Fix test and add test without updating the parameter input for Galaxy >=21.01

Author: nsoranzo

bioblend/_tests/TestGalaxyInvocations.py

@@ -175,23 +175,26 @@ def test_rerun_invocation(self):
         history = self.gi.histories.show_history(rerun_invocation["history_id"], contents=True)
         assert len(history) == 3
 
-    @test_util.skip_unless_galaxy("release_24.02")
+    @test_util.skip_unless_galaxy("release_21.01")
     def test_rerun_invocation_with_input_params(self):
         threeline_dataset_id = self._test_dataset(self.history_id, contents="A\nB\nC")
         invocation = self._invoke_x_random_lines_workflow(threeline_dataset_id)
         self.gi.invocations.wait_for_invocation(invocation["id"])
-        params = {
-            "how_many": {
-                "parameter_value": "1",
-                "label": "how_many",
-            }
-        }
+        rerun_invocation = self.gi.invocations.rerun_invocation(invocation["id"], history_id=self.history_id)
+        self.gi.invocations.wait_for_invocation(rerun_invocation["id"])
+
+    @test_util.skip_unless_galaxy("release_24.2")
+    def test_rerun_invocation_with_input_params_changed(self):
+        threeline_dataset_id = self._test_dataset(self.history_id, contents="A\nB\nC")
+        invocation = self._invoke_x_random_lines_workflow(threeline_dataset_id)
+        self.gi.invocations.wait_for_invocation(invocation["id"])
+        inputs_update = {"how_many": 1}
         rerun_invocation = self.gi.invocations.rerun_invocation(
-            invocation["id"], params_update=params, history_id=self.history_id
+            invocation["id"], inputs_update=inputs_update, history_id=self.history_id
         )
         self.gi.invocations.wait_for_invocation(rerun_invocation["id"])
         rerun_request = self.gi.invocations.get_invocation_request(rerun_invocation["id"])
-        assert rerun_request["inputs"]["how_many"] == "1"
+        assert rerun_request["inputs"]["how_many"] == 1
 
     def _invoke_workflow(self) -> dict[str, Any]:
         dataset = {"src": "hda", "id": self.dataset_id}
@@ -213,7 +216,7 @@ def _invoke_pause_workflow(self) -> dict[str, Any]:
     def _invoke_x_random_lines_workflow(self, dataset_id: str) -> dict[str, Any]:
         return self.gi.workflows.invoke_workflow(
             self.x_random_lines_workflow_id,
-            inputs={"from_what": {"src": "hda", "id": dataset_id}, "how_many": "2"},
+            inputs={"from_what": {"src": "hda", "id": dataset_id}, "how_many": 2},
             history_id=self.history_id,
             inputs_by="name",
         )

bioblend/galaxy/invocations/__init__.py

@@ -250,20 +250,32 @@ def rerun_invocation(
                 raise
             # Galaxy release_24.1 or earlier
             invocation = self.show_invocation(invocation_id)
+            workflow_step_id_to_index = {
+                step["workflow_step_id"]: index for index, step in enumerate(invocation["steps"])
+            }
+            # Merge input_step_parameters (indexed by label) into inputs (indexed by step index)
+            inputs = invocation["inputs"]
+            for param_input_dict in invocation["input_step_parameters"].values():
+                workflow_step_id = param_input_dict["workflow_step_id"]
+                workflow_step_index = workflow_step_id_to_index[workflow_step_id]
+                inputs[str(workflow_step_index)] = param_input_dict
             payload = {
-                "inputs": invocation["inputs"],
+                "inputs": inputs,
                 "instance": True,
-                "params": invocation["input_step_parameters"],
                 "workflow_id": invocation["workflow_id"],
             }
         else:
             # Drop history_id from the payload as we will set history later
             payload.pop("history_id")
         workflow_id = payload["workflow_id"]
         if inputs_update:
-            payload.setdefault("inputs", {}).update(inputs_update)
+            if payload.get("inputs") is None:
+                payload["inputs"] = {}
+            payload["inputs"].update(inputs_update)
         if params_update:
-            payload.setdefault("params", {}).update(params_update)
+            if payload.get("parameters") is None:
+                payload["parameters"] = {}
+            payload["parameters"].update(params_update)
         if replacement_params:
             payload["replacement_params"] = replacement_params
         if history_id:
@@ -407,7 +419,7 @@ def get_invocation_request(self, invocation_id: str) -> dict[str, Any]:
         :return: The invocation request.
 
         .. note::
-          This method works only on Galaxy 24.02 or later.
+          This method works only on Galaxy 24.2 or later.
         """
         url = self._make_url(invocation_id) + "/request"
         return self._get(url=url)