Typing fixes after rebase

galaxyproject · Nov 22, 2021 · 55380de · 55380de
1 parent 3e5efab
commit 55380de
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Showing 2 changed files with 7 additions and 9 deletions.
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -356,10 +356,9 @@ def normalize_workflow_format(self, trans, as_dict):
             # create a temporary file for the workflow if it is provided
             # as JSON, to make it parseable by the WorkflowProxy
             if workflow_path is None:
-                f = tempfile.NamedTemporaryFile(delete=False)
-                json.dump(as_dict, f)
-                workflow_path = f.name
-                f.close()
+                with tempfile.NamedTemporaryFile(mode="w+", delete=False) as f:
+                    json.dump(as_dict, f)
+                    workflow_path = f.name
                 if object_id:
                     workflow_path += "#" + object_id
                 wf_proxy = workflow_proxy(workflow_path)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
@@ -3,7 +3,7 @@
 import os
 import shlex
 import tempfile
-from typing import Any, cast, Dict, List
+from typing import Any, cast, Dict, List, Optional, Union
 
 from galaxy import model
 from galaxy.files import ProvidesUserFileSourcesUserContext
@@ -249,9 +249,8 @@ def wrap_input(input_values, input):
                 )
                 input_values[input.name] = wrapper
             elif isinstance(input, FieldTypeToolParameter):
-                if value is None:
-                    field_wrapper = None
-                else:
+                field_wrapper: Optional[Union[InputValueWrapper, DatasetFilenameWrapper]] = None
+                if value:
                     assert "value" in value, value
                     assert "src" in value, value
                     src = value["src"]
@@ -260,7 +259,7 @@ def wrap_input(input_values, input):
                     elif src == "hda":
                         field_wrapper = DatasetFilenameWrapper(value["value"],
                                                                datatypes_registry=self.app.datatypes_registry,
-                                                               tool=self,
+                                                               tool=self.tool,
                                                                name=input.name)
                     else:
                         raise ValueError(f"src should be 'json' or 'hda' but is '{src}'")