Test case WIP...

Author: jmchilton

lib/galaxy/tool_util/parameters/case.py

@@ -0,0 +1,70 @@
+from dataclasses import dataclass
+from typing import (
+    Any,
+    Dict,
+    List,
+)
+
+from .models import (
+    DataCollectionParameterModel,
+    DataParameterModel,
+    FloatParameterModel,
+    IntegerParameterModel,
+    parameters_by_name,
+    ToolParameterBundle,
+    ToolParameterT,
+)
+from .state import TestCaseToolState
+
+
+@dataclass
+class TestCaseStateAndWarnings:
+    tool_state: TestCaseToolState
+    warnings: List[str]
+
+
+def legacy_from_string(parameter: ToolParameterT, value: str, 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.
+    We have to maintain backward compatibility on these for older Galaxy tool profile versions.
+    """
+    is_string = isinstance(value, str)
+    result_value: Any = value
+    if is_string and isinstance(parameter, (IntegerParameterModel,)):
+        warnings.append(
+            f"Implicitly converted {parameter.name} to an integer from a string value, please use 'value_json' to define this test input parameter value instead."
+        )
+        result_value = int(value)
+    elif is_string and isinstance(parameter, (FloatParameterModel,)):
+        warnings.append(
+            f"Implicitly converted {parameter.name} to a floating point number from a string value, please use 'value_json' to define this test input parameter value instead."
+        )
+        result_value = float(value)
+    return result_value
+
+
+def test_case_state(
+    test_dict: Dict[str, Any], tool_parameter_bundle: ToolParameterBundle, profile: str
+) -> TestCaseStateAndWarnings:
+    warnings: List[str] = []
+    inputs = test_dict["inputs"]
+    state = {}
+    by_name = parameters_by_name(tool_parameter_bundle)
+    for input in inputs:
+        input_name = input["name"]
+        if input_name not in by_name:
+            raise Exception(f"Cannot find tool parameter for {input_name}")
+        tool_parameter_model = by_name[input_name]
+        input_value = input["value"]
+        input_value = legacy_from_string(tool_parameter_model, input_value, warnings, profile)
+        if isinstance(tool_parameter_model, (DataParameterModel,)):
+            pass
+        elif isinstance(tool_parameter_model, (DataCollectionParameterModel,)):
+            pass
+
+        state[input_name] = input_value
+
+    tool_state = TestCaseToolState(state)
+    tool_state.validate(tool_parameter_bundle)
+    return TestCaseStateAndWarnings(tool_state, warnings)