fix(test): force Virtuoso checkpoint after loading test data

Virtuoso may not fully index inserted data before queries run,
causing flaky SELECT failures despite ASK checks passing. Run an
explicit checkpoint via isql after data loading and replace ASK
verification with SELECT queries that confirm data is queryable.

Author: arcangelo7

tests/load_test_data.py

@@ -80,20 +80,21 @@ def load_data(data_file, endpoint="http://localhost:9999/sparql"):
             _process_chunk(triples[i:i + chunk_size], client, (i // chunk_size) + 1, total_chunks)
 
 
-def _verify_data_loaded(endpoint="http://localhost:9999/sparql", timeout=30):
-    """Wait until a broad sample of test data is queryable in Virtuoso."""
+def _verify_data_loaded(endpoint="http://localhost:9999/sparql", timeout=60):
+    """Wait until test data is fully queryable in Virtuoso via SELECT."""
     checks = [
-        'ASK { GRAPH <https://github.com/arcangelo7/time_agnostic/br/> { <https://github.com/arcangelo7/time_agnostic/br/2> ?p ?o } }',
-        'ASK { GRAPH <https://github.com/arcangelo7/time_agnostic/id/> { <https://github.com/arcangelo7/time_agnostic/id/27139> ?p ?o } }',
-        'ASK { GRAPH <https://github.com/arcangelo7/time_agnostic/ar/> { <https://github.com/arcangelo7/time_agnostic/ar/15519> ?p ?o } }',
+        ('SELECT ?p ?o WHERE { GRAPH ?g { <https://github.com/arcangelo7/time_agnostic/br/31830> ?p ?o } }', 1),
+        ('SELECT ?p ?o WHERE { GRAPH ?g { <https://github.com/arcangelo7/time_agnostic/id/27139> ?p ?o } }', 1),
+        ('SELECT ?p ?o WHERE { GRAPH ?g { <https://github.com/arcangelo7/time_agnostic/ar/15519> ?p ?o } }', 1),
     ]
     start_time = time.time()
     with SPARQLClient(endpoint) as client:
-        for check in checks:
+        for query, min_results in checks:
             while True:
                 if time.time() - start_time > timeout:
-                    raise TimeoutError(f"Data verification timed out: {check}")
-                if client.ask(check):
+                    raise TimeoutError(f"Data verification timed out: {query}")
+                result = client.query(query)
+                if len(result["results"]["bindings"]) >= min_results:
                     break
                 time.sleep(1)
     print("Data verification passed.")

tests/start-test-database.sh

@@ -45,5 +45,9 @@ docker exec test-virtuoso /opt/virtuoso-opensource/bin/isql -U dba -P dba exec="
 echo "Loading test data..."
 uv run python tests/load_test_data.py
 
+# Force Virtuoso to flush transaction log to disk
+echo "Running Virtuoso checkpoint..."
+docker exec test-virtuoso /opt/virtuoso-opensource/bin/isql -U dba -P dba exec="checkpoint;"
+
 echo "Setup completed."
-echo "Virtuoso DB: http://localhost:9999/sparql" 
+echo "Virtuoso DB: http://localhost:9999/sparql"