Merge pull request #18743 from jmchilton/parameter_models_rework_test…

…_case_xml

Improvements to parameter models for test case inputs

lib/galaxy/tool_util/models.py

@@ -48,7 +48,7 @@ def parse_tool(tool_source: ToolSource) -> ParsedTool:
     version = tool_source.parse_version()
     name = tool_source.parse_name()
     description = tool_source.parse_description()
-    inputs = input_models_for_tool_source(tool_source).input_models
+    inputs = input_models_for_tool_source(tool_source).parameters
     outputs = from_tool_source(tool_source)
     citations = tool_source.parse_citations()
     license = tool_source.parse_license()

lib/galaxy/tool_util/parameters/__init__.py

@@ -62,6 +62,7 @@
     repeat_inputs_to_array,
     validate_explicit_conditional_test_value,
     visit_input_values,
+    VISITOR_NO_REPLACEMENT,
 )
 
 __all__ = (
@@ -116,6 +117,7 @@
     "keys_starting_with",
     "visit_input_values",
     "repeat_inputs_to_array",
+    "VISITOR_NO_REPLACEMENT",
     "decode",
     "encode",
     "WorkflowStepToolState",

lib/galaxy/tool_util/parameters/case.py

@@ -12,10 +12,13 @@
 from packaging.version import Version
 
 from galaxy.tool_util.parser.interface import (
+    TestCollectionDef,
     ToolSource,
     ToolSourceTest,
     ToolSourceTestInput,
     ToolSourceTestInputs,
+    xml_data_input_to_json,
+    XmlTestCollectionDefDict,
 )
 from galaxy.util import asbool
 from .factory import input_models_for_tool_source
@@ -25,6 +28,7 @@
     ConditionalWhen,
     DataCollectionParameterModel,
     DataColumnParameterModel,
+    DataParameterModel,
     FloatParameterModel,
     IntegerParameterModel,
     RepeatParameterModel,
@@ -249,8 +253,26 @@ def _merge_into_state(
     else:
         test_input = _input_for(state_path, inputs)
         if test_input is not None:
+            input_value: Any
             if isinstance(tool_input, (DataCollectionParameterModel,)):
-                input_value = test_input.get("attributes", {}).get("collection")
+                input_value = TestCollectionDef.from_dict(
+                    cast(XmlTestCollectionDefDict, test_input.get("attributes", {}).get("collection"))
+                ).test_format_to_dict()
+            elif isinstance(tool_input, (DataParameterModel,)):
+                data_tool_input = cast(DataParameterModel, tool_input)
+                if data_tool_input.multiple:
+                    value = test_input["value"]
+                    input_value_list = []
+                    if value:
+                        test_input_values = cast(str, value).split(",")
+                        for test_input_value in test_input_values:
+                            instance_test_input = test_input.copy()
+                            instance_test_input["value"] = test_input_value
+                            input_value = xml_data_input_to_json(test_input)
+                            input_value_list.append(input_value)
+                    input_value = input_value_list
+                else:
+                    input_value = xml_data_input_to_json(test_input)
             else:
                 input_value = test_input["value"]
                 input_value = legacy_from_string(tool_input, input_value, warnings, profile)
@@ -299,6 +321,6 @@ def validate_test_cases_for_tool_source(
     test_cases: List[ToolSourceTest] = tool_source.parse_tests_to_dict()["tests"]
     results_by_test: List[TestCaseStateValidationResult] = []
     for test_case in test_cases:
-        validation_result = test_case_validation(test_case, tool_parameter_bundle.input_models, profile)
+        validation_result = test_case_validation(test_case, tool_parameter_bundle.parameters, profile)
         results_by_test.append(validation_result)
     return results_by_test

lib/galaxy/tool_util/parameters/factory.py

@@ -319,7 +319,7 @@ def _from_input_source_cwl(input_source: CwlInputSource) -> ToolParameterT:
 
 
 def input_models_from_json(json: List[Dict[str, Any]]) -> ToolParameterBundle:
-    return ToolParameterBundleModel(input_models=json)
+    return ToolParameterBundleModel(parameters=json)
 
