Add support for the new "cancelling" invocation state

CHANGELOG.md

@@ -7,6 +7,8 @@
 * Classes defined in ``bioblend.galaxy.objects.wrappers`` are no more
   re-exported by ``bioblend.galaxy.objects``.
 
+* Added support for the new "cancelling" invocation state.
+
 ### BioBlend v1.2.0 - 2023-06-30
 
 * Dropped support for Galaxy releases 17.09-19.01. Added support for Galaxy

bioblend/_tests/TestGalaxyInvocations.py

@@ -19,21 +19,24 @@ def setUp(self):
         self.workflow_id = self.gi.workflows.import_workflow_from_local_path(path)["id"]
         self.history_id = self.gi.histories.create_history(name="TestGalaxyInvocations")["id"]
         self.dataset_id = self._test_dataset(self.history_id)
+        path = test_util.get_abspath(os.path.join("data", "test_workflow_pause.ga"))
+        self.pause_workflow_id = self.gi.workflows.import_workflow_from_local_path(path)["id"]
 
     def tearDown(self):
         self.gi.histories.delete_history(self.history_id, purge=True)
 
     @test_util.skip_unless_galaxy("release_19.09")
     def test_cancel_invocation(self):
-        invocation = self._invoke_workflow()
-
+        invocation = self._invoke_pause_workflow()
         invocation_id = invocation["id"]
         invocations = self.gi.invocations.get_invocations()
-        assert len(invocations) == 1
-        assert invocations[0]["id"] == invocation_id
-        self.gi.invocations.cancel_invocation(invocation_id)
+        assert invocation_id in [inv["id"] for inv in invocations]
+
         invocation = self.gi.invocations.show_invocation(invocation_id)
-        assert invocation["state"] == "cancelled"
+        assert invocation["state"] in ["new", "ready"]
+
+        invocation = self.gi.invocations.cancel_invocation(invocation_id)
+        assert invocation["state"] in ["cancelled", "cancelling"]
 
     @test_util.skip_unless_galaxy("release_20.01")
     def test_get_invocations(self):
@@ -111,14 +114,7 @@ def test_get_invocation_jobs_summary(self):
     @test_util.skip_unless_tool("cat1")
     @test_util.skip_unless_tool("cat")
     def test_workflow_scheduling(self):
-        path = test_util.get_abspath(os.path.join("data", "test_workflow_pause.ga"))
-        workflow = self.gi.workflows.import_workflow_from_local_path(path)
-
-        invocation = self.gi.workflows.invoke_workflow(
-            workflow["id"],
-            inputs={"0": {"src": "hda", "id": self.dataset_id}},
-            history_id=self.history_id,
-        )
+        invocation = self._invoke_pause_workflow()
         invocation_id = invocation["id"]
 
         def invocation_steps_by_order_index() -> Dict[int, Dict[str, Any]]:
@@ -154,3 +150,10 @@ def _invoke_workflow(self) -> Dict[str, Any]:
             history_id=self.history_id,
             inputs_by="name",
         )
+
+    def _invoke_pause_workflow(self) -> Dict[str, Any]:
+        return self.gi.workflows.invoke_workflow(
+            self.pause_workflow_id,
+            inputs={"0": {"src": "hda", "id": self.dataset_id}},
+            history_id=self.history_id,
+        )

bioblend/_tests/TestGalaxyObjects.py

@@ -355,7 +355,7 @@ def test_sorted_steps_by(self):
     def test_cancel(self):
         inv = self._obj_invoke_workflow()
         inv.cancel()
-        assert inv.state == "cancelled"
+        assert inv.state in ["cancelled", "cancelling"]
 
     def test_wait(self):
         inv = self._obj_invoke_workflow()

bioblend/_tests/TestGalaxyWorkflows.py

@@ -102,20 +102,18 @@ def test_cancelling_workflow_scheduling(self):
         assert len(invocations) == 0
 
         invocation = self.gi.workflows.invoke_workflow(
-            workflow["id"],
+            workflow_id,
             inputs={"0": {"src": "hda", "id": dataset1_id}},
         )
         invocation_id = invocation["id"]
         invocations = self.gi.workflows.get_invocations(workflow_id)
-        assert len(invocations) == 1
-        assert invocations[0]["id"] == invocation_id
+        assert invocation_id in [inv["id"] for inv in invocations]
 
         invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
         assert invocation["state"] in ["new", "ready"]
 
-        self.gi.workflows.cancel_invocation(workflow_id, invocation_id)
-        invocation = self.gi.invocations.wait_for_invocation(invocation_id, check=False)
-        assert invocation["state"] == "cancelled"
+        invocation = self.gi.workflows.cancel_invocation(workflow_id, invocation_id)
+        assert invocation["state"] in ["cancelled", "cancelling"]
 
     def test_import_export_workflow_from_local_path(self):
         with pytest.raises(TypeError):

bioblend/galaxy/invocations/__init__.py

@@ -24,7 +24,7 @@
 log = logging.getLogger(__name__)
 
 INVOCATION_TERMINAL_STATES = {"cancelled", "failed", "scheduled"}
-# Invocation non-terminal states are: 'new', 'ready'
+# Invocation non-terminal states are: "cancelling", "new", "ready"
 
 
 class InvocationClient(Client):