mypy fixes...

jmchilton · Aug 11, 2024 · b3a12b9 · b3a12b9
1 parent 477a1a1
commit b3a12b9
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Showing 5 changed files with 9 additions and 8 deletions.
diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
@@ -74,7 +74,7 @@ def to_dict(self):
         }
 
 
-def legacy_from_string(parameter: ToolParameterT, value: str, warnings: List[str], profile: str) -> Any:
+def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings: List[str], profile: str) -> Any:
     """Convert string values in XML test cases into typed variants.
 
     This should only be used when parsing XML test cases into a TestCaseToolState object.
@@ -131,7 +131,7 @@ def test_case_state(
     warnings: List[str] = []
     inputs: ToolSourceTestInputs = test_dict["inputs"]
     unhandled_inputs = []
-    state = {}
+    state: Dict[str, Any] = {}
 
     handled_inputs = _merge_level_into_state(tool_parameter_bundle, inputs, state, profile, warnings, None)
 

diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
@@ -211,7 +211,7 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
             Union[BooleanParameterModel, SelectParameterModel], _from_input_source_galaxy(test_param_input_source)
         )
         whens = []
-        default_value = cond_test_parameter_default_value(test_parameter)
+        default_test_value = cond_test_parameter_default_value(test_parameter)
         for value, case_inputs_sources in input_source.parse_when_input_sources():
             if isinstance(test_parameter, BooleanParameterModel):
                 # TODO: investigate truevalue/falsevalue when...
@@ -221,7 +221,7 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
 
             tool_parameter_models = input_models_for_page(case_inputs_sources)
             is_default_when = False
-            if typed_value == default_value:
+            if typed_value == default_test_value:
                 is_default_when = True
             whens.append(
                 ConditionalWhen(discriminator=value, parameters=tool_parameter_models, is_default_when=is_default_when)

diff --git a/lib/galaxy/tool_util/parameters/scripts/validate_test_cases.py b/lib/galaxy/tool_util/parameters/scripts/validate_test_cases.py
@@ -51,7 +51,7 @@ def arg_parser() -> argparse.ArgumentParser:
 @dataclass
 class ToolTestValidationResults:
     tool_id: str
-    tool_version: str
+    tool_version: Optional[str]
     tool_profile: str
     tool_path: str
     results: List[TestCaseStateValidationResult]
@@ -103,7 +103,7 @@ def validate_tool(tool_path, latest) -> ToolTestValidationResults:
         load_error = e
         results = []
     return ToolTestValidationResults(
-        tool_source.parse_id(),
+        tool_id,
         tool_source.parse_version(),
         tool_source.parse_profile(),
         tool_path,

diff --git a/lib/galaxy/tool_util/verify/parse.py b/lib/galaxy/tool_util/verify/parse.py
@@ -156,7 +156,7 @@ def _description_from_tool_source(
     return ToolTestDescription.from_tool_source_dict(processed_test_dict)
 
 
-def _tool_id_and_version(tool_source: ToolSource, tool_guid: Optional[str]) -> Tuple[str, Optional[str]]:
+def _tool_id_and_version(tool_source: ToolSource, tool_guid: Optional[str]) -> Tuple[str, str]:
     tool_id = tool_guid or tool_source.parse_id()
     assert tool_id
     tool_version = parse_tool_version_with_defaults(tool_id, tool_source)

diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
@@ -6,6 +6,7 @@
 from galaxy.tool_util.parameters.case import (
     test_case_state as case_state,
     validate_test_cases_for_tool_source,
+    TestCaseStateValidationResult,
 )
 from galaxy.tool_util.parser.factory import get_tool_source
 from galaxy.tool_util.parser.interface import ToolSourceTest
@@ -119,7 +120,7 @@ def _validate_path(tool_path: str):
         assert tool_state.state_representation == "test_case_xml"
 
 
-def validate_test_cases_for(tool_name: str, **kwd) -> List[List[str]]:
+def validate_test_cases_for(tool_name: str, **kwd) -> List[TestCaseStateValidationResult]:
     test_tool_directory = functional_test_tool_directory()
     tool_path = os.path.join(test_tool_directory, f"{tool_name}.xml")
     tool_source = get_tool_source(tool_path)