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Don't fail if reporting invalid parameter values

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which can contain None values.
Fixes the following traceback:
```
TypeError: sequence item 0: expected str instance, NoneType found
  File "galaxy/web/framework/decorators.py", line 346, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/tools.py", line 247, in build
    return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
  File "galaxy/tools/__init__.py", line 2509, in to_json
    populate_state(request_context, self.inputs, params.__dict__, state_inputs, state_errors)
  File "galaxy/tools/parameters/__init__.py", line 412, in populate_state
    _populate_state_legacy(
  File "galaxy/tools/parameters/__init__.py", line 625, in _populate_state_legacy
    check_param(request_context, input, param_value, context, simple_errors=simple_errors)
  File "galaxy/tools/parameters/__init__.py", line 246, in check_param
    value = param.from_json(value, trans, param_values)
  File "galaxy/tools/parameters/basic.py", line 1045, in from_json
    f"invalid options ({','.join(set(value) - set(legal_values))!r}) were selected (valid options: {','.join(legal_values)})",
```
Where `None` was in values. Note also that pyright underlined these
lines, not sure why mypy has ignored this error.
This commit is contained in:
mvdbeek
2024-04-16 17:41:31 +02:00
parent 3c2db48ae6
commit 48168faa35
1 changed files with 8 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/tools/parameters/basic.py
+8 -2
View File
@@ -892,6 +892,11 @@ class BaseURLToolParameter(HiddenToolParameter):
return d
def iter_to_string(iterable: typing.Iterable[typing.Any]) -> typing.Generator[str, None, None]:
for item in iterable:
yield str(item)
class SelectToolParameter(ToolParameter):
"""
Parameter that takes on one (or many) or a specific set of values.
@@ -1041,8 +1046,9 @@ class SelectToolParameter(ToolParameter):
elif set(value).issubset(set(fallback_values.keys())):
return [fallback_values[v] for v in value]
else:
invalid_options = iter_to_string(set(value) - set(legal_values))
raise ParameterValueError(
f"invalid options ({','.join(set(value) - set(legal_values))!r}) were selected (valid options: {','.join(legal_values)})",
f"invalid options ({','.join(invalid_options)!r}) were selected (valid options: {','.join(iter_to_string(legal_values))})",
self.name,
is_dynamic=self.is_dynamic,
)
@@ -1066,7 +1072,7 @@ class SelectToolParameter(ToolParameter):
return value
else:
raise ParameterValueError(
f"an invalid option ({value!r}) was selected (valid options: {','.join(legal_values)})",
f"an invalid option ({value!r}) was selected (valid options: {','.join(iter_to_string(legal_values))})",
self.name,
value,
is_dynamic=self.is_dynamic,