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 +137,29 @@ 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 Readout(Reagent):
     """Description of a readout"""
 
@@ -292,6 +316,47 @@ 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"
+    protocol_id: Optional[str] = Field(default=None, title="Protocol ID", description="DOI for protocols.io")
+    iacuc_protocol: str = Field(..., title="IACUC protocol")
+    start_date: date = Field(..., title="Start date")
+    experimenter_full_name: str = Field(
+        ...,
+        description="First and last name of the experimenter.",
+        title="Experimenter full name",
+    )
+    where_performed: Annotated[Union[Organization.AIND, Organization.JAX],
+                               Field(..., title="Where performed", discriminator="name")]
+    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")
+    notes: Optional[str] = Field(default=None, title="Notes")
+
+
+class CatheterMaintenance(AindModel):
+    """Description of a catheter maintenance procedure"""
+
+    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")
+    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"
+    )
+    health_assessment: Optional[str] = Field(default=None, title="Health assessment")
+    pantent: bool = Field(default=True, title="Catheter patent")
+    notes: Optional[str] = Field(default=None, title="Notes")
+
+
 class Craniotomy(AindModel):
     """Description of craniotomy procedure"""
 
@@ -495,6 +560,28 @@ class IntraCisternalMagnaInjection(BrainInjection):
     injection_volume_unit: VolumeUnit = Field(VolumeUnit.NL, title="Injection volume unit")
 
 
+class BloodCollection(AindModel):
+    """Description of a blood collection procedure"""
+
+    procedure_type: Literal["Blood collection"] = "Blood collection"
+    protocol_id = Optional[str] = Field(default=None, title="Protocol ID", description="DOI for protocols.io")
+    iacuc_protcol: str = Field(..., title="IACUC protocol")
+    start_date: date = Field(..., title="Start date")
+    experimenter_full_name: str = Field(
+        ...,
+        description="First and last name of the experimenter.",
+        title="Experimenter full name",
+    )
+    injection: List[IntraperitonealInjection] = Field(..., title="IP injections")
+    injection_time: int = Field(..., title="Relative injection time")
+    collection_time: int = Field(..., title="Relative collection time")
+    time_unit: TimeUnit = Field(default=TimeUnit.M, title="Time unit")
+    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")
+    notes: Optional[str] = Field(default=None, title="Notes"
+
+
 class TrainingProtocol(AindModel):
     """Description of an animal training protocol"""
 
@@ -658,7 +745,15 @@ class Procedures(AindCoreModel):
     )
     subject_procedures: List[
         Annotated[
-            Union[Surgery, TrainingProtocol, WaterRestriction, OtherSubjectProcedure],
+            Union[
+                BloodCollection,
+                CatheterImplant,
+                CatheterMaintenance,
+                Surgery,
+                TrainingProtocol,
+                WaterRestriction,
+                OtherSubjectProcedure
+            ],
             Field(discriminator="procedure_type"),
         ]
     ] = Field(default=[], title="Subject Procedures")