provide string default in pharm info func

Author: elewis2

pori_python/graphkb/genes.py

@@ -370,7 +370,7 @@ def get_pharmacogenomic_info(
 
 
 def get_gene_linked_pharmacogenomic_info(
-    conn: GraphKBConnection, source: str
+    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE_NAME
 ) -> Tuple[List[str], Dict[str, Tuple[str, List[str]]]]:
     """
     Return two lists from GraphKB, one of pharmacogenomic genes and one of associated variants.

tests/test_graphkb/test_genes.py

@@ -18,7 +18,6 @@
     get_pharmacogenomic_info,
     get_preferred_gene_name,
     get_therapeutic_associated_genes,
-    PREFERRED_GENE_SOURCE_NAME,
 )
 from pori_python.graphkb.util import get_rid
 
@@ -172,7 +171,7 @@ def test_get_pharmacogenomic_info(conn):
     EXCLUDE_BCGSC_TESTS, reason="excluding BCGSC-specific tests (requires CGL loader))"
 )
 def test_get_gene_linked_pharmacogenomic_info(conn):
-    genes, matches = get_gene_linked_pharmacogenomic_info(conn, PREFERRED_GENE_SOURCE_NAME)
+    genes, matches = get_gene_linked_pharmacogenomic_info(conn)
     for gene in PHARMACOGENOMIC_INITIAL_GENES:
         assert gene in genes, f"{gene} not found in get_pharmacogenomic_info"
         for rid, variant_info in matches.items():