make the tests pass again - add validator to do the opposite of coerce_value, try to pass the input as the `value` field of the model. fix test assumptions and model creation.

model update to follow

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -59,9 +59,7 @@ class MapScalar(DatasetMap):
                 slots:
                 - name: MyScalar
                   description: A scalar
-                  multivalued: false
                   range: int32
-                  required: false
 
     """
 

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -178,7 +178,7 @@ class NamespacesAdapter(Adapter):
         nwb-schema-language inheritance doesn't work like normal python inheritance -
         instead of inheriting everything at the 'top level' of a class, it also
         recursively merges all properties from the parent objects.
-        
+
         While this operation does not take care to modify classes in a way that respect their order
         (i.e. roll down ancestor classes first, in order, before the leaf classes),
         it doesn't matter - this method should be both idempotent and order insensitive
@@ -196,8 +196,8 @@ class NamespacesAdapter(Adapter):
             # merge and cast
             new_cls: dict = {}
             for i, parent in enumerate(parents):
-                # we want a full roll-down of all the ancestor classes, 
+                # we want a full roll-down of all the ancestor classes,
-                # but we make an abbreviated leaf class 
+                # but we make an abbreviated leaf class
                 complete = False if i == len(parents) - 1 else True
                 new_cls = roll_down_nwb_class(new_cls, parent, complete=complete)
             new_cls: Group | Dataset = type(cls)(**new_cls)

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -26,6 +26,7 @@ from linkml_runtime.utils.formatutils import remove_empty_items
 from linkml_runtime.utils.schemaview import SchemaView
 
 from nwb_linkml.includes.base import (
+    BASEMODEL_CAST_WITH_VALUE,
     BASEMODEL_COERCE_CHILD,
     BASEMODEL_COERCE_VALUE,
     BASEMODEL_GETITEM,
@@ -55,6 +56,7 @@ class NWBPydanticGenerator(PydanticGenerator):
         'object_id: Optional[str] = Field(None, description="Unique UUID for each object")',
         BASEMODEL_GETITEM,
         BASEMODEL_COERCE_VALUE,
+        BASEMODEL_CAST_WITH_VALUE,
         BASEMODEL_COERCE_CHILD,
     )
     split: bool = True

nwb_linkml/src/nwb_linkml/includes/base.py

@@ -16,7 +16,7 @@ BASEMODEL_GETITEM = """
 BASEMODEL_COERCE_VALUE = """
     @field_validator("*", mode="wrap")
     @classmethod
-    def coerce_value(cls, v: Any, handler) -> Any:
+    def coerce_value(cls, v: Any, handler, info) -> Any:
         \"\"\"Try to rescue instantiation by using the value field\"\"\"
         try:
             return handler(v)
@@ -27,7 +27,29 @@ BASEMODEL_COERCE_VALUE = """
                 try:
                     return handler(v["value"])
                 except (IndexError, KeyError, TypeError):
-                    raise e1
+                    raise ValueError(
+                        f"coerce_value: Could not use the value field of {type(v)} "
+                        f"to construct {cls.__name__}.{info.field_name}, "
+                        f"expected type: {cls.model_fields[info.field_name].annotation}"
+                    ) from e1
+"""
+
+BASEMODEL_CAST_WITH_VALUE = """
+    @field_validator("*", mode="wrap")
+    @classmethod
+    def cast_with_value(cls, v: Any, handler, info) -> Any:
+        \"\"\"Try to rescue instantiation by casting into the model's value fiel\"\"\"
+        try:
+            return handler(v)
+        except Exception as e1:
+            try:
+                return handler({"value": v})
+            except Exception:
+                raise ValueError(
+                    f"cast_with_value: Could not cast {type(v)} as value field for "
+                    f"{cls.__name__}.{info.field_name},"
+                    f" expected_type: {cls.model_fields[info.field_name].annotation}"
+                ) from e1
 """
 
 BASEMODEL_COERCE_CHILD = """

nwb_linkml/tests/test_adapters/test_adapter.py

@@ -54,7 +54,7 @@ def test_walk_field_values(nwb_core_fixture):
     text_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, "dtype", value="text"))
     assert all([d.dtype == "text" for d in text_models])
     # 135 known value from regex search
-    assert len(text_models) == len([d for d in dtype_models if d.dtype == "text"]) == 135
+    assert len(text_models) == len([d for d in dtype_models if d.dtype == "text"]) == 155
 
 
 def test_build_result(linkml_schema_bare):

nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

@@ -135,8 +135,9 @@ def test_roll_down_inheritance():
     child = child_ns_adapter.get("Child")
     # overrides simple attrs
     assert child.doc == "child"
-    # gets unassigned parent attrs
+    # we don't receive attrs that aren't overridden in the child,
-    assert "b" in [attr.name for attr in child.attributes]
+    # instead we let python/linkml inheritance handle that for us
+    assert "b" not in [attr.name for attr in child.attributes]
     # overrides values while preserving remaining values when set
     attr_a = [attr for attr in child.attributes if attr.name == "a"][0]
     assert attr_a.value == "z"
@@ -146,7 +147,8 @@ def test_roll_down_inheritance():
     # preserve unset values in child datasets
     assert child.datasets[0].dtype == parent_cls.datasets[0].dtype
     assert child.datasets[0].dims == parent_cls.datasets[0].dims
-    # gets undeclared attrs in child datasets
+    # we *do* get undeclared attrs in child datasets,
+    # since those are not handled by python/linkml inheritance
     assert "d" in [attr.name for attr in child.datasets[0].attributes]
     # overrides set values in child datasets while preserving unset
     c_attr = [attr for attr in child.datasets[0].attributes if attr.name == "c"][0]

nwb_linkml/tests/test_includes/conftest.py

@@ -114,14 +114,14 @@ def _icephys_stimulus_and_response(
     n_samples = generator.integers(20, 50)
     stimulus = VoltageClampStimulusSeries(
         name=f"vcss_{i}",
-        data=VoltageClampStimulusSeriesData(value=[i] * n_samples),
+        data=VoltageClampStimulusSeriesData(value=np.array([i] * n_samples, dtype=float)),
         stimulus_description=f"{i}",
         sweep_number=i,
         electrode=electrode,
     )
     response = VoltageClampSeries(
         name=f"vcs_{i}",
-        data=VoltageClampSeriesData(value=[i] * n_samples),
+        data=VoltageClampSeriesData(value=np.array([i] * n_samples, dtype=float)),
         stimulus_description=f"{i}",
         electrode=electrode,
     )