 
 def tool_parameter_bundle_from_json(json: Dict[str, Any]) -> ToolParameterBundleModel:
@@ -328,7 +328,7 @@ def tool_parameter_bundle_from_json(json: Dict[str, Any]) -> ToolParameterBundle
 
 def input_models_for_tool_source(tool_source: ToolSource) -> ToolParameterBundleModel:
     pages = tool_source.parse_input_pages()
-    return ToolParameterBundleModel(input_models=input_models_for_pages(pages))
+    return ToolParameterBundleModel(parameters=input_models_for_pages(pages))
 
 
 def input_models_for_pages(pages: PagesSource) -> List[ToolParameterT]:

lib/galaxy/tool_util/parameters/models.py

@@ -41,7 +41,8 @@
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.tool_util.parser.interface import (
     DrillDownOptionsDict,
-    TestCollectionDefDict,
+    JsonTestCollectionDefDict,
+    JsonTestDatasetDefDict,
 )
 from ._types import (
     cast_as_type,
@@ -312,9 +313,9 @@ def py_type_internal(self) -> Type:
     def py_type_test_case(self) -> Type:
         base_model: Type
         if self.multiple:
-            base_model = str
+            base_model = list_type(JsonTestDatasetDefDict)
         else:
-            base_model = str
+            base_model = JsonTestDatasetDefDict
         return optional_if_needed(base_model, self.optional)
 
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
@@ -372,7 +373,7 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
         elif state_representation == "workflow_step_linked":
             return dynamic_model_information_from_py_type(self, ConnectedValue)
         elif state_representation == "test_case_xml":
-            return dynamic_model_information_from_py_type(self, TestCollectionDefDict)
+            return dynamic_model_information_from_py_type(self, JsonTestCollectionDefDict)
         else:
             raise NotImplementedError(
                 f"Have not implemented data collection parameter models for state representation {state_representation}"
@@ -1164,12 +1165,11 @@ class ToolParameterModel(RootModel):
 class ToolParameterBundle(Protocol):
     """An object having a dictionary of input models (i.e. a 'Tool')"""
 
-    # TODO: rename to parameters to align with ConditionalWhen and Repeat.
-    input_models: List[ToolParameterT]
+    parameters: List[ToolParameterT]
 
 
 class ToolParameterBundleModel(BaseModel):
-    input_models: List[ToolParameterT]
+    parameters: List[ToolParameterT]
 
 
 def to_simple_model(input_parameter: Union[ToolParameterModel, ToolParameterT]) -> ToolParameterT:
@@ -1180,10 +1180,8 @@ def to_simple_model(input_parameter: Union[ToolParameterModel, ToolParameterT])
         return cast(ToolParameterT, input_parameter)
 
 
-def simple_input_models(
-    input_models: Union[List[ToolParameterModel], List[ToolParameterT]]
-) -> Iterable[ToolParameterT]:
-    return [to_simple_model(m) for m in input_models]
+def simple_input_models(parameters: Union[List[ToolParameterModel], List[ToolParameterT]]) -> Iterable[ToolParameterT]:
+    return [to_simple_model(m) for m in parameters]
 
 
 def create_model_strict(*args, **kwd) -> Type[BaseModel]:
@@ -1194,27 +1192,27 @@ def create_model_strict(*args, **kwd) -> Type[BaseModel]:
 
 
 def create_request_model(tool: ToolParameterBundle, name: str = "DynamicModelForTool") -> Type[BaseModel]:
-    return create_field_model(tool.input_models, name, "request")
+    return create_field_model(tool.parameters, name, "request")
 
 
 def create_request_internal_model(tool: ToolParameterBundle, name: str = "DynamicModelForTool") -> Type[BaseModel]:
-    return create_field_model(tool.input_models, name, "request_internal")
+    return create_field_model(tool.parameters, name, "request_internal")
 
 
 def create_job_internal_model(tool: ToolParameterBundle, name: str = "DynamicModelForTool") -> Type[BaseModel]:
-    return create_field_model(tool.input_models, name, "job_internal")
+    return create_field_model(tool.parameters, name, "job_internal")
 
 
 def create_test_case_model(tool: ToolParameterBundle, name: str = "DynamicModelForTool") -> Type[BaseModel]:
-    return create_field_model(tool.input_models, name, "test_case_xml")
+    return create_field_model(tool.parameters, name, "test_case_xml")
 
