opentrons 8.6.0a1__py3-none-any.whl

opentrons/protocols/models/json_protocol.py

@@ -0,0 +1,679 @@
+"""
+This was initially generated by datamodel-codegen from the protocol schema in
+shared-data. It's been modified by hand to be more friendly.
+
+TODO: 20210330 Amit - consider moving this to opentrons-shared-data.
+"""
+
+from __future__ import annotations
+
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import ConfigDict, BaseModel, Field
+from typing_extensions import Literal
+
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
+from opentrons_shared_data.protocol import types
+
+CommandAspirate: types.AspirateCommandId = "aspirate"
+CommandDispense: types.DispenseCommandId = "dispense"
+CommandAirGap: types.AirGapCommandId = "airGap"
+CommandBlowout: types.BlowoutCommandId = "blowout"
+CommandTouchTip: types.TouchTipCommandId = "touchTip"
+CommandPickUpTip: types.PickUpTipCommandId = "pickUpTip"
+CommandDropTip: types.DropTipCommandId = "dropTip"
+CommandMoveToSlot: types.MoveToSlotCommandId = "moveToSlot"
+CommandMoveToWell: types.MoveToWellCommandId = "moveToWell"
+CommandDelay: types.DelayCommandId = "delay"
+CommandMagneticModuleEngage: types.MagneticModuleEngageCommandId = (
+    "magneticModule/engageMagnet"
+)
+CommandMagneticModuleDisengage: types.MagneticModuleDisengageCommandId = (
+    "magneticModule/disengageMagnet"
+)
+CommandTemperatureModuleSetTarget: types.TemperatureModuleSetTargetCommandId = (
+    "temperatureModule/setTargetTemperature"
+)
+CommandTemperatureModuleAwait: types.TemperatureModuleAwaitCommandId = (
+    "temperatureModule/awaitTemperature"
+)
+CommandTemperatureModuleDeactivate: types.TemperatureModuleDeactivateCommandId = (
+    "temperatureModule/deactivate"
+)
+CommandThermocyclerSetTargetBlock: types.ThermocyclerSetTargetBlockCommandId = (
+    "thermocycler/setTargetBlockTemperature"
+)
+CommandThermocyclerSetTargetLid: types.ThermocyclerSetTargetLidCommandId = (
+    "thermocycler/setTargetLidTemperature"
+)
+CommandThermocyclerAwaitLidTemperature: types.ThermocyclerAwaitLidTemperatureCommandId = (
+    "thermocycler/awaitLidTemperature"
+)
+CommandThermocyclerAwaitBlockTemperature: types.ThermocyclerAwaitBlockTemperatureCommandId = (
+    "thermocycler/awaitBlockTemperature"
+)
+CommandThermocyclerDeactivateBlock: types.ThermocyclerDeactivateBlockCommandId = (
+    "thermocycler/deactivateBlock"
+)
+CommandThermocyclerDeactivateLid: types.ThermocyclerDeactivateLidCommandId = (
+    "thermocycler/deactivateLid"
+)
+CommandThermocyclerOpenLid: types.ThermocyclerOpenLidCommandId = "thermocycler/openLid"
+CommandThermocyclerCloseLid: types.ThermocyclerCloseLidCommandId = (
+    "thermocycler/closeLid"
+)
+CommandThermocyclerRunProfile: types.ThermocyclerRunProfileCommandId = (
+    "thermocycler/runProfile"
+)
+CommandThermocyclerAwaitProfile: types.ThermocyclerAwaitProfileCommandId = (
+    "thermocycler/awaitProfileComplete"
+)
+
+
+class Metadata(BaseModel):
+    """
+    Optional metadata about the protocol
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    protocolName: Optional[str] = Field(
+        None, description="A short, human-readable name for the protocol"
+    )
+    author: Optional[str] = Field(
+        None, description="The author or organization who created the protocol"
+    )
+    description: Optional[Optional[str]] = Field(
+        None, description="A text description of the protocol."
