refactor(api, robot-server, shared-data): replace v3 deck definition …

…with v4 in protocol api and engine (#13854)

Switches V3 Deck to V4 in Protocol API and Engine, removes automatically loaded fixed trash from empty runs and maintenance runs, and introduces legacy fixed trash loading for older protocols.

api/src/opentrons/execute.py

@@ -39,6 +39,8 @@
 from opentrons.protocols import parse
 from opentrons.protocols.api_support.deck_type import (
     guess_from_global_config as guess_deck_type_from_global_config,
+    should_load_fixed_trash,
+    should_load_fixed_trash_for_python_protocol,
 )
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.execution import execute as execute_apiv2
@@ -536,6 +538,7 @@ def _create_live_context_pe(
             config=_get_protocol_engine_config(),
             drop_tips_after_run=False,
             post_run_hardware_state=PostRunHardwareState.STAY_ENGAGED_IN_PLACE,
+            load_fixed_trash=should_load_fixed_trash_for_python_protocol(api_version),
         )
     )
 
@@ -609,6 +612,7 @@ async def run(protocol_source: ProtocolSource) -> None:
         protocol_engine = await create_protocol_engine(
             hardware_api=hardware_api.wrapped(),
             config=_get_protocol_engine_config(),
+            load_fixed_trash=should_load_fixed_trash(protocol_source.config),
         )
 
         protocol_runner = create_protocol_runner(

api/src/opentrons/protocol_api/core/engine/instrument.py

@@ -18,7 +18,7 @@
 from opentrons.protocol_engine.errors.exceptions import TipNotAttachedError
 from opentrons.protocol_engine.clients import SyncClient as EngineClient
 from opentrons.protocols.api_support.definitions import MAX_SUPPORTED_VERSION
-from opentrons.types import Point
+from opentrons.types import Point, DeckSlotName
 
 from opentrons_shared_data.pipette.dev_types import PipetteNameType
 
@@ -409,13 +409,7 @@ def _move_to_waste_chute(
             slot_origin_to_tip_a1 = _waste_chute_dimensions.SLOT_ORIGIN_TO_1_OR_8_TIP_A1
 
         # TODO: All of this logic to compute the destination coordinate belongs in Protocol Engine.
-        slot_d3 = next(
-            s
-            for s in self._protocol_core.get_deck_definition()["locations"][
-                "orderedSlots"
-            ]
-            if s["id"] == "D3"
-        )
+        slot_d3 = self._protocol_core.get_slot_definition(DeckSlotName.SLOT_D3)
         slot_d3_origin = Point(*slot_d3["position"])
         destination_point = slot_d3_origin + slot_origin_to_tip_a1
 

api/src/opentrons/protocol_api/core/engine/protocol.py

@@ -4,7 +4,7 @@
 from opentrons.protocol_api import _waste_chute_dimensions
 
 from opentrons.protocol_engine.commands import LoadModuleResult
-from opentrons_shared_data.deck.dev_types import DeckDefinitionV3, SlotDefV3
+from opentrons_shared_data.deck.dev_types import DeckDefinitionV4, SlotDefV3
 from opentrons_shared_data.labware.labware_definition import LabwareDefinition
 from opentrons_shared_data.labware.dev_types import LabwareDefinition as LabwareDefDict
 from opentrons_shared_data.pipette.dev_types import PipetteNameType
@@ -102,17 +102,20 @@ def robot_type(self) -> RobotType:
         return self._engine_client.state.config.robot_type
 
     @property
-    def fixed_trash(self) -> LabwareCore:
+    def fixed_trash(self) -> Optional[LabwareCore]:
         """Get the fixed trash labware."""
         trash_id = self._engine_client.state.labware.get_fixed_trash_id()
-        return self._labware_cores_by_id[trash_id]
+        if trash_id is not None:
+            return self._labware_cores_by_id[trash_id]
+        return None
 
     def _load_fixed_trash(self) -> None:
         trash_id = self._engine_client.state.labware.get_fixed_trash_id()
-        self._labware_cores_by_id[trash_id] = LabwareCore(
-            labware_id=trash_id,
-            engine_client=self._engine_client,
-        )
+        if trash_id is not None:
+            self._labware_cores_by_id[trash_id] = LabwareCore(
+                labware_id=trash_id,
+                engine_client=self._engine_client,
+            )
 
     def get_max_speeds(self) -> AxisMaxSpeeds:
         """Get a control interface for maximum move speeds."""
@@ -532,11 +535,12 @@ def set_last_location(
         self._last_location = location
         self._last_mount = mount
 