 
 def create_workflow_step_model(tool: ToolParameterBundle, name: str = "DynamicModelForTool") -> Type[BaseModel]:
-    return create_field_model(tool.input_models, name, "workflow_step")
+    return create_field_model(tool.parameters, name, "workflow_step")
 
 
 def create_workflow_step_linked_model(tool: ToolParameterBundle, name: str = "DynamicModelForTool") -> Type[BaseModel]:
-    return create_field_model(tool.input_models, name, "workflow_step_linked")
+    return create_field_model(tool.parameters, name, "workflow_step_linked")
 
 
 def create_field_model(

lib/galaxy/tool_util/parameters/state.py

@@ -39,8 +39,8 @@ def __init__(self, input_state: Dict[str, Any]):
     def _validate(self, pydantic_model: Type[BaseModel]) -> None:
         validate_against_model(pydantic_model, self.input_state)
 
-    def validate(self, input_models: HasToolParameters) -> None:
-        base_model = self.parameter_model_for(input_models)
+    def validate(self, parameters: HasToolParameters) -> None:
+        base_model = self.parameter_model_for(parameters)
         if base_model is None:
             raise NotImplementedError(
                 f"Validating tool state against state representation {self.state_representation} is not implemented."
@@ -53,64 +53,64 @@ def state_representation(self) -> StateRepresentationT:
         """Get state representation of the inputs."""
 
     @classmethod
-    def parameter_model_for(cls, input_models: HasToolParameters) -> Type[BaseModel]:
+    def parameter_model_for(cls, parameters: HasToolParameters) -> Type[BaseModel]:
         bundle: ToolParameterBundle
-        if isinstance(input_models, list):
-            bundle = ToolParameterBundleModel(input_models=input_models)
+        if isinstance(parameters, list):
+            bundle = ToolParameterBundleModel(parameters=parameters)
         else:
-            bundle = input_models
+            bundle = parameters
         return cls._parameter_model_for(bundle)
 
     @classmethod
     @abstractmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
         """Return a model type for this tool state kind."""
 
 
 class RequestToolState(ToolState):
     state_representation: Literal["request"] = "request"
 
     @classmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
-        return create_request_model(input_models)
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_request_model(parameters)
 
 
 class RequestInternalToolState(ToolState):
     state_representation: Literal["request_internal"] = "request_internal"
 
     @classmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
-        return create_request_internal_model(input_models)
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_request_internal_model(parameters)
 
 
 class JobInternalToolState(ToolState):
     state_representation: Literal["job_internal"] = "job_internal"
 
     @classmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
-        return create_job_internal_model(input_models)
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_job_internal_model(parameters)
 
 
 class TestCaseToolState(ToolState):
     state_representation: Literal["test_case_xml"] = "test_case_xml"
 
     @classmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
         # implement a test case model...
-        return create_test_case_model(input_models)
+        return create_test_case_model(parameters)
 
 
 class WorkflowStepToolState(ToolState):
     state_representation: Literal["workflow_step"] = "workflow_step"
 
     @classmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
-        return create_workflow_step_model(input_models)
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_workflow_step_model(parameters)
 
 
 class WorkflowStepLinkedToolState(ToolState):
     state_representation: Literal["workflow_step_linked"] = "workflow_step_linked"
 
     @classmethod
-    def _parameter_model_for(cls, input_models: ToolParameterBundle) -> Type[BaseModel]:
-        return create_workflow_step_linked_model(input_models)
+    def _parameter_model_for(cls, parameters: ToolParameterBundle) -> Type[BaseModel]:
+        return create_workflow_step_linked_model(parameters)

lib/galaxy/tool_util/parameters/visitor.py

@@ -34,7 +34,7 @@ def visit_input_values(
     no_replacement_value=VISITOR_NO_REPLACEMENT,
 ) -> Dict[str, Any]:
     return _visit_input_values(
-        simple_input_models(input_models.input_models),
+        simple_input_models(input_models.parameters),
         tool_state.input_state,
         callback=callback,
         no_replacement_value=no_replacement_value,