+    )
+    created: Optional[float] = Field(
+        None, description="UNIX timestamp when this file was created"
+    )
+    lastModified: Optional[Optional[float]] = Field(
+        None, description="UNIX timestamp when this file was last modified"
+    )
+    category: Optional[Optional[str]] = Field(
+        None, description='Category of protocol (eg, "Basic Pipetting")'
+    )
+    subcategory: Optional[Optional[str]] = Field(
+        None, description='Subcategory of protocol (eg, "Cell Plating")'
+    )
+    tags: Optional[List[str]] = Field(
+        None, description="Tags to be used in searching for this protocol"
+    )
+
+
+class DesignerApplication(BaseModel):
+    """
+    Optional data & metadata not required to execute the protocol, used by the
+    application that created this protocol
+    """
+
+    name: Optional[str] = Field(
+        None,
+        description="Name of the application that created the protocol. Should "
+        "be namespaced under the organization or individual who "
+        'owns the organization, eg "opentrons/protocol-designer"',
+    )
+    version: Optional[str] = Field(
+        None, description="Version of the application that created the protocol"
+    )
+    data: Optional[Dict[str, Any]] = Field(
+        None, description="Any data used by the application that created this protocol"
+    )
+
+
+class Robot(BaseModel):
+    model: Literal["OT-2 Standard"] = Field(
+        ...,
+        description="Model of the robot this protocol is written for "
+        "(currently only OT-2 Standard is supported)",
+    )
+
+
+class ModuleOnlyParams(BaseModel):
+    module: str
+
+
+class OffsetFromBottomMm(BaseModel):
+    """
+    Offset from bottom of well in millimeters
+    """
+
+    offsetFromBottomMm: float = Field(
+        ..., description="Millimeters for pipette location offsets"
+    )
+
+
+class PipetteAccessParams(BaseModel):
+    pipette: str
+    labware: str
+    well: str
+
+
+class VolumeParams(BaseModel):
+    volume: float
+
+
+class FlowRate(BaseModel):
+    flowRate: float = Field(
+        ..., description="Flow rate in uL/sec. Must be greater than 0", ge=0.0
+    )
+
+
+class Params2(PipetteAccessParams, OffsetFromBottomMm):
+    pass
+
+
+class Params1(Params2, FlowRate):
+    pass
+
+
+class Params(Params1, Params2, VolumeParams):
+    pass
+
+
+class LiquidCommand(BaseModel):
+    """
+    Aspirate / dispense / air gap commands
+    """
+
+    command: Literal["aspirate", "dispense", "airGap"]
+    params: Params
+
+
+class BlowoutCommand(BaseModel):
+    """
+    Blowout command
+    """
+
+    command: Literal["blowout"]
+    params: Params1
+
+
+class TouchTipCommand(BaseModel):
+    """
+    Touch tip commands
+    """
+
+    command: Literal["touchTip"]
+    params: Params2
+
+
+class PickUpDropTipCommand(BaseModel):
+    """
+    Pick up tip / drop tip commands
+    """
+
+    command: Literal["pickUpTip", "dropTip"]
+    params: PipetteAccessParams
+
+
+class Offset(BaseModel):
+    """
+    Optional offset from slot bottom left corner, in mm
+    """
+
+    x: float
+    y: float
+    z: float
+
+
+class Params3(BaseModel):
+    pipette: str
+    slot: str = Field(
+        ...,
+        description="string '1'-'12', or special string 'span7_8_10_11' signify "
+        "it's a slot on the OT-2 deck. If it's a UUID, it's the "
+        "slot on the module referenced by that ID.",
+    )
+    offset: Optional[Offset] = Field(
+        None, description="Optional offset from slot bottom left corner, in mm"
+    )
+    minimumZHeight: Optional[float] = Field(
+        None,
+        description="Optional minimal Z margin in mm. If this is larger than "
+        "the API's default safe Z margin, it will make the arc "
+        "higher. If it's smaller, it will have no effect. Specifying "
+        "this for movements that would not arc (moving within the "
+        "same well in the same labware) will cause an arc movement "
+        "instead.",
+        ge=0.0,
+    )
+    forceDirect: Optional[bool] = Field(
+        None,
+        description="Default is false. If true, moving from one labware/well to "
+        "another will not arc to the default safe z, but instead will "
+        "move directly to the specified location. This will also force "
+        "the 'minimumZHeight' param to be ignored. A 'direct' movement "
+        "is in X/Y/Z simultaneously",
+    )
+
+
+class MoveToSlotCommand(BaseModel):
+    """
+    Move to slot command. NOTE: this is an EXPERIMENTAL command, its behavior is
+    subject to change in future releases.
