@opentrons/shared-data 0.0.0-alpha.2 → 0.0.1-alpha.1

package/python/build/lib/opentrons_shared_data/protocol/constants.py

@@ -0,0 +1,98 @@
+from typing import TYPE_CHECKING
+from enum import Enum
+
+
+if TYPE_CHECKING:
+    from .dev_types import (
+        DelayCommandId,
+        BlowoutCommandId,
+        PickUpTipCommandId,
+        DropTipCommandId,
+        AspirateCommandId,
+        DispenseCommandId,
+        TouchTipCommandId,
+        MoveToSlotCommandId,
+        AirGapCommandId,
+        MagneticModuleEngageCommandId,
+        MagneticModuleDisengageCommandId,
+        TemperatureModuleSetTargetCommandId,
+        TemperatureModuleAwaitCommandId,
+        TemperatureModuleDeactivateCommandId,
+        ThermocyclerSetTargetBlockCommandId,
+        ThermocyclerSetTargetLidCommandId,
+        ThermocyclerAwaitBlockTemperatureCommandId,
+        ThermocyclerAwaitLidTemperatureCommandId,
+        ThermocyclerOpenLidCommandId,
+        ThermocyclerCloseLidCommandId,
+        ThermocyclerDeactivateLidCommandId,
+        ThermocyclerDeactivateBlockCommandId,
+        ThermocyclerRunProfileCommandId,
+        ThermocyclerAwaitProfileCommandId,
+        MoveToWellCommandId,
+    )
+
+
+class JsonPipetteCommand(Enum):
+    airGap: "AirGapCommandId" = "airGap"
+    blowout: "BlowoutCommandId" = "blowout"
+    pickUpTip: "PickUpTipCommandId" = "pickUpTip"
+    dropTip: "DropTipCommandId" = "dropTip"
+    aspirate: "AspirateCommandId" = "aspirate"
+    dispense: "DispenseCommandId" = "dispense"
+    touchTip: "TouchTipCommandId" = "touchTip"
+    moveToSlot: "MoveToSlotCommandId" = "moveToSlot"
+    moveToWell: "MoveToWellCommandId" = "moveToWell"
+
+
+class JsonRobotCommand(Enum):
+    delay: "DelayCommandId" = "delay"
+
+
+class JsonMagneticModuleCommand(Enum):
+    magneticModuleEngageMagnet: "MagneticModuleEngageCommandId" = (
+        "magneticModule/engageMagnet"
+    )
+    magneticModuleDisengageMagnet: "MagneticModuleDisengageCommandId" = (
+        "magneticModule/disengageMagnet"
+    )
+
+
+class JsonTemperatureModuleCommand(Enum):
+    temperatureModuleSetTargetTemperature: "TemperatureModuleSetTargetCommandId" = (
+        "temperatureModule/setTargetTemperature"
+    )
+    temperatureModuleDeactivate: "TemperatureModuleDeactivateCommandId" = (
+        "temperatureModule/deactivate"
+    )
+    temperatureModuleAwaitTemperature: "TemperatureModuleAwaitCommandId" = (
+        "temperatureModule/awaitTemperature"
+    )
+
+
+class JsonThermocyclerCommand(Enum):
+    thermocyclerSetTargetBlockTemperature: "ThermocyclerSetTargetBlockCommandId" = (
+        "thermocycler/setTargetBlockTemperature"
+    )
+    thermocyclerSetTargetLidTemperature: "ThermocyclerSetTargetLidCommandId" = (
+        "thermocycler/setTargetLidTemperature"
+    )
+    thermocyclerAwaitBlockTemperature: "ThermocyclerAwaitBlockTemperatureCommandId" = (
+        "thermocycler/awaitBlockTemperature"
+    )
+    thermocyclerAwaitLidTemperature: "ThermocyclerAwaitLidTemperatureCommandId" = (
+        "thermocycler/awaitLidTemperature"
+    )
+    thermocyclerOpenLid: "ThermocyclerOpenLidCommandId" = "thermocycler/openLid"
+    thermocyclerCloseLid: "ThermocyclerCloseLidCommandId" = "thermocycler/closeLid"
+    thermocyclerDeactivateBlock: "ThermocyclerDeactivateBlockCommandId" = (
