Feat 1147 interoception

src/aind_data_schema/core/procedures.py

@@ -6,6 +6,7 @@
 from typing import List, Literal, Optional, Set, Union
 
 from aind_data_schema_models.mouse_anatomy import MouseAnatomicalStructure
+from aind_data_schema_models.organizations import Organization
 from aind_data_schema_models.pid_names import PIDName
 from aind_data_schema_models.species import Species
 from aind_data_schema_models.specimen_procedure_types import SpecimenProcedureType
@@ -136,6 +137,38 @@ class VirusPrepType(str, Enum):
     PURIFIED = "Purified"
 
 
+class CatheterMaterial(str, Enum):
+    """Type of catheter material"""
+
+    NAKED = "Naked"
+    SILICONE = "VAB silicone"
+    MESH = "VAB mesh"
+
+
+class CatheterDesign(str, Enum):
+    """Type of catheter design"""
+
+    MAGNETIC = "Magnetic"
+    NONMAGNETIC = "Non-magnetic"
+    NA = "N/A"
+
+
+class CatheterPort(str, Enum):
+    """Type of catheter port"""
+
+    SINGLE = "Single"
+    DOUBLE = "Double"
+
+
+class CatheterPatency(str, Enum):
+    """Patency of catheter"""
+
+    NOT_PATENT = "Not patent"
+    PATENT = "Patent"
+    ONLY_PUSH = "Only push"
+    ONLY_PULL = "Only pull"
+
+
 class Readout(Reagent):
     """Description of a readout"""
 
@@ -292,6 +325,45 @@ class OtherSubjectProcedure(AindModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
+class CatheterImplant(AindModel):
+    """Description of a catheter implant procedure"""
+
+    procedure_type: Literal["Catheter Implant"] = "Catheter implant"
+    where_performed: Organization.CATHETER_IMPLANT_INSTITUTIONS = Field(..., title="Where performed")
+    catheter_material: CatheterMaterial = Field(..., title="Catheter material")
+    catheter_design: CatheterDesign = Field(..., title="Catheter design")
+    catheter_port: CatheterPort = Field(..., title="Catheter port")
+    targeted_vessel: MouseAnatomicalStructure.BLOOD_VESSELS = Field(..., title="Targeted blood vessel")
+
+
+class CatheterMaintenance(AindModel):
+    """Description of a single catheter maintenance procedure"""
+
+    procedure_type: Literal["Catheter maintenance"] = "Catheter maintenance"
+    start_date: date = Field(..., title="Start date")
+    experimenter_full_name: str = Field(
+        ...,
+        description="First and last name of the experimenter.",
+        title="Experimenter full name",
+    )
+    animal_weight_prior: Decimal = Field(
+        ..., title="Animal weight (g)", description="Animal weight before procedure"
+    )
+    weight_unit: MassUnit = Field(default=MassUnit.G, title="Weight unit")
+    health_assessment: Optional[str] = Field(default=None, title="Health assessment")
+    patent: CatheterPatency = Field(..., title="Catheter patent")
+    notes: Optional[str] = Field(default=None, title="Notes")
+
+
+class CatheterMaintenanceRecord(AindModel):
+    """Description of catheter maintenance record"""
+
+    procedure_type: Literal["Catheter maintenance"] = "Catheter maintenance"
+    protocol_id: Optional[str] = Field(default=None, title="Protocol ID", description="DOI for protocols.io")
+    iacuc_protocol: str = Field(..., title="IACUC protocol")
+    catheter_maintenance: List[CatheterMaintenance] = Field(..., title="Cathether maintenance")
+
+
 class Craniotomy(AindModel):
     """Description of craniotomy procedure"""
 
@@ -415,6 +487,7 @@ class IntraperitonealInjection(Injection):
     """Description of an intraperitoneal injection procedure"""
 
     procedure_type: Literal["Intraperitoneal injection"] = "Intraperitoneal injection"
+    time: Optional[AwareDatetimeWithDefault] = Field(default=None, title="Injection time")
     injection_volume: Decimal = Field(..., title="Injection volume (uL)")
     injection_volume_unit: VolumeUnit = Field(default=VolumeUnit.UL, title="Injection volume unit")
 
@@ -495,6 +568,16 @@ class IntraCisternalMagnaInjection(BrainInjection):
     injection_volume_unit: VolumeUnit = Field(VolumeUnit.NL, title="Injection volume unit")
 
 
+class BloodCollection(AindModel):
+    """Description of a single blood collection"""
+
+    procedure_type: Literal["Blood collection"] = "Blood collection"
+    time: AwareDatetimeWithDefault = Field(..., title="Collection time")
+    collection_volume: Decimal = Field(..., title="Collection volume")
+    collection_volume_unit: VolumeUnit = Field(..., title="Collection volume unit")
+    collection_method: Optional[str] = Field(default=None, title="Collection method for terminal collection")
+
+
 class TrainingProtocol(AindModel):
     """Description of an animal training protocol"""
 
@@ -624,6 +707,8 @@ class Surgery(AindModel):
     procedures: List[
         Annotated[
             Union[
+                BloodCollection,
+                CatheterImplant,
                 Craniotomy,
                 FiberImplant,
                 Headframe,
@@ -658,7 +743,13 @@ class Procedures(AindCoreModel):
     )
     subject_procedures: List[
         Annotated[
-            Union[Surgery, TrainingProtocol, WaterRestriction, OtherSubjectProcedure],
+            Union[
+                CatheterMaintenance,
+                Surgery,
+                TrainingProtocol,
+                WaterRestriction,
+                OtherSubjectProcedure
+            ],
             Field(discriminator="procedure_type"),
         ]
     ] = Field(default=[], title="Subject Procedures")