+    """
+
+    command: Literal["moveToSlot"]
+    params: Params3
+
+
+class DelayCommandParams(BaseModel):
+    wait: Union[Literal[True], float] = Field(
+        ...,
+        description="either a number of seconds to wait (fractional values OK), "
+        "or `true` to wait indefinitely until the user manually "
+        "resumes the protocol",
+    )
+    message: Optional[str] = Field(
+        None, description="optional message describing the delay"
+    )
+
+
+class DelayCommand(BaseModel):
+    """
+    Delay command
+    """
+
+    command: Literal["delay"]
+    params: DelayCommandParams
+
+
+class Params5(BaseModel):
+    engageHeight: float = Field(
+        ...,
+        description="Height in mm(*) from bottom plane of labware (above if positive, "
+        "below if negative). *NOTE: for magneticModuleV1 (aka GEN1), these "
+        "are not true mm but an arbitrary unit equal to 0.5mm. So "
+        "`engageHeight: 2` means 1mm above the labware plane if the "
+        "command is for a GEN1 magnetic module, but would mean 2mm "
+        "above the labware plane for GEN2 module",
+    )
+    module: str
+
+
+class MagneticModuleEngageCommand(BaseModel):
+    """
+    Magnetic module engage command. Engages magnet to specified height
+    """
+
+    command: Literal["magneticModule/engageMagnet"]
+    params: Params5
+
+
+class MagneticModuleDisengageCommand(BaseModel):
+    """
+    Magnetic module disengage command. Moves magnet down to disengaged (home) position
+    """
+
+    command: Literal["magneticModule/disengageMagnet"]
+    params: ModuleOnlyParams
+
+
+class Params6(BaseModel):
+    module: str
+    temperature: float
+
+
+class TemperatureModuleSetTargetCommand(BaseModel):
+    """
+    Temperature module set target temperature command. Module will begin moving
+    to the target temperature. This command is non-blocking, it does not delay
+    until the temperature is reached.
+    """
+
+    command: Literal["temperatureModule/setTargetTemperature"]
+    params: Params6
+
+
+class Params7(BaseModel):
+    module: str
+    temperature: float
+
+
+class TemperatureModuleAwaitTemperatureCommand(BaseModel):
+    """
+    Temperature module await temperature command. Delay further protocol execution
+    until the specified temperature is reached.
+    """
+
+    command: Literal["temperatureModule/awaitTemperature"]
+    params: Params7
+
+
+class TemperatureModuleDeactivateCommand(BaseModel):
+    """
+    Temperature module deactivate command. Module will stop actively controlling
+    its temperature and drift to ambient temperature.
+    """
+
+    command: Literal["temperatureModule/deactivate"]
+    params: ModuleOnlyParams
+
+
+class Params8(BaseModel):
+    module: str
+    temperature: float
+    volume: Optional[float] = None
+
+
+class ThermocyclerSetTargetBlockTemperatureCommand(BaseModel):
+    """
+    Thermocycler set target block temperature command. Lid will begin moving to
+    the target temperature. This command is non-blocking, it does not delay until
+    the temperature is reached.
+    """
+
+    command: Literal["thermocycler/setTargetBlockTemperature"]
+    params: Params8
+
+
+class Params9(BaseModel):
+    module: str
+    temperature: float
+
+
+class ThermocyclerSetTargetLidTemperatureCommand(BaseModel):
+    """
+    Thermocycler set target lid temperature command. Lid will begin moving to the
+    target temperature. This command is non-blocking, it does not delay until
+    the temperature is reached.
+    """
+
+    command: Literal["thermocycler/setTargetLidTemperature"]
+    params: Params9
+
+
+class Params10(BaseModel):
+    module: str
+    temperature: float
+
+
+class ThermocyclerAwaitBlockTemperatureCommand(BaseModel):
+    """
+    Thermocycler await block temperature command. Delay further protocol execution
+    until the specified temperature is reached.
+    """
+
+    command: Literal["thermocycler/awaitBlockTemperature"]
+    params: Params10
+
+
+class Params11(BaseModel):
+    module: str
+    temperature: float
+
+
+class ThermocyclerAwaitLidTemperatureCommand(BaseModel):
+    """
+    Thermocycler await lid temperature command. Delay further protocol execution
+    until the specified temperature is reached.
