one last model generation

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -31,6 +31,7 @@ from nwb_linkml.includes.base import (
     BASEMODEL_COERCE_VALUE,
     BASEMODEL_EXTRA_TO_VALUE,
     BASEMODEL_GETITEM,
+    BASEMODEL_SERIALIZER,
 )
 from nwb_linkml.includes.hdmf import (
     DYNAMIC_TABLE_IMPORTS,
@@ -60,12 +61,20 @@ class NWBPydanticGenerator(PydanticGenerator):
         BASEMODEL_CAST_WITH_VALUE,
         BASEMODEL_COERCE_CHILD,
         BASEMODEL_EXTRA_TO_VALUE,
+        BASEMODEL_SERIALIZER,
     )
     split: bool = True
     imports: list[Import] = field(
         default_factory=lambda: [
             Import(module="numpy", alias="np"),
-            Import(module="pydantic", objects=[ObjectImport(name="model_validator")]),
+            Import(
+                module="pydantic",
+                objects=[
+                    ObjectImport(name="model_validator"),
+                    ObjectImport(name="model_serializer"),
+                ],
+            ),
+            Import(module="pdb"),
         ]
     )
 
@@ -294,12 +303,15 @@ class AfterGenerateClass:
             else:  # pragma: no cover - for completeness, shouldn't happen
                 cls.imports = DYNAMIC_TABLE_IMPORTS.model_copy()
         elif cls.cls.name == "VectorData":
-            cls.cls.bases = ["VectorDataMixin"]
+            cls.cls.bases = ["VectorDataMixin[T]", "Generic[T]"]
             # make ``value`` generic on T
             if "value" in cls.cls.attributes:
                 cls.cls.attributes["value"].range = "Optional[T]"
         elif cls.cls.name == "VectorIndex":
-            cls.cls.bases = ["VectorIndexMixin"]
+            cls.cls.bases = ["VectorIndexMixin[T]", "Generic[T]"]
+            # make ``value`` generic on T
+            if "value" in cls.cls.attributes:
+                cls.cls.attributes["value"].range = "Optional[T]"
         elif cls.cls.name == "DynamicTableRegion":
             cls.cls.bases = ["DynamicTableRegionMixin", "VectorData"]
         elif cls.cls.name == "AlignedDynamicTable":

nwb_linkml/src/nwb_linkml/includes/base.py

@@ -88,3 +88,17 @@ BASEMODEL_EXTRA_TO_VALUE = """
                     v["value"] = extras
         return v
 """
+
+BASEMODEL_SERIALIZER = """
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR":str(e), "TYPE": str(type(self))}
+            if 'Circular reference' in str(e):
+                return {"REFERENCE":"REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = ('indent', 'include', 'exclude', 'context', 'by_alias', 'exclude_unset', 'exclude_defaults', 'exclude_none', 'round_trip', 'warnings', 'serialize_as_any')
+            return self.model_dump_json(**{k:v for k,v in info.__dict__.items() if k in json_dump_fields})
+"""

nwb_linkml/src/nwb_linkml/io/hdf5.py

@@ -171,23 +171,7 @@ def _load_node(
             del args[".specloc"]
 
         model = provider.get_class(obj.attrs["namespace"], obj.attrs["neurodata_type"])
-        # 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:

nwb_linkml/tests/test_io/test_io_nwb.py

@@ -2,6 +2,7 @@
 Placeholder test module to test reading from pynwb-generated NWB file
 """
 
+import pdb
 from datetime import datetime
 
 import numpy as np
@@ -11,6 +12,7 @@ from numpydantic.interface.hdf5 import H5Proxy
 from pydantic import BaseModel
 from pynwb import NWBHDF5IO
 from pynwb import NWBFile as PyNWBFile
+from pydantic_core import to_json
 
 from nwb_linkml.io.hdf5 import HDF5IO
 from nwb_models.models import NWBFile
@@ -29,6 +31,13 @@ def test_read_from_nwbfile(nwb_file):
 @pytest.fixture(scope="module")
 def read_nwbfile(nwb_file) -> NWBFile:
     res = HDF5IO(nwb_file).read()
+
+    def fallback(*args, **kwargs):
+        pdb.set_trace()
+
+    to_json(res, fallback=fallback)
+
+    pdb.set_trace()
     return res
 
 
@@ -63,6 +72,7 @@ def test_nwbfile_base(read_nwbfile, read_pynwb):
     """
     Base attributes on top-level nwbfile are correct
     """
+
     _compare_attrs(read_nwbfile, read_pynwb)
 
 

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_base.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -32,6 +33,7 @@ from pydantic import (
     RootModel,
     ValidationInfo,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -134,6 +136,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_behavior.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import (
     NWBDataInterface,
@@ -115,6 +124,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_device.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -8,7 +9,15 @@ from enum import Enum
 from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import NWBContainer
 
