Pass a sparql connection object to get_dataset_metadata

* wqflask/wqflask/database.py (database_connection): New function.
* wqflask/wqflask/views.py: Import sparql_connection
(show_trait_page): Pass sparql_connection object to
get_dataset_metadata.

2 files changed, 13 insertions, 1 deletions

diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 663e2ebf..d2929488 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -1,6 +1,7 @@
 # Module to initialize sqlalchemy with flask
 import os
 import sys
+from SPARQLWrapper import JSON, SPARQLWrapper
 from typing import Tuple, Protocol, Any, Iterator
 from urllib.parse import urlparse
 import importlib
@@ -60,3 +61,10 @@ def database_connection() -> Iterator[Connection]:
         yield connection
     finally:
         connection.close()
+
+
+def sparql_connection():
+    """Create a sparql objection that is used to query RDF"""
+    return SPARQLWrapper(
+        get_setting("SPARQL_ENDPOINT")
+    )
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8a0bede3..1b34e2f8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -90,6 +90,7 @@ from base.webqtlConfig import TMPDIR
 from base.webqtlConfig import GENERATED_IMAGE_DIR
 
 from wqflask.database import database_connection
+from wqflask.database import sparql_connection
 
 import jobs.jobs as jobs
 
@@ -491,7 +492,10 @@ def show_trait_page():
         metadata = (
             template_vars.dataset.accession_id
             .bind(
-                lambda idx: get_dataset_metadata(f"GN{idx}")
+                lambda idx: get_dataset_metadata(
+                    sparql_connection(),
+                    f"GN{idx}"
+                )
             )
         ).data