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refactor: move ground wire information into its own procedures #1243

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refactor: move ground wire information into its own procedures #1243

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492ca7b
refactor: move ground wire information into its own procedures
dbirman Jan 16, 2025
39abb47
fix: removing ground_electrode_location from MyomatrixThread
dbirman Jan 16, 2025
1197acb
refactor: add description for hole and embed in Myomatrix procedure
dbirman Jan 23, 2025
c654698
feat: deprecate ProtectiveMaterialReplacement
dbirman Jan 23, 2025
43e27d1
chore: remove reference to deprecated procedure
dbirman Jan 23, 2025
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22 changes: 16 additions & 6 deletions src/aind_data_schema/core/procedures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -361,18 +361,26 @@ class Headframe(DataModel):
well_type: Optional[str] = Field(default=None, title="Well type")


class GroundWireImplant(DataModel):
"""Ground wire implant procedure"""

procedure_type: Literal["Ground wire implant"] = "Ground wire implant"
ground_electrode_location: MouseAnatomicalStructure.ONE_OF = Field(..., title="Location of ground electrode")
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Would it be valuable to have a sublist of structures that we anticipate using for the ground electrode. We currently use BODY_PARTS for the EMG ground wire position, could we make a list called something ~ GROUND_WIRE_PARTS or GROUND_WIRE_LOCATIONS that has all of those plus brain? The full list of anatomical structures is super long and for people using the GUI it will be impossible to navigate


ground_wire_hole: Optional[int] = Field(default=None, title="Ground wire hole")
ground_wire_material: Optional[GroundWireMaterial] = Field(default=None, title="Ground wire material")
ground_wire_diameter: Optional[Decimal] = Field(default=None, title="Ground wire diameter")
ground_wire_diameter_unit: Optional[SizeUnit] = Field(default=None, title="Ground wire diameter unit")


class ProtectiveMaterialReplacement(DataModel):
"""Description of a protective material replacement procedure in preparation for ephys recording"""

procedure_type: Literal["Ground wire"] = "Ground wire"
procedure_type: Literal["Protective material"] = "Protective material"
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(default=None, title="Ground wire hole")
ground_wire_material: Optional[GroundWireMaterial] = Field(default=None, title="Ground wire material")
ground_wire_diameter: Optional[Decimal] = Field(default=None, title="Ground wire diameter")
ground_wire_diameter_unit: Optional[SizeUnit] = Field(default=None, title="Ground wire diameter unit")
well_part_number: Optional[str] = Field(default=None, title="Well part number")
well_type: Optional[str] = Field(default=None, title="Well type")

Expand Down Expand Up @@ -623,7 +631,9 @@ class MyomatrixContact(DataModel):
class MyomatrixThread(DataModel):
"""Description of a thread of a myomatrix array"""

ground_electrode_location: MouseAnatomicalStructure.BODY_PARTS = Field(..., title="Location of ground electrode")
ground_electrode: bool = Field(
..., title="Connected to a ground electrode", description="Ground electrode implant is in a separate procedure"
)
contacts: List[MyomatrixContact] = Field(..., title="Contacts")


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