0613,W0621
+def test_get_wiki_entries_by_symbol(rdf_setup):  # pylint: disable=W0613,W0621
     """Test that wiki entries are fetched correctly by symbol"""
-    sparql_conf = get_sparql_auth_conf(fxtr_app_config)
+    sparql_conf = get_sparql_auth_conf()
     result = get_wiki_entries_by_symbol(
         symbol="ckb",
         sparql_uri=sparql_conf["sparql_endpoint"],
@@ -260,9 +260,9 @@ and C1QL3 (CTRP13).",
 
 
 @pytest.mark.rdf
-def test_get_comment_history(fxtr_app_config, rdf_setup):  # pylint: disable=W0613,W0621
+def test_get_comment_history(rdf_setup):  # pylint: disable=W0613,W0621
     """Test fetching a comment's history from RDF"""
-    sparql_conf = get_sparql_auth_conf(fxtr_app_config)
+    sparql_conf = get_sparql_auth_conf()
     result = get_comment_history(
         comment_id=1158,
         sparql_uri=sparql_conf["sparql_endpoint"],
@@ -353,9 +353,9 @@ Possible 3' UTR variants.",
 
 
 @pytest.mark.rdf
-def test_update_wiki_comment(fxtr_app_config, rdf_setup):  # pylint: disable=W0613,W0621
+def test_update_wiki_comment(rdf_setup):  # pylint: disable=W0613,W0621
     """Test that a comment is updated correctly"""
-    sparql_conf = get_sparql_auth_conf(fxtr_app_config)
+    sparql_conf = get_sparql_auth_conf()
     update_wiki_comment(
         insert_dict={
             "Id": 230,