-    def get_deck_definition(self) -> DeckDefinitionV3:
+    def get_deck_definition(self) -> DeckDefinitionV4:
         """Get the geometry definition of the robot's deck."""
         return self._engine_client.state.labware.get_deck_definition()
 
     def get_slot_definition(self, slot: DeckSlotName) -> SlotDefV3:
+        """Get the slot definition from the robot's deck."""
         return self._engine_client.state.labware.get_slot_definition(slot)
 
     def _ensure_module_location(

api/src/opentrons/protocol_api/core/legacy/deck.py

@@ -4,12 +4,10 @@
 import logging
 from collections import UserDict
 from typing import Dict, Optional, List, Union
-from typing_extensions import Protocol
+from typing_extensions import Protocol, Final
+
+from opentrons_shared_data.deck import load as load_deck
 
-from opentrons_shared_data.deck import (
-    DEFAULT_DECK_DEFINITION_VERSION,
-    load as load_deck,
-)
 from opentrons_shared_data.deck.dev_types import SlotDefV3
 from opentrons_shared_data.labware.dev_types import LabwareUri
 
@@ -34,6 +32,9 @@
 FIXED_TRASH_ID = "fixedTrash"
 
 
+DEFAULT_LEGACY_DECK_DEFINITION_VERSION: Final = 3
+
+
 class DeckItem(Protocol):
     @property
     def highest_z(self) -> float:
@@ -50,7 +51,7 @@ class Deck(UserDict):  # type: ignore[type-arg]
     def __init__(self, deck_type: str) -> None:
         super().__init__()
         self._definition = load_deck(
-            name=deck_type, version=DEFAULT_DECK_DEFINITION_VERSION
+            name=deck_type, version=DEFAULT_LEGACY_DECK_DEFINITION_VERSION
         )
         self._positions = {}
         for slot in self._definition["locations"]["orderedSlots"]:

api/src/opentrons/protocol_api/core/legacy/legacy_protocol_core.py

@@ -1,7 +1,7 @@
 import logging
 from typing import Dict, List, Optional, Set, Union, cast, Tuple
 
-from opentrons_shared_data.deck.dev_types import DeckDefinitionV3
+from opentrons_shared_data.deck.dev_types import DeckDefinitionV4, SlotDefV3
 from opentrons_shared_data.labware.dev_types import LabwareDefinition
 from opentrons_shared_data.pipette.dev_types import PipetteNameType
 from opentrons_shared_data.robot.dev_types import RobotType
@@ -452,10 +452,14 @@ def get_labware_on_labware(
     ) -> Optional[LegacyLabwareCore]:
         assert False, "get_labware_on_labware only supported on engine core"
 
-    def get_deck_definition(self) -> DeckDefinitionV3:
+    def get_deck_definition(self) -> DeckDefinitionV4:
         """Get the geometry definition of the robot's deck."""
         assert False, "get_deck_definition only supported on engine core"
 
+    def get_slot_definition(self, slot: DeckSlotName) -> SlotDefV3:
+        """Get the slot definition from the robot's deck."""
+        assert False, "get_slot_definition only supported on engine core"
+
     def get_slot_item(
         self, slot_name: DeckSlotName
     ) -> Union[LegacyLabwareCore, legacy_module_core.LegacyModuleCore, None]:

api/src/opentrons/protocol_api/core/protocol.py

@@ -5,7 +5,7 @@
 from abc import abstractmethod, ABC
 from typing import Generic, List, Optional, Union, Tuple
 
-from opentrons_shared_data.deck.dev_types import DeckDefinitionV3
+from opentrons_shared_data.deck.dev_types import DeckDefinitionV4, SlotDefV3
 from opentrons_shared_data.pipette.dev_types import PipetteNameType
 from opentrons_shared_data.labware.dev_types import LabwareDefinition
 from opentrons_shared_data.robot.dev_types import RobotType
@@ -28,7 +28,7 @@ class AbstractProtocol(
 ):
     @property
     @abstractmethod
-    def fixed_trash(self) -> LabwareCoreType:
+    def fixed_trash(self) -> Optional[LabwareCoreType]:
         """Get the fixed trash labware core."""
         ...
 
@@ -154,9 +154,14 @@ def set_last_location(
         ...
 
     @abstractmethod
-    def get_deck_definition(self) -> DeckDefinitionV3:
+    def get_deck_definition(self) -> DeckDefinitionV4:
         """Get the geometry definition of the robot's deck."""
 
