opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Generate somewhat valid SafeStringWrapper-wrapped class names

Browse Source 
I don't think there's any downside, and the upside is that we can use
https://github.com/kensho-technologies/pytest-annotate to kickstart type
annotations. Applying collected annotations (e.g. `pyannotate --py3
--type-info ./annotations.json lib/galaxy/workflow/run.py` currently fails with:
```
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/.venv/bin/pyannotate", line 8, in <module>
    sys.exit(main())
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/__main__.py", line 122, in main
    data = generate_annotations_json_string(
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/main.py", line 60, in generate_annotations_json_string
    signature = unify_type_comments(item.type_comments)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/main.py", line 27, in unify_type_comments
    arg_types, return_type = infer_annotation(type_comments)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/infer.py", line 45, in infer_annotation
    arg_types, return_type = parse_type_comment(comment)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/parse.py", line 216, in parse_type_comment
    return Parser(comment).parse()
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/parse.py", line 225, in __init__
    self.tokens = tokenize(comment)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/parse.py", line 193, in tokenize
    raise ParseError(original)
pyannotate_tools.annotations.parse.ParseError: Invalid type comment: (galaxy.app.UniverseApplication, Dict, Dict[str, galaxy.model.HistoryDatasetAssociation], Dict[Union[galaxy.security.object_wrapper:SafeStringWrapper(str:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>), str], Union[galaxy.security.object_wrapper.CallableSafeStringWrapper, galaxy.security.object_wrapper:SafeStringWrapper(str:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>), str]]) -> None
```
This fixes that.
This commit is contained in:
mvdbeek
2022-09-22 10:55:29 +02:00
parent 77182eb7f1
commit ac27540c57
1 changed files with 3 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/security/object_wrapper.py
+3 -1
View File
@@ -168,7 +168,9 @@ def wrap_with_safe_string(value, no_wrap_classes=None):
value_mod = inspect.getmodule(value)
if value_mod:
wrapped_class_name = f"{value_mod.__name__}.{wrapped_class_name}"
wrapped_class_name = f"SafeStringWrapper({wrapped_class_name}:{','.join(sorted(map(str, no_wrap_classes)))})"
wrapped_class_name = (
f"SafeStringWrapper__{wrapped_class_name}__{'__'.join(sorted([c.__name__ for c in no_wrap_classes]))}"
)
do_wrap_func_name = f"__do_wrap_{wrapped_class_name}"
do_wrap_func = __do_wrap
global_dict = globals()