From 4c7a0cc3d8ec6efb64f198a3d6786104d6e72bf7 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 20 Jan 2025 15:15:27 +0000
Subject: [PATCH] Add type annotations

---
 lib/galaxy/managers/workflows.py   | 7 +++++--
 lib/galaxy/tool_util/cwl/parser.py | 5 +++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index ecb0b7a719ae..162596abb1ff 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -46,7 +46,10 @@
     joinedload,
     subqueryload,
 )
-from typing_extensions import Annotated
+from typing_extensions import (
+    Annotated,
+    TypeAlias,
+)
 
 from galaxy import (
     exceptions,
@@ -1827,7 +1830,7 @@ def __module_from_dict(
             self.add_item_annotation(sa_session, trans.get_user(), step, annotation)
 
         # Stick this in the step temporarily
-        DictConnection = Dict[str, Union[int, str]]
+        DictConnection: TypeAlias = Dict[str, Union[int, str]]
         temp_input_connections: Dict[str, Union[List[DictConnection], DictConnection]] = step_dict.get(
             "input_connections", {}
         )
diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index e4a4ff83fb20..5533261c560c 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -15,6 +15,7 @@
 from typing import (
     Dict,
     List,
+    Optional,
     overload,
     Union,
 )
@@ -531,7 +532,7 @@ class WorkflowProxy:
     def __init__(self, workflow, workflow_path=None):
         self._workflow = workflow
         self._workflow_path = workflow_path
-        self._step_proxies = None
+        self._step_proxies: Optional[List[Union[SubworkflowStepProxy, ToolStepProxy]]] = None
 
     @property
     def cwl_id(self):
@@ -562,7 +563,7 @@ def get_outputs_for_label(self, label):
 
     def tool_reference_proxies(self):
         """Fetch tool source definitions for all referenced tools."""
-        references = []
+        references: List[ToolProxy] = []
         for step in self.step_proxies():
             references.extend(step.tool_reference_proxies())
         return references