+        "thermocycler/deactivateBlock"
+    )
+    thermocyclerDeactivateLid: "ThermocyclerDeactivateLidCommandId" = (
+        "thermocycler/deactivateLid"
+    )
+    thermocyclerRunProfile: "ThermocyclerRunProfileCommandId" = (
+        "thermocycler/runProfile"
+    )
+    thermocyclerAwaitProfileComplete: "ThermocyclerAwaitProfileCommandId" = (
+        "thermocycler/awaitProfileComplete"
+    )

package/python/build/lib/opentrons_shared_data/protocol/dev_types.py

@@ -0,0 +1,436 @@
+"""
+opentrons_shared_data.protocol.dev_types: types for json protocols
+"""
+
+from typing import Any, Dict, List, Optional, Union
+from enum import Enum
+
+from typing_extensions import TypedDict, Literal
+from ..pipette.dev_types import PipetteName
+from ..labware.dev_types import LabwareDefinition
+from ..module.dev_types import ModuleModel
+
+SlotSpan = Literal["span7_8_10_11"]
+
+
+class BlowoutLocation(Enum):
+    SOURCE = "source well"
+    DEST = "destination well"
+    TRASH = "trash"
+
+
+LiquidHandlingCommand = Union[
+    Literal["transfer"], Literal["consolidate"], Literal["distribute"]
+]
+
+
+class LabwareRequirement(TypedDict):
+    slot: str
+    definitionId: str
+    displayName: str
+
+
+Metadata = TypedDict(
+    "Metadata",
+    {
+        "protocolName": str,
+        "protocol-name": str,
+        "author": str,
+        "description": Optional[str],
+        "created": int,
+        "lastModified": Optional[int],
+        "last-modified": Optional[int],
+        "category": Optional[str],
+        "subcategory": Optional[str],
+        "tags": List[str],
+    },
+    total=False,
+)
+
+AspirateCommandId = Literal["aspirate"]
+DispenseCommandId = Literal["dispense"]
+AirGapCommandId = Literal["airGap"]
+BlowoutCommandId = Literal["blowout"]
+TouchTipCommandId = Literal["touchTip"]
+PickUpTipCommandId = Literal["pickUpTip"]
+DropTipCommandId = Literal["dropTip"]
+MoveToSlotCommandId = Literal["moveToSlot"]
+MoveToWellCommandId = Literal["moveToWell"]
+DelayCommandId = Literal["delay"]
+MagneticModuleEngageCommandId = Literal["magneticModule/engageMagnet"]
+MagneticModuleDisengageCommandId = Literal["magneticModule/disengageMagnet"]
+TemperatureModuleSetTargetCommandId = Literal["temperatureModule/setTargetTemperature"]
+TemperatureModuleAwaitCommandId = Literal["temperatureModule/awaitTemperature"]
+TemperatureModuleDeactivateCommandId = Literal["temperatureModule/deactivate"]
+ThermocyclerSetTargetBlockCommandId = Literal["thermocycler/setTargetBlockTemperature"]
+ThermocyclerSetTargetLidCommandId = Literal["thermocycler/setTargetLidTemperature"]
+ThermocyclerAwaitLidTemperatureCommandId = Literal["thermocycler/awaitLidTemperature"]
+ThermocyclerAwaitBlockTemperatureCommandId = Literal[
+    "thermocycler/awaitBlockTemperature"
+]
+ThermocyclerDeactivateBlockCommandId = Literal["thermocycler/deactivateBlock"]
+ThermocyclerDeactivateLidCommandId = Literal["thermocycler/deactivateLid"]
+ThermocyclerOpenLidCommandId = Literal["thermocycler/openLid"]
+ThermocyclerCloseLidCommandId = Literal["thermocycler/closeLid"]
+ThermocyclerRunProfileCommandId = Literal["thermocycler/runProfile"]
+ThermocyclerAwaitProfileCommandId = Literal["thermocycler/awaitProfileComplete"]
+
+
+class NamedOffset(TypedDict):
+    x: float
+    y: float
+    z: float
+
+
+class ModuleRequirement(TypedDict):