+    # TODO(jbl 10-30-2023) this method may no longer need to exist post deck config work being completed
+    @abstractmethod
+    def get_slot_definition(self, slot: DeckSlotName) -> SlotDefV3:
+        """Get the slot definition from the robot's deck."""
+
     @abstractmethod
     def get_slot_item(
         self, slot_name: DeckSlotName

api/src/opentrons/protocol_api/deck.py

@@ -65,13 +65,47 @@ def __init__(
         self._core_map = core_map
         self._api_version = api_version
 
-        self._protocol_core.robot_type
-
-        deck_locations = protocol_core.get_deck_definition()["locations"]
+        # TODO(jbl 10-30-2023) this hardcoding should be removed once slots are refactored to work with deck config
+        if self._protocol_core.robot_type == "OT-2 Standard":
+            ordered_slot_ids = [
+                "1",
+                "2",
+                "3",
+                "4",
+                "5",
+                "6",
+                "7",
+                "8",
+                "9",
+                "10",
+                "11",
+                "12",
+            ]
+        else:
+            ordered_slot_ids = [
+                "D1",
+                "D2",
+                "D3",
+                "C1",
+                "C2",
+                "C3",
+                "B1",
+                "B2",
+                "B3",
+                "A1",
+                "A2",
+                "A3",
+            ]
 
         self._slot_definitions_by_name = {
-            slot["id"]: slot for slot in deck_locations["orderedSlots"]
+            slot_id: self._protocol_core.get_slot_definition(
+                DeckSlotName.from_primitive(slot_id)
+            )
+            for slot_id in ordered_slot_ids
         }
+
+        deck_locations = protocol_core.get_deck_definition()["locations"]
+
         self._calibration_positions = [
             CalibrationPosition(
                 id=point["id"],

api/src/opentrons/protocol_api/instrument_context.py

@@ -16,6 +16,7 @@
 from opentrons.protocols.advanced_control.mix import mix_from_kwargs
 from opentrons.protocols.advanced_control import transfers
 
+from opentrons.protocols.api_support.deck_type import NoTrashDefinedError
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.api_support import instrument
 from opentrons.protocols.api_support.util import (
@@ -84,7 +85,7 @@ def __init__(
         broker: LegacyBroker,
         api_version: APIVersion,
         tip_racks: List[labware.Labware],
-        trash: labware.Labware,
+        trash: Optional[labware.Labware],
         requested_as: str,
     ) -> None:
         super().__init__(broker)
@@ -99,7 +100,7 @@ def __init__(
             default_dispense=_DEFAULT_DISPENSE_CLEARANCE,
         )
 
-        self.trash_container = trash
+        self._trash = trash
         self.requested_as = requested_as
 
     @property  # type: ignore
@@ -1422,6 +1423,10 @@ def trash_container(self) -> labware.Labware:
 
         By default, the trash container is in slot A3 on Flex and in slot 12 on OT-2.
         """
+        if self._trash is None:
+            raise NoTrashDefinedError(
+                "No trash container has been defined in this protocol."
+            )
         return self._trash
 
     @trash_container.setter

api/src/opentrons/protocol_api/protocol_context.py

@@ -23,6 +23,7 @@
 from opentrons.commands import protocol_commands as cmds, types as cmd_types
 from opentrons.commands.publisher import CommandPublisher, publish
 from opentrons.protocols.api_support import instrument as instrument_support
+from opentrons.protocols.api_support.deck_type import NoTrashDefinedError
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.api_support.util import (
     AxisMaxSpeeds,
@@ -822,13 +823,19 @@ def load_instrument(
                 log=logger,
             )
 
+        trash: Optional[Labware]
+        try:
+            trash = self.fixed_trash
+        except NoTrashDefinedError:
+            trash = None
+
         instrument = InstrumentContext(
             core=instrument_core,
             protocol_core=self._core,
             broker=self._broker,
             api_version=self._api_version,
             tip_racks=tip_racks,
-            trash=self.fixed_trash,
+            trash=trash,
             requested_as=instrument_name,
         )
 
@@ -985,17 +992,23 @@ def fixed_trash(self) -> Labware:
         It has one well and should be accessed like labware in your protocol.
         e.g. ``protocol.fixed_trash['A1']``
         """
-        return self._core_map.get(self._core.fixed_trash)
+        fixed_trash = self._core_map.get(self._core.fixed_trash)
+        if fixed_trash is None:
+            raise NoTrashDefinedError(
+                "No trash container has been defined in this protocol."
+            )
+        return fixed_trash
 
     def _load_fixed_trash(self) -> None:
         fixed_trash_core = self._core.fixed_trash
-        fixed_trash = Labware(
-            core=fixed_trash_core,
-            api_version=self._api_version,
-            protocol_core=self._core,
-            core_map=self._core_map,
-        )
-        self._core_map.add(fixed_trash_core, fixed_trash)
+        if fixed_trash_core is not None:
+            fixed_trash = Labware(
+                core=fixed_trash_core,
+                api_version=self._api_version,
+                protocol_core=self._core,
+                core_map=self._core_map,
+            )
+            self._core_map.add(fixed_trash_core, fixed_trash)
 
     @requires_version(2, 5)
     def set_rail_lights(self, on: bool) -> None: