From ced2175a1f7eb3537ed7717e1e19e048c139a9c3 Mon Sep 17 00:00:00 2001
From: ahiuchingau <20424172+ahiuchingau@users.noreply.github.com>
Date: Tue, 30 Apr 2024 17:31:54 -0400
Subject: [PATCH] add absorbance reader command to protocol engine 1

---
 .../commands/absorbance_reader/__init__.py    |  1 +
 .../commands/absorbance_reader/run_profile.py | 68 +++++++++++++++++++
 .../state/module_substates/__init__.py        |  5 +-
 .../absorbance_reader_substate.py             | 22 ++++++
 4 files changed, 95 insertions(+), 1 deletion(-)
 create mode 100644 api/src/opentrons/protocol_engine/commands/absorbance_reader/__init__.py
 create mode 100644 api/src/opentrons/protocol_engine/commands/absorbance_reader/run_profile.py
 create mode 100644 api/src/opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py

diff --git a/api/src/opentrons/protocol_engine/commands/absorbance_reader/__init__.py b/api/src/opentrons/protocol_engine/commands/absorbance_reader/__init__.py
new file mode 100644
index 000000000000..9a273d2a9be1
--- /dev/null
+++ b/api/src/opentrons/protocol_engine/commands/absorbance_reader/__init__.py
@@ -0,0 +1 @@
+"""Command models for Absorbance Reader commands."""
diff --git a/api/src/opentrons/protocol_engine/commands/absorbance_reader/run_profile.py b/api/src/opentrons/protocol_engine/commands/absorbance_reader/run_profile.py
new file mode 100644
index 000000000000..467f1d7cac04
--- /dev/null
+++ b/api/src/opentrons/protocol_engine/commands/absorbance_reader/run_profile.py
@@ -0,0 +1,68 @@
+"""Command models to execute a Thermocycler profile."""
+from __future__ import annotations
+from typing import List, Optional, TYPE_CHECKING
+from typing_extensions import Literal, Type
+
+from pydantic import BaseModel, Field
+
+from opentrons.hardware_control.modules.types import ThermocyclerStep
+
+from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate
+
+if TYPE_CHECKING:
+    from opentrons.protocol_engine.state import StateView
+    from opentrons.protocol_engine.execution import EquipmentHandler
+
+
+RunProfileCommandType = Literal["thermocycler/runProfile"]
+
+
+class AbsorbanceReadParams(BaseModel):
+    """Input parameters for a single absorbance reading."""
+
+    moduleId: str = Field(..., description="Unique ID of the Thermocycler.")
+    sampleWavelength: float = Field(..., description="Sample wavelength in nm.")
+
+
+class AbsorbanceReadResult(BaseModel):
+    """Result data from running an aborbance reading."""
+
+    data: List[float] = Field(..., description="Absorbance data points.")
+
+
+class AbsorbanceReadImpl(AbstractCommandImpl[AbsorbanceReadParams, AbsorbanceReadResult]):
+    """Execution implementation of a Thermocycler's run profile command."""
+
+    def __init__(
+        self,
+        state_view: StateView,
+        equipment: EquipmentHandler,
+        **unused_dependencies: object,
+    ) -> None:
+        self._state_view = state_view
+        self._equipment = equipment
+
+    async def execute(self, params: AbsorbanceReadParams) -> AbsorbanceReadResult:
+        """Initiate a single absorbance measurement."""
+        # TODO: Implement this
+        return AbsorbanceReadResult(data=[])
+
+
+class AbsorbanceRead(BaseCommand[AbsorbanceReadParams, AbsorbanceReadResult]):
+    """A command to execute a Thermocycler profile run."""
+
+    # TODO: fix this
+    commandType: AbsorbanceReadCommandType = "absorbanceReader/measure"
+    params: AbsorbanceReadParams
+    result: Optional[AbsorbanceReadResult]
+
+    _ImplementationCls: Type[AbsorbanceReadImpl] = AbsorbanceReadImpl
+
+
+class RunProfileCreate(BaseCommandCreate[AbsorbanceReadParams]):
+    """A request to execute a Thermocycler profile run."""
+
+    commandType: AbsorbanceReadCommandType = "absorbanceReader/measure"
+    params: AbsorbanceReadParams
+
+    _CommandCls: Type[AbsorbanceRead] = AbsorbanceRead
diff --git a/api/src/opentrons/protocol_engine/state/module_substates/__init__.py b/api/src/opentrons/protocol_engine/state/module_substates/__init__.py
index 2e9b18ba17ba..3865982612be 100644
--- a/api/src/opentrons/protocol_engine/state/module_substates/__init__.py
+++ b/api/src/opentrons/protocol_engine/state/module_substates/__init__.py
@@ -12,7 +12,7 @@
     ThermocyclerModuleId,
 )
 from .magnetic_block_substate import MagneticBlockSubState, MagneticBlockId
-
+from .absorbance_reader_substate import AbsorbanceReaderSubState, AbsorbanceReaderId
 
 ModuleSubStateType = Union[
     HeaterShakerModuleSubState,
@@ -20,6 +20,7 @@
     TemperatureModuleSubState,
     ThermocyclerModuleSubState,
     MagneticBlockSubState,
+    AbsorbanceReaderSubState,
 ]
 
 __all__ = [
@@ -33,6 +34,8 @@
     "ThermocyclerModuleId",
     "MagneticBlockSubState",
     "MagneticBlockId",
+    "AbsorbanceReaderSubState",
+    "AbsorbanceReaderId",
     # Union of all module substates
     "ModuleSubStateType",
 ]
diff --git a/api/src/opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py b/api/src/opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py
new file mode 100644
index 000000000000..5b1cada15cc7
--- /dev/null
+++ b/api/src/opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py
@@ -0,0 +1,22 @@
+"""Heater-Shaker Module sub-state."""
+from dataclasses import dataclass
+from typing import NewType, List
+
+from opentrons.protocol_engine.types import (
+    TemperatureRange,
+    SpeedRange,
+    HeaterShakerLatchStatus,
+)
+
+AbsorbanceReaderId = NewType("AbsorbanceReaderId", str)
+
+
+@dataclass(frozen=True)
+class AbsorbanceReaderSubState:
+    """Absorbance-Plate-Reader-specific state."""
+
+    module_id: AbsorbanceReaderId
+    is_lid_open: bool
+    is_loaded: bool
+    sample_wavelength: int
+    supported_wavelengths: List[int]