Repair calls to gene_set loaders

monarch-initiative · Sep 19, 2023 · 74a55ca · 74a55ca
1 parent 43207e3
commit 74a55ca
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/src/ontogpt/utils/gene_set_utils.py b/src/ontogpt/utils/gene_set_utils.py
@@ -155,7 +155,7 @@ def load_gene_sets(
     """
     gene_sets = []
     for input_path in glob.glob(f"{path}/*.yaml"):
-        gene_set = parse_gene_set(input_path)
+        gene_set = parse_gene_set(input_path, format="yaml")
         gene_sets.append(gene_set)
         if not gene_set.gene_ids and not gene_set.gene_symbols:
             raise ValueError(f"Gene set {gene_set.name} has no gene symbols or ids")

diff --git a/tests/unit/test_utils/test_gene_set_utils.py b/tests/unit/test_utils/test_gene_set_utils.py
@@ -35,7 +35,7 @@ def test_load_gene_sets(self):
 
     def test_populate(self):
         """Test population of gene set."""
-        gene_set = parse_gene_set(GENE_SETS_DIR / "Yamanaka-TFs.yaml")
+        gene_set = parse_gene_set(GENE_SETS_DIR / "Yamanaka-TFs.yaml", format="yaml")
         self.assertEqual(len(gene_set.gene_ids), 4)
         fill_missing_gene_set_values(gene_set)
         # print(yaml.dump(gene_set.dict(), sort_keys=False))