add ground_wire procedure (#812)

* add ground_wire procedure

* added to subject list

* added hole number to probe insertion in session

* added material and diameter

* added PtIr

* updates to protective material replacement

* rearranged

* spelling

* examples

* update example

* linting

Author: saskiad

examples/ephys_session.json

@@ -47,6 +47,7 @@
                   "z": "1000",
                   "unit": "micrometer"
                },
+               "implant_hole_number": null,
                "ephys_probes": [
                   {
                      "name": "Probe A",
@@ -88,7 +89,8 @@
                   "y": "1000",
                   "z": "1000",
                   "unit": "micrometer"
-               }
+               },
+               "implant_hole_number": null
             }
          ],
          "detectors": [],

src/aind_data_schema/core/procedures.py

@@ -89,6 +89,7 @@ class Side(str, Enum):
 class ProtectiveMaterial(str, Enum):
     """Name of material applied to craniotomy"""
 
+    AGAROSE = "Agarose"
     DURAGEL = "Duragel"
     KWIK_CAST = "Kwik-Cast"
     SORTA_CLEAR = "SORTA-clear"
@@ -121,6 +122,13 @@ class HeadframeMaterial(str, Enum):
     WHITE_ZIRCONIA = "White Zirconia"
 
 
+class GroundWireMaterial(str, Enum):
+    """Ground wire material name"""
+
+    SILVER = "Silver"
+    PLATINUM_IRIDIUM = "Platinum iridium"
+
+
 class VirusPrepType(str, Enum):
     """Type of virus preparation"""
 
@@ -299,6 +307,22 @@ class Headframe(AindModel):
     well_type: Optional[str] = Field(None, title="Well type")
 
 
+class ProtectiveMaterialReplacement(AindModel):
+    """Description of a protective material replacement procedure in preparation for ephys recording"""
+
+    procedure_type: Literal["Ground wire"] = "Ground wire"
+    protocol_id: str = Field(..., title="Protocol ID", description="DOI for protocols.io")
+    protective_material: ProtectiveMaterial = Field(
+        ..., title="Protective material", description="New material being applied"
+        )
+    ground_wire_hole: Optional[int] = Field(None, title="Ground wire hole")
+    ground_wire_material: Optional[GroundWireMaterial] = Field(None, title="Ground wire material")
+    ground_wire_diameter: Optional[Decimal] = Field(None, title="Ground wire diameter")
+    ground_wire_diameter_unit: SizeUnit = Field(SizeUnit.IN, title="Ground wire diameter unit")
+    well_part_number: Optional[str] = Field(None, title="Well part number")
+    well_type: Optional[str] = Field(None, title="Well type")
+
+
 class TarsVirusIdentifiers(AindModel):
     """TARS data for a viral prep"""
 
@@ -557,8 +581,9 @@ class Surgery(AindModel):
                 IntraperitonealInjection,
                 IontophoresisInjection,
                 NanojectInjection,
-                Perfusion,
                 OtherSubjectProcedure,
+                Perfusion,
+                ProtectiveMaterialReplacement,
                 RetroOrbitalInjection,
             ],
             Field(discriminator="procedure_type"),

src/aind_data_schema/core/session.py

@@ -173,6 +173,7 @@ class ManipulatorModule(DomeModule):
         ...,
         title="Manipulator coordinates",
     )
+    implant_hole_number: Optional[int] = Field(None, title="Implant hole number")
 
 
 class EphysProbeConfig(AindModel):