+    slot: str
+    model: "ModuleModel"
+
+
+class RobotRequirement(TypedDict):
+    model: Literal["OT-2 Standard"]
+
+
+class PipetteRequirement(TypedDict):
+    mount: Union[Literal["left"], Literal["right"]]
+    name: PipetteName
+
+
+class PipetteAccessParams(TypedDict):
+    pipette: str
+    labware: str
+    well: str
+
+
+class FlowRateParams(TypedDict):
+    flowRate: float
+
+
+class PipetteAccessWithOffsetParams(PipetteAccessParams):
+    offsetFromBottomMm: float
+
+
+class StandardLiquidHandlingParams(PipetteAccessWithOffsetParams, FlowRateParams):
+    volume: float
+
+
+class AspirateCommand(TypedDict):
+    command: AspirateCommandId
+    params: StandardLiquidHandlingParams
+
+
+class DispenseCommand(TypedDict):
+    command: DispenseCommandId
+    params: StandardLiquidHandlingParams
+
+
+class AirGapCommand(TypedDict):
+    command: AirGapCommandId
+    params: StandardLiquidHandlingParams
+
+
+class BlowoutParams(PipetteAccessWithOffsetParams, FlowRateParams):
+    pass
+
+
+class BlowoutCommand(TypedDict):
+    command: BlowoutCommandId
+    params: BlowoutParams
+
+
+class TouchTipParams(PipetteAccessParams):
+    offsetFromBottomMm: float
+
+
+class TouchTipCommand(TypedDict):
+    command: TouchTipCommandId
+    params: TouchTipParams
+
+
+class PickUpTipCommand(TypedDict):
+    command: PickUpTipCommandId
+    params: PipetteAccessParams
+
+
+class DropTipCommand(TypedDict):
+    command: DropTipCommandId
+    params: PipetteAccessParams
+
+
+class MoveToSlotParams(TypedDict, total=False):
+    pipette: str
+    slot: str
+    offset: NamedOffset
+    minimumZHeight: float
+    forceDirect: bool
+
+
+class MoveToSlotCommand(TypedDict):
+    command: MoveToSlotCommandId
+    params: MoveToSlotParams
+
+
+class MoveToWellParams(PipetteAccessParams, total=False):
+    offset: NamedOffset
+    minimumZHeight: float
+    forceDirect: bool
+
+
+class MoveToWellCommand(TypedDict):
+    command: MoveToWellCommandId
+    params: MoveToWellParams
+
+
+class DelayParams(TypedDict, total=False):
+    wait: Union[float, bool]
+    message: str
+
+
+class DelayCommand(TypedDict):
+    command: DelayCommandId
+    params: DelayParams
+
+
+class ModuleIDParams(TypedDict):
+    module: str
+
+
+class MagneticModuleEngageParams(ModuleIDParams):
+    engageHeight: float
+
+
+class MagneticModuleEngageCommand(TypedDict):
+    command: MagneticModuleEngageCommandId
+    params: MagneticModuleEngageParams
+
+
+class MagneticModuleDisengageCommand(TypedDict):
+    command: MagneticModuleDisengageCommandId
+    params: ModuleIDParams
+
+
+class TemperatureParams(ModuleIDParams):
+    temperature: float
+
+
+class TemperatureModuleSetTargetCommand(TypedDict):
+    command: TemperatureModuleSetTargetCommandId
+    params: TemperatureParams
+
+
+class TemperatureModuleAwaitCommand(TypedDict):
+    command: TemperatureModuleAwaitCommandId
+    params: TemperatureParams
+
+
+class TemperatureModuleDeactivateCommand(TypedDict):
+    command: TemperatureModuleDeactivateCommandId
+    params: ModuleIDParams
+
+
+class ThermocyclerSetTargetBlockParams(TemperatureParams, total=False):
+    volume: float
+
+
+class ThermocyclerSetTargetBlockCommand(TypedDict):
+    command: ThermocyclerSetTargetBlockCommandId
+    params: ThermocyclerSetTargetBlockParams
+
+
