From baa5471af72a93cc0bd2f54d7b3471e5dc9615d6 Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <sneakers-the-rat@protonmail.com>
Date: Fri, 26 Jul 2024 21:58:07 -0700
Subject: [PATCH] getting started doing hdmf mixins but am tired

---
 .../src/nwb_linkml/generators/pydantic.py     |  2 +-
 .../src/nwb_linkml/includes/__init__.py       |  0
 nwb_linkml/src/nwb_linkml/includes/hdmf.py    | 37 +++++++++++++++++++
 .../{includes.py => includes/types.py}        |  0
 nwb_linkml/src/nwb_linkml/lang_elements.py    |  9 -----
 5 files changed, 38 insertions(+), 10 deletions(-)
 create mode 100644 nwb_linkml/src/nwb_linkml/includes/__init__.py
 create mode 100644 nwb_linkml/src/nwb_linkml/includes/hdmf.py
 rename nwb_linkml/src/nwb_linkml/{includes.py => includes/types.py} (100%)

diff --git a/nwb_linkml/src/nwb_linkml/generators/pydantic.py b/nwb_linkml/src/nwb_linkml/generators/pydantic.py
index 1b15468..f35b4d9 100644
--- a/nwb_linkml/src/nwb_linkml/generators/pydantic.py
+++ b/nwb_linkml/src/nwb_linkml/generators/pydantic.py
@@ -62,7 +62,7 @@ from pydantic import BaseModel
 
 from nwb_linkml.maps import flat_to_nptyping
 from nwb_linkml.maps.naming import module_case, version_module_case
-from nwb_linkml.includes import ModelTypeString, _get_name, NamedString, NamedImports
+from nwb_linkml.includes.types import ModelTypeString, _get_name, NamedString, NamedImports
 
 OPTIONAL_PATTERN = re.compile(r"Optional\[([\w\.]*)\]")
 
diff --git a/nwb_linkml/src/nwb_linkml/includes/__init__.py b/nwb_linkml/src/nwb_linkml/includes/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/nwb_linkml/src/nwb_linkml/includes/hdmf.py b/nwb_linkml/src/nwb_linkml/includes/hdmf.py
new file mode 100644
index 0000000..ee81b39
--- /dev/null
+++ b/nwb_linkml/src/nwb_linkml/includes/hdmf.py
@@ -0,0 +1,37 @@
+"""
+Special types for mimicking HDMF special case behavior
+"""
+
+from typing import Optional
+from pydantic import BaseModel, field_validator, ConfigDict, model_validator
+
+
+class DynamicTableMixin(BaseModel):
+    model_config = ConfigDict(extra='allow')
+
+    @model_validator(mode='after')
+    def ensure_equal_length(cls, model: 'DynamicTableMixin') -> 'DynamicTableMixin':
+        """
+        Ensure all vectors are of equal length
+        """
+        raise NotImplementedError('TODO')
+
+    @model_validator(mode="after")
+    def create_index_backrefs(cls, model: 'DynamicTableMixin') -> 'DynamicTableMixin':
+        """
+        Ensure that vectordata with vectorindexes know about them
+        """
+        raise NotImplementedError('TODO')
+
+    def __getitem__(self, item):
+        raise NotImplementedError('TODO')
+
+    def __setitem__(self, key, value):
+        raise NotImplementedError('TODO')
+
+
+
+class VectorDataMixin(BaseModel):
+    index: Optional[BaseModel] = None
+
+
diff --git a/nwb_linkml/src/nwb_linkml/includes.py b/nwb_linkml/src/nwb_linkml/includes/types.py
similarity index 100%
rename from nwb_linkml/src/nwb_linkml/includes.py
rename to nwb_linkml/src/nwb_linkml/includes/types.py
diff --git a/nwb_linkml/src/nwb_linkml/lang_elements.py b/nwb_linkml/src/nwb_linkml/lang_elements.py
index d35a767..7bb68c4 100644
--- a/nwb_linkml/src/nwb_linkml/lang_elements.py
+++ b/nwb_linkml/src/nwb_linkml/lang_elements.py
@@ -7,20 +7,12 @@ from typing import List
 
 from linkml_runtime.linkml_model import (
     ClassDefinition,
-    EnumDefinition,
-    PermissibleValue,
     Prefix,
     SchemaDefinition,
     TypeDefinition,
 )
 
 from nwb_linkml.maps import flat_to_linkml, flat_to_np
-from nwb_schema_language.datamodel.nwb_schema_pydantic import FlatDtype as FlatDtype_source
-
-FlatDType = EnumDefinition(
-    name="FlatDType",
-    permissible_values=[PermissibleValue(p) for p in FlatDtype_source.__members__],
-)
 
 
 def _make_dtypes() -> List[TypeDefinition]:
@@ -59,7 +51,6 @@ NwbLangSchema = SchemaDefinition(
     name="nwb.language",
     id="nwb.language",
     description="Adapter objects to mimic the behavior of elements in the nwb-schema-language",
-    enums=[FlatDType],
     classes=[AnyType],
     types=DTypeTypes,
     imports=["linkml:types"],