Schema inference enhancements

CHANGELOG.md

@@ -5,6 +5,8 @@
 ### Features
 
 ### Bug fixes
+* Fixed the JSON schema inference warning on excluded fields; also improved error message reporting of which method
+  triggered the error. [PR #1037](https://github.com/catalystneuro/neuroconv/pull/1037)
 
 ### Improvements
 

src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py

@@ -315,7 +315,6 @@ def add_to_nwbfile(
 
                 metadata['Ecephys']['ElectricalSeries'] = dict(name=my_name, description=my_description)
 
-        The default is False (append mode).
         starting_time : float, optional
             Sets the starting time of the ElectricalSeries to a manually set value.
         stub_test : bool, default: False

src/neuroconv/nwbconverter.py

@@ -319,7 +319,7 @@ def get_conversion_options_schema(self) -> dict:
             version="0.1.0",
         )
         for interface_name, data_interface in self.data_interface_objects.items():
-            conversion_options_schema["properties"].update(
-                {interface_name: unroot_schema(data_interface.get_conversion_options_schema())}
-            )
+
+            schema = data_interface.get_conversion_options_schema()
+            conversion_options_schema["properties"].update({interface_name: unroot_schema(schema)})
         return conversion_options_schema

src/neuroconv/utils/json_schema.py

@@ -102,6 +102,9 @@ def get_json_schema_from_method_signature(method: Callable, exclude: Optional[li
     exclude = exclude or []
     exclude += ["self", "cls"]
 
+    split_qualname = method.__qualname__.split(".")[1:]
+    method_display = ".".join(split_qualname[1:]) if "<" not in split_qualname[-1] else split_qualname[0]
+
     signature = inspect.signature(obj=method)
     parameters = signature.parameters
     additional_properties = False
@@ -140,10 +143,13 @@ def get_json_schema_from_method_signature(method: Callable, exclude: Optional[li
     # Attempt to find descriptions within the docstring of the method
     parsed_docstring = docstring_parser.parse(method.__doc__)
     for parameter_in_docstring in parsed_docstring.params:
+        if parameter_in_docstring.arg_name in exclude:
+            continue
+
         if parameter_in_docstring.arg_name not in json_schema["properties"]:
             message = (
-                f"The argument_name '{parameter_in_docstring.arg_name}' from the docstring not occur in the "
-                "method signature, possibly due to a typo."
+                f"The argument_name '{parameter_in_docstring.arg_name}' from the docstring of method "
+                f"'{method_display}' does not occur in the signature, possibly due to a typo."
             )
             warnings.warn(message=message, stacklevel=2)
             continue

tests/test_minimal/test_utils/test_get_json_schema_from_method_signature.py

@@ -4,9 +4,10 @@
 import pytest
 from jsonschema import validate
 from pydantic import DirectoryPath, FilePath
+from pynwb import NWBFile
 
 from neuroconv.datainterfaces import AlphaOmegaRecordingInterface
-from neuroconv.utils import ArrayType, get_json_schema_from_method_signature
+from neuroconv.utils import ArrayType, DeepDict, get_json_schema_from_method_signature
 
 
 def test_get_json_schema_from_method_signature_basic():
@@ -299,8 +300,119 @@ def method_with_typo_in_docstring(integer: int):
     with pytest.warns(expected_warning=UserWarning) as warning_info:
         test_json_schema = get_json_schema_from_method_signature(method=method_with_typo_in_docstring)
 
+    assert len(warning_info) == 1
+
+    expected_warning_message = (
+        "The argument_name 'integ' from the docstring of method 'method_with_typo_in_docstring' does not occur in "
+        "the signature, possibly due to a typo."
+    )
+    assert warning_info[0].message.args[0] == expected_warning_message
+
+    expected_json_schema = {
+        "properties": {"integer": {"type": "integer"}},
+        "required": ["integer"],
+        "type": "object",
+        "additionalProperties": False,
+    }
+
+    assert test_json_schema == expected_json_schema
+
+
+def test_get_json_schema_from_method_signature_docstring_warning_with_exclusions():
+    def method_with_typo_in_docstring_and_exclusions(integer: int, nwbfile: NWBFile, metadata: DeepDict):
+        """
+        This is a docstring with a typo in the argument name.
+
+        Parameters
+        ----------
+        integ : int
+            This is an integer.
+        nwbfile : pynwb.NWBFile
+            An in-memory NWBFile object.
+        metadata : neuroconv.utils.DeepDict
+            A dictionary-like object that allows for deep access and modification.
+        """
+        pass
+
+    with pytest.warns(expected_warning=UserWarning) as warning_info:
+        test_json_schema = get_json_schema_from_method_signature(
+            method=method_with_typo_in_docstring_and_exclusions, exclude=["nwbfile", "metadata"]
+        )
+
+    assert len(warning_info) == 1
+
+    expected_warning_message = (
+        "The argument_name 'integ' from the docstring of method 'method_with_typo_in_docstring_and_exclusions' "
+        "does not occur in the signature, possibly due to a typo."
+    )
+    assert warning_info[0].message.args[0] == expected_warning_message
+
+    expected_json_schema = {
+        "properties": {"integer": {"type": "integer"}},
+        "required": ["integer"],
+        "type": "object",
+        "additionalProperties": False,
+    }
+
+    assert test_json_schema == expected_json_schema
+
+
+def test_get_json_schema_from_method_signature_docstring_warning_from_bound_method():
+    class TestClass:
+        def test_bound_method(self, integer: int):
+            """
+            This is a docstring with a typo in the argument name.
+
+            Parameters
+            ----------
+            integ : int
+                This is an integer.
+            """
+            pass
+
+    with pytest.warns(expected_warning=UserWarning) as warning_info:
+        test_json_schema = get_json_schema_from_method_signature(method=TestClass.test_bound_method)
+
+    assert len(warning_info) == 1
+
+    expected_warning_message = (
+        "The argument_name 'integ' from the docstring of method 'TestClass.test_bound_method' does not occur in the "
+        "signature, possibly due to a typo."
+    )
+    assert warning_info[0].message.args[0] == expected_warning_message
+
+    expected_json_schema = {
+        "properties": {"integer": {"type": "integer"}},
+        "required": ["integer"],
+        "type": "object",
+        "additionalProperties": False,
+    }
+
+    assert test_json_schema == expected_json_schema
+
+
+def test_get_json_schema_from_method_signature_docstring_warning_from_class_method():
+    class TestClass:
+        @classmethod
+        def test_class_method(self, integer: int):
+            """
+            This is a docstring with a typo in the argument name.
+
+            Parameters
+            ----------
+            integ : int
+                This is an integer.
+            """
+            pass
+
+    with pytest.warns(expected_warning=UserWarning) as warning_info:
+        test_json_schema = get_json_schema_from_method_signature(method=TestClass.test_class_method)
+
+    assert len(warning_info) == 1
+
     expected_warning_message = (
-        "The argument_name 'integ' from the docstring not occur in the method signature, possibly due to a typo."
+        "The argument_name 'integ' from the docstring of method 'TestClass.test_class_method' does not occur in the "
+        "signature, possibly due to a typo."
     )
     assert warning_info[0].message.args[0] == expected_warning_message