+class ThermocyclerSetTargetLidCommand(TypedDict):
+    command: ThermocyclerSetTargetLidCommandId
+    params: TemperatureParams
+
+
+class ThermocyclerAwaitLidTemperatureCommand(TypedDict):
+    command: ThermocyclerAwaitLidTemperatureCommandId
+    params: TemperatureParams
+
+
+class ThermocyclerAwaitBlockTemperatureCommand(TypedDict):
+    command: ThermocyclerAwaitBlockTemperatureCommandId
+    params: TemperatureParams
+
+
+class ThermocyclerDeactivateBlockCommand(TypedDict):
+    command: ThermocyclerDeactivateBlockCommandId
+    params: ModuleIDParams
+
+
+class ThermocyclerDeactivateLidCommand(TypedDict):
+    command: ThermocyclerDeactivateLidCommandId
+    params: ModuleIDParams
+
+
+class ThermocyclerOpenLidCommand(TypedDict):
+    command: ThermocyclerOpenLidCommandId
+    params: ModuleIDParams
+
+
+class ThermocyclerCloseLidCommand(TypedDict):
+    command: ThermocyclerCloseLidCommandId
+    params: ModuleIDParams
+
+
+class ThermocyclerCycle(TypedDict):
+    temperature: float
+    holdTime: float
+
+
+class ThermocyclerRunProfileParams(TypedDict):
+    module: str
+    volume: float
+    profile: List[ThermocyclerCycle]
+
+
+class ThermocyclerRunProfileCommand(TypedDict):
+    command: ThermocyclerRunProfileCommandId
+    params: ThermocyclerRunProfileParams
+
+
+class ThermocyclerAwaitProfileCommand(TypedDict):
+    command: ThermocyclerAwaitProfileCommandId
+    params: ModuleIDParams
+
+
+ThermocyclerCommand = Union[
+    ThermocyclerAwaitProfileCommand,
+    ThermocyclerRunProfileCommand,
+    ThermocyclerCloseLidCommand,
+    ThermocyclerOpenLidCommand,
+    ThermocyclerDeactivateLidCommand,
+    ThermocyclerDeactivateBlockCommand,
+    ThermocyclerAwaitBlockTemperatureCommand,
+    ThermocyclerAwaitLidTemperatureCommand,
+    ThermocyclerSetTargetLidCommand,
+    ThermocyclerSetTargetBlockCommand,
+]
+ThermocyclerCommandId = Union[
+    ThermocyclerAwaitProfileCommandId,
+    ThermocyclerRunProfileCommandId,
+    ThermocyclerCloseLidCommandId,
+    ThermocyclerOpenLidCommandId,
+    ThermocyclerDeactivateLidCommandId,
+    ThermocyclerDeactivateBlockCommandId,
+    ThermocyclerAwaitBlockTemperatureCommandId,
+    ThermocyclerAwaitLidTemperatureCommandId,
+    ThermocyclerSetTargetLidCommandId,
+    ThermocyclerSetTargetBlockCommandId,
+]
+
+TemperatureModuleCommand = Union[
+    TemperatureModuleAwaitCommand,
+    TemperatureModuleSetTargetCommand,
+    TemperatureModuleDeactivateCommand,
+]
+TemperatureModuleCommandId = Union[
+    TemperatureModuleAwaitCommandId,
+    TemperatureModuleSetTargetCommandId,
+    TemperatureModuleDeactivateCommandId,
+]
+
+MagneticModuleCommand = Union[
+    MagneticModuleEngageCommand, MagneticModuleDisengageCommand
+]
+MagneticModuleCommandId = Union[
+    MagneticModuleEngageCommandId, MagneticModuleDisengageCommandId
+]
+
+
+ModuleCommand = Union[
+    ThermocyclerCommand, TemperatureModuleCommand, MagneticModuleCommand
+]
+ModuleCommandId = Union[
+    ThermocyclerCommandId, TemperatureModuleCommandId, MagneticModuleCommandId
+]
+
+PipetteCommand = Union[
+    AspirateCommand,
+    DispenseCommand,
+    AirGapCommand,
+    BlowoutCommand,
+    TouchTipCommand,
+    PickUpTipCommand,
+    DropTipCommand,
+    MoveToSlotCommand,
+    MoveToWellCommand,
+]
+PipetteCommandId = Union[
+    AspirateCommandId,
+    DispenseCommandId,
