cast to value in container classes

docs/meta/todo.md

@@ -53,6 +53,9 @@ Loading
 - [ ] Top-level containers are still a little janky, eg. how `ProcessingModule` just accepts 
   extra args rather than properly abstracting `value` as a `__getitem__(self, key) -> T:` 
 
+Changes to linkml
+- [ ] Allow parameterizing "extra" fields, so we don't have to stuff things into `value` dicts
+
 ## Docs TODOs
 
 ```{todolist}

nwb_linkml/src/nwb_linkml/adapters/group.py

@@ -129,7 +129,7 @@ class GroupAdapter(ClassAdapter):
             # We are a top-level container class like ProcessingModule
             base = self.build_base()
             # remove all the attributes and replace with child slot
-            base.classes[0].attributes = [slot]
+            base.classes[0].attributes.append(slot)
             return base
 
     def handle_container_slot(self, cls: Group) -> BuildResult:

nwb_linkml/src/nwb_linkml/includes/base.py

@@ -65,7 +65,10 @@ BASEMODEL_COERCE_CHILD = """
                 annotation = annotation.__args__[0]
             try:
                 if issubclass(annotation, type(v)) and annotation is not type(v):
-                    v = annotation(**{**v.__dict__, **v.__pydantic_extra__})
+                    if v.__pydantic_extra__:
+                        v = annotation(**{**v.__dict__, **v.__pydantic_extra__})
+                    else:
+                        v = annotation(**v.__dict__)            
             except TypeError:
                 # fine, annotation is a non-class type like a TypeVar
                 pass

nwb_linkml/src/nwb_linkml/io/hdf5.py

@@ -35,7 +35,7 @@ import h5py
 import networkx as nx
 import numpy as np
 from numpydantic.interface.hdf5 import H5ArrayPath
-from pydantic import BaseModel
+from pydantic import BaseModel, ValidationError
 from tqdm import tqdm
 
 from nwb_linkml.maps.hdf5 import (
@@ -167,7 +167,24 @@ def _load_node(
 
     if "neurodata_type" in obj.attrs:
         model = provider.get_class(obj.attrs["namespace"], obj.attrs["neurodata_type"])
-        return model(**args)
+        try:
+            return model(**args)
+        except ValidationError as e1:
+            # try to restack extra fields into ``value``
+            if "value" in model.model_fields:
+                value_dict = {
+                    key: val for key, val in args.items() if key not in model.model_fields
+                }
+                for k in value_dict:
+                    del args[k]
+                args["value"] = value_dict
+                try:
+                    return model(**args)
+                except Exception as e2:
+                    raise e2 from e1
+            else:
+                raise e1
+
     else:
         if "name" in args:
             del args["name"]