+    """
+
+    command: Literal["thermocycler/awaitLidTemperature"]
+    params: Params11
+
+
+class ThermocyclerDeactivateBlockCommand(BaseModel):
+    """
+    Thermocycler deactivate block command. Module will stop actively controlling
+    its block temperature.
+    """
+
+    command: Literal["thermocycler/deactivateBlock"]
+    params: ModuleOnlyParams
+
+
+class ThermocyclerDeactivateLidCommand(BaseModel):
+    """
+    Thermocycler deactivate lid command. Module will stop actively controlling
+    its lid temperature.
+    """
+
+    command: Literal["thermocycler/deactivateLid"]
+    params: ModuleOnlyParams
+
+
+class ThermocyclerOpenLidCommand(BaseModel):
+    """
+    Thermocycler open lid command. This command will block until the lid is
+    fully open.
+    """
+
+    command: Literal["thermocycler/openLid"]
+    params: ModuleOnlyParams
+
+
+class ThermocyclerCloseLidCommand(BaseModel):
+    """
+    Thermocycler close lid command. This command will block until the lid is
+    fully closed.
+    """
+
+    command: Literal["thermocycler/closeLid"]
+    params: ModuleOnlyParams
+
+
+class ProfileItem(BaseModel):
+    temperature: float = Field(..., description="Target temperature of profile step")
+    holdTime: float = Field(
+        ..., description="Time (in seconds) to hold once temperature is reached"
+    )
+
+
+class Params12(BaseModel):
+    module: str
+    profile: List[ProfileItem]
+    volume: float
+
+
+class ThermocyclerRunProfile(BaseModel):
+    """
+    Thermocycler run profile command. Begin running the specified profile steps on
+    the thermocycler. This command is non-blocking, it does not delay protocol
+    execution outside of thermocycler steps. No more thermocycler commands should
+    be given until a 'thermocycler/awaitProfileComplete' command is executed.
+    """
+
+    command: Literal["thermocycler/runProfile"]
+    params: Params12
+
+
+class ThermocyclerAwaitProfileCompleteCommand(BaseModel):
+    """
+    Thermocycler await profile complete command. Blocks further protocol
+    execution until profile execution is complete.
+    """
+
+    command: Literal["thermocycler/awaitProfileComplete"]
+    params: ModuleOnlyParams
+
+
+class Offset1(BaseModel):
+    """
+    Optional offset from well bottom center, in mm
+    """
+
+    x: float
+    y: float
+    z: float
+
+
+class Params13(BaseModel):
+    pipette: str
+    labware: str
+    well: str
+    offset: Optional[Offset1] = Field(
+        None, description="Optional offset from well bottom center, in mm"
+    )
+    minimumZHeight: Optional[float] = Field(
+        None,
+        description="Optional minimal Z margin in mm. If this is larger than "
+        "the API's default safe Z margin, it will make the arc higher. "
+        "If it's smaller, it will have no effect. Specifying this for "
+        "movements that would not arc (moving within the same well in "
+        "the same labware) will cause an arc movement instead.",
+        ge=0.0,
+    )
+    forceDirect: Optional[bool] = Field(
+        None,
+        description="Default is false. If true, moving from one labware/well "
+        "to another will not arc to the default safe z, but instead "
+        "will move directly to the specified location. This will also "
+        "force the 'minimumZHeight' param to be ignored. A 'direct' "
+        "movement is in X/Y/Z simultaneously",
+    )
+
+
+class MoveToWellCommand(BaseModel):
+    """
+    Move to well command. Move the pipette's critical point to the specified well
+    in a labware, with an optional offset. The pipette's critical point is a
+    reference point on the pipette. The critical point can be one of the following:
+    (1) Single-channel pipette with no tip: end of nozzle. (2) Multi-channel
+    pipette with no tip: end of backmost nozzle. (3) Single-channel pipette with
+    a tip: end of tip. (4) Multi-channel pipette with tip: end of tip on backmost
+    nozzle.
