From 1d527d8f715daff0e4d3c266d14eb7bc6337d31d Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <sneakers-the-rat@protonmail.com>
Date: Wed, 31 Jul 2024 01:54:14 -0700
Subject: [PATCH] fix hdmf forwardrefs, remove numpy types temporarily

---
 nwb_linkml/src/nwb_linkml/includes/hdmf.py | 10 +++++-----
 nwb_linkml/src/nwb_linkml/lang_elements.py |  9 +++++----
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/nwb_linkml/src/nwb_linkml/includes/hdmf.py b/nwb_linkml/src/nwb_linkml/includes/hdmf.py
index 9027ae6..10aa05f 100644
--- a/nwb_linkml/src/nwb_linkml/includes/hdmf.py
+++ b/nwb_linkml/src/nwb_linkml/includes/hdmf.py
@@ -22,7 +22,7 @@ class DynamicTableMixin(BaseModel):
     """
 
     model_config = ConfigDict(extra="allow")
-    __pydantic_extra__: Dict[str, Union[list, "NDArray", "VectorData"]]
+    __pydantic_extra__: Dict[str, Union[list, "NDArray", "VectorDataMixin"]]
     NON_COLUMN_FIELDS: ClassVar[tuple[str]] = (
         "name",
         "colnames",
@@ -33,15 +33,15 @@ class DynamicTableMixin(BaseModel):
     colnames: List[str] = Field(default_factory=list)
 
     @property
-    def _columns(self) -> Dict[str, Union[list, "NDArray", "VectorData"]]:
+    def _columns(self) -> Dict[str, Union[list, "NDArray", "VectorDataMixin"]]:
         return {k: getattr(self, k) for i, k in enumerate(self.colnames)}
 
     @property
-    def _columns_list(self) -> List[Union[list, "NDArray", "VectorData"]]:
+    def _columns_list(self) -> List[Union[list, "NDArray", "VectorDataMixin"]]:
         return [getattr(self, k) for i, k in enumerate(self.colnames)]
 
     @overload
-    def __getitem__(self, item: str) -> Union[list, "NDArray", "VectorData"]: ...
+    def __getitem__(self, item: str) -> Union[list, "NDArray", "VectorDataMixin"]: ...
 
     @overload
     def __getitem__(self, item: int) -> DataFrame: ...
@@ -54,7 +54,7 @@ class DynamicTableMixin(BaseModel):
         DataFrame,
         list,
         "NDArray",
-        "VectorData",
+        "VectorDataMixin",
     ]: ...
 
     @overload
diff --git a/nwb_linkml/src/nwb_linkml/lang_elements.py b/nwb_linkml/src/nwb_linkml/lang_elements.py
index 7bb68c4..4ebd6d4 100644
--- a/nwb_linkml/src/nwb_linkml/lang_elements.py
+++ b/nwb_linkml/src/nwb_linkml/lang_elements.py
@@ -12,7 +12,7 @@ from linkml_runtime.linkml_model import (
     TypeDefinition,
 )
 
-from nwb_linkml.maps import flat_to_linkml, flat_to_np
+from nwb_linkml.maps import flat_to_linkml
 
 
 def _make_dtypes() -> List[TypeDefinition]:
@@ -27,12 +27,13 @@ def _make_dtypes() -> List[TypeDefinition]:
         if nwbtype.startswith("uint"):
             amin = 0
 
-        np_type = flat_to_np[nwbtype]
+        # FIXME: Restore numpy types when we wrap them :)
+        # np_type = flat_to_np[nwbtype]
 
-        repr_string = f"np.{np_type.__name__}" if np_type.__module__ == "numpy" else None
+        # repr_string = f"np.{np_type.__name__}" if np_type.__module__ == "numpy" else None
 
         atype = TypeDefinition(
-            name=nwbtype, minimum_value=amin, typeof=linkmltype, repr=repr_string
+            name=nwbtype, minimum_value=amin, typeof=linkmltype, # repr=repr_string
         )
         DTypeTypes.append(atype)
     return DTypeTypes