Use test fixtures to set-up a test named graph.

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

3 files changed, 47 insertions, 5 deletions

diff --git a/tests/fixtures/__init__.py b/tests/fixtures/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tests/fixtures/__init__.py
diff --git a/tests/fixtures/rdf.py b/tests/fixtures/rdf.py
new file mode 100644
index 0000000..a5fd711
--- /dev/null
+++ b/tests/fixtures/rdf.py
@@ -0,0 +1,41 @@
+"""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("")
+    sparql_conf.from_envvar("GN3_SECRETS")
+    sparql_conf.from_envvar("GN3_CONF")
+    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"])
+    # 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)
diff --git a/tests/unit/db/rdf/test_wiki.py b/tests/unit/db/rdf/test_wiki.py
index 99ecab0..a1500e9 100644
--- a/tests/unit/db/rdf/test_wiki.py
+++ b/tests/unit/db/rdf/test_wiki.py
@@ -1,6 +1,6 @@
 """Tests for gn3/db/rdf/wiki.py"""
 from unittest import TestCase
-
+from tests.fixtures.rdf import rdf_setup, get_sparql_auth_conf
 import pytest
 import os
 
@@ -12,6 +12,7 @@ from gn3.db.rdf.wiki import (
 )
 
 
+SPARQL_CONF = get_sparql_auth_conf()
 GRAPH = "<http://cd-test.genenetwork.org>"
 
 
@@ -168,11 +169,11 @@ def test_sanitize_result(result, expected):
 
 
 @pytest.mark.rdf
-def test_get_wiki_entries_by_symbol():
+def test_get_wiki_entries_by_symbol(rdf_setup):
     """Test that wiki entries are fetched correctly by symbol"""
     result = get_wiki_entries_by_symbol(
         symbol="ckb",
-        sparql_uri=os.environ.get("SPARQL_ENDPOINT", "http://localhost:9082/sparql"),
+        sparql_uri=SPARQL_CONF["sparql_endpoint"],
         graph=GRAPH,
     )
     expected = {
@@ -239,10 +240,10 @@ def test_get_wiki_entries_by_symbol():
 
 
 @pytest.mark.rdf
-def test_get_comment_history():
+def test_get_comment_history(rdf_setup):
     result = get_comment_history(
         comment_id=1158,
-        sparql_uri=os.environ.get("SPARQL_ENDPOINT", "http://localhost:9082/sparql"),
+        sparql_uri=SPARQL_CONF["sparql_endpoint"],
         graph=GRAPH,
     )
     expected = {