+    """
+
+    command: Literal["moveToWell"]
+    params: Params13
+
+
+AllCommands = Union[
+    LiquidCommand,
+    BlowoutCommand,
+    TouchTipCommand,
+    PickUpDropTipCommand,
+    MoveToSlotCommand,
+    DelayCommand,
+    MagneticModuleEngageCommand,
+    MagneticModuleDisengageCommand,
+    TemperatureModuleSetTargetCommand,
+    TemperatureModuleAwaitTemperatureCommand,
+    TemperatureModuleDeactivateCommand,
+    ThermocyclerSetTargetBlockTemperatureCommand,
+    ThermocyclerSetTargetLidTemperatureCommand,
+    ThermocyclerAwaitBlockTemperatureCommand,
+    ThermocyclerAwaitLidTemperatureCommand,
+    ThermocyclerDeactivateBlockCommand,
+    ThermocyclerDeactivateLidCommand,
+    ThermocyclerOpenLidCommand,
+    ThermocyclerCloseLidCommand,
+    ThermocyclerRunProfile,
+    ThermocyclerAwaitProfileCompleteCommand,
+    MoveToWellCommand,
+]
+
+
+class Pipettes(BaseModel):
+    """
+    Fields describing an individual pipette
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    mount: Literal["left", "right"] = Field(
+        ..., description="Where the pipette is mounted"
+    )
+    name: str = Field(
+        ...,
+        description="Name of a pipette. Does not contain info about specific "
+        "model/version. Should match keys in pipetteNameSpecs.json file",
+    )
+
+
+class Labware(BaseModel):
+    """
+    Fields describing a single labware on the deck
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    slot: str = Field(
+        ...,
+        description="string '1'-'12', or special string 'span7_8_10_11' signify "
+        "it's a slot on the OT-2 deck. If it's a UUID, it's the "
+        "slot on the module referenced by that ID.",
+    )
+    definitionId: str = Field(
+        ..., description='reference to this labware\'s ID in "labwareDefinitions"'
+    )
+    displayName: Optional[str] = Field(
+        None,
+        description="An optional human-readable nickname for this labware. "
+        'Eg "Buffer Trough"',
+    )
+
+
+class Modules(BaseModel):
+    """
+    Fields describing a single module on the deck
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    slot: str = Field(
+        ...,
+        description="string '1'-'12', or special string 'span7_8_10_11' signify "
+        "it's a slot on the OT-2 deck. If it's a UUID, it's the "
+        "slot on the module referenced by that ID.",
+    )
+    model: str = Field(
+        ...,
+        description="model of module. Eg 'magneticModuleV1' or 'magneticModuleV2'. "
+        "This should match a top-level key in "
+        "shared-data/module/definitions/2.json",
+    )
+
+
+class Model(BaseModel):
+    otSharedSchema: Optional[
+        Literal["#/protocol/schemas/5", "#/protocol/schemas/4"]
+    ] = Field(
+        None,
+        alias="$otSharedSchema",
+        description="The path to a valid Opentrons shared schema relative to "
+        "the shared-data directory, without its extension.",
+    )
+    schemaVersion: Literal[1, 2, 3, 4, 5] = Field(
+        ..., description="Schema version of a protocol is a single integer"
+    )
+    metadata: Metadata = Field(..., description="Optional metadata about the protocol")
+    designerApplication: Optional[DesignerApplication] = Field(
+        None,
+        description="Optional data & metadata not required to execute the protocol, "
+        "used by the application that created this protocol",
+    )
+    robot: Robot
+    pipettes: Dict[str, Pipettes] = Field(
+        ...,
+        description="The pipettes used in this protocol, keyed by an arbitrary "
+        "unique ID",
+    )
+    labwareDefinitions: Dict[str, LabwareDefinition] = Field(
+        ...,
+        description="All labware definitions used by labware in this protocol, "
+        "keyed by UUID",
+    )
+    labware: Dict[str, Labware] = Field(
+        ...,
+        description="All types of labware used in this protocol, and references "
+        "to their definitions",
+    )
+    modules: Optional[Dict[str, Modules]] = Field(
+        None, description="All modules used in this protocol"
+    )
+    commands: List[AllCommands] = Field(
+        ...,
+        description="An array of command objects representing steps to be executed "
+        "on the robot",
+    )
+    commandAnnotations: Optional[Dict[str, Any]] = Field(
+        None,
+        description="An optional object of annotations associated with commands. "
+        "Its usage has not yet been defined, so its shape is not "
+        "enforced by this schema.",
+    )