+    AirGapCommandId,
+    BlowoutCommandId,
+    TouchTipCommandId,
+    PickUpTipCommandId,
+    DropTipCommandId,
+    MoveToSlotCommandId,
+    MoveToWellCommandId,
+]
+
+RobotCommand = Union[DelayCommand]
+RobotCommandId = Union[DelayCommandId]
+
+Command = Union[ModuleCommand, PipetteCommand, RobotCommand]
+CommandId = Union[ModuleCommandId, PipetteCommandId, RobotCommandId]
+
+V3Command = Union[PipetteCommand, RobotCommand]
+V3CommandId = Union[PipetteCommandId, RobotCommandId]
+
+
+class DesignerApplication(TypedDict):
+    name: str
+    version: str
+    data: Dict[str, Any]
+
+
+JsonProtocolV4 = TypedDict(
+    "JsonProtocolV4",
+    {
+        "$otSharedSchema": Literal["#/protocol/schemas/4"],
+        "schemaVersion": Literal[4],
+        "metadata": Metadata,
+        "robot": RobotRequirement,
+        "pipettes": Dict[str, PipetteRequirement],
+        "labware": Dict[str, LabwareRequirement],
+        "labwareDefinitions": Dict[str, LabwareDefinition],
+        "modules": Dict[str, ModuleRequirement],
+        "commands": List[Command],
+        "commandAnnotations": Dict[str, Any],
+        "designerApplication": DesignerApplication,
+    },
+    total=False,
+)
+
+JsonProtocolV5 = TypedDict(
+    "JsonProtocolV5",
+    {
+        "$otSharedSchema": Literal["#/protocol/schemas/5"],
+        "schemaVersion": Literal[5],
+        "metadata": Metadata,
+        "robot": RobotRequirement,
+        "pipettes": Dict[str, PipetteRequirement],
+        "labware": Dict[str, LabwareRequirement],
+        "labwareDefinitions": Dict[str, LabwareDefinition],
+        "modules": Dict[str, ModuleRequirement],
+        "commands": List[Command],
+        "commandAnnotations": Dict[str, Any],
+        "designerApplication": DesignerApplication,
+    },
+    total=False,
+)
+
+
+class JsonProtocolV3(TypedDict, total=False):
+    schemaVersion: Literal[3]
+    metadata: Metadata
+    robot: RobotRequirement
+    pipettes: Dict[str, PipetteRequirement]
+    labware: Dict[str, LabwareRequirement]
+    labwareDefinitions: Dict[str, LabwareDefinition]
+    commands: List[V3Command]
+    commandAnnotations: Dict[str, Any]
+    designerApplication: DesignerApplication
+
+
+# todo(mm, 2022-03-18): Should this include JsonProtocolV5?
+JsonProtocol = Union[JsonProtocolV4, JsonProtocolV3]

package/python/build/lib/opentrons_shared_data/protocol/models/__init__.py

@@ -0,0 +1,45 @@
+"""Protocol file reading interfaces."""
+from . import protocol_schema_v6, protocol_schema_v7
+from .protocol_schema_v6 import ProtocolSchemaV6
+from .protocol_schema_v7 import ProtocolSchemaV7
+from .shared_models import (
+    Liquid,
+    Labware,
+    CommandAnnotation,
+    Location,
+    ProfileStep,
+    WellLocation,
+    OffsetVector,
+    Dimensions,
+    GroupMetadata,
+    Shape,
+    WellDefinition,
+    Metadata,
+    Module,
+    Pipette,
+    Robot,
+    DesignerApplication,
+)
+
+__all__ = [
+    "ProtocolSchemaV6",
+    "protocol_schema_v6",
+    "ProtocolSchemaV7",
+    "protocol_schema_v7",
+    "Liquid",
+    "Labware",
+    "CommandAnnotation",
+    "Location",
+    "ProfileStep",
+    "WellLocation",
+    "OffsetVector",
+    "Dimensions",
+    "GroupMetadata",
+    "Shape",
+    "WellDefinition",
+    "Metadata",
+    "Module",
+    "Pipette",
+    "Robot",
+    "DesignerApplication",
+]