@@ -108,6 +117,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_ecephys.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -17,6 +18,7 @@ from pydantic import (
     RootModel,
     ValidationInfo,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -126,6 +128,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_epoch.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -17,6 +18,7 @@ from pydantic import (
     RootModel,
     ValidationInfo,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -124,6 +126,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_file.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import (
     Images,
@@ -137,6 +146,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_icephys.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -17,6 +18,7 @@ from pydantic import (
     RootModel,
     ValidationInfo,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -133,6 +135,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_image.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import (
     Image,
@@ -116,6 +125,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_misc.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -17,6 +18,7 @@ from pydantic import (
     RootModel,
     ValidationInfo,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -126,6 +128,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_ogen.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import (
     NWBContainer,
@@ -115,6 +124,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_ophys.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -17,6 +18,7 @@ from pydantic import (
     RootModel,
     ValidationInfo,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -133,6 +135,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/core_nwb_retinotopy.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import NWBDataInterface
 
@@ -109,6 +118,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/namespace.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -8,7 +9,15 @@ from enum import Enum
 from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...core.v2_7_0.core_nwb_base import (
     Image,
@@ -280,6 +289,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_8_0/hdmf_common_base.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -8,7 +9,15 @@ from enum import Enum
 from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 
 metamodel_version = "None"
@@ -106,6 +115,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_8_0/hdmf_common_sparse.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...hdmf_common.v1_8_0.hdmf_common_base import Container
 
@@ -109,6 +118,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_8_0/hdmf_common_table.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -32,6 +33,7 @@ from pydantic import (
     ValidationInfo,
     ValidatorFunctionWrapHandler,
     field_validator,
+    model_serializer,
     model_validator,
 )
 
@@ -133,6 +135,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}
@@ -908,7 +936,7 @@ linkml_meta = LinkMLMeta(
 )
 
 
-class VectorData(VectorDataMixin):
+class VectorData(VectorDataMixin[T], Generic[T]):
     """
     An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on.
     """
@@ -922,7 +950,7 @@ class VectorData(VectorDataMixin):
     value: Optional[T] = Field(None)
 
 
-class VectorIndex(VectorIndexMixin):
+class VectorIndex(VectorIndexMixin[T], Generic[T]):
     """
     Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\".
     """
@@ -936,14 +964,7 @@ class VectorIndex(VectorIndexMixin):
         None, description="""Reference to the target dataset that this index applies to."""
     )
     description: str = Field(..., description="""Description of what these vectors represent.""")
-    value: Optional[
+    value: Optional[T] = Field(None)
-        Union[
-            NDArray[Shape["* dim0"], Any],
-            NDArray[Shape["* dim0, * dim1"], Any],
-            NDArray[Shape["* dim0, * dim1, * dim2"], Any],
-            NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], Any],
-        ]
-    ] = Field(None)
 
 
 class ElementIdentifiers(ElementIdentifiersMixin, Data):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_8_0/namespace.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -8,7 +9,15 @@ from enum import Enum
 from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...hdmf_common.v1_8_0.hdmf_common_base import Container, Data, SimpleMultiContainer
 from ...hdmf_common.v1_8_0.hdmf_common_sparse import CSRMatrix
@@ -117,6 +126,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/hdmf_experimental/v0_5_0/hdmf_experimental_experimental.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...hdmf_common.v1_8_0.hdmf_common_table import VectorData
 
@@ -109,6 +118,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/hdmf_experimental/v0_5_0/hdmf_experimental_resources.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -9,7 +10,15 @@ from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from numpydantic import NDArray, Shape
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...hdmf_common.v1_8_0.hdmf_common_base import Container, Data
 
@@ -109,6 +118,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/models/pydantic/hdmf_experimental/v0_5_0/namespace.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pdb
 import re
 import sys
 from datetime import date, datetime, time
@@ -8,7 +9,15 @@ from enum import Enum
 from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator,
+    model_serializer,
+    model_validator,
+)
 
 from ...hdmf_common.v1_8_0.hdmf_common_base import Container, Data, SimpleMultiContainer
 from ...hdmf_common.v1_8_0.hdmf_common_sparse import CSRMatrix
@@ -127,6 +136,32 @@ class ConfiguredBaseModel(BaseModel):
                     v["value"] = extras
         return v
 
+    @model_serializer(mode="wrap", when_used="json")
+    def serialize_model(self, nxt, info) -> Dict[str, Any]:
+        try:
+            return nxt(self, info)
+        except Exception as e:
+            return {"ERROR": str(e), "TYPE": str(type(self))}
+            if "Circular reference" in str(e):
+                return {"REFERENCE": "REFERENCE"}
+            pdb.set_trace()
+            json_dump_fields = (
+                "indent",
+                "include",
+                "exclude",
+                "context",
+                "by_alias",
+                "exclude_unset",
+                "exclude_defaults",
+                "exclude_none",
+                "round_trip",
+                "warnings",
+                "serialize_as_any",
+            )
+            return self.model_dump_json(
+                **{k: v for k, v in info.__dict__.items() if k in json_dump_fields}
+            )
+
 
 class LinkMLMeta(RootModel):
     root: Dict[str, Any] = {}

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.nwb.language.yaml

@@ -5,7 +5,7 @@ annotations:
     value: 'False'
   namespace:
     tag: namespace
-    value: hdmf-experimental
+    value: core
 description: Adapter objects to mimic the behavior of elements in the nwb-schema-language
 id: nwb.language
 imports:

nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.nwb.language.yaml

@@ -5,7 +5,7 @@ annotations:
     value: 'False'
   namespace:
     tag: namespace
-    value: hdmf-experimental
+    value: core
 description: Adapter objects to mimic the behavior of elements in the nwb-schema-language
 id: nwb.language
 imports: