Ephys Improvements (#979)

* initial commit

* examples

* Update procedures.py

* adding `default=` field

* linters

* adding `default` to any optional field missing it

Author: Sun-flow

examples/bergamo_ophys_session.json

@@ -162,6 +162,6 @@
    "headframe_registration": null,
    "reward_delivery": null,
    "reward_consumed_total": null,
-   "reward_consumed_unit": "microliter",
+   "reward_consumed_unit": "milliliter",
    "notes": null
 }

examples/ephys_session.json

@@ -388,6 +388,6 @@
    "headframe_registration": null,
    "reward_delivery": null,
    "reward_consumed_total": null,
-   "reward_consumed_unit": "microliter",
+   "reward_consumed_unit": "milliliter",
    "notes": null
 }

examples/mri_session.json

@@ -153,6 +153,6 @@
    "headframe_registration": null,
    "reward_delivery": null,
    "reward_consumed_total": null,
-   "reward_consumed_unit": "microliter",
+   "reward_consumed_unit": "milliliter",
    "notes": "There was some information about this scan session"
 }

examples/multiplane_ophys_session.json

@@ -282,6 +282,6 @@
    "headframe_registration": null,
    "reward_delivery": null,
    "reward_consumed_total": null,
-   "reward_consumed_unit": "microliter",
+   "reward_consumed_unit": "milliliter",
    "notes": null
 }

examples/ophys_session.json

@@ -87,6 +87,6 @@
    "headframe_registration": null,
    "reward_delivery": null,
    "reward_consumed_total": null,
-   "reward_consumed_unit": "microliter",
+   "reward_consumed_unit": "milliliter",
    "notes": null
 }

src/aind_data_schema/core/procedures.py

@@ -277,7 +277,7 @@ class Anaesthetic(AindModel):
     type: str = Field(..., title="Type")
     duration: Decimal = Field(..., title="Duration")
     duration_unit: TimeUnit = Field(default=TimeUnit.M, title="Duration unit")
-    level: Decimal = Field(..., title="Level (percent)", ge=1, le=5)
+    level: Optional[Decimal] = Field(default=None, title="Level (percent)", ge=1, le=5)
 
 
 class OtherSubjectProcedure(AindModel):
@@ -583,7 +583,7 @@ class Surgery(AindModel):
         description="First and last name of the experimenter.",
         title="Experimenter full name",
     )
-    iacuc_protocol: Optional[str] = Field(None, title="IACUC protocol")
+    iacuc_protocol: Optional[str] = Field(default=None, title="IACUC protocol")
     animal_weight_prior: Optional[Decimal] = Field(
         default=None, title="Animal weight (g)", description="Animal weight before procedure"
     )

src/aind_data_schema/core/session.py

@@ -208,7 +208,7 @@ class ManipulatorModule(DomeModule):
     """A dome module connected to a 3-axis manipulator"""
 
     primary_targeted_structure: str = Field(..., title="Targeted structure")
-    other_targeted_structure: Optional[List[str]] = Field(None, title="Other targeted structure")
+    other_targeted_structure: Optional[List[str]] = Field(default=None, title="Other targeted structure")
     targeted_ccf_coordinates: List[CcfCoords] = Field(
         default=[],
         title="Targeted CCF coordinates",
@@ -217,11 +217,11 @@ class ManipulatorModule(DomeModule):
         ...,
         title="Manipulator coordinates",
     )
-    bregma_coordinates: Optional[Coordinates3d] = Field(None, title="Bregma coordinates")
-    surface_z: Optional[Decimal] = Field(None, title="Surface z")
+    bregma_coordinates: Optional[Coordinates3d] = Field(default=None, title="Bregma coordinates")
+    surface_z: Optional[Decimal] = Field(default=None, title="Surface z")
     surface_z_unit: SizeUnit = Field(SizeUnit.UM, title="Surface z unit")
-    dye: Optional[str] = Field(None, title="Dye")
-    implant_hole_number: Optional[int] = Field(None, title="Implant hole number")
+    dye: Optional[str] = Field(default=None, title="Dye")
+    implant_hole_number: Optional[int] = Field(default=None, title="Implant hole number")
 
 
 class FiberModule(ManipulatorModule):
@@ -511,7 +511,7 @@ class StimulusEpoch(AindModel):
                 Field(discriminator="stimulus_type"),
             ]
         ]
-    ] = Field(None, title="Stimulus parameters")
+    ] = Field(default=None, title="Stimulus parameters")
     stimulus_device_names: List[str] = Field(default=[], title="Stimulus devices")
     speaker_config: Optional[SpeakerConfig] = Field(default=None, title="Speaker Config")
     light_source_config: Optional[List[LIGHT_SOURCE_CONFIGS]] = Field(
@@ -582,7 +582,7 @@ class Session(AindCoreModel):
     headframe_registration: Optional[Affine3dTransform] = Field(
         None, title="Headframe registration", description="MRI transform matrix for headframe"
     )
-    reward_delivery: Optional[RewardDeliveryConfig] = Field(None, title="Reward delivery")
-    reward_consumed_total: Optional[Decimal] = Field(None, title="Total reward consumed (uL)")
-    reward_consumed_unit: VolumeUnit = Field(VolumeUnit.UL, title="Reward consumed unit")
-    notes: Optional[str] = Field(None, title="Notes")
+    reward_delivery: Optional[RewardDeliveryConfig] = Field(default=None, title="Reward delivery")
+    reward_consumed_total: Optional[Decimal] = Field(default=None, title="Total reward consumed (mL)")
+    reward_consumed_unit: VolumeUnit = Field(VolumeUnit.ML, title="Reward consumed unit")
+    notes: Optional[str] = Field(default=None, title="Notes")