Merge pull request #199 from nsoranzo/gxformat2_fixes

Fix integer order_index step keys in native workflow loading

Author: jmchilton

gxformat2/normalized/_native.py

@@ -216,7 +216,7 @@ def _normalize_native_for_validation(data: dict[str, Any]) -> dict[str, Any]:
         for key, step in data["steps"].items():
             if isinstance(step, dict):
                 step = _normalize_step_for_validation(step)
-            steps[key] = step
+            steps[str(key)] = step  # Galaxy may use integer order_index as keys
         data["steps"] = steps
     return data
 

tests/test_load_native.py

@@ -31,6 +31,19 @@ def test_valid_tags_accepted(self):
         result = load_native(wf, strict=True)
         assert result.tags == ["a", "b"]
 
+    def test_integer_step_keys_rejected(self):
+        wf = {
+            **MINIMAL_WORKFLOW,
+            "steps": {
+                0: {
+                    "id": 0,
+                    "type": "data_input",
+                },
+            },
+        }
+        with pytest.raises(ValidationError, match="Input should be a valid string"):
+            load_native(wf, strict=True)
+
 
 class TestLoadNativeLax:
     """Lax mode normalizes known quirks."""
@@ -127,6 +140,20 @@ def test_action_arguments_dict_unchanged(self):
         pja = result.steps["0"].post_job_actions["RenameOut"]
         assert pja.action_arguments == {"newname": "renamed"}
 
+    def test_integer_step_keys_normalized_to_strings(self):
+        """Galaxy serializes steps with integer order_index keys; lax mode converts them to strings."""
+        wf = {
+            **MINIMAL_WORKFLOW,
+            "steps": {
+                0: {
+                    "id": 0,
+                    "type": "data_input",
+                },
+            },
+        }
+        result = load_native(wf, strict=False)
+        assert set(result.steps.keys()) == {"0"}
+
     def test_does_not_mutate_input(self):
         wf = {**MINIMAL_WORKFLOW, "tags": "a,b"}
         original_tags = wf["tags"]