Feat 45 missing fields

src/aind_slims_api/core.py

@@ -353,6 +353,7 @@ def add_model(
                 exclude=fields_to_exclude,
                 **kwargs,
                 by_alias=True,
+                context="slims_post",
             ),
         )
         return type(model).model_validate(rtn)
@@ -377,9 +378,7 @@ def update_model(self, model: SlimsBaseModel, *args, **kwargs):
             model._slims_table,
             model.pk,
             model.model_dump(
-                include=fields_to_include,
-                by_alias=True,
-                **kwargs,
+                include=fields_to_include, by_alias=True, **kwargs, context="slims_post"
             ),
         )
         return type(model).model_validate(rtn)

src/aind_slims_api/models/base.py

@@ -4,8 +4,13 @@
 import logging
 from datetime import datetime
 from typing import ClassVar, Optional
-
-from pydantic import BaseModel, ValidationInfo, field_serializer, field_validator
+from pydantic import (
+    BaseModel,
+    ValidationInfo,
+    field_serializer,
+    field_validator,
+    SerializationInfo,
+)
 from slims.internal import Column as SlimsColumn  # type: ignore
 
 from aind_slims_api.models.utils import _find_unit_spec
@@ -63,15 +68,18 @@ def _validate(cls, value, info: ValidationInfo):
             return value
 
     @field_serializer("*")
-    def _serialize(self, field, info):
-        """Serialize a field, accounts for Quantities and datetime"""
+    def _serialize(self, field, info: SerializationInfo):
+        """Serialize a field, accounts for Quantities and datetime."""
         unit_spec = _find_unit_spec(self.model_fields[info.field_name])
         if unit_spec and field is not None:
-            quantity = {
-                "amount": field,
-                "unit_display": unit_spec.preferred_unit,
-            }
-            return quantity
+            if info.context == "slims_post":
+                quantity = {
+                    "amount": field,
+                    "unit_display": unit_spec.preferred_unit,
+                }
+                return quantity
+            else:
+                return field
         elif isinstance(field, datetime):
             return int(field.timestamp() * 10**3)
         else:

src/aind_slims_api/models/ecephys_session.py

@@ -72,6 +72,11 @@ class SlimsGroupOfSessionsRunStep(SlimsExperimentRunStep):
         serialization_alias="xprs_cf_activeMousePlatform",
         validation_alias="xprs_cf_activeMousePlatform",
     )
+    instrument_pk: Optional[int] = Field(
+        default=None,
+        serialization_alias="xprs_cf_fk_instrumentJson",
+        validation_alias="xprs_cf_fk_instrumentJson",
+    )
     # TODO: add device calibrations once we have an example
     # device_calibrations_attachment: Optional[str] = Field(
     #     default=None,
@@ -373,6 +378,26 @@ class SlimsEphysInsertionResult(SlimsBaseModel):
     }
 
 
+class SlimsInstrumentRdrc(SlimsBaseModel):
+    """Model for Instrument Rdrc"""
+
+    pk: Optional[int] = Field(
+        default=None, serialization_alias="rdrc_pk", validation_alias="rdrc_pk"
+    )
+    name: Optional[str] = Field(
+        default=None, serialization_alias="rdrc_name", validation_alias="rdrc_name"
+    )
+    created_on: Optional[datetime] = Field(
+        default=None,
+        serialization_alias="rdrc_createdOn",
+        validation_alias="rdrc_createdOn",
+    )
+    _slims_table = "ReferenceDataRecord"
+    _base_fetch_filters: ClassVar[dict[str, str]] = {
+        "rdty_name": "AIND Instruments",
+    }
+
+
 class SlimsDomeModuleRdrc(SlimsBaseModel):
     """Model for Dome Module Reference Data"""
 
@@ -392,15 +417,15 @@ class SlimsDomeModuleRdrc(SlimsBaseModel):
         serialization_alias="rdrc_cf_probeName",
         validation_alias="rdrc_cf_probeName",
     )
-    primary_targeted_structure: Optional[str] = Field(
+    primary_targeted_structure_pk: Optional[int] = Field(
         default=None,
-        serialization_alias="rdrc_cf_fk_primaryTargetedStructure_display",
-        validation_alias="rdrc_cf_fk_primaryTargetedStructure_display",
+        serialization_alias="rdrc_cf_fk_primaryTargetedStructure",
+        validation_alias="rdrc_cf_fk_primaryTargetedStructure",
     )
-    secondary_targeted_structures: Optional[List] = Field(
+    secondary_targeted_structures_pk: Optional[List] = Field(
         default=None,
-        serialization_alias="rdrc_cf_fk_secondaryTargetedStructures2_display",
-        validation_alias="rdrc_cf_fk_secondaryTargetedStructures2_display",
+        serialization_alias="rdrc_cf_fk_secondaryTargetedStructures",
+        validation_alias="rdrc_cf_fk_secondaryTargetedStructures",
     )
     arc_angle: Annotated[float | None, UnitSpec("degree", "°")] = Field(
         default=None,
@@ -504,6 +529,26 @@ class SlimsDomeModuleRdrc(SlimsBaseModel):
     }
 
 
+class SlimsBrainStructureRdrc(SlimsBaseModel):
+    """Model for Brain Structure Reference Data"""
+
+    pk: Optional[int] = Field(
+        default=None, serialization_alias="rdrc_pk", validation_alias="rdrc_pk"
+    )
+    name: Optional[str] = Field(
+        default=None, serialization_alias="rdrc_name", validation_alias="rdrc_name"
+    )
+    created_on: Optional[datetime] = Field(
+        default=None,
+        serialization_alias="rdrc_createdOn",
+        validation_alias="rdrc_createdOn",
+    )
+    _slims_table = "ReferenceDataRecord"
+    _base_fetch_filters: ClassVar[dict[str, str]] = {
+        "rdty_name": "CCF brain structures",
+    }
+
+
 class SlimsFiberConnectionsRdrc(SlimsBaseModel):
     """Model for Fiber Connections Reference Data"""
 
@@ -539,7 +584,7 @@ class SlimsRewardDeliveryRdrc(SlimsBaseModel):
 
     pk: Optional[int] = Field(serialization_alias="rdrc_pk", validation_alias="rdrc_pk")
     reward_spouts_pk: Optional[int] = Field(
-        default=[],
+        default=None,
         serialization_alias="rdrc_cf_fk_rewardSpouts",
         validation_alias="rdrc_cf_fk_